From 9fe0165e4671179a1e5c7a619e2590b01e69226f Mon Sep 17 00:00:00 2001
From: Chris Black <chris@ckblack.org>
Date: Mon, 23 Feb 2026 01:11:34 -0800
Subject: [PATCH 01/75] first draft of fn to parse restart dates out of event
 files

---
 modules/data.land/NAMESPACE                   |  1 +
 .../data.land/R/events_to_crop_cycle_starts.R | 52 +++++++++++++++++++
 .../man/events_to_crop_cycle_starts.Rd        | 44 ++++++++++++++++
 .../test-events_to_crop_cycle_starts.R        | 50 ++++++++++++++++++
 4 files changed, 147 insertions(+)
 create mode 100644 modules/data.land/R/events_to_crop_cycle_starts.R
 create mode 100644 modules/data.land/man/events_to_crop_cycle_starts.Rd
 create mode 100644 modules/data.land/tests/testthat/test-events_to_crop_cycle_starts.R

diff --git a/modules/data.land/NAMESPACE b/modules/data.land/NAMESPACE
index 58bf6b196d8..a3dec8b5a33 100644
--- a/modules/data.land/NAMESPACE
+++ b/modules/data.land/NAMESPACE
@@ -18,6 +18,7 @@ export(download_package_rm)
 export(ens_veg_module)
 export(eto_to_etc)
 export(eto_to_etc_bism)
+export(events_to_crop_cycle_starts)
 export(extract.stringCode)
 export(extract_FIA)
 export(extract_NEON_veg)
diff --git a/modules/data.land/R/events_to_crop_cycle_starts.R b/modules/data.land/R/events_to_crop_cycle_starts.R
new file mode 100644
index 00000000000..3d766d7b637
--- /dev/null
+++ b/modules/data.land/R/events_to_crop_cycle_starts.R
@@ -0,0 +1,52 @@
+#' Extract the first planting date of each crop cycle
+#'
+#' Reads a (JSON) management events file and finds the planting events at which
+#' the site changes from from one crop to another, ignoring repeat plantings of
+#' the same crop.
+#' These are the dates when single-PFT models will need to restart to update
+#' their crop parameterization.
+#'
+#' TODO: For now this function requires each planting event to specify a
+#' `crop` attribute, but note that this is not enforced by v0.1 of the PEcAn
+#' events schema. The schema instead allows each site object to specify a
+#' site-level `PFT` attribute that is implied constant over time.
+#' As I write this I think the schema may need to change to require a crop or
+#' PFT identifier be specified for every planting event.
+#'
+#' @param event_json path to an `events.json` file
+#'
+#' @return data frame with columns `site_id`, `date`, `crop`,
+#'  with one row per detected crop cycle.
+#' @export
+#' @author Chris Black
+#'
+#' @examples
+#' # Not currently runnable because file does not list crop in planting events.
+#' # Revisit after deciding if schema update is warranted.
+#' \dontrun{
+#' evts <- system.file(
+#'   "events_fixtures/events_site1_site2.json",
+#'   package = "PEcAn.data.land"
+#' )
+#' events_to_crop_cycle_starts(evts)
+#' }
+events_to_crop_cycle_starts <- function(event_json) {
+  jsonlite::read_json(event_json) |>
+    dplyr::bind_rows() |>
+    dplyr::mutate(events = purrr::map(.data$events, as.data.frame)) |>
+    tidyr::unnest(.data$events) |>
+    dplyr::mutate(date = as.Date(.data$date)) |>
+    find_crop_changes()
+}
+
+# helper for events_to_crop_cyle_starts,
+# mostly to ease unit testing
+find_crop_changes <- function(event_df) {
+  event_df |>
+    dplyr::filter(.data$event_type == "planting") |>
+    dplyr::arrange(.data$site_id, .data$date) |>
+    dplyr::mutate(crop_cycle_id = dplyr::consecutive_id(.data$site_id, .data$crop)) |>
+    dplyr::group_by(.data$site_id, .data$crop_cycle_id) |>
+    dplyr::slice_min(.data$date) |>
+    dplyr::select("site_id", "date", "crop")
+}
diff --git a/modules/data.land/man/events_to_crop_cycle_starts.Rd b/modules/data.land/man/events_to_crop_cycle_starts.Rd
new file mode 100644
index 00000000000..c3677bf0cf6
--- /dev/null
+++ b/modules/data.land/man/events_to_crop_cycle_starts.Rd
@@ -0,0 +1,44 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/events_to_crop_cycle_starts.R
+\name{events_to_crop_cycle_starts}
+\alias{events_to_crop_cycle_starts}
+\title{Extract the first planting date of each crop cycle}
+\usage{
+events_to_crop_cycle_starts(event_json)
+}
+\arguments{
+\item{event_json}{path to an `events.json` file}
+}
+\value{
+data frame with columns `site_id`, `date`, `crop`,
+ with one row per detected crop cycle.
+}
+\description{
+Reads a (JSON) management events file and finds the planting events at which
+the site changes from from one crop to another, ignoring repeat plantings of
+the same crop.
+These are the dates when single-PFT models will need to restart to update
+their crop parameterization.
+}
+\details{
+TODO: For now this function requires each planting event to specify a
+`crop` attribute, but note that this is not enforced by v0.1 of the PEcAn
+events schema. The schema instead allows each site object to specify a
+site-level `PFT` attribute that is implied constant over time.
+As I write this I think the schema may need to change to require a crop or
+PFT identifier be specified for every planting event.
+}
+\examples{
+# Not currently runnable because file does not list crop in planting events.
+# Revisit after deciding if schema update is warranted.
+\dontrun{
+evts <- system.file(
+  "events_fixtures/events_site1_site2.json",
+  package = "PEcAn.data.land"
+)
+events_to_crop_cycle_starts(evts)
+}
+}
+\author{
+Chris Black
+}
diff --git a/modules/data.land/tests/testthat/test-events_to_crop_cycle_starts.R b/modules/data.land/tests/testthat/test-events_to_crop_cycle_starts.R
new file mode 100644
index 00000000000..e075bfc6bde
--- /dev/null
+++ b/modules/data.land/tests/testthat/test-events_to_crop_cycle_starts.R
@@ -0,0 +1,50 @@
+test_that("non-planting events are ignored", {
+  dat <- dplyr::tribble(
+    ~site_id, ~date, ~event_type, ~crop,
+    "a", "2016-01-01", "planting", "almond",
+    "a", "2016-05-01", "irrigation", NA_character_,
+    "a", "2017-01-01", "planting", "almond",
+    "a", "2017-05-15", "fertilization", NA_character_,
+  )
+  res <- find_crop_changes(dat)
+  expect_equal(nrow(res), 1)
+  expect_equal(res$date, "2016-01-01")
+  expect_equal(res, find_crop_changes(dat[-c(2, 4), ]))
+})
+
+test_that("nonconsecutive runs of the same crop counted separately", {
+  dat <- dplyr::tribble(
+    ~site_id, ~date, ~event_type, ~crop,
+    "b", "2016-03-01", "planting", "tomato",
+    "b", "2017-03-05", "planting", "tomato",
+    "b", "2018-04-15", "planting", "potato",
+    "b", "2018-08-01", "planting", "tomato",
+  )
+  res <- find_crop_changes(dat)
+  expect_equal(nrow(res), 3)
+  expect_equal(res$date, dat$date[c(1, 3, 4)])
+})
+
+test_that("sites are counted separately", {
+  dat <- dplyr::tribble(
+    ~site_id, ~date, ~event_type, ~crop,
+    "a", "2016-03-01", "planting", "grape",
+    "b", "2016-03-01", "planting", "grape",
+    "c", "2023-03-01", "planting", "grape",
+  )
+  res <- find_crop_changes(dat)
+  expect_equal(nrow(res), 3)
+  expect_equal(res$date, dat$date)
+  expect_equal(res$site_id, dat$site_id)
+})
+
+test_that("reads from JSON", {
+  skip("needs schema update")
+  path <- system.file(
+    "events_fixtures/events_site1.json",
+    package = "PEcAn.data.land"
+  )
+  res <- events_to_crop_cycle_starts(path)
+  expect_equal(res$date, "2022-02-19")
+  expect_equal(res$crop, "EX1")
+})

From 4708176828f580897879abe0ff92b6dd5cbef721 Mon Sep 17 00:00:00 2001
From: Chris Black <chris@ckblack.org>
Date: Fri, 27 Feb 2026 12:12:49 -0800
Subject: [PATCH 02/75] Update
 modules/data.land/tests/testthat/test-events_to_crop_cycle_starts.R

---
 .../data.land/tests/testthat/test-events_to_crop_cycle_starts.R  | 1 -
 1 file changed, 1 deletion(-)

diff --git a/modules/data.land/tests/testthat/test-events_to_crop_cycle_starts.R b/modules/data.land/tests/testthat/test-events_to_crop_cycle_starts.R
index e075bfc6bde..19c92de805b 100644
--- a/modules/data.land/tests/testthat/test-events_to_crop_cycle_starts.R
+++ b/modules/data.land/tests/testthat/test-events_to_crop_cycle_starts.R
@@ -39,7 +39,6 @@ test_that("sites are counted separately", {
 })
 
 test_that("reads from JSON", {
-  skip("needs schema update")
   path <- system.file(
     "events_fixtures/events_site1.json",
     package = "PEcAn.data.land"

From d8df7d02913b63303470ff51f3d8266192dcf2b5 Mon Sep 17 00:00:00 2001
From: Chris Black <chris@ckblack.org>
Date: Wed, 25 Feb 2026 02:52:33 -0800
Subject: [PATCH 03/75] require crop id in planting and harvest; add docs on
 event properties

---
 .../03_topical_pages/02_pecan_standards.Rmd   | 80 ++++++++++++++++++
 modules/data.land/R/validate_events.R         | 11 ++-
 .../inst/events_fixtures/events_site1.json    |  6 +-
 .../events_fixtures/events_site1_site2.json   | 10 +--
 .../data.land/inst/events_schema_v0.1.1.json  | 81 +++++++++++++++++++
 modules/data.land/man/validate_events_json.Rd |  6 +-
 6 files changed, 182 insertions(+), 12 deletions(-)
 create mode 100644 modules/data.land/inst/events_schema_v0.1.1.json

diff --git a/book_source/03_topical_pages/02_pecan_standards.Rmd b/book_source/03_topical_pages/02_pecan_standards.Rmd
index b4e81427cb7..ad1bd488082 100644
--- a/book_source/03_topical_pages/02_pecan_standards.Rmd
+++ b/book_source/03_topical_pages/02_pecan_standards.Rmd
@@ -97,6 +97,86 @@ See the [Soil Data] section on more into on creating a standard soil data file.
 
 See the [Vegetation Data] section on more info on creating a standard vegetation data file
 
+### Management events
+
+Externally imposed changes in system state, such as planting and harvest or tillage of crop systems, are represented as a sequence of "events" that are each defined by a date, event type, and one or more event-specific properties that describe the kind and magnitude of change imposed. PEcAn passes the same representation of a given event to all models, but interpretation of all properties -- including dates and event types -- is necessarily model-specific and could include ignoring an event entirely.
+
+Event types are defined by the PEcAn events spec, which is currently provided as a JSON schema file bundled into the PEcAn.data.land package (TODO consider exposing this in a more linkable format?). Valid events files are stored as JSON, with each events file containing an array of sites. Each site contains an id, a schema version, and an array of events, usually recorded in date order. Each event has a date, an event type, and one or more values from the required and optional properties that are documented below for each event type. Any event is also allowed to contain arbitrary additional properties not mentioned in the spec; PEcAn will pass these on to models with no further validation.
+
+The currently supported event types are: planting, harvest, irrigation, fertilization, and tillage. Each of these is described briefly below. You will note that all of them are focused on agronomic management of croplands; future work will extend this framework to include disturbance of unmanaged systems such as fire, inundation or insect outbreaks.
+
+
+#### planting
+
+Addition of live biomass that is expected to grow according to the model's plant growth rules. The current spec expects a "planting" to be a transplantation of leafed-out seedlings; models which represent planting as addition of unsprouted seeds might choose to adjust the date to account for germination time.
+
+Required properties:
+
+* `crop_code`: a machine-readable identifier that specifies what type of plant was added. Should preferably be short and use only characters that are safe in filenames.
+* `leaf_c_kg_m2`: Amount of leaf biomass added. 
+
+Optional properties:
+
+* `wood_c_kg_m2`: Biomass added as aboveground stems. Assumed zero if not specified.
+* `fine_root_c_kg_m2`: Biomass added to belowground roots. Assumed zero if not specified.
+* `cultivar`: Identifier for finer-grainer plant type identifiers that will be meaningful to models with detailed growth parameterizations but likely ignored by PFT-based models.
+* `crop_display`: A human-readable name for the added plant type.
+
+#### harvest
+
+Removal of biomass from the living pool, either by transferring it to dead (litter) biomass or by removing it from the system. Specified as a fraction of live biomass.
+
+Required properties:
+* `crop_code`: A machine_readable identifier that specifies what type of plant was harvested.
+* `frac_above_removed_0to1`: Fraction of existing aboveground biomass removed from the system.
+
+Optional properties:
+
+* `frac_below_removed_0to1`: Fraction of existing beloweground biomass removed from the system. Assumed zero if not specified.
+* `frac_above_to_litter_0to1`, `frac_below_to_litter_0to1`: fraction of existing above- or below-ground live biomass converted to dead litter. Assumed zero if not specified.
+* `cultivar`: Identifier for finer-grainer plant type identifiers that will be meaningful to models with detailed growth parameterizations but likely ignored by PFT-based models.
+* `crop_display`: A human-readable name for the added plant type.
+
+#### irrigation
+
+Addition of water to the system beyond that specified as precipitation in met files. Note that only the total amount of water is specified and not the application rate; assumptions about the duration of the event will be model-specific.
+
+Required properties:
+
+* `method`: How water was applied. One of "soil", "canopy", "flood".
+* `amount_mm`: Amount of water applied.
+
+Optional properties:
+
+* `immed_evap_frac_0to1`: fraction of the applied water that evaporates before reaching the soil water pool.
+
+#### fertilization
+
+Addition of exogenous nutrients, including non-crop carbon (e.g. manure, compost). Nutrients other than N and C are not currently included but may be added in future schemas.
+
+Required properties:
+
+* at least one of `org_c_kg_m2`, `nh4_n_kg_m2`, `no3_n_kg_m2`, which are respectively the amount of organic C, ammonium N, and nitrate N added.
+
+Optional properties:
+
+* any of `org_c_kg_m2`, `nh4_n_kg_m2`, `no3_n_kg_m2` not already counted as required. All are assumed zero if not specified.
+* `org_n_kg_m2`: the amount of N added in organic compounds. Assumed zero if not specified. If specifying, you probably want to specify `org_c_kg_m2` as well but the schema does not enforce this.
+
+#### tillage
+
+Physical disturbance of the soil and litter pools. Models differ greatly in their representation of tillage effects and this spec intentionally limits its representation to a simple intensity score whose maximum should be interpreted as "the most complete possible mixing/disturbance." Whether this is sufficient detail will be re-evaluated in future revisions.
+
+Required properties:
+
+* `tillage_eff_0to1`: Relative tillage intensity, with 0 meaning no disturbance at all and 1 meaning the most complete disturbance possible.
+
+Optional properties:
+
+* `intensity_category`: string giving additional information on the type or amount of tillage performed.
+* `depth_m`: Depth of soil affected by the event.
+
+
 ## Output Standards
 
 * created by `model2netcdf` functions
diff --git a/modules/data.land/R/validate_events.R b/modules/data.land/R/validate_events.R
index 95ebd486960..a24b9ce2201 100644
--- a/modules/data.land/R/validate_events.R
+++ b/modules/data.land/R/validate_events.R
@@ -1,7 +1,7 @@
 #' Validate PEcAn events JSON against schema v0.1.0
 #'
 #' Validates a PEcAn events JSON file (single-site object or an array of site
-#' objects) against the bundled JSON Schema (draft 2020-12) using the AJV
+#' objects) against the bundled JSON Schema using the AJV
 #' engine.
 #'
 #' - Logs an error and returns FALSE if the JSON file does not exist or does
@@ -10,6 +10,7 @@
 #'   not installed, so calling code can proceed without a hard dependency.
 #'
 #' @param events_json character. Path to the JSON file to validate.
+#' @param schema_version character. Version of the PEcAn events schema to validate against.
 #' @param verbose logical. When `TRUE`, include detailed AJV messages on error.
 #'
 #' @return Logical TRUE if valid, FALSE if invalid.
@@ -22,7 +23,7 @@
 #' #                                package = "PEcAn.data.land"))
 #'
 #' @export
-validate_events_json <- function(events_json, verbose = TRUE) {
+validate_events_json <- function(events_json, schema_version = "0.1.1", verbose = TRUE) {
   if (!file.exists(events_json)) {
     PEcAn.logger::logger.error(glue::glue("events_json file does not exist: {events_json}"))
     return(FALSE)
@@ -33,7 +34,11 @@ validate_events_json <- function(events_json, verbose = TRUE) {
     return(NA)
   }
 
-  schema <- system.file("events_schema_v0.1.0.json", package = "PEcAn.data.land", mustWork = TRUE)
+  schema <- system.file(
+    paste0("events_schema_v", schema_version, ".json"),
+    package = "PEcAn.data.land",
+    mustWork = TRUE
+  )
   ok <- jsonvalidate::json_validate(events_json, schema = schema, engine = "ajv", verbose = verbose, error = FALSE)
   if (isTRUE(ok)) {
     PEcAn.logger::logger.info(glue::glue("events_json file is valid: {events_json}"))
diff --git a/modules/data.land/inst/events_fixtures/events_site1.json b/modules/data.land/inst/events_fixtures/events_site1.json
index 19605953a19..d2b583e4475 100644
--- a/modules/data.land/inst/events_fixtures/events_site1.json
+++ b/modules/data.land/inst/events_fixtures/events_site1.json
@@ -1,6 +1,6 @@
 [
   {
-    "pecan_events_version": "0.1.0",
+    "pecan_events_version": "0.1.1",
     "site_id": "EX1",
     "events": [
       {
@@ -29,11 +29,13 @@
       {
         "event_type": "planting",
         "date": "2022-02-19",
-        "leaf_c_kg_m2": 0.01
+        "leaf_c_kg_m2": 0.01,
+        "crop_code": "Mo17"
       },
       {
         "event_type": "harvest",
         "date": "2022-09-07",
+        "crop_code": "Mo17",
         "frac_above_removed_0to1": 0.1,
         "frac_below_removed_0to1": 0.0,
         "frac_above_to_litter_0to1": 0.0,
diff --git a/modules/data.land/inst/events_fixtures/events_site1_site2.json b/modules/data.land/inst/events_fixtures/events_site1_site2.json
index 84a2ee195d6..fb2cc151249 100644
--- a/modules/data.land/inst/events_fixtures/events_site1_site2.json
+++ b/modules/data.land/inst/events_fixtures/events_site1_site2.json
@@ -1,8 +1,7 @@
 [
   {
-    "pecan_events_version": "0.1.0",
+    "pecan_events_version": "0.1.1",
     "site_id": "S1",
-    "pft": "PFT",
     "events": [
       {
         "event_type": "tillage",
@@ -12,6 +11,7 @@
       {
         "event_type": "harvest",
         "date": "2022-09-01",
+        "crop_code": "wheat",
         "frac_above_removed_0to1": 0.2,
         "frac_below_removed_0to1": 0.0,
         "frac_above_to_litter_0to1": 0.0,
@@ -20,14 +20,14 @@
     ]
   },
   {
-    "pecan_events_version": "0.1.0",
+    "pecan_events_version": "0.1.1",
     "site_id": "S2",
-    "pft": "PFT",
     "events": [
       {
         "event_type": "planting",
         "date": "2022-03-01",
-        "leaf_c_kg_m2": 0.01
+        "leaf_c_kg_m2": 0.01,
+        "crop_code": "maize"
       },
       {
         "event_type": "irrigation",
diff --git a/modules/data.land/inst/events_schema_v0.1.1.json b/modules/data.land/inst/events_schema_v0.1.1.json
new file mode 100644
index 00000000000..71af1ccbd60
--- /dev/null
+++ b/modules/data.land/inst/events_schema_v0.1.1.json
@@ -0,0 +1,81 @@
+{
+  "$schema": "https://json-schema.org/draft/2020-12/schema",
+  "$id": "https://pecanproject.org/schema/events-mvp-0-1-1.json",
+  "oneOf": [
+    { "$ref": "#/$defs/site" },
+    { "type": "array", "items": { "$ref": "#/$defs/site" } }
+  ],
+  "$defs": {
+    "site": {
+      "type": "object",
+      "required": ["pecan_events_version", "site_id", "events"],
+      "properties": {
+        "pecan_events_version": { "type": "string", "const": "0.1.1" },
+        "site_id": { "type": "string", "minLength": 1 },
+        "ensemble_id": { "type": ["string", "null"], "minLength": 1 },
+        "geometry_uri": { "type": ["string", "null"], "format": "uri" },
+        "provenance": { "type": "object", "additionalProperties": true },
+        "events": {
+          "type": "array",
+          "items": {
+            "type": "object",
+            "required": ["event_type", "date"],
+            "properties": {
+              "event_type": {
+                "type": "string",
+                "enum": ["planting", "harvest", "irrigation", "fertilization", "tillage"]
+              },
+              "date": { "type": "string", "pattern": "^\\d{4}-\\d{2}-\\d{2}$" },
+              "fraction_area": { "type": "number", "minimum": 0, "maximum": 1, "default": 1.0 },
+              "source": { "type": "string" },
+
+              "leaf_c_kg_m2": { "type": "number", "minimum": 0 },
+              "wood_c_kg_m2": { "type": "number", "minimum": 0 },
+              "fine_root_c_kg_m2": { "type": "number", "minimum": 0 },
+              "coarse_root_c_kg_m2": { "type": "number", "minimum": 0 },
+              "cultivar": { "type": "string" },
+              "crop_code": { "type": "string" },
+              "crop_display": { "type": "string" },
+
+              "frac_above_removed_0to1": { "type": "number", "minimum": 0, "maximum": 1 },
+              "frac_below_removed_0to1": { "type": "number", "minimum": 0, "maximum": 1 },
+              "frac_above_to_litter_0to1": { "type": "number", "minimum": 0, "maximum": 1 },
+              "frac_below_to_litter_0to1": { "type": "number", "minimum": 0, "maximum": 1 },
+
+              "amount_mm": { "type": "number", "minimum": 0 },
+              "method": { "type": "string", "enum": ["soil", "canopy", "flood"] },
+              "immed_evap_frac_0to1": { "type": "number", "minimum": 0, "maximum": 1 },
+
+              "org_c_kg_m2": { "type": "number", "minimum": 0 },
+              "org_n_kg_m2": { "type": "number", "minimum": 0 },
+              "nh4_n_kg_m2": { "type": "number", "minimum": 0 },
+              "no3_n_kg_m2": { "type": "number", "minimum": 0 },
+
+              "tillage_eff_0to1": { "type": "number", "minimum": 0 },
+              "intensity_category": { "type": "string" },
+              "depth_m": { "type": "number", "minimum": 0 }
+            },
+            "allOf": [
+              { "if": { "properties": { "event_type": { "const": "planting" } } },
+                "then": { "required": ["crop_code", "leaf_c_kg_m2"] } },
+              { "if": { "properties": { "event_type": { "const": "harvest" } } },
+                "then": { "required": ["crop_code", "frac_above_removed_0to1"] } },
+              { "if": { "properties": { "event_type": { "const": "irrigation" } } },
+                "then": { "required": ["amount_mm", "method"] } },
+              { "if": { "properties": { "event_type": { "const": "fertilization" } } },
+                "then": { "anyOf": [
+                  { "required": ["org_c_kg_m2"] },
+                  { "required": ["nh4_n_kg_m2"] },
+                  { "required": ["no3_n_kg_m2"] }
+                ] } },
+              { "if": { "properties": { "event_type": { "const": "tillage" } } },
+                "then": { "required": ["tillage_eff_0to1"] } }
+            ],
+            "additionalProperties": true
+          }
+        }
+      },
+      "additionalProperties": false
+    }
+  }
+}
diff --git a/modules/data.land/man/validate_events_json.Rd b/modules/data.land/man/validate_events_json.Rd
index bab649c3a3c..db37833fe49 100644
--- a/modules/data.land/man/validate_events_json.Rd
+++ b/modules/data.land/man/validate_events_json.Rd
@@ -4,11 +4,13 @@
 \alias{validate_events_json}
 \title{Validate PEcAn events JSON against schema v0.1.0}
 \usage{
-validate_events_json(events_json, verbose = TRUE)
+validate_events_json(events_json, schema_version = "0.1.1", verbose = TRUE)
 }
 \arguments{
 \item{events_json}{character. Path to the JSON file to validate.}
 
+\item{schema_version}{character. Version of the PEcAn events schema to validate against.}
+
 \item{verbose}{logical. When `TRUE`, include detailed AJV messages on error.}
 }
 \value{
@@ -17,7 +19,7 @@ NA if validator unavailable.
 }
 \description{
 Validates a PEcAn events JSON file (single-site object or an array of site
-objects) against the bundled JSON Schema (draft 2020-12) using the AJV
+objects) against the bundled JSON Schema using the AJV
 engine.
 }
 \details{

From 24db91241b426a8dec141a3931809769e037f3f4 Mon Sep 17 00:00:00 2001
From: Chris Black <chris@ckblack.org>
Date: Wed, 25 Feb 2026 03:22:09 -0800
Subject: [PATCH 04/75] right, we said optional for harvest

---
 book_source/03_topical_pages/02_pecan_standards.Rmd | 2 +-
 modules/data.land/inst/events_schema_v0.1.1.json    | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/book_source/03_topical_pages/02_pecan_standards.Rmd b/book_source/03_topical_pages/02_pecan_standards.Rmd
index ad1bd488082..29605b65b7e 100644
--- a/book_source/03_topical_pages/02_pecan_standards.Rmd
+++ b/book_source/03_topical_pages/02_pecan_standards.Rmd
@@ -127,13 +127,13 @@ Optional properties:
 Removal of biomass from the living pool, either by transferring it to dead (litter) biomass or by removing it from the system. Specified as a fraction of live biomass.
 
 Required properties:
-* `crop_code`: A machine_readable identifier that specifies what type of plant was harvested.
 * `frac_above_removed_0to1`: Fraction of existing aboveground biomass removed from the system.
 
 Optional properties:
 
 * `frac_below_removed_0to1`: Fraction of existing beloweground biomass removed from the system. Assumed zero if not specified.
 * `frac_above_to_litter_0to1`, `frac_below_to_litter_0to1`: fraction of existing above- or below-ground live biomass converted to dead litter. Assumed zero if not specified.
+* `crop_code`: A machine_readable identifier that specifies what type of plant was harvested.
 * `cultivar`: Identifier for finer-grainer plant type identifiers that will be meaningful to models with detailed growth parameterizations but likely ignored by PFT-based models.
 * `crop_display`: A human-readable name for the added plant type.
 
diff --git a/modules/data.land/inst/events_schema_v0.1.1.json b/modules/data.land/inst/events_schema_v0.1.1.json
index 71af1ccbd60..14e5b8c7002 100644
--- a/modules/data.land/inst/events_schema_v0.1.1.json
+++ b/modules/data.land/inst/events_schema_v0.1.1.json
@@ -59,7 +59,7 @@
               { "if": { "properties": { "event_type": { "const": "planting" } } },
                 "then": { "required": ["crop_code", "leaf_c_kg_m2"] } },
               { "if": { "properties": { "event_type": { "const": "harvest" } } },
-                "then": { "required": ["crop_code", "frac_above_removed_0to1"] } },
+                "then": { "required": ["frac_above_removed_0to1"] } },
               { "if": { "properties": { "event_type": { "const": "irrigation" } } },
                 "then": { "required": ["amount_mm", "method"] } },
               { "if": { "properties": { "event_type": { "const": "fertilization" } } },

From 7d145c859f6f319ec32acfb07781af2dc880e4c0 Mon Sep 17 00:00:00 2001
From: Chris Black <chris@ckblack.org>
Date: Wed, 25 Feb 2026 03:37:04 -0800
Subject: [PATCH 05/75] changelog

---
 CHANGELOG.md              | 1 +
 modules/data.land/NEWS.md | 1 +
 2 files changed, 2 insertions(+)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index a8246e87abf..4330150845b 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -36,6 +36,7 @@ For more information about this file see also [Keep a Changelog](http://keepacha
   `MCMCpack`, `mvtnorm`, `neonUtilities`, `neonstore`, `PEcAn.benchmark`,
   `PEcAn.visualization`, `rjags`, `sirt`, and `sp` from `Imports` to
   `Suggests` (@omkarrr2533, #3599).
+- Management events specified via `events.json` are now required to specify a crop code for each planting event, so that models can know when to restart with a different PFT (#3828, #3836).
 
 
 
diff --git a/modules/data.land/NEWS.md b/modules/data.land/NEWS.md
index 9c2f9481ea0..bb23a8fedf1 100644
--- a/modules/data.land/NEWS.md
+++ b/modules/data.land/NEWS.md
@@ -23,6 +23,7 @@
   `neonstore`, `PEcAn.benchmark`, `PEcAn.visualization`, `rjags`, `sirt`, and
   `sp` are now suggested rather than required. They are only needed for
   specific optional functionality. (#3599)
+* Updated `validate_events_json()` to use events schema v0.1.1 by default. The previous default v0.1.0 is still available by setting `schema_version="0.1.0"`.
 
 # PEcAn.data.land 1.9.0
 

From 67e055dabf938f23441b805be9c7ec6397ffe0b4 Mon Sep 17 00:00:00 2001
From: Alexey Shiklomanov <alexey.shiklomanov@gmail.com>
Date: Fri, 27 Mar 2026 10:34:58 -0400
Subject: [PATCH 06/75] WIP changes

---
 .Renviron                                     |    0
 modules/data.atmosphere/DESCRIPTION           |    3 -
 .../inst/sipnet-restart-workflow/workflow.R   |  285 +
 pixi.lock                                     | 5572 +++++++++++++++++
 pixi.toml                                     |   95 +
 5 files changed, 5952 insertions(+), 3 deletions(-)
 create mode 100644 .Renviron
 create mode 100644 modules/data.land/inst/sipnet-restart-workflow/workflow.R
 create mode 100644 pixi.lock
 create mode 100644 pixi.toml

diff --git a/.Renviron b/.Renviron
new file mode 100644
index 00000000000..e69de29bb2d
diff --git a/modules/data.atmosphere/DESCRIPTION b/modules/data.atmosphere/DESCRIPTION
index 624278a61f6..f6061884332 100644
--- a/modules/data.atmosphere/DESCRIPTION
+++ b/modules/data.atmosphere/DESCRIPTION
@@ -41,14 +41,12 @@ Imports:
     MASS,
     mgcv,
     ncdf4 (>= 1.15),
-    nneo,
     PEcAn.DB,
     PEcAn.logger,
     PEcAn.remote,
     PEcAn.utils,
     purrr (>= 0.2.3),
     raster,
-    REddyProc,
     reshape2,
     rlang (>= 0.2.0),
     sf,
@@ -59,7 +57,6 @@ Imports:
     tibble,
     tidyr,
     tidyselect,
-    truncnorm,
     units,
     utils,
     XML (>= 3.98-1.4),
diff --git a/modules/data.land/inst/sipnet-restart-workflow/workflow.R b/modules/data.land/inst/sipnet-restart-workflow/workflow.R
new file mode 100644
index 00000000000..5a92c5a8197
--- /dev/null
+++ b/modules/data.land/inst/sipnet-restart-workflow/workflow.R
@@ -0,0 +1,285 @@
+#!/usr/bin/env Rscript
+
+# devtools::install("~/projects/pecan/sipnet-events/modules/data.remote", upgrade = FALSE)
+# devtools::install("~/projects/pecan/sipnet-events/base/workflow", upgrade = FALSE)
+# devtools::install("~/projects/pecan/sipnet-events/models/sipnet", upgrade = FALSE)
+
+# devtools::load_all("~/projects/pecan/sipnet-events/modules/data.land")
+# devtools::load_all("~/projects/pecan/sipnet-events/models/sipnet")
+
+# Pick a parcel from irrigation
+pid <- 39011
+
+irrigation_path <- "/projectnb/dietzelab/ccmmf/usr/ashiklom/event-outputs/irrigation_10000.parquet"
+
+# Find the closest design point to that parcel to use existing met
+parcel_path <- "/projectnb/dietzelab/ccmmf/LandIQ-harmonized-v4.1/parcels.gpkg"
+parcel <- sf::read_sf(
+  parcel_path,
+  query = glue::glue("SELECT * FROM parcels WHERE parcel_id = {pid}")
+)
+
+dp_path <- "/projectnb/dietzelab/ccmmf/management/irrigation/design_points.csv"
+design_points <- read.csv(dp_path) |>
+  sf::st_as_sf(coords = c("lon", "lat"), crs = 4326) |>
+  sf::st_transform(sf::st_crs(parcel))
+dp_idx <- sf::st_nearest_feature(parcel, design_points)
+site_id <- design_points[dp_idx, ][["id"]]
+
+# site1 <- "~/projects/pecan/sipnet-events/modules/data.land/inst/events_fixtures/events_site1.json"
+# site1_multi <- "~/projects/pecan/sipnet-events/modules/data.land/inst/events_fixtures/events_site1_multi.json"
+# site_12 <- "~/projects/pecan/sipnet-events/modules/data.land/inst/events_fixtures/events_site1_site2.json"
+
+binary <- "/projectnb/dietzelab/ccmmf/usr/ashiklom/pecan/sipnet/sipnet"
+met <- file.path(
+  "/projectnb/dietzelab/ccmmf/ensemble/ERA5_SIPNET",
+  site_id,
+  "ERA5.1.2016-01-01.2024-12-31.clim"
+)
+stopifnot(file.exists(met))
+
+# Make the events.json
+planting <- fs::dir_ls(
+  "/projectnb/dietzelab/ccmmf/management/event_files",
+  regexp = "planting_statewide_.*\\.parquet"
+) |>
+  arrow::open_dataset() |>
+  dplyr::collect() |>
+  dplyr::filter(.data$site_id == as.character(.env$pid)) |>
+  dplyr::mutate(date = as.Date(.data$date)) |>
+  tibble::as_tibble()
+
+code_pft_mapping <- planting |>
+  dplyr::distinct(crop_code = .data$code, .data$PFT)
+
+planting_events <- planting |>
+  dplyr::select(
+    "site_id", "event_type", "date",
+    "crop_code" = "code",
+    "leaf_c_kg_m2" = "C_LEAF",
+    "wood_c_kg_m2" = "C_STEM",
+    "fine_root_c_kg_m2" = "C_FINEROOT",
+    "coarse_root_c_kg_m2" = "C_COARSEROOT",
+    "leaf_n_kg_m2" = "N_LEAF",
+    "wood_n_kg_m2" = "N_STEM",
+    "fine_root_n_kg_m2" = "N_FINEROOT",
+    "coarse_root_n_kg_m2" = "N_COARSEROOT"
+  )
+
+# Harvest
+mslsp_path <- "/projectnb/dietzelab/ccmmf/management/phenology/matched_landiq_mslsp_v4.1"
+phenology <- fs::dir_ls(mslsp_path, glob = "*.parquet") |>
+  arrow::open_dataset() |>
+  dplyr::filter(.data$parcel_id == .env$pid, !is.na(.data$mslsp_cycle)) |>
+  dplyr::collect() |>
+  tibble::as_tibble() |>
+  dplyr::arrange(.data$year, .data$mslsp_cycle) |>
+  dplyr::relocate(
+    "year", "mslsp_cycle", dplyr::starts_with("landiq_"),
+  )
+
+# Dummy values for testing
+harvest_events <- phenology |>
+  dplyr::mutate(
+    event_type = "harvest",
+    site_id = as.character(.data$parcel_id),
+    frac_above_removed_0to1 = 0.85
+  ) |>
+  dplyr::select(
+    "site_id", "event_type", "date" = mslsp_OGMn, "frac_above_removed_0to1"
+  )
+
+start_date <- min(planting$date)
+end_date <- max(harvest$date)
+
+irrigation_events <- arrow::open_dataset(irrigation_path) |>
+  dplyr::filter(
+    .data$parcel_id == .env$pid,
+    .data$ens_id == "irr_ens_001"
+  ) |>
+  dplyr::select(-"ens_id") |>
+  dplyr::collect() |>
+  tibble::as_tibble() |>
+  dplyr::filter(.data$date <= .env$end_date) |>
+  dplyr::mutate(
+    event_type = "irrigation",
+    site_id = as.character(.data$parcel_id),
+    .keep = "unused"
+  ) |>
+  dplyr::relocate("site_id", "event_type", "date")
+
+make_event_list <- function(df) {
+  df2list <- function(df) {
+    as.list(df) |> purrr::list_transpose()
+  }
+  df |>
+    tidyr::nest(.by = "site_id", .key = "events") |>
+    dplyr::mutate(events = purrr::map(.data$events, df2list))
+}
+
+planting_n <- make_event_list(planting_events)
+harvest_n <- make_event_list(harvest_events)
+irrigation_n <- make_event_list(irrigation_events)
+all_events <- planting_n |>
+  dplyr::full_join(harvest_n, by = "site_id") |>
+  dplyr::full_join(irrigation_n, by = "site_id") |>
+  dplyr::mutate(
+    events = dplyr::starts_with("events") |>
+      dplyr::across() |>
+      purrr::pmap(c) |>
+      purrr::map(unname),
+    .keep = "unused"
+  )
+
+jsonlite::toJSON(all_events, pretty = TRUE, auto_unbox = TRUE)
+
+################################################################################
+events_json <- site1
+
+outdir <- normalizePath("_test/segments")
+dir.create(outdir, showWarnings = FALSE)
+
+settings <- PEcAn.settings::as.Settings(list(
+  outdir = file.path(outdir, "out"),
+  rundir = file.path(outdir, "run"),
+  modeloutdir = file.path(outdir, "out"),
+  pfts = list(list(
+    name = "grassland",
+    constants = list(num = 1)
+  )),
+  model = list(
+    type = "SIPNET",
+    binary = binary,
+    revision = "v2"
+  ),
+  run = list(
+    site = list(
+      id = site_id,
+      name = site_id,
+      lat = 32.71585,
+      lon = -115.47163
+    ),
+    start.date = start_date,
+    end.date = end_date,
+    inputs = list(met = list(path = met))
+  ),
+  host = list(
+    name = "localhost"
+  )
+))
+
+events <- jsonlite::fromJSON(events_json, simplifyVector = FALSE)
+# TODO: Iterate over events
+site_events_obj <- events[[1]]
+
+site_id <- site_events_obj[["site_id"]]
+site_events_list <- site_events_obj[["events"]]
+site_events_common <- site_events_obj
+site_events_common[["events"]] <- NULL
+
+crop_cycles <- events_to_crop_cycle_starts(site1_multi)
+
+# Empty example
+# crop_cycles <- tibble::tibble(
+#   site_id = character(0),
+#   date = as.Date(NULL),
+#   crop_code = character(0)
+# )
+
+# Get segments
+segments <- tibble::tibble(
+  start_date = c(start_date, crop_cycles[["date"]]),
+  end_date = c(crop_cycles[["date"]] - 1, end_date)
+) |>
+  dplyr::mutate(segment_id = dplyr::row_number())
+
+################################################################################
+
+for (isegment in seq_len(nrow(segments))) {
+  # isegment <- 1
+  segment <- segments[isegment, ]
+  segment_id <- sprintf("%03d", isegment)
+  dstart <- segment[["start_date"]]
+  dend <- segment[["end_date"]]
+
+  segment_dir <- file.path(outdir, paste0("segment_", segment_id))
+  if (dir.exists(segment_dir)) {
+    unlink(segment_dir, recursive = TRUE)
+  }
+  dir.create(segment_dir, showWarnings = FALSE, recursive = TRUE)
+
+  # Filter events to relevant dates
+  events_sub <- site_events_list |>
+    purrr::keep(~as.Date(.x[["date"]]) >= dstart) |>
+    purrr::keep(~as.Date(.x[["date"]]) <= dend)
+
+  # Segment-separated events file
+  eventfile <- file.path(segment_dir, "events.json")
+  segment_event_obj <- list(c(site_events_common, events = list(events_sub)) )
+  jsonlite::write_json(segment_event_obj, eventfile, auto_unbox = TRUE)
+
+  segment_eventfile <- PEcAn.SIPNET::write.events.SIPNET(eventfile, segment_dir)
+
+  # Subset the met to only the dates in this segment. SIPNET does not respect
+  # start/end date, only the dates in the .clim file.
+  met_orig <- read.table(settings[[c("run", "inputs", "met", "path")]])
+  met_segment <- met_orig |>
+    # Create a date from the year + DOY
+    dplyr::mutate(date = as.Date(paste0(V2, "-01-01")) + V3) |>
+    dplyr::filter(date >= dstart, date <= dend) |>
+    dplyr::select(-c("date"))
+  met_segment_file <- file.path(segment_dir, "met.clim")
+  write.table(
+    met_segment,
+    met_segment_file,
+    quote = FALSE,
+    sep = "\t",
+    row.names = FALSE,
+    col.names = FALSE
+  )
+
+  # Segment-specific settings
+  segment_outdir <- file.path(segment_dir, "out")
+  dir.create(segment_outdir, showWarnings = FALSE, recursive = TRUE)
+  segment_rundir <- file.path(segment_dir, "run")
+  dir.create(segment_rundir, showWarnings = FALSE, recursive = TRUE)
+  segment_rundir_withid <- file.path(segment_rundir, segment_id)
+  dir.create(segment_rundir_withid, showWarnings = FALSE, recursive = TRUE)
+
+  segment_settings <- settings
+  segment_settings[["outdir"]] <- segment_outdir
+  segment_settings[["rundir"]] <- segment_rundir
+  segment_settings[["modeloutdir"]] <- segment_rundir
+  segment_settings[[c("run", "start.date")]] <- dstart
+  segment_settings[[c("run", "end.date")]] <- dend
+  segment_settings[[c("run", "inputs", "met", "path")]] <- met_segment_file
+  segment_settings[[c("run", "inputs", "events")]] <- list(path = segment_eventfile)
+
+  if (isegment > 1) {
+    # For isegment > 1, we restart from the *previous* segment's restart.out
+    segment_settings[[c("model", "restart_in")]] <- restart_out
+  }
+  # ...and now, define a new restart.out for *this* segment
+  restart_out <- file.path(segment_dir, "restart.out")
+  segment_settings[[c("model", "restart_out")]] <- restart_out
+
+  # Write runs file
+  writeLines(segment_id, file.path(segment_rundir, "runs.txt"))
+
+  # TODO: Logic to get the trait values corresponding to the segment's PFT.
+  # 1. Cross-reference crop_code against PFT
+  # 2. Get traits from PFT posterior file.
+  segment_traits <- list(list())
+
+  config <- PEcAn.SIPNET::write.config.SIPNET(
+    defaults = settings[["pfts"]],
+    trait.values = segment_traits,
+    settings = segment_settings,
+    run.id = segment_id
+  )
+
+  runs <- PEcAn.workflow::start_model_runs(segment_settings, write = FALSE)
+}
+
+# TODO: Post processing. Combine all the segments together and return output in
+# PEcAn standard.
diff --git a/pixi.lock b/pixi.lock
new file mode 100644
index 00000000000..729d04086a2
--- /dev/null
+++ b/pixi.lock
@@ -0,0 +1,5572 @@
+version: 6
+environments:
+  default:
+    channels:
+    - url: https://conda.anaconda.org/conda-forge/
+    options:
+      pypi-prerelease-mode: if-necessary-or-explicit
+    packages:
+      linux-64:
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/_openmp_mutex-4.5-20_gnu.conda
+      - conda: https://conda.anaconda.org/conda-forge/noarch/_r-mutex-1.0.1-anacondar_1.tar.bz2
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/air-0.8.2-hb17b654_0.conda
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/attr-2.5.2-hb03c661_1.conda
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/aws-c-auth-0.9.3-hef928c7_0.conda
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/aws-c-cal-0.9.13-h2c9d079_1.conda
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/aws-c-common-0.12.6-hb03c661_0.conda
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/aws-c-compression-0.3.1-h8b1a151_9.conda
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/aws-c-event-stream-0.5.7-h28f887f_1.conda
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/aws-c-http-0.10.7-ha8fc4e3_5.conda
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/aws-c-io-0.23.3-hdaf4b65_5.conda
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/aws-c-mqtt-0.13.3-hc63082f_11.conda
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/aws-c-s3-0.11.3-h06ab39a_1.conda
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/aws-c-sdkutils-0.2.4-h8b1a151_4.conda
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/aws-checksums-0.2.7-h8b1a151_5.conda
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/aws-crt-cpp-0.35.4-h8824e59_0.conda
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/aws-sdk-cpp-1.11.606-h20b40b1_10.conda
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/azure-core-cpp-1.16.2-h206d751_0.conda
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+- conda: https://conda.anaconda.org/conda-forge/linux-64/xorg-libice-1.1.2-hb9d3cd8_0.conda
+  sha256: c12396aabb21244c212e488bbdc4abcdef0b7404b15761d9329f5a4a39113c4b
+  md5: fb901ff28063514abb6046c9ec2c4a45
+  depends:
+  - __glibc >=2.17,<3.0.a0
+  - libgcc >=13
+  license: MIT
+  license_family: MIT
+  size: 58628
+  timestamp: 1734227592886
+- conda: https://conda.anaconda.org/conda-forge/linux-64/xorg-libsm-1.2.6-he73a12e_0.conda
+  sha256: 277841c43a39f738927145930ff963c5ce4c4dacf66637a3d95d802a64173250
+  md5: 1c74ff8c35dcadf952a16f752ca5aa49
+  depends:
+  - __glibc >=2.17,<3.0.a0
+  - libgcc >=13
+  - libuuid >=2.38.1,<3.0a0
+  - xorg-libice >=1.1.2,<2.0a0
+  license: MIT
+  license_family: MIT
+  size: 27590
+  timestamp: 1741896361728
+- conda: https://conda.anaconda.org/conda-forge/linux-64/xorg-libx11-1.8.13-he1eb515_0.conda
+  sha256: 516d4060139dbb4de49a4dcdc6317a9353fb39ebd47789c14e6fe52de0deee42
+  md5: 861fb6ccbc677bb9a9fb2468430b9c6a
+  depends:
+  - __glibc >=2.17,<3.0.a0
+  - libgcc >=14
+  - libxcb >=1.17.0,<2.0a0
+  license: MIT
+  license_family: MIT
+  size: 839652
+  timestamp: 1770819209719
+- conda: https://conda.anaconda.org/conda-forge/linux-64/xorg-libxau-1.0.12-hb03c661_1.conda
+  sha256: 6bc6ab7a90a5d8ac94c7e300cc10beb0500eeba4b99822768ca2f2ef356f731b
+  md5: b2895afaf55bf96a8c8282a2e47a5de0
+  depends:
+  - __glibc >=2.17,<3.0.a0
+  - libgcc >=14
+  license: MIT
+  license_family: MIT
+  size: 15321
+  timestamp: 1762976464266
+- conda: https://conda.anaconda.org/conda-forge/linux-64/xorg-libxdmcp-1.1.5-hb03c661_1.conda
+  sha256: 25d255fb2eef929d21ff660a0c687d38a6d2ccfbcbf0cc6aa738b12af6e9d142
+  md5: 1dafce8548e38671bea82e3f5c6ce22f
+  depends:
+  - __glibc >=2.17,<3.0.a0
+  - libgcc >=14
+  license: MIT
+  license_family: MIT
+  size: 20591
+  timestamp: 1762976546182
+- conda: https://conda.anaconda.org/conda-forge/linux-64/xorg-libxext-1.3.7-hb03c661_0.conda
+  sha256: 79c60fc6acfd3d713d6340d3b4e296836a0f8c51602327b32794625826bd052f
+  md5: 34e54f03dfea3e7a2dcf1453a85f1085
+  depends:
+  - __glibc >=2.17,<3.0.a0
+  - libgcc >=14
+  - xorg-libx11 >=1.8.12,<2.0a0
+  license: MIT
+  license_family: MIT
+  size: 50326
+  timestamp: 1769445253162
+- conda: https://conda.anaconda.org/conda-forge/linux-64/xorg-libxrender-0.9.12-hb9d3cd8_0.conda
+  sha256: 044c7b3153c224c6cedd4484dd91b389d2d7fd9c776ad0f4a34f099b3389f4a1
+  md5: 96d57aba173e878a2089d5638016dc5e
+  depends:
+  - __glibc >=2.17,<3.0.a0
+  - libgcc >=13
+  - xorg-libx11 >=1.8.10,<2.0a0
+  license: MIT
+  license_family: MIT
+  size: 33005
+  timestamp: 1734229037766
+- conda: https://conda.anaconda.org/conda-forge/linux-64/xorg-libxt-1.3.1-hb9d3cd8_0.conda
+  sha256: a8afba4a55b7b530eb5c8ad89737d60d60bc151a03fbef7a2182461256953f0e
+  md5: 279b0de5f6ba95457190a1c459a64e31
+  depends:
+  - __glibc >=2.17,<3.0.a0
+  - libgcc >=13
+  - xorg-libice >=1.1.1,<2.0a0
+  - xorg-libsm >=1.2.4,<2.0a0
+  - xorg-libx11 >=1.8.10,<2.0a0
+  license: MIT
+  license_family: MIT
+  size: 379686
+  timestamp: 1731860547604
+- conda: https://conda.anaconda.org/conda-forge/linux-64/zeromq-4.3.5-h41580af_10.conda
+  sha256: 325d370b28e2b9cc1f765c5b4cdb394c91a5d958fbd15da1a14607a28fee09f6
+  md5: 755b096086851e1193f3b10347415d7c
+  depends:
+  - libgcc >=14
+  - __glibc >=2.17,<3.0.a0
+  - libstdcxx >=14
+  - krb5 >=1.22.2,<1.23.0a0
+  - libsodium >=1.0.21,<1.0.22.0a0
+  license: MPL-2.0
+  license_family: MOZILLA
+  size: 311150
+  timestamp: 1772476812121
+- conda: https://conda.anaconda.org/conda-forge/linux-64/zlib-1.3.1-hb9d3cd8_2.conda
+  sha256: 5d7c0e5f0005f74112a34a7425179f4eb6e73c92f5d109e6af4ddeca407c92ab
+  md5: c9f075ab2f33b3bbee9e62d4ad0a6cd8
+  depends:
+  - __glibc >=2.17,<3.0.a0
+  - libgcc >=13
+  - libzlib 1.3.1 hb9d3cd8_2
+  license: Zlib
+  license_family: Other
+  size: 92286
+  timestamp: 1727963153079
+- conda: https://conda.anaconda.org/conda-forge/linux-64/zstd-1.5.7-hb78ec9c_6.conda
+  sha256: 68f0206ca6e98fea941e5717cec780ed2873ffabc0e1ed34428c061e2c6268c7
+  md5: 4a13eeac0b5c8e5b8ab496e6c4ddd829
+  depends:
+  - __glibc >=2.17,<3.0.a0
+  - libzlib >=1.3.1,<2.0a0
+  license: BSD-3-Clause
+  license_family: BSD
+  size: 601375
+  timestamp: 1764777111296
diff --git a/pixi.toml b/pixi.toml
new file mode 100644
index 00000000000..d837eada88a
--- /dev/null
+++ b/pixi.toml
@@ -0,0 +1,95 @@
+[workspace]
+authors = ["Alexey Shiklomanov <alexey.shiklomanov@gmail.com>"]
+channels = ["conda-forge"]
+name = "cimis-et-complete"
+platforms = ["linux-64"]
+version = "0.1.0"
+
+[tasks]
+[tasks.install_package]
+args = [{arg = "pkg"}]
+cmd = 'Rscript -e "install.packages(\"{{ pkg }} \")"'
+
+[tasks.rdinst]
+args = [{arg = "path"}]
+cmd = 'Rscript -e "devtools::install(\"{{ path }}\", upgrade = FALSE)"'
+
+[tasks.rdoc]
+args = [{arg = "path"}]
+cmd = 'Rscript -e "devtools::document(\"{{ path }}\")"'
+
+[tasks.inst_local]
+depends-on = [
+  {task = "rdinst", args = ["base/logger"]},
+  {task = "rdinst", args = ["base/utils"]},
+  {task = "rdinst", args = ["base/remote"]},
+  {task = "rdinst", args = ["base/db"]},
+  {task = "rdinst", args = ["modules/data.land"]},
+  {task = "rdinst", args = ["modules/data.atmosphere"]},
+  {task = "rdinst", args = ["models/sipnet"]},
+]
+
+[tasks.targets]
+args = [{arg = "tar_project", default = "small"}]
+cmd = "TAR_PROJECT={{ tar_project }} Rscript -e 'targets::tar_make()'"
+
+[tasks.outdated]
+args = [{arg = "tar_project", default = "small"}]
+cmd = "TAR_PROJECT={{ tar_project }} Rscript -e 'targets::tar_outdated()'"
+
+[tasks.target_build]
+depends-on = [
+  {task = "rdinst", args = ["modules/data.land"]},
+  {task = "targets"}
+]
+
+[dependencies]
+r = ">=4"
+r-roxygen2 = "==7.3.3"
+r-abind = ">=1.4.5"
+r-arrow = "*"
+r-coda = "*"
+r-curl = "*"
+r-dbplyr = ">=2.4.0"
+r-devtools = "*"
+r-dplyr = ">=1.1.2"
+r-dplR = "*"
+r-foreach = "*"
+r-fs = "*"
+r-future = "*"
+r-furrr = "*"
+r-httr = "*"
+r-httr2 = "*"
+r-jsonlite = "*"
+r-lubridate = "*"
+r-magrittr = "*"
+r-nanoarrow = "*"
+r-ncdf4 = ">=1.15"
+r-purrr = "*"
+r-rlang = "*"
+r-sf = "*"
+r-stringi = "*"
+r-stringr = "*"
+r-terra = "*"
+r-testthat = "*"
+r-tibble = "*"
+r-tidyr = "*"
+r-tidyselect = "*"
+r-withr = "*"
+r-xml = ">=3.98"
+r-dbi = "*"
+r-glue = "*"
+"r-R.utils" = "*"
+r-units = "*"
+r-urltools = "*"
+r-languageserver = ">=0.3.17,<0.4"
+r-targets = ">=1.12.0,<2"
+r-here = ">=1.0.2,<2"
+r-tarchetypes = ">=0.14.0,<0.15"
+r-ggplot2 = ">=4.0.2,<5"
+r-mirai = ">=2.6.1,<3"
+r-clustermq = ">=0.9.8,<0.10"
+r-crew = ">=1.3.0,<2"
+"r-crew.cluster" = ">=0.4.0,<0.5"
+air = ">=0.8.2,<0.9"
+r-visnetwork = ">=2.1.4,<3"

From dac5a9ece82f00e70dd87c4ac96c6b4446804c72 Mon Sep 17 00:00:00 2001
From: Alexey Shiklomanov <alexey.shiklomanov@gmail.com>
Date: Fri, 27 Mar 2026 11:31:36 -0400
Subject: [PATCH 07/75] split prepare events from run workflow

---
 modules/data.land/.Rbuildignore               |   1 +
 .../01-prepare-events.R                       | 122 +++++++++++++++
 .../{workflow.R => 02-run-sipnet.R}           | 142 ++----------------
 .../inst/sipnet-restart-workflow/config.yml   |  20 +++
 pixi.lock                                     | 118 +++++++++++++++
 pixi.toml                                     |   6 +-
 6 files changed, 276 insertions(+), 133 deletions(-)
 create mode 100644 modules/data.land/inst/sipnet-restart-workflow/01-prepare-events.R
 rename modules/data.land/inst/sipnet-restart-workflow/{workflow.R => 02-run-sipnet.R} (50%)
 create mode 100644 modules/data.land/inst/sipnet-restart-workflow/config.yml

diff --git a/modules/data.land/.Rbuildignore b/modules/data.land/.Rbuildignore
index edd7e377255..d8e715679ba 100644
--- a/modules/data.land/.Rbuildignore
+++ b/modules/data.land/.Rbuildignore
@@ -2,3 +2,4 @@ contrib
 data-raw
 ^docs$
 .*venv/
+.*/sipnet-restart-workflow/
diff --git a/modules/data.land/inst/sipnet-restart-workflow/01-prepare-events.R b/modules/data.land/inst/sipnet-restart-workflow/01-prepare-events.R
new file mode 100644
index 00000000000..a3571a934a1
--- /dev/null
+++ b/modules/data.land/inst/sipnet-restart-workflow/01-prepare-events.R
@@ -0,0 +1,122 @@
+#!/usr/bin/env Rscript
+
+config <- config::get(file = "modules/data.land/inst/sipnet-restart-workflow/config.yml")
+
+# Pick a parcel from irrigation
+pid <- config[["parcel_id"]]
+site_id <- config[["site_id"]]
+
+# Find the closest design point to that parcel to use existing met
+if (is.null(site_id)) {
+  parcel_path <- config[["parcel_path"]]
+  parcel <- sf::read_sf(
+    parcel_path,
+    query = glue::glue("SELECT * FROM parcels WHERE parcel_id = {pid}")
+  )
+
+  dp_path <- config[["dp_path"]]
+  design_points <- read.csv(dp_path) |>
+    sf::st_as_sf(coords = c("lon", "lat"), crs = 4326) |>
+    sf::st_transform(sf::st_crs(parcel))
+  dp_idx <- sf::st_nearest_feature(parcel, design_points)
+  site_id <- design_points[dp_idx, ][["id"]]
+}
+
+met <- file.path(
+  config[["met_dir"]],
+  site_id,
+  "ERA5.1.2016-01-01.2024-12-31.clim"
+)
+stopifnot(file.exists(met))
+
+# Make the events.json
+planting <- fs::dir_ls(
+  config[["planting_events_dir"]],
+  regexp = "planting_statewide_.*\\.parquet"
+) |>
+  arrow::open_dataset() |>
+  dplyr::collect() |>
+  dplyr::filter(.data$site_id == as.character(.env$pid)) |>
+  dplyr::mutate(date = as.Date(.data$date)) |>
+  tibble::as_tibble()
+
+code_pft_mapping <- planting |>
+  dplyr::distinct(crop_code = .data$code, .data$PFT)
+
+planting_events <- planting |>
+  dplyr::select(
+    "site_id", "event_type", "date",
+    "crop_code" = "code",
+    "leaf_c_kg_m2" = "C_LEAF",
+    "wood_c_kg_m2" = "C_STEM",
+    "fine_root_c_kg_m2" = "C_FINEROOT",
+    "coarse_root_c_kg_m2" = "C_COARSEROOT",
+    "leaf_n_kg_m2" = "N_LEAF",
+    "wood_n_kg_m2" = "N_STEM",
+    "fine_root_n_kg_m2" = "N_FINEROOT",
+    "coarse_root_n_kg_m2" = "N_COARSEROOT"
+  )
+
+# Harvest
+mslsp_path <- config[["mslsp_path"]]
+phenology <- fs::dir_ls(mslsp_path, glob = "*.parquet") |>
+  arrow::open_dataset() |>
+  dplyr::filter(.data$parcel_id == .env$pid, !is.na(.data$mslsp_cycle)) |>
+  dplyr::collect() |>
+  tibble::as_tibble() |>
+  dplyr::arrange(.data$year, .data$mslsp_cycle) |>
+  dplyr::relocate(
+    "year", "mslsp_cycle", dplyr::starts_with("landiq_"),
+  )
+
+# Dummy values for testing
+harvest_events <- phenology |>
+  dplyr::mutate(
+    event_type = "harvest",
+    site_id = as.character(.data$parcel_id),
+    frac_above_removed_0to1 = 0.85
+  ) |>
+  dplyr::select(
+    "site_id", "event_type", "date" = mslsp_OGMn, "frac_above_removed_0to1"
+  )
+
+start_date <- min(planting$date)
+end_date <- max(harvest_events$date)
+
+irrigation_path <- config[["irrigation_path"]]
+
+irrigation_events <- arrow::open_dataset(irrigation_path) |>
+  dplyr::filter(
+    .data$parcel_id == .env$pid,
+    .data$ens_id == "irr_ens_001"
+  ) |>
+  dplyr::select(-"ens_id") |>
+  dplyr::collect() |>
+  tibble::as_tibble() |>
+  dplyr::filter(.data$date <= .env$end_date) |>
+  dplyr::mutate(
+    event_type = "irrigation",
+    site_id = as.character(.data$parcel_id),
+    .keep = "unused"
+  ) |>
+  dplyr::relocate("site_id", "event_type", "date")
+
+make_event_list <- function(df) {
+  df2list <- function(df) {
+    as.list(df) |> purrr::list_transpose()
+  }
+  df |>
+    tidyr::nest(.by = "site_id", .key = "events") |>
+    dplyr::mutate(events = purrr::map(.data$events, df2list))
+}
+
+planting_n <- make_event_list(planting_events)
+harvest_n <- make_event_list(harvest_events)
+irrigation_n <- make_event_list(irrigation_events)
+all_events <- dplyr::bind_rows(planting_n, harvest_n, irrigation_n) |>
+  dplyr::summarize(events = list(c(events)), .by = "site_id") |>
+  dplyr::mutate(pecan_events_version = "0.1.1", .before = "site_id")
+
+outdir_root <- fs::dir_create(config[["outdir_root"]])
+events_json_file <- fs::path(outdir_root, "events.json")
+jsonlite::write_json(all_events, events_json_file, pretty = TRUE, auto_unbox = TRUE)
diff --git a/modules/data.land/inst/sipnet-restart-workflow/workflow.R b/modules/data.land/inst/sipnet-restart-workflow/02-run-sipnet.R
similarity index 50%
rename from modules/data.land/inst/sipnet-restart-workflow/workflow.R
rename to modules/data.land/inst/sipnet-restart-workflow/02-run-sipnet.R
index 5a92c5a8197..f4e446ef7a3 100644
--- a/modules/data.land/inst/sipnet-restart-workflow/workflow.R
+++ b/modules/data.land/inst/sipnet-restart-workflow/02-run-sipnet.R
@@ -1,143 +1,24 @@
 #!/usr/bin/env Rscript
 
-# devtools::install("~/projects/pecan/sipnet-events/modules/data.remote", upgrade = FALSE)
-# devtools::install("~/projects/pecan/sipnet-events/base/workflow", upgrade = FALSE)
-# devtools::install("~/projects/pecan/sipnet-events/models/sipnet", upgrade = FALSE)
+devtools::load_all("~/projects/pecan/sipnet-events/modules/data.land")
+devtools::load_all("~/projects/pecan/sipnet-events/models/sipnet")
 
-# devtools::load_all("~/projects/pecan/sipnet-events/modules/data.land")
-# devtools::load_all("~/projects/pecan/sipnet-events/models/sipnet")
+config <- config::get(file = "modules/data.land/inst/sipnet-restart-workflow/config.yml")
 
-# Pick a parcel from irrigation
-pid <- 39011
+outdir_root <- config[["outdir_root"]]
 
-irrigation_path <- "/projectnb/dietzelab/ccmmf/usr/ashiklom/event-outputs/irrigation_10000.parquet"
+binary <- config[["sipnet_binary"]]
+stopifnot(file.exists(binary))
 
-# Find the closest design point to that parcel to use existing met
-parcel_path <- "/projectnb/dietzelab/ccmmf/LandIQ-harmonized-v4.1/parcels.gpkg"
-parcel <- sf::read_sf(
-  parcel_path,
-  query = glue::glue("SELECT * FROM parcels WHERE parcel_id = {pid}")
-)
+site_id <- config[["site_id"]]
 
-dp_path <- "/projectnb/dietzelab/ccmmf/management/irrigation/design_points.csv"
-design_points <- read.csv(dp_path) |>
-  sf::st_as_sf(coords = c("lon", "lat"), crs = 4326) |>
-  sf::st_transform(sf::st_crs(parcel))
-dp_idx <- sf::st_nearest_feature(parcel, design_points)
-site_id <- design_points[dp_idx, ][["id"]]
+events_json_file <- fs::path(outdir_root, "events.json")
+events <- jsonlite::read_json(events_json_file, simplifyVector = FALSE)
 
-# site1 <- "~/projects/pecan/sipnet-events/modules/data.land/inst/events_fixtures/events_site1.json"
-# site1_multi <- "~/projects/pecan/sipnet-events/modules/data.land/inst/events_fixtures/events_site1_multi.json"
-# site_12 <- "~/projects/pecan/sipnet-events/modules/data.land/inst/events_fixtures/events_site1_site2.json"
-
-binary <- "/projectnb/dietzelab/ccmmf/usr/ashiklom/pecan/sipnet/sipnet"
-met <- file.path(
-  "/projectnb/dietzelab/ccmmf/ensemble/ERA5_SIPNET",
-  site_id,
-  "ERA5.1.2016-01-01.2024-12-31.clim"
-)
-stopifnot(file.exists(met))
-
-# Make the events.json
-planting <- fs::dir_ls(
-  "/projectnb/dietzelab/ccmmf/management/event_files",
-  regexp = "planting_statewide_.*\\.parquet"
-) |>
-  arrow::open_dataset() |>
-  dplyr::collect() |>
-  dplyr::filter(.data$site_id == as.character(.env$pid)) |>
-  dplyr::mutate(date = as.Date(.data$date)) |>
-  tibble::as_tibble()
-
-code_pft_mapping <- planting |>
-  dplyr::distinct(crop_code = .data$code, .data$PFT)
-
-planting_events <- planting |>
-  dplyr::select(
-    "site_id", "event_type", "date",
-    "crop_code" = "code",
-    "leaf_c_kg_m2" = "C_LEAF",
-    "wood_c_kg_m2" = "C_STEM",
-    "fine_root_c_kg_m2" = "C_FINEROOT",
-    "coarse_root_c_kg_m2" = "C_COARSEROOT",
-    "leaf_n_kg_m2" = "N_LEAF",
-    "wood_n_kg_m2" = "N_STEM",
-    "fine_root_n_kg_m2" = "N_FINEROOT",
-    "coarse_root_n_kg_m2" = "N_COARSEROOT"
-  )
-
-# Harvest
-mslsp_path <- "/projectnb/dietzelab/ccmmf/management/phenology/matched_landiq_mslsp_v4.1"
-phenology <- fs::dir_ls(mslsp_path, glob = "*.parquet") |>
-  arrow::open_dataset() |>
-  dplyr::filter(.data$parcel_id == .env$pid, !is.na(.data$mslsp_cycle)) |>
-  dplyr::collect() |>
-  tibble::as_tibble() |>
-  dplyr::arrange(.data$year, .data$mslsp_cycle) |>
-  dplyr::relocate(
-    "year", "mslsp_cycle", dplyr::starts_with("landiq_"),
-  )
-
-# Dummy values for testing
-harvest_events <- phenology |>
-  dplyr::mutate(
-    event_type = "harvest",
-    site_id = as.character(.data$parcel_id),
-    frac_above_removed_0to1 = 0.85
-  ) |>
-  dplyr::select(
-    "site_id", "event_type", "date" = mslsp_OGMn, "frac_above_removed_0to1"
-  )
-
-start_date <- min(planting$date)
-end_date <- max(harvest$date)
-
-irrigation_events <- arrow::open_dataset(irrigation_path) |>
-  dplyr::filter(
-    .data$parcel_id == .env$pid,
-    .data$ens_id == "irr_ens_001"
-  ) |>
-  dplyr::select(-"ens_id") |>
-  dplyr::collect() |>
-  tibble::as_tibble() |>
-  dplyr::filter(.data$date <= .env$end_date) |>
-  dplyr::mutate(
-    event_type = "irrigation",
-    site_id = as.character(.data$parcel_id),
-    .keep = "unused"
-  ) |>
-  dplyr::relocate("site_id", "event_type", "date")
-
-make_event_list <- function(df) {
-  df2list <- function(df) {
-    as.list(df) |> purrr::list_transpose()
-  }
-  df |>
-    tidyr::nest(.by = "site_id", .key = "events") |>
-    dplyr::mutate(events = purrr::map(.data$events, df2list))
-}
-
-planting_n <- make_event_list(planting_events)
-harvest_n <- make_event_list(harvest_events)
-irrigation_n <- make_event_list(irrigation_events)
-all_events <- planting_n |>
-  dplyr::full_join(harvest_n, by = "site_id") |>
-  dplyr::full_join(irrigation_n, by = "site_id") |>
-  dplyr::mutate(
-    events = dplyr::starts_with("events") |>
-      dplyr::across() |>
-      purrr::pmap(c) |>
-      purrr::map(unname),
-    .keep = "unused"
-  )
-
-jsonlite::toJSON(all_events, pretty = TRUE, auto_unbox = TRUE)
+dates <- purrr::
 
 ################################################################################
-events_json <- site1
-
-outdir <- normalizePath("_test/segments")
-dir.create(outdir, showWarnings = FALSE)
+outdir <- fs::path(outdir_root, "segments") |> fs::dir_create()
 
 settings <- PEcAn.settings::as.Settings(list(
   outdir = file.path(outdir, "out"),
@@ -168,7 +49,6 @@ settings <- PEcAn.settings::as.Settings(list(
   )
 ))
 
-events <- jsonlite::fromJSON(events_json, simplifyVector = FALSE)
 # TODO: Iterate over events
 site_events_obj <- events[[1]]
 
diff --git a/modules/data.land/inst/sipnet-restart-workflow/config.yml b/modules/data.land/inst/sipnet-restart-workflow/config.yml
new file mode 100644
index 00000000000..032e814ae3d
--- /dev/null
+++ b/modules/data.land/inst/sipnet-restart-workflow/config.yml
@@ -0,0 +1,20 @@
+default:
+  parcel_id: 39011
+  site_id: "cf1c223d4e408116"
+  outdir_root: "modules/data.land/inst/sipnet-restart-workflow/_test"
+  irrigation_path: "/projectnb/dietzelab/ccmmf/usr/ashiklom/event-outputs/irrigation_10000.parquet"
+  parcel_path: "/projectnb/dietzelab/ccmmf/LandIQ-harmonized-v4.1/parcels.gpkg"
+  dp_path: "/projectnb/dietzelab/ccmmf/management/irrigation/design_points.csv"
+  sipnet_binary: "/projectnb/dietzelab/ccmmf/usr/ashiklom/pecan/sipnet/sipnet"
+  met_dir: "/projectnb/dietzelab/ccmmf/ensemble/ERA5_SIPNET"
+  planting_events_dir: "/projectnb/dietzelab/ccmmf/management/event_files"
+  mslsp_path: "/projectnb/dietzelab/ccmmf/management/phenology/matched_landiq_mslsp_v4.1"
+
+ashiklom:
+  irrigation_path: !expr path.expand("~/data/irrigation-events-out/irrigation_10000.parquet")
+  parcel_path: !expr path.expand("~/data/LandIQ-harmonized-v4.1/parcels.gpkg") 
+  dp_path: !expr path.expand("~/data/design_points.csv")
+  sipnet_binary: !expr normalizePath("../_helpers/sipnet/sipnet.master", mustWork = TRUE)
+  met_dir: !expr path.expand("~/data/ERA5-site-processed")
+  planting_events_dir: !expr path.expand("~/data/event-files/planting")
+  mslsp_path: !expr path.expand("~/data/matched_landiq_mslsp_v4.1")
diff --git a/pixi.lock b/pixi.lock
index 729d04086a2..9335daab155 100644
--- a/pixi.lock
+++ b/pixi.lock
@@ -187,6 +187,7 @@ environments:
       - conda: https://conda.anaconda.org/conda-forge/linux-64/r-class-7.3_23-r45h54b55ab_1.conda
       - conda: https://conda.anaconda.org/conda-forge/linux-64/r-classint-0.4_11-r45heaba542_1.conda
       - conda: https://conda.anaconda.org/conda-forge/linux-64/r-cli-3.6.5-r45h3697838_1.conda
+      - conda: https://conda.anaconda.org/conda-forge/noarch/r-cliapp-0.1.2-r45hc72bb7e_2.conda
       - conda: https://conda.anaconda.org/conda-forge/noarch/r-clipr-0.8.0-r45hc72bb7e_4.conda
       - conda: https://conda.anaconda.org/conda-forge/linux-64/r-cluster-2.1.8.2-r45heaba542_0.conda
       - conda: https://conda.anaconda.org/conda-forge/linux-64/r-clustermq-0.9.8-r45hded8526_1.conda
@@ -218,6 +219,7 @@ environments:
       - conda: https://conda.anaconda.org/conda-forge/linux-64/r-fansi-1.0.7-r45h54b55ab_0.conda
       - conda: https://conda.anaconda.org/conda-forge/linux-64/r-farver-2.1.2-r45h3697838_2.conda
       - conda: https://conda.anaconda.org/conda-forge/linux-64/r-fastmap-1.2.0-r45h3697838_2.conda
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/r-filelock-1.0.3-r45h54b55ab_2.conda
       - conda: https://conda.anaconda.org/conda-forge/noarch/r-fontawesome-0.5.3-r45hc72bb7e_1.conda
       - conda: https://conda.anaconda.org/conda-forge/noarch/r-foreach-1.5.2-r45hc72bb7e_4.conda
       - conda: https://conda.anaconda.org/conda-forge/linux-64/r-foreign-0.8_91-r45h54b55ab_0.conda
@@ -259,6 +261,7 @@ environments:
       - conda: https://conda.anaconda.org/conda-forge/noarch/r-lintr-3.3.0_1-r45hc72bb7e_0.conda
       - conda: https://conda.anaconda.org/conda-forge/noarch/r-listenv-0.10.1-r45hc72bb7e_0.conda
       - conda: https://conda.anaconda.org/conda-forge/linux-64/r-lme4-1.1_38-r45h3697838_0.conda
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/r-lpsolve-5.6.23-r45h54b55ab_1.conda
       - conda: https://conda.anaconda.org/conda-forge/linux-64/r-lubridate-1.9.5-r45h54b55ab_0.conda
       - conda: https://conda.anaconda.org/conda-forge/linux-64/r-magrittr-2.0.4-r45h54b55ab_0.conda
       - conda: https://conda.anaconda.org/conda-forge/linux-64/r-mass-7.3_65-r45h54b55ab_0.conda
@@ -280,15 +283,18 @@ environments:
       - conda: https://conda.anaconda.org/conda-forge/linux-64/r-nnet-7.3_20-r45h54b55ab_1.conda
       - conda: https://conda.anaconda.org/conda-forge/linux-64/r-openssl-2.3.5-r45h68c19f5_0.conda
       - conda: https://conda.anaconda.org/conda-forge/noarch/r-otel-0.2.0-r45hc72bb7e_1.conda
+      - conda: https://conda.anaconda.org/conda-forge/noarch/r-pak-0.9.2-r45hc72bb7e_0.conda
       - conda: https://conda.anaconda.org/conda-forge/linux-64/r-parallelly-1.46.1-r45h54b55ab_0.conda
       - conda: https://conda.anaconda.org/conda-forge/noarch/r-pillar-1.11.1-r45hc72bb7e_0.conda
       - conda: https://conda.anaconda.org/conda-forge/noarch/r-pkgbuild-1.4.8-r45hc72bb7e_1.conda
+      - conda: https://conda.anaconda.org/conda-forge/noarch/r-pkgcache-2.2.4-r45hc72bb7e_1.conda
       - conda: https://conda.anaconda.org/conda-forge/noarch/r-pkgconfig-2.0.3-r45hc72bb7e_5.conda
       - conda: https://conda.anaconda.org/conda-forge/noarch/r-pkgdown-2.2.0-r45hc72bb7e_0.conda
       - conda: https://conda.anaconda.org/conda-forge/noarch/r-pkgload-1.5.0-r45hc72bb7e_0.conda
       - conda: https://conda.anaconda.org/conda-forge/linux-64/r-plyr-1.8.9-r45h3697838_3.conda
       - conda: https://conda.anaconda.org/conda-forge/linux-64/r-png-0.1_8-r45h6b2d295_3.conda
       - conda: https://conda.anaconda.org/conda-forge/noarch/r-praise-1.0.0-r45hc72bb7e_1009.conda
+      - conda: https://conda.anaconda.org/conda-forge/noarch/r-prettycode-1.1.0-r45hc72bb7e_5.conda
       - conda: https://conda.anaconda.org/conda-forge/noarch/r-prettyunits-1.2.0-r45hc72bb7e_2.conda
       - conda: https://conda.anaconda.org/conda-forge/linux-64/r-processx-3.8.6-r45h54b55ab_1.conda
       - conda: https://conda.anaconda.org/conda-forge/linux-64/r-profvis-0.4.0-r45h54b55ab_1.conda
@@ -328,6 +334,7 @@ environments:
       - conda: https://conda.anaconda.org/conda-forge/linux-64/r-sass-0.4.10-r45h3697838_1.conda
       - conda: https://conda.anaconda.org/conda-forge/noarch/r-scales-1.4.0-r45hc72bb7e_1.conda
       - conda: https://conda.anaconda.org/conda-forge/linux-64/r-secretbase-1.2.0-r45h54b55ab_0.conda
+      - conda: https://conda.anaconda.org/conda-forge/noarch/r-selectr-0.5_1-r45hc72bb7e_0.conda
       - conda: https://conda.anaconda.org/conda-forge/noarch/r-sessioninfo-1.2.3-r45hc72bb7e_1.conda
       - conda: https://conda.anaconda.org/conda-forge/linux-64/r-sf-1.1_0-r45h1d36251_0.conda
       - conda: https://conda.anaconda.org/conda-forge/noarch/r-shiny-1.13.0-r45h785f33e_0.conda
@@ -2747,6 +2754,25 @@ packages:
   license_family: MIT
   size: 1311871
   timestamp: 1757414956557
+- conda: https://conda.anaconda.org/conda-forge/noarch/r-cliapp-0.1.2-r45hc72bb7e_2.conda
+  sha256: e6f8e916018d958aab7742fc4dca39d11e9fd71a6c9cbf706ae48b3f4aa68963
+  md5: eda926ce6830fc811ca06adde8ae3630
+  depends:
+  - r-base >=4.5,<4.6.0a0
+  - r-cli
+  - r-crayon
+  - r-fansi
+  - r-glue >=1.3.0
+  - r-prettycode
+  - r-progress >=1.2.0
+  - r-r6
+  - r-selectr
+  - r-withr
+  - r-xml2
+  license: MIT
+  license_family: MIT
+  size: 248879
+  timestamp: 1757835846605
 - conda: https://conda.anaconda.org/conda-forge/noarch/r-clipr-0.8.0-r45hc72bb7e_4.conda
   sha256: df9c2315dcc8e271947d6fee8d805f1723ce1f41be4369aa820f572d272c042d
   md5: 5deda37b255bc9dc837d00b89dbf2a21
@@ -3188,6 +3214,17 @@ packages:
   license_family: MIT
   size: 73870
   timestamp: 1757421441326
+- conda: https://conda.anaconda.org/conda-forge/linux-64/r-filelock-1.0.3-r45h54b55ab_2.conda
+  sha256: 669a2a6ac19e9ca817b7e6b6ec30643fbf08e423380987f356c3106b596d671a
+  md5: 67bb6dd33b269b3b3d8d6d6c7d7264c8
+  depends:
+  - __glibc >=2.17,<3.0.a0
+  - libgcc >=14
+  - r-base >=4.5,<4.6.0a0
+  license: MIT
+  license_family: MIT
+  size: 33681
+  timestamp: 1757575946026
 - conda: https://conda.anaconda.org/conda-forge/noarch/r-fontawesome-0.5.3-r45hc72bb7e_1.conda
   sha256: 865df12d8cdd8cf577abc8f785a0aa4ee50b4f8751256dffe4676a350943d591
   md5: e9fccb3617ec9776569c6496fa254e64
@@ -3745,6 +3782,17 @@ packages:
   license_family: GPL3
   size: 4684719
   timestamp: 1764694208302
+- conda: https://conda.anaconda.org/conda-forge/linux-64/r-lpsolve-5.6.23-r45h54b55ab_1.conda
+  sha256: 44570160d4d90327de321f2631f6143747a7dff4772012de27f63b66f764e8aa
+  md5: b55b20eef247b07cf9a194dab27adc0d
+  depends:
+  - __glibc >=2.17,<3.0.a0
+  - libgcc >=14
+  - r-base >=4.5,<4.6.0a0
+  license: LGPL-2.0-only
+  license_family: LGPL
+  size: 378203
+  timestamp: 1757495634048
 - conda: https://conda.anaconda.org/conda-forge/linux-64/r-lubridate-1.9.5-r45h54b55ab_0.conda
   sha256: 169ffbb02cd134949c806d521666a5b6fce7d59ea2ca39346c27a13b179a6627
   md5: cec48e713c16eb74b4984019282ad03a
@@ -4006,6 +4054,36 @@ packages:
   license_family: MIT
   size: 286342
   timestamp: 1761151056217
+- conda: https://conda.anaconda.org/conda-forge/noarch/r-pak-0.9.2-r45hc72bb7e_0.conda
+  sha256: 5d8b370c69e88f806d0f163dac91e69d24fe65743c43472fe36099658d8042e8
+  md5: 6a487c2d5e67a5fc80d6619de02c708c
+  depends:
+  - r-assertthat
+  - r-base >=4.5,<4.6.0a0
+  - r-base64enc
+  - r-callr >=3.0.0.9002
+  - r-cli >=1.0.0
+  - r-cliapp >=0.0.0.9002
+  - r-crayon >=1.3.4
+  - r-curl >=3.2
+  - r-desc >=1.2.0
+  - r-filelock >=1.0.2
+  - r-glue >=1.3.0
+  - r-jsonlite
+  - r-lpsolve
+  - r-pkgbuild >=1.0.2
+  - r-pkgcache >=1.0.3
+  - r-prettyunits
+  - r-processx >=3.2.1
+  - r-ps >=1.3.0
+  - r-r6
+  - r-rematch2
+  - r-rprojroot >=1.3.2
+  - r-tibble
+  license: GPL-3.0-only
+  license_family: GPL3
+  size: 5820251
+  timestamp: 1766394791414
 - conda: https://conda.anaconda.org/conda-forge/linux-64/r-parallelly-1.46.1-r45h54b55ab_0.conda
   sha256: bf80a25cead88176880121ea7fefba2d143d1919420bcbef4b640cdad863a1ad
   md5: a3b330fbc5ec2832ad37243a46817df4
@@ -4051,6 +4129,24 @@ packages:
   license_family: GPL3
   size: 221277
   timestamp: 1757496221
+- conda: https://conda.anaconda.org/conda-forge/noarch/r-pkgcache-2.2.4-r45hc72bb7e_1.conda
+  sha256: 7cd5e76b7e4dfbd40aeb0a3bc1b8171dbf045571476c53b0c2d4e02e9d87496f
+  md5: c2f0a882d15573cda41289201873077c
+  depends:
+  - r-base >=4.5,<4.6.0a0
+  - r-callr >=2.0.4.9000
+  - r-cli >=3.2.0
+  - r-curl >=3.2
+  - r-filelock
+  - r-jsonlite
+  - r-prettyunits
+  - r-processx >=3.3.0.9001
+  - r-r6
+  - r-rappdirs
+  license: MIT
+  license_family: MIT
+  size: 921394
+  timestamp: 1758416361320
 - conda: https://conda.anaconda.org/conda-forge/noarch/r-pkgconfig-2.0.3-r45hc72bb7e_5.conda
   sha256: fda425435a533e86da5f0fc89cf45c9f889a4e6f1e2ed536ca23662a8461602c
   md5: 40a5fdd06c7e7880758a021cf2df6c12
@@ -4142,6 +4238,17 @@ packages:
   license_family: MIT
   size: 25995
   timestamp: 1757447352187
+- conda: https://conda.anaconda.org/conda-forge/noarch/r-prettycode-1.1.0-r45hc72bb7e_5.conda
+  sha256: fdac4ff464bf1fd8dfd33cff7f76143ca120296d9ea59d8c0b0a001d5d5b7b16
+  md5: a8d5f73a68f4d4171c40cfbb3c195477
+  depends:
+  - r-base >=4.5,<4.6.0a0
+  - r-crayon
+  - r-withr
+  license: MIT
+  license_family: MIT
+  size: 251464
+  timestamp: 1757801114578
 - conda: https://conda.anaconda.org/conda-forge/noarch/r-prettyunits-1.2.0-r45hc72bb7e_2.conda
   sha256: 0306580de6e867b9060595f5eedde4dbf531ee89c16dd3738dde995b30f3fe14
   md5: 07465728b1fd99d28b286156dac895a3
@@ -4661,6 +4768,17 @@ packages:
   license_family: GPL3
   size: 93507
   timestamp: 1770286893349
+- conda: https://conda.anaconda.org/conda-forge/noarch/r-selectr-0.5_1-r45hc72bb7e_0.conda
+  sha256: d5d4dddd88a5c282c345897bb9faaac4dcc2bca5e63269aec32fa6b21a77bfad
+  md5: cf2e9902cba2ba0ec9368910a6ae908e
+  depends:
+  - r-base >=4.5,<4.6.0a0
+  - r-r6
+  - r-stringr
+  license: BSD-3-Clause
+  license_family: BSD
+  size: 478871
+  timestamp: 1765968903101
 - conda: https://conda.anaconda.org/conda-forge/noarch/r-sessioninfo-1.2.3-r45hc72bb7e_1.conda
   sha256: 83749d9ea9422d89e8e59e93dfee6423297e83a1fab325b03d412700784773bc
   md5: e2d98358063814d40bcb9150b45fb6e9
diff --git a/pixi.toml b/pixi.toml
index d837eada88a..8bef15217b3 100644
--- a/pixi.toml
+++ b/pixi.toml
@@ -6,9 +6,9 @@ platforms = ["linux-64"]
 version = "0.1.0"
 
 [tasks]
-[tasks.install_package]
+[tasks.pak]
 args = [{arg = "pkg"}]
-cmd = 'Rscript -e "install.packages(\"{{ pkg }} \")"'
+cmd = 'Rscript -e "pak::pak(\"{{ pkg }}\")"'
 
 [tasks.rdinst]
 args = [{arg = "path"}]
@@ -27,6 +27,7 @@ depends-on = [
   {task = "rdinst", args = ["modules/data.land"]},
   {task = "rdinst", args = ["modules/data.atmosphere"]},
   {task = "rdinst", args = ["models/sipnet"]},
+  {task = "rdinst", args = ["base/settings"]}
 ]
 
 [tasks.targets]
@@ -93,3 +94,4 @@ r-crew = ">=1.3.0,<2"
 "r-crew.cluster" = ">=0.4.0,<0.5"
 air = ">=0.8.2,<0.9"
 r-visnetwork = ">=2.1.4,<3"
+r-pak = "*"

From 175f15a05eeba0804477c071a528a0af7bc92717 Mon Sep 17 00:00:00 2001
From: Alexey Shiklomanov <alexey.shiklomanov@gmail.com>
Date: Fri, 27 Mar 2026 13:18:56 -0400
Subject: [PATCH 08/75] wip changes

---
 .../01-prepare-events.R                       |  9 +---
 .../sipnet-restart-workflow/02-run-sipnet.R   | 44 +++++++++++++------
 pixi.lock                                     | 28 ++++++++++++
 pixi.toml                                     |  1 +
 4 files changed, 60 insertions(+), 22 deletions(-)

diff --git a/modules/data.land/inst/sipnet-restart-workflow/01-prepare-events.R b/modules/data.land/inst/sipnet-restart-workflow/01-prepare-events.R
index a3571a934a1..724bc75064c 100644
--- a/modules/data.land/inst/sipnet-restart-workflow/01-prepare-events.R
+++ b/modules/data.land/inst/sipnet-restart-workflow/01-prepare-events.R
@@ -22,13 +22,6 @@ if (is.null(site_id)) {
   site_id <- design_points[dp_idx, ][["id"]]
 }
 
-met <- file.path(
-  config[["met_dir"]],
-  site_id,
-  "ERA5.1.2016-01-01.2024-12-31.clim"
-)
-stopifnot(file.exists(met))
-
 # Make the events.json
 planting <- fs::dir_ls(
   config[["planting_events_dir"]],
@@ -114,7 +107,7 @@ planting_n <- make_event_list(planting_events)
 harvest_n <- make_event_list(harvest_events)
 irrigation_n <- make_event_list(irrigation_events)
 all_events <- dplyr::bind_rows(planting_n, harvest_n, irrigation_n) |>
-  dplyr::summarize(events = list(c(events)), .by = "site_id") |>
+  dplyr::summarize(events = list(purrr::list_c(.data$events)), .by = "site_id") |>
   dplyr::mutate(pecan_events_version = "0.1.1", .before = "site_id")
 
 outdir_root <- fs::dir_create(config[["outdir_root"]])
diff --git a/modules/data.land/inst/sipnet-restart-workflow/02-run-sipnet.R b/modules/data.land/inst/sipnet-restart-workflow/02-run-sipnet.R
index f4e446ef7a3..c8247d4762f 100644
--- a/modules/data.land/inst/sipnet-restart-workflow/02-run-sipnet.R
+++ b/modules/data.land/inst/sipnet-restart-workflow/02-run-sipnet.R
@@ -15,7 +15,20 @@ site_id <- config[["site_id"]]
 events_json_file <- fs::path(outdir_root, "events.json")
 events <- jsonlite::read_json(events_json_file, simplifyVector = FALSE)
 
-dates <- purrr::
+all_dates <- events |>
+  purrr::pluck(1, "events") |>
+  purrr::map_chr("date") |>
+  as.Date()
+
+start_date <- min(all_dates)
+end_date <- max(all_dates)
+
+met <- file.path(
+  config[["met_dir"]],
+  site_id,
+  "ERA5.1.2016-01-01.2024-12-31.clim"
+)
+stopifnot(file.exists(met))
 
 ################################################################################
 outdir <- fs::path(outdir_root, "segments") |> fs::dir_create()
@@ -49,6 +62,14 @@ settings <- PEcAn.settings::as.Settings(list(
   )
 ))
 
+crop_cycles <- events_to_crop_cycle_starts(events_json_file)
+# Empty example
+# crop_cycles <- tibble::tibble(
+#   site_id = character(0),
+#   date = as.Date(NULL),
+#   crop_code = character(0)
+# )
+
 # TODO: Iterate over events
 site_events_obj <- events[[1]]
 
@@ -57,15 +78,6 @@ site_events_list <- site_events_obj[["events"]]
 site_events_common <- site_events_obj
 site_events_common[["events"]] <- NULL
 
-crop_cycles <- events_to_crop_cycle_starts(site1_multi)
-
-# Empty example
-# crop_cycles <- tibble::tibble(
-#   site_id = character(0),
-#   date = as.Date(NULL),
-#   crop_code = character(0)
-# )
-
 # Get segments
 segments <- tibble::tibble(
   start_date = c(start_date, crop_cycles[["date"]]),
@@ -95,20 +107,24 @@ for (isegment in seq_len(nrow(segments))) {
 
   # Segment-separated events file
   eventfile <- file.path(segment_dir, "events.json")
-  segment_event_obj <- list(c(site_events_common, events = list(events_sub)) )
-  jsonlite::write_json(segment_event_obj, eventfile, auto_unbox = TRUE)
+  segment_event_obj <- list(c(site_events_common, events = list(events_sub)))
+  jsonlite::write_json(segment_event_obj, eventfile, auto_unbox = TRUE, pretty = TRUE)
 
   segment_eventfile <- PEcAn.SIPNET::write.events.SIPNET(eventfile, segment_dir)
 
+  metpath <- settings[[c("run", "inputs", "met", "path")]]
+  met_segment_file <- file.path(segment_dir, "met.clim")
+
   # Subset the met to only the dates in this segment. SIPNET does not respect
   # start/end date, only the dates in the .clim file.
-  met_orig <- read.table(settings[[c("run", "inputs", "met", "path")]])
+  # TODO: Use `split_inputs.SIPNET` here instead...
+
+  met_orig <- read.table(metpath)
   met_segment <- met_orig |>
     # Create a date from the year + DOY
     dplyr::mutate(date = as.Date(paste0(V2, "-01-01")) + V3) |>
     dplyr::filter(date >= dstart, date <= dend) |>
     dplyr::select(-c("date"))
-  met_segment_file <- file.path(segment_dir, "met.clim")
   write.table(
     met_segment,
     met_segment_file,
diff --git a/pixi.lock b/pixi.lock
index 9335daab155..41766fa290c 100644
--- a/pixi.lock
+++ b/pixi.lock
@@ -250,6 +250,7 @@ environments:
       - conda: https://conda.anaconda.org/conda-forge/noarch/r-iterators-1.0.14-r45hc72bb7e_4.conda
       - conda: https://conda.anaconda.org/conda-forge/noarch/r-jquerylib-0.1.4-r45hc72bb7e_4.conda
       - conda: https://conda.anaconda.org/conda-forge/linux-64/r-jsonlite-2.0.0-r45h54b55ab_1.conda
+      - conda: https://conda.anaconda.org/conda-forge/noarch/r-jsonvalidate-1.5.0-r45hc72bb7e_1.conda
       - conda: https://conda.anaconda.org/conda-forge/linux-64/r-kernsmooth-2.23_26-r45ha0a88a1_1.conda
       - conda: https://conda.anaconda.org/conda-forge/noarch/r-knitr-1.51-r45hc72bb7e_0.conda
       - conda: https://conda.anaconda.org/conda-forge/noarch/r-labeling-0.4.3-r45hc72bb7e_2.conda
@@ -363,6 +364,7 @@ environments:
       - conda: https://conda.anaconda.org/conda-forge/linux-64/r-urltools-1.7.3.1-r45h3697838_1.conda
       - conda: https://conda.anaconda.org/conda-forge/noarch/r-usethis-3.2.1-r45hc72bb7e_1.conda
       - conda: https://conda.anaconda.org/conda-forge/linux-64/r-utf8-1.2.6-r45h54b55ab_1.conda
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/r-v8-8.0.1-r45h3697838_0.conda
       - conda: https://conda.anaconda.org/conda-forge/linux-64/r-vctrs-0.7.1-r45h3697838_0.conda
       - conda: https://conda.anaconda.org/conda-forge/noarch/r-viridislite-0.4.3-r45hc72bb7e_0.conda
       - conda: https://conda.anaconda.org/conda-forge/noarch/r-visnetwork-2.1.4-r45hc72bb7e_1.conda
@@ -3623,6 +3625,17 @@ packages:
   license_family: MIT
   size: 638574
   timestamp: 1757419590757
+- conda: https://conda.anaconda.org/conda-forge/noarch/r-jsonvalidate-1.5.0-r45hc72bb7e_1.conda
+  sha256: 12921f3fe9e72d4c6396eb0847151df200951ee08a7f19047ead3eed7592d171
+  md5: 39c5b5dbabffaee26021620971fd6b1b
+  depends:
+  - r-base >=4.5,<4.6.0a0
+  - r-r6
+  - r-v8
+  license: MIT
+  license_family: MIT
+  size: 169177
+  timestamp: 1758511478721
 - conda: https://conda.anaconda.org/conda-forge/linux-64/r-kernsmooth-2.23_26-r45ha0a88a1_1.conda
   sha256: 032d445f1a7e4f35e5762a28ffefe90f6f68cc2bc3b6806e0d0fba89bb1e5b43
   md5: bd7ceffa31a5b9980641d9b40c27e85d
@@ -5253,6 +5266,21 @@ packages:
   license_family: APACHE
   size: 147244
   timestamp: 1757424673681
+- conda: https://conda.anaconda.org/conda-forge/linux-64/r-v8-8.0.1-r45h3697838_0.conda
+  sha256: d5b7ddd15efe71500090da3a2bd79453c5a4432bf9d87483ad2be1129b5cf0b4
+  md5: 1861207714878e6df085591005681dc7
+  depends:
+  - __glibc >=2.17,<3.0.a0
+  - libgcc >=14
+  - libstdcxx >=14
+  - r-base >=4.5,<4.6.0a0
+  - r-curl >=1.0
+  - r-jsonlite >=1.0
+  - r-rcpp >=0.12.12
+  license: MIT
+  license_family: MIT
+  size: 10399678
+  timestamp: 1760099076903
 - conda: https://conda.anaconda.org/conda-forge/linux-64/r-vctrs-0.7.1-r45h3697838_0.conda
   sha256: 25033570039c1a0ff96356fc4f867c268fc299b379a5e4e4f41ba1263cdce162
   md5: f6e3a62834212f3a44fa4a0a97fedcde
diff --git a/pixi.toml b/pixi.toml
index 8bef15217b3..f5a7a8ccd76 100644
--- a/pixi.toml
+++ b/pixi.toml
@@ -95,3 +95,4 @@ r-crew = ">=1.3.0,<2"
 air = ">=0.8.2,<0.9"
 r-visnetwork = ">=2.1.4,<3"
 r-pak = "*"
+r-jsonvalidate = ">=1.5.0,<2"

From a97a9463bb410163304b880cadbadc6fe1b55bfe Mon Sep 17 00:00:00 2001
From: Alexey Shiklomanov <alexey.shiklomanov@gmail.com>
Date: Fri, 27 Mar 2026 13:34:14 -0400
Subject: [PATCH 09/75] remove .Renviron

---
 .Renviron | 0
 1 file changed, 0 insertions(+), 0 deletions(-)
 delete mode 100644 .Renviron

diff --git a/.Renviron b/.Renviron
deleted file mode 100644
index e69de29bb2d..00000000000

From 4174200fe4556e4300712e12ed4dfc613569e11b Mon Sep 17 00:00:00 2001
From: Alexey Shiklomanov <alexey.shiklomanov@gmail.com>
Date: Fri, 27 Mar 2026 16:17:30 -0400
Subject: [PATCH 10/75] sipnet output workaround

---
 models/sipnet/R/model2netcdf.SIPNET.R | 29 ++++++++++++++++++++++++++-
 1 file changed, 28 insertions(+), 1 deletion(-)

diff --git a/models/sipnet/R/model2netcdf.SIPNET.R b/models/sipnet/R/model2netcdf.SIPNET.R
index 480467d2c8f..b7793b4f2b7 100644
--- a/models/sipnet/R/model2netcdf.SIPNET.R
+++ b/models/sipnet/R/model2netcdf.SIPNET.R
@@ -64,7 +64,34 @@ model2netcdf.SIPNET <- function(outdir, sitelat, sitelon, start_date, end_date,
   # if the first line starts with "year", there is no Notes line.
   first_line <- readLines(sipnet_out_file, n = 1)
   skip_n <- if (grepl("^year", first_line)) 0 else 1
-  sipnet_output <- utils::read.table(sipnet_out_file, header = T, skip = skip_n, sep = "")
+  # Temporary workaround until
+  # https://github.com/PecanProject/sipnet/issues/304 is resolved.
+  sipnet_output <- tryCatch({
+    utils::read.table(sipnet_out_file, header = TRUE, skip = skip_n, sep = "")
+  }, error = function(err) {
+    PEcAn.logger::logger.warn(
+      "Failed to read using `read.table`. ",
+      "Trying to parse output manually."
+    )
+    raw_lines <- readLines(sipnet_out_file)
+    raw_header <- raw_lines[[1 + skip_n]]
+    raw_body <- tail(raw_lines, -(1 + skip_n))
+    # SIPNET output is right-aligned with the column names in the header.
+    # We use this to figure out where the numbers end if there are no spaces.
+    token_matches <- gregexpr("\\S+", raw_header, perl = TRUE)
+    proc_header <- regmatches(raw_header, token_matches)[[1]]
+    col_ends <- token_matches[[1]] + attr(token_matches[[1]], "match.length") - 1
+    col_starts <- c(1, head(col_ends, -1) + 1)
+    col_widths <- col_ends - col_starts + 1
+    result <- read.fwf(
+      textConnection(raw_body),
+      widths = col_widths,
+      col.names = proc_header,
+      na.strings = c("nan", "-nan")
+    )
+    result[] <- lapply(result, as.numeric)
+    result
+  })
   #sipnet_output_dims <- dim(sipnet_output)
   
   ### Determine number of years and output timestep

From 236fb4a85ef2bb04b0365fdaa5b3dd3da2247096 Mon Sep 17 00:00:00 2001
From: Alexey Shiklomanov <alexey.shiklomanov@gmail.com>
Date: Fri, 27 Mar 2026 16:17:43 -0400
Subject: [PATCH 11/75] pixi dependencies

---
 pixi.lock | 144 ++++++++++++++++++++++++++++++++++++++++++++++++++++++
 pixi.toml |   5 ++
 2 files changed, 149 insertions(+)

diff --git a/pixi.lock b/pixi.lock
index 41766fa290c..d988cdf7e37 100644
--- a/pixi.lock
+++ b/pixi.lock
@@ -61,6 +61,7 @@ environments:
       - conda: https://conda.anaconda.org/conda-forge/linux-64/hdf4-4.2.15-h2a13503_7.conda
       - conda: https://conda.anaconda.org/conda-forge/linux-64/hdf5-1.14.6-nompi_h19486de_106.conda
       - conda: https://conda.anaconda.org/conda-forge/linux-64/icu-78.3-h33c6efd_0.conda
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/jags-4.3.2-h647a790_1.conda
       - conda: https://conda.anaconda.org/conda-forge/linux-64/json-c-0.18-h6688a6e_0.conda
       - conda: https://conda.anaconda.org/conda-forge/noarch/kernel-headers_linux-64-4.18.0-he073ed8_9.conda
       - conda: https://conda.anaconda.org/conda-forge/linux-64/keyutils-1.6.3-hb9d3cd8_0.conda
@@ -210,6 +211,7 @@ environments:
       - conda: https://conda.anaconda.org/conda-forge/noarch/r-devtools-2.4.6-r45hc72bb7e_0.conda
       - conda: https://conda.anaconda.org/conda-forge/linux-64/r-diffobj-0.3.6-r45h54b55ab_1.conda
       - conda: https://conda.anaconda.org/conda-forge/linux-64/r-digest-0.6.39-r45h3697838_0.conda
+      - conda: https://conda.anaconda.org/conda-forge/noarch/r-doparallel-1.0.17-r45hc72bb7e_4.conda
       - conda: https://conda.anaconda.org/conda-forge/noarch/r-downlit-0.4.5-r45hc72bb7e_0.conda
       - conda: https://conda.anaconda.org/conda-forge/linux-64/r-dplr-1.7.8-r45heaba542_1.conda
       - conda: https://conda.anaconda.org/conda-forge/linux-64/r-dplyr-1.2.0-r45h3697838_0.conda
@@ -316,13 +318,17 @@ environments:
       - conda: https://conda.anaconda.org/conda-forge/noarch/r-rcolorbrewer-1.1_3-r45h785f33e_4.conda
       - conda: https://conda.anaconda.org/conda-forge/linux-64/r-rcpp-1.1.1-r45h3697838_0.conda
       - conda: https://conda.anaconda.org/conda-forge/linux-64/r-rcppeigen-0.3.4.0.2-r45h3704496_1.conda
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/r-rcpptoml-0.2.3-r45h3697838_1.conda
       - conda: https://conda.anaconda.org/conda-forge/noarch/r-rdpack-2.6.6-r45hc72bb7e_0.conda
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/r-readr-2.2.0-r45h3697838_0.conda
       - conda: https://conda.anaconda.org/conda-forge/noarch/r-recommended-4.5-r45hd8ed1ab_1008.conda
       - conda: https://conda.anaconda.org/conda-forge/noarch/r-reformulas-0.4.4-r45hc72bb7e_0.conda
       - conda: https://conda.anaconda.org/conda-forge/noarch/r-rematch2-2.1.2-r45hc72bb7e_5.conda
       - conda: https://conda.anaconda.org/conda-forge/noarch/r-remotes-2.5.0-r45hc72bb7e_2.conda
       - conda: https://conda.anaconda.org/conda-forge/noarch/r-repr-1.1.7-r45h785f33e_2.conda
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/r-reticulate-1.45.0-r45h3697838_0.conda
       - conda: https://conda.anaconda.org/conda-forge/noarch/r-rex-1.2.1-r45hc72bb7e_4.conda
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/r-rjags-4_17-r45h3697838_1.conda
       - conda: https://conda.anaconda.org/conda-forge/linux-64/r-rlang-1.1.7-r45h3697838_0.conda
       - conda: https://conda.anaconda.org/conda-forge/noarch/r-rmarkdown-2.30-r45hc72bb7e_0.conda
       - conda: https://conda.anaconda.org/conda-forge/linux-64/r-roxygen2-7.3.3-r45h3697838_1.conda
@@ -359,6 +365,7 @@ environments:
       - conda: https://conda.anaconda.org/conda-forge/linux-64/r-timechange-0.4.0-r45h3697838_0.conda
       - conda: https://conda.anaconda.org/conda-forge/noarch/r-tinytex-0.58-r45hc72bb7e_0.conda
       - conda: https://conda.anaconda.org/conda-forge/linux-64/r-triebeard-0.4.1-r45h3697838_4.conda
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/r-tzdb-0.5.0-r45h3697838_2.conda
       - conda: https://conda.anaconda.org/conda-forge/linux-64/r-units-1.0_0-r45h3697838_0.conda
       - conda: https://conda.anaconda.org/conda-forge/noarch/r-urlchecker-1.0.1-r45hc72bb7e_4.conda
       - conda: https://conda.anaconda.org/conda-forge/linux-64/r-urltools-1.7.3.1-r45h3697838_1.conda
@@ -368,6 +375,7 @@ environments:
       - conda: https://conda.anaconda.org/conda-forge/linux-64/r-vctrs-0.7.1-r45h3697838_0.conda
       - conda: https://conda.anaconda.org/conda-forge/noarch/r-viridislite-0.4.3-r45hc72bb7e_0.conda
       - conda: https://conda.anaconda.org/conda-forge/noarch/r-visnetwork-2.1.4-r45hc72bb7e_1.conda
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/r-vroom-1.7.0-r45h3697838_0.conda
       - conda: https://conda.anaconda.org/conda-forge/noarch/r-waldo-0.6.2-r45hc72bb7e_1.conda
       - conda: https://conda.anaconda.org/conda-forge/noarch/r-whisker-0.4.1-r45hc72bb7e_3.conda
       - conda: https://conda.anaconda.org/conda-forge/noarch/r-withr-3.0.2-r45hc72bb7e_1.conda
@@ -1063,6 +1071,21 @@ packages:
   license_family: MIT
   size: 12723451
   timestamp: 1773822285671
+- conda: https://conda.anaconda.org/conda-forge/linux-64/jags-4.3.2-h647a790_1.conda
+  sha256: fbd5005100423c1baa95c7e5a962f636d12fcb40d08897b1d2a6a9925e093871
+  md5: 3888dd884df92d5ea9993dc8338e91bc
+  depends:
+  - __glibc >=2.17,<3.0.a0
+  - libblas >=3.9.0,<4.0a0
+  - libgcc-ng >=12
+  - libgfortran-ng
+  - libgfortran5 >=12.4.0
+  - liblapack >=3.9.0,<4.0a0
+  - libstdcxx-ng >=12
+  license: GPL-2.0-only
+  license_family: GPL
+  size: 1013020
+  timestamp: 1721907912966
 - conda: https://conda.anaconda.org/conda-forge/linux-64/json-c-0.18-h6688a6e_0.conda
   sha256: 09e706cb388d3ea977fabcee8e28384bdaad8ce1fc49340df5f868a2bd95a7da
   md5: 38f5dbc9ac808e31c00650f7be1db93f
@@ -3078,6 +3101,17 @@ packages:
   license_family: GPL2
   size: 218412
   timestamp: 1763566744987
+- conda: https://conda.anaconda.org/conda-forge/noarch/r-doparallel-1.0.17-r45hc72bb7e_4.conda
+  sha256: 2edd40491f63166d242e4e092f37c793a9c51c45fc8eae6132c11d5831706205
+  md5: af58987665d786f31bfd45264cb72ae4
+  depends:
+  - r-base >=4.5,<4.6.0a0
+  - r-foreach >=1.2.0
+  - r-iterators >=1.0.0
+  license: GPL-2.0-only
+  license_family: GPL2
+  size: 200811
+  timestamp: 1757511066319
 - conda: https://conda.anaconda.org/conda-forge/noarch/r-downlit-0.4.5-r45hc72bb7e_0.conda
   sha256: 73396f3432df8aac38aeb15f27ebdecb216d3b63bfa3c87fc6b996acf27b82f8
   md5: 49850c61c12fbd8dd19b30d9bc81833f
@@ -4522,6 +4556,19 @@ packages:
   license_family: GPL2
   size: 1496128
   timestamp: 1757496030112
+- conda: https://conda.anaconda.org/conda-forge/linux-64/r-rcpptoml-0.2.3-r45h3697838_1.conda
+  sha256: 8e10fa6f550c83cdc99175443ecc92db178369e82a7dcb743e1fe7ce87d39530
+  md5: 707ba8dabbbffd03f5907406a0fe8368
+  depends:
+  - __glibc >=2.17,<3.0.a0
+  - libgcc >=14
+  - libstdcxx >=14
+  - r-base >=4.5,<4.6.0a0
+  - r-rcpp >=0.11.5
+  license: GPL-2.0-or-later
+  license_family: GPL2
+  size: 227793
+  timestamp: 1757490566643
 - conda: https://conda.anaconda.org/conda-forge/noarch/r-rdpack-2.6.6-r45hc72bb7e_0.conda
   sha256: e53806a09281774eb7c5e6e8572278dc4e82994d41bdc92a5e18793711301865
   md5: 2b9eb11b885d45d9810089deb8078f02
@@ -4533,6 +4580,29 @@ packages:
   license_family: GPL3
   size: 638016
   timestamp: 1770551164495
+- conda: https://conda.anaconda.org/conda-forge/linux-64/r-readr-2.2.0-r45h3697838_0.conda
+  sha256: 06a42932d182259540fd53dca6ac6e988bb28b70d4b09d5786b4260928090598
+  md5: a5f0d7d99d912486b2d93a576fadb8e0
+  depends:
+  - __glibc >=2.17,<3.0.a0
+  - libgcc >=14
+  - libstdcxx >=14
+  - r-base >=4.5,<4.6.0a0
+  - r-cli
+  - r-clipr
+  - r-cpp11
+  - r-crayon
+  - r-hms >=0.4.1
+  - r-lifecycle >=0.2.0
+  - r-r6
+  - r-rlang
+  - r-tibble
+  - r-tzdb >=0.1.1
+  - r-vroom >=1.5.4
+  license: MIT
+  license_family: MIT
+  size: 808559
+  timestamp: 1771573588021
 - conda: https://conda.anaconda.org/conda-forge/noarch/r-recommended-4.5-r45hd8ed1ab_1008.conda
   sha256: aabe4c91dd234e4cadc51f5a83cd501d269682d6e34320b336595fda71fbfb17
   md5: 340c190b18b45a12a1359d78467fba78
@@ -4600,6 +4670,27 @@ packages:
   license_family: GPL3
   size: 147271
   timestamp: 1757481783597
+- conda: https://conda.anaconda.org/conda-forge/linux-64/r-reticulate-1.45.0-r45h3697838_0.conda
+  sha256: a24dd07d3f234effd6175b1f4aef8e7841896fe2d0f1bd95f7e37873b20109a5
+  md5: d12318e8af8655d396b1f26ffb99fe09
+  depends:
+  - __glibc >=2.17,<3.0.a0
+  - libgcc >=14
+  - libstdcxx >=14
+  - r-base >=4.5,<4.6.0a0
+  - r-here
+  - r-jsonlite
+  - r-matrix
+  - r-png
+  - r-rappdirs
+  - r-rcpp >=1.0.7
+  - r-rcpptoml
+  - r-rlang
+  - r-withr
+  license: Apache-2.0
+  license_family: APACHE
+  size: 1916204
+  timestamp: 1771004475839
 - conda: https://conda.anaconda.org/conda-forge/noarch/r-rex-1.2.1-r45hc72bb7e_4.conda
   sha256: e8f6a44ed24e37df7a9a311ac00355294d09e0ad92e1aef9d0fc06045ec6c382
   md5: 461e9fef868aacbde6b73ba681ebce34
@@ -4611,6 +4702,20 @@ packages:
   license_family: MIT
   size: 126090
   timestamp: 1757451641758
+- conda: https://conda.anaconda.org/conda-forge/linux-64/r-rjags-4_17-r45h3697838_1.conda
+  sha256: b0d732923793090f4e91112a03a1bbb0f71e7180d6c89f95853ebf48fe0bb61e
+  md5: 3ef4fb93f36b0534412e661042f5403e
+  depends:
+  - __glibc >=2.17,<3.0.a0
+  - jags 4.*
+  - libgcc >=14
+  - libstdcxx >=14
+  - r-base >=4.5,<4.6.0a0
+  - r-coda >=0.13
+  license: GPL-2.0-only
+  license_family: GPL2
+  size: 149658
+  timestamp: 1757622623100
 - conda: https://conda.anaconda.org/conda-forge/linux-64/r-rlang-1.1.7-r45h3697838_0.conda
   sha256: dd4df06afcc68d95473939cc1a6ff2b2fa190412ddefac214da1a48a87441d9f
   md5: 4623f836bbe3b849519dd29cf55881a9
@@ -5186,6 +5291,19 @@ packages:
   license_family: MIT
   size: 185274
   timestamp: 1757482938729
+- conda: https://conda.anaconda.org/conda-forge/linux-64/r-tzdb-0.5.0-r45h3697838_2.conda
+  sha256: d5e6baaf4063a7fb2c462e6f1a5ffda1c8928eb4b943887e4989e8eac9a98916
+  md5: 54673c8b5186c85794f0bd40d7c49bb4
+  depends:
+  - __glibc >=2.17,<3.0.a0
+  - libgcc >=14
+  - libstdcxx >=14
+  - r-base >=4.5,<4.6.0a0
+  - r-cpp11 >=0.5.2
+  license: MIT
+  license_family: MIT
+  size: 555420
+  timestamp: 1757490039639
 - conda: https://conda.anaconda.org/conda-forge/linux-64/r-units-1.0_0-r45h3697838_0.conda
   sha256: 8d8fe2da1482f3c7496d0959c05fb67a7db164e674343d01c74c6f417e01399a
   md5: d2caba583b30269a834a053307f80a66
@@ -5319,6 +5437,32 @@ packages:
   license_family: MIT
   size: 3724506
   timestamp: 1757566751580
+- conda: https://conda.anaconda.org/conda-forge/linux-64/r-vroom-1.7.0-r45h3697838_0.conda
+  sha256: 71b7da0c90cbcc0430f34a30a38b71c754bc6fa90dbf955438be2db3021c693f
+  md5: e43318d3f2be7d5adf0c06d79520ac8f
+  depends:
+  - __glibc >=2.17,<3.0.a0
+  - libgcc >=14
+  - libstdcxx >=14
+  - r-base >=4.5,<4.6.0a0
+  - r-bit64
+  - r-cli
+  - r-cpp11 >=0.2.0
+  - r-crayon
+  - r-glue
+  - r-hms
+  - r-lifecycle
+  - r-progress >=1.2.1
+  - r-rlang >=0.4.2
+  - r-tibble >=2.0.0
+  - r-tidyselect
+  - r-tzdb >=0.1.1
+  - r-vctrs >=0.2.0
+  - r-withr
+  license: MIT
+  license_family: MIT
+  size: 935533
+  timestamp: 1769540679531
 - conda: https://conda.anaconda.org/conda-forge/noarch/r-waldo-0.6.2-r45hc72bb7e_1.conda
   sha256: 57eb80cb919524dde77b4c19f257ac9b327aba900e28298d990fa622f30b6f09
   md5: 86406bcc46061e27fe7ec24f73eb6676
diff --git a/pixi.toml b/pixi.toml
index f5a7a8ccd76..0520d9a0cbb 100644
--- a/pixi.toml
+++ b/pixi.toml
@@ -96,3 +96,8 @@ air = ">=0.8.2,<0.9"
 r-visnetwork = ">=2.1.4,<3"
 r-pak = "*"
 r-jsonvalidate = ">=1.5.0,<2"
+r-rjags = ">=4_17,<5"
+r-rcpptoml = ">=0.2.3,<0.3"
+r-doparallel = ">=1.0.17,<2"
+r-reticulate = ">=1.45.0,<2"
+r-readr = ">=2.2.0,<3"

From b093d75b96a028c13ecb1c558bee112ae1dcb941 Mon Sep 17 00:00:00 2001
From: Alexey Shiklomanov <alexey.shiklomanov@gmail.com>
Date: Fri, 27 Mar 2026 16:17:54 -0400
Subject: [PATCH 12/75] crop --> crop_code for parsing crop cycles

---
 modules/data.land/R/events_to_crop_cycle_starts.R | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/modules/data.land/R/events_to_crop_cycle_starts.R b/modules/data.land/R/events_to_crop_cycle_starts.R
index 3d766d7b637..c9a64ebd1c4 100644
--- a/modules/data.land/R/events_to_crop_cycle_starts.R
+++ b/modules/data.land/R/events_to_crop_cycle_starts.R
@@ -45,8 +45,8 @@ find_crop_changes <- function(event_df) {
   event_df |>
     dplyr::filter(.data$event_type == "planting") |>
     dplyr::arrange(.data$site_id, .data$date) |>
-    dplyr::mutate(crop_cycle_id = dplyr::consecutive_id(.data$site_id, .data$crop)) |>
+    dplyr::mutate(crop_cycle_id = dplyr::consecutive_id(.data$site_id, .data$crop_code)) |>
     dplyr::group_by(.data$site_id, .data$crop_cycle_id) |>
     dplyr::slice_min(.data$date) |>
-    dplyr::select("site_id", "date", "crop")
+    dplyr::select("site_id", "date", "crop_code")
 }

From c47817cc11c3d8195811ab12761d6952f692354c Mon Sep 17 00:00:00 2001
From: Alexey Shiklomanov <alexey.shiklomanov@gmail.com>
Date: Fri, 27 Mar 2026 16:18:08 -0400
Subject: [PATCH 13/75] working run-sipnet workflow

---
 .../sipnet-restart-workflow/02-run-sipnet.R   | 50 +++++++++++--------
 1 file changed, 28 insertions(+), 22 deletions(-)

diff --git a/modules/data.land/inst/sipnet-restart-workflow/02-run-sipnet.R b/modules/data.land/inst/sipnet-restart-workflow/02-run-sipnet.R
index c8247d4762f..6b59709410f 100644
--- a/modules/data.land/inst/sipnet-restart-workflow/02-run-sipnet.R
+++ b/modules/data.land/inst/sipnet-restart-workflow/02-run-sipnet.R
@@ -1,7 +1,7 @@
 #!/usr/bin/env Rscript
 
-devtools::load_all("~/projects/pecan/sipnet-events/modules/data.land")
-devtools::load_all("~/projects/pecan/sipnet-events/models/sipnet")
+devtools::load_all("modules/data.land")
+devtools::load_all("models/sipnet")
 
 config <- config::get(file = "modules/data.land/inst/sipnet-restart-workflow/config.yml")
 
@@ -11,6 +11,10 @@ binary <- config[["sipnet_binary"]]
 stopifnot(file.exists(binary))
 
 site_id <- config[["site_id"]]
+dp_data <- read.csv(config[["dp_path"]]) |>
+  dplyr::filter(.data$id == .env$site_id)
+site_lat <- dp_data[["lat"]]
+site_lon <- dp_data[["lon"]]
 
 events_json_file <- fs::path(outdir_root, "events.json")
 events <- jsonlite::read_json(events_json_file, simplifyVector = FALSE)
@@ -50,8 +54,8 @@ settings <- PEcAn.settings::as.Settings(list(
     site = list(
       id = site_id,
       name = site_id,
-      lat = 32.71585,
-      lon = -115.47163
+      lat = site_lat,
+      lon = site_lon
     ),
     start.date = start_date,
     end.date = end_date,
@@ -88,7 +92,7 @@ segments <- tibble::tibble(
 ################################################################################
 
 for (isegment in seq_len(nrow(segments))) {
-  # isegment <- 1
+  message("Running segment ", isegment)
   segment <- segments[isegment, ]
   segment_id <- sprintf("%03d", isegment)
   dstart <- segment[["start_date"]]
@@ -113,30 +117,22 @@ for (isegment in seq_len(nrow(segments))) {
   segment_eventfile <- PEcAn.SIPNET::write.events.SIPNET(eventfile, segment_dir)
 
   metpath <- settings[[c("run", "inputs", "met", "path")]]
-  met_segment_file <- file.path(segment_dir, "met.clim")
 
   # Subset the met to only the dates in this segment. SIPNET does not respect
   # start/end date, only the dates in the .clim file.
-  # TODO: Use `split_inputs.SIPNET` here instead...
-
-  met_orig <- read.table(metpath)
-  met_segment <- met_orig |>
-    # Create a date from the year + DOY
-    dplyr::mutate(date = as.Date(paste0(V2, "-01-01")) + V3) |>
-    dplyr::filter(date >= dstart, date <= dend) |>
-    dplyr::select(-c("date"))
-  write.table(
-    met_segment,
-    met_segment_file,
-    quote = FALSE,
-    sep = "\t",
-    row.names = FALSE,
-    col.names = FALSE
+  met_segment_file <- split_inputs.SIPNET(
+    dstart,
+    dend,
+    metpath,
+    outpath = segment_dir,
+    overwrite = TRUE
   )
 
   # Segment-specific settings
   segment_outdir <- file.path(segment_dir, "out")
   dir.create(segment_outdir, showWarnings = FALSE, recursive = TRUE)
+  segment_outdir_withid <- file.path(segment_outdir, segment_id)
+  # Don't need to create the outdir here because it is created by write.configs
   segment_rundir <- file.path(segment_dir, "run")
   dir.create(segment_rundir, showWarnings = FALSE, recursive = TRUE)
   segment_rundir_withid <- file.path(segment_rundir, segment_id)
@@ -144,8 +140,8 @@ for (isegment in seq_len(nrow(segments))) {
 
   segment_settings <- settings
   segment_settings[["outdir"]] <- segment_outdir
+  segment_settings[["modeloutdir"]] <- segment_outdir
   segment_settings[["rundir"]] <- segment_rundir
-  segment_settings[["modeloutdir"]] <- segment_rundir
   segment_settings[[c("run", "start.date")]] <- dstart
   segment_settings[[c("run", "end.date")]] <- dend
   segment_settings[[c("run", "inputs", "met", "path")]] <- met_segment_file
@@ -175,6 +171,16 @@ for (isegment in seq_len(nrow(segments))) {
   )
 
   runs <- PEcAn.workflow::start_model_runs(segment_settings, write = FALSE)
+
+  model2netcdf.SIPNET(
+    outdir = segment_outdir_withid,
+    sitelat = segment_settings[[c("run", "site", "lat")]],
+    sitelon = segment_settings[[c("run", "site", "lon")]],
+    start_date = dstart,
+    end_date = dend,
+    revision = segment_settings[[c("model", "revision")]],
+    overwrite = TRUE
+  )
 }
 
 # TODO: Post processing. Combine all the segments together and return output in

From 4bf352f5247d8ac860fa4f9ee5e2de243140cf6a Mon Sep 17 00:00:00 2001
From: Alexey Shiklomanov <alexey.shiklomanov@gmail.com>
Date: Fri, 3 Apr 2026 10:44:30 -0400
Subject: [PATCH 14/75] add cdo and r-stars to pixi environment

---
 pixi.lock | 377 +++++++++++++++++++++++++++++++++++++++++++++++-------
 pixi.toml |   2 +
 2 files changed, 334 insertions(+), 45 deletions(-)

diff --git a/pixi.lock b/pixi.lock
index d988cdf7e37..3e0ca16fa62 100644
--- a/pixi.lock
+++ b/pixi.lock
@@ -36,7 +36,12 @@ environments:
       - conda: https://conda.anaconda.org/conda-forge/linux-64/c-ares-1.34.6-hb03c661_0.conda
       - conda: https://conda.anaconda.org/conda-forge/noarch/ca-certificates-2026.2.25-hbd8a1cb_0.conda
       - conda: https://conda.anaconda.org/conda-forge/linux-64/cairo-1.18.4-he90730b_1.conda
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/cdo-2.5.0-hbf53078_5.conda
       - conda: https://conda.anaconda.org/conda-forge/linux-64/curl-8.19.0-hcf29cc6_0.conda
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/eccodes-2.46.0-h83bc92c_0.conda
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/expat-2.7.4-hecca717_0.conda
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/fftw-3.3.10-nompi_h3b011a4_112.conda
+      - conda: https://conda.anaconda.org/conda-forge/noarch/findlibs-0.1.2-pyhd8ed1ab_0.conda
       - conda: https://conda.anaconda.org/conda-forge/noarch/font-ttf-dejavu-sans-mono-2.37-hab24e00_0.tar.bz2
       - conda: https://conda.anaconda.org/conda-forge/noarch/font-ttf-inconsolata-3.000-h77eed37_0.tar.bz2
       - conda: https://conda.anaconda.org/conda-forge/noarch/font-ttf-source-code-pro-2.038-h77eed37_0.tar.bz2
@@ -44,6 +49,7 @@ environments:
       - conda: https://conda.anaconda.org/conda-forge/linux-64/fontconfig-2.17.1-h27c8c51_0.conda
       - conda: https://conda.anaconda.org/conda-forge/noarch/fonts-conda-ecosystem-1-0.tar.bz2
       - conda: https://conda.anaconda.org/conda-forge/noarch/fonts-conda-forge-1-hc364b38_1.conda
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/freeglut-3.2.2-ha6d2627_3.conda
       - conda: https://conda.anaconda.org/conda-forge/linux-64/freexl-2.0.0-h9dce30a_2.conda
       - conda: https://conda.anaconda.org/conda-forge/linux-64/fribidi-1.0.16-hb03c661_0.conda
       - conda: https://conda.anaconda.org/conda-forge/linux-64/gcc_impl_linux-64-15.2.0-he420e7e_18.conda
@@ -62,6 +68,7 @@ environments:
       - conda: https://conda.anaconda.org/conda-forge/linux-64/hdf5-1.14.6-nompi_h19486de_106.conda
       - conda: https://conda.anaconda.org/conda-forge/linux-64/icu-78.3-h33c6efd_0.conda
       - conda: https://conda.anaconda.org/conda-forge/linux-64/jags-4.3.2-h647a790_1.conda
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/jasper-4.2.9-h1588d4d_1.conda
       - conda: https://conda.anaconda.org/conda-forge/linux-64/json-c-0.18-h6688a6e_0.conda
       - conda: https://conda.anaconda.org/conda-forge/noarch/kernel-headers_linux-64-4.18.0-he073ed8_9.conda
       - conda: https://conda.anaconda.org/conda-forge/linux-64/keyutils-1.6.3-hb9d3cd8_0.conda
@@ -100,7 +107,11 @@ environments:
       - conda: https://conda.anaconda.org/conda-forge/linux-64/libgfortran-ng-15.2.0-h69a702a_18.conda
       - conda: https://conda.anaconda.org/conda-forge/linux-64/libgfortran5-15.2.0-h68bc16d_18.conda
       - conda: https://conda.anaconda.org/conda-forge/linux-64/libgit2-1.9.2-hc20babb_0.conda
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/libgl-1.7.0-ha4b6fd6_2.conda
       - conda: https://conda.anaconda.org/conda-forge/linux-64/libglib-2.86.4-h6548e54_1.conda
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/libglu-9.0.3-h5888daf_1.conda
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/libglvnd-1.7.0-ha4b6fd6_2.conda
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/libglx-1.7.0-ha4b6fd6_2.conda
       - conda: https://conda.anaconda.org/conda-forge/linux-64/libgomp-15.2.0-he0feb66_18.conda
       - conda: https://conda.anaconda.org/conda-forge/linux-64/libgoogle-cloud-2.39.0-hdb79228_0.conda
       - conda: https://conda.anaconda.org/conda-forge/linux-64/libgoogle-cloud-storage-2.39.0-hdbdcf42_0.conda
@@ -113,10 +124,11 @@ environments:
       - conda: https://conda.anaconda.org/conda-forge/linux-64/liblapack-3.11.0-5_h47877c9_openblas.conda
       - conda: https://conda.anaconda.org/conda-forge/linux-64/liblzma-5.8.2-hb03c661_0.conda
       - conda: https://conda.anaconda.org/conda-forge/linux-64/libmpdec-4.0.0-hb03c661_1.conda
-      - conda: https://conda.anaconda.org/conda-forge/linux-64/libnetcdf-4.10.0-nompi_hbf2fc22_100.conda
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/libnetcdf-4.9.3-nompi_hbf2fc22_104.conda
       - conda: https://conda.anaconda.org/conda-forge/linux-64/libnghttp2-1.68.1-h877daf1_0.conda
       - conda: https://conda.anaconda.org/conda-forge/linux-64/libnsl-2.0.1-hb9d3cd8_1.conda
       - conda: https://conda.anaconda.org/conda-forge/linux-64/libopenblas-0.3.30-pthreads_h94d23a6_4.conda
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/libopengl-1.7.0-ha4b6fd6_2.conda
       - conda: https://conda.anaconda.org/conda-forge/linux-64/libopentelemetry-cpp-1.21.0-hb9b0907_1.conda
       - conda: https://conda.anaconda.org/conda-forge/linux-64/libopentelemetry-cpp-headers-1.21.0-ha770c72_1.conda
       - conda: https://conda.anaconda.org/conda-forge/linux-64/libparquet-22.0.0-h7376487_10_cpu.conda
@@ -147,15 +159,17 @@ environments:
       - conda: https://conda.anaconda.org/conda-forge/linux-64/libzlib-1.3.1-hb9d3cd8_2.conda
       - conda: https://conda.anaconda.org/conda-forge/linux-64/lz4-c-1.10.0-h5888daf_1.conda
       - conda: https://conda.anaconda.org/conda-forge/linux-64/lzo-2.10-h280c20c_1002.conda
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/magics-4.16.0-h637ef6b_3.conda
+      - conda: https://conda.anaconda.org/conda-forge/noarch/magics-python-1.5.8-pyhd8ed1ab_1.conda
       - conda: https://conda.anaconda.org/conda-forge/linux-64/make-4.4.1-hb9d3cd8_2.conda
       - conda: https://conda.anaconda.org/conda-forge/linux-64/mbedtls-3.6.3.1-h5888daf_0.conda
       - conda: https://conda.anaconda.org/conda-forge/linux-64/minizip-4.0.10-h05a5f5f_0.conda
       - conda: https://conda.anaconda.org/conda-forge/linux-64/muparser-2.3.5-h5888daf_0.conda
       - conda: https://conda.anaconda.org/conda-forge/linux-64/ncurses-6.5-h2d0b736_3.conda
       - conda: https://conda.anaconda.org/conda-forge/linux-64/nlohmann_json-3.12.0-h54a6638_1.conda
-      - conda: https://conda.anaconda.org/conda-forge/linux-64/nlopt-2.10.1-np2py314h6477eea_2.conda
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/nlopt-2.10.1-np2py314h7173366_2.conda
       - conda: https://conda.anaconda.org/conda-forge/linux-64/nng-1.11-h5888daf_0.conda
-      - conda: https://conda.anaconda.org/conda-forge/linux-64/numpy-2.4.3-py314h2b28147_0.conda
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/numpy-2.4.3-py314hd4f4903_0.conda
       - conda: https://conda.anaconda.org/conda-forge/linux-64/openssl-3.6.1-h35e630c_1.conda
       - conda: https://conda.anaconda.org/conda-forge/linux-64/orc-2.2.2-h19cb568_0.conda
       - conda: https://conda.anaconda.org/conda-forge/linux-64/pandoc-3.9.0.1-ha770c72_0.conda
@@ -165,8 +179,8 @@ environments:
       - conda: https://conda.anaconda.org/conda-forge/linux-64/proj-9.7.1-he0df7b0_3.conda
       - conda: https://conda.anaconda.org/conda-forge/linux-64/prometheus-cpp-1.3.0-ha5d0236_0.conda
       - conda: https://conda.anaconda.org/conda-forge/linux-64/pthread-stubs-0.4-hb9d3cd8_1002.conda
-      - conda: https://conda.anaconda.org/conda-forge/linux-64/python-3.14.3-h32b2ec7_101_cp314.conda
-      - conda: https://conda.anaconda.org/conda-forge/noarch/python_abi-3.14-8_cp314.conda
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/python-3.14.3-he1279bd_1_cp314t.conda
+      - conda: https://conda.anaconda.org/conda-forge/noarch/python_abi-3.14-8_cp314t.conda
       - conda: https://conda.anaconda.org/conda-forge/noarch/r-4.5-r45hd8ed1ab_1009.conda
       - conda: https://conda.anaconda.org/conda-forge/noarch/r-abind-1.4_8-r45hc72bb7e_1.conda
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+  timestamp: 1773492082997
 - conda: https://conda.anaconda.org/conda-forge/linux-64/nng-1.11-h5888daf_0.conda
   sha256: e9c0a46c046fdffa22eb1f77030c95c46d2d6ec5cfaea89fc23710735f2c8d33
   md5: 9b929cfa0d6353227bae3cd63ecd7940
@@ -2307,24 +2522,24 @@ packages:
   license_family: MIT
   size: 255583
   timestamp: 1748924914867
-- conda: https://conda.anaconda.org/conda-forge/linux-64/numpy-2.4.3-py314h2b28147_0.conda
-  sha256: f2ba8cb0d86a6461a6bcf0d315c80c7076083f72c6733c9290086640723f79ec
-  md5: 36f5b7eb328bdc204954a2225cf908e2
+- conda: https://conda.anaconda.org/conda-forge/linux-64/numpy-2.4.3-py314hd4f4903_0.conda
+  sha256: 80bdebe25269b3a0ea5e3eae2ef7159615d4aa3a74b2aa1b408f35b5812312b7
+  md5: ee2b2bb9e96a9cd64d68492842559adf
   depends:
   - python
   - libstdcxx >=14
   - libgcc >=14
   - __glibc >=2.17,<3.0.a0
-  - python_abi 3.14.* *_cp314
+  - python_abi 3.14.* *_cp314t
   - libcblas >=3.9.0,<4.0a0
-  - liblapack >=3.9.0,<4.0a0
   - libblas >=3.9.0,<4.0a0
+  - liblapack >=3.9.0,<4.0a0
   constrains:
   - numpy-base <0a0
   license: BSD-3-Clause
   license_family: BSD
-  size: 8927860
-  timestamp: 1773839233468
+  size: 8972010
+  timestamp: 1773839212779
 - conda: https://conda.anaconda.org/conda-forge/linux-64/openssl-3.6.1-h35e630c_1.conda
   sha256: 44c877f8af015332a5d12f5ff0fb20ca32f896526a7d0cdb30c769df1144fb5c
   md5: f61eb8cd60ff9057122a3d338b99c00f
@@ -2447,10 +2662,10 @@ packages:
   license_family: MIT
   size: 8252
   timestamp: 1726802366959
-- conda: https://conda.anaconda.org/conda-forge/linux-64/python-3.14.3-h32b2ec7_101_cp314.conda
-  build_number: 101
-  sha256: cb0628c5f1732f889f53a877484da98f5a0e0f47326622671396fb4f2b0cd6bd
-  md5: c014ad06e60441661737121d3eae8a60
+- conda: https://conda.anaconda.org/conda-forge/linux-64/python-3.14.3-he1279bd_1_cp314t.conda
+  build_number: 1
+  sha256: 4212a85ccc69264eaf9e68b77ff9b504e78935a53d0923fa409900084418edce
+  md5: 19b5d632d02f56f9f95ce07dc1e086b5
   depends:
   - __glibc >=2.17,<3.0.a0
   - bzip2 >=1.0.8,<2.0a0
@@ -2465,25 +2680,27 @@ packages:
   - libzlib >=1.3.1,<2.0a0
   - ncurses >=6.5,<7.0a0
   - openssl >=3.5.5,<4.0a0
-  - python_abi 3.14.* *_cp314
+  - python_abi 3.14.* *_cp314t
   - readline >=8.3,<9.0a0
   - tk >=8.6.13,<8.7.0a0
   - tzdata
   - zstd >=1.5.7,<1.6.0a0
+  track_features:
+  - py_freethreading
   license: Python-2.0
-  size: 36702440
-  timestamp: 1770675584356
-  python_site_packages_path: lib/python3.14/site-packages
-- conda: https://conda.anaconda.org/conda-forge/noarch/python_abi-3.14-8_cp314.conda
+  size: 47583647
+  timestamp: 1770675516163
+  python_site_packages_path: lib/python3.14t/site-packages
+- conda: https://conda.anaconda.org/conda-forge/noarch/python_abi-3.14-8_cp314t.conda
   build_number: 8
-  sha256: ad6d2e9ac39751cc0529dd1566a26751a0bf2542adb0c232533d32e176e21db5
-  md5: 0539938c55b6b1a59b560e843ad864a4
+  sha256: d9ed2538fba61265a330ee1b1afe99a4bb23ace706172b9464546c7e01259d63
+  md5: 3251796e09870c978e0f69fa05e38fb6
   constrains:
-  - python 3.14.* *_cp314
+  - python 3.14.* *_cp314t
   license: BSD-3-Clause
   license_family: BSD
-  size: 6989
-  timestamp: 1752805904792
+  size: 7020
+  timestamp: 1752805919426
 - conda: https://conda.anaconda.org/conda-forge/noarch/r-4.5-r45hd8ed1ab_1009.conda
   sha256: 2af0ddd26c10dd1326774e57f9aa47607bd0c51b6a4122e8b68a023358280861
   md5: cc1055fbf899ff061909f934af18a20b
@@ -4025,19 +4242,19 @@ packages:
   license_family: APACHE
   size: 225802
   timestamp: 1764331882493
-- conda: https://conda.anaconda.org/conda-forge/linux-64/r-ncdf4-1.24-r45h8a39af1_4.conda
-  sha256: 906db096beae7d0fee62f90e6cb969196afc6c1eee1e9e840c3e771038f6f78c
-  md5: 2bb14f5b8bcf7c5dadda50e773ae0527
+- conda: https://conda.anaconda.org/conda-forge/linux-64/r-ncdf4-1.24-r45h5f38480_3.conda
+  sha256: c884ac3901bc53e0317d7e19f28102d722baf27502df8b9b4715cea5c1bf0750
+  md5: e075e7fc47e3c2c7ecaa85c628bc87fc
   depends:
   - __glibc >=2.17,<3.0.a0
   - hdf5 >=1.14.6,<1.14.7.0a0
   - libgcc >=14
-  - libnetcdf >=4.10.0,<4.10.1.0a0
+  - libnetcdf >=4.9.3,<4.9.4.0a0
   - r-base >=4.5,<4.6.0a0
   license: GPL-3.0-or-later
   license_family: GPL3
-  size: 300037
-  timestamp: 1772304020267
+  size: 299918
+  timestamp: 1757542673765
 - conda: https://conda.anaconda.org/conda-forge/linux-64/r-nlme-3.1_168-r45heaba542_1.conda
   sha256: da4b17286e9df1c5db0de78534ee49ace3990e380a601e2e4369a80d31c7642e
   md5: b75eb6b18bf2dcdc4f72c3f9cdc310b6
@@ -4996,6 +5213,20 @@ packages:
   license_family: GPL3
   size: 155963
   timestamp: 1757509276008
+- conda: https://conda.anaconda.org/conda-forge/noarch/r-stars-0.7_1-r45hc72bb7e_0.conda
+  sha256: f432d5b9d7ddad97f0aeb99fbb9e69459054cd3e1428170f7d9dae0639103154
+  md5: 6da2005783692518aef1c4f435859c26
+  depends:
+  - r-abind
+  - r-base >=4.5,<4.6.0a0
+  - r-classint >=0.4_1
+  - r-rlang
+  - r-sf >=1.0_19
+  - r-units
+  license: Apache-2.0
+  license_family: APACHE
+  size: 4407203
+  timestamp: 1770994555091
 - conda: https://conda.anaconda.org/conda-forge/linux-64/r-stringi-1.8.7-r45h3d52c89_2.conda
   sha256: 6d0d8d6f1465b3486996edaef7ccd1020cb2fcca1e69b543fc52dbad5262079b
   md5: c7ce6f26b92398224c78b92c653b94c1
@@ -5647,6 +5878,18 @@ packages:
   license_family: GPL
   size: 228948
   timestamp: 1746562045847
+- conda: https://conda.anaconda.org/conda-forge/linux-64/simplejson-3.20.2-py314h56549f7_1.conda
+  sha256: 7ef960870a6827599537fb434550848d75ce4bb5bf6ac3bc5317a80f941f8955
+  md5: 3f9d3f6f3e67369b6b82112fc1144db6
+  depends:
+  - __glibc >=2.17,<3.0.a0
+  - libgcc >=14
+  - python >=3.14,<3.15.0a0
+  - python_abi 3.14.* *_cp314t
+  license: MIT
+  license_family: MIT
+  size: 136662
+  timestamp: 1762507051896
 - conda: https://conda.anaconda.org/conda-forge/linux-64/snappy-1.2.2-h03e3b7b_1.conda
   sha256: 48f3f6a76c34b2cfe80de9ce7f2283ecb55d5ed47367ba91e8bb8104e12b8f11
   md5: 98b6c9dc80eb87b2519b97bcf7e578dd
@@ -5715,6 +5958,16 @@ packages:
   license: LicenseRef-Public-Domain
   size: 119135
   timestamp: 1767016325805
+- conda: https://conda.anaconda.org/conda-forge/linux-64/udunits2-2.2.28-h40f5838_3.conda
+  sha256: 7beb28a13dd4206c54ed994434d843aabda57fc9e5a0835c2f504c77336a4087
+  md5: 6bb8deb138f87c9d48320ac21b87e7a1
+  depends:
+  - libexpat >=2.5.0,<3.0a0
+  - libgcc-ng >=12
+  - libudunits2 2.2.28 h40f5838_3
+  license: LicenseRef-BSD-UCAR
+  size: 112783
+  timestamp: 1696525549258
 - conda: https://conda.anaconda.org/conda-forge/linux-64/uriparser-0.9.8-hac33072_0.conda
   sha256: 2aad2aeff7c69a2d7eecd7b662eef756b27d6a6b96f3e2c2a7071340ce14543e
   md5: d71d3a66528853c0a1ac2c02d79a0284
@@ -5802,6 +6055,30 @@ packages:
   license_family: MIT
   size: 50326
   timestamp: 1769445253162
+- conda: https://conda.anaconda.org/conda-forge/linux-64/xorg-libxfixes-6.0.2-hb03c661_0.conda
+  sha256: 83c4c99d60b8784a611351220452a0a85b080668188dce5dfa394b723d7b64f4
+  md5: ba231da7fccf9ea1e768caf5c7099b84
+  depends:
+  - __glibc >=2.17,<3.0.a0
+  - libgcc >=14
+  - xorg-libx11 >=1.8.12,<2.0a0
+  license: MIT
+  license_family: MIT
+  size: 20071
+  timestamp: 1759282564045
+- conda: https://conda.anaconda.org/conda-forge/linux-64/xorg-libxi-1.8.2-hb9d3cd8_0.conda
+  sha256: 1a724b47d98d7880f26da40e45f01728e7638e6ec69f35a3e11f92acd05f9e7a
+  md5: 17dcc85db3c7886650b8908b183d6876
+  depends:
+  - __glibc >=2.17,<3.0.a0
+  - libgcc >=13
+  - xorg-libx11 >=1.8.10,<2.0a0
+  - xorg-libxext >=1.3.6,<2.0a0
+  - xorg-libxfixes >=6.0.1,<7.0a0
+  license: MIT
+  license_family: MIT
+  size: 47179
+  timestamp: 1727799254088
 - conda: https://conda.anaconda.org/conda-forge/linux-64/xorg-libxrender-0.9.12-hb9d3cd8_0.conda
   sha256: 044c7b3153c224c6cedd4484dd91b389d2d7fd9c776ad0f4a34f099b3389f4a1
   md5: 96d57aba173e878a2089d5638016dc5e
@@ -5826,6 +6103,16 @@ packages:
   license_family: MIT
   size: 379686
   timestamp: 1731860547604
+- conda: https://conda.anaconda.org/conda-forge/linux-64/xorg-xorgproto-2025.1-hb03c661_0.conda
+  sha256: 7a8c64938428c2bfd016359f9cb3c44f94acc256c6167dbdade9f2a1f5ca7a36
+  md5: aa8d21be4b461ce612d8f5fb791decae
+  depends:
+  - __glibc >=2.17,<3.0.a0
+  - libgcc >=14
+  license: MIT
+  license_family: MIT
+  size: 570010
+  timestamp: 1766154256151
 - conda: https://conda.anaconda.org/conda-forge/linux-64/zeromq-4.3.5-h41580af_10.conda
   sha256: 325d370b28e2b9cc1f765c5b4cdb394c91a5d958fbd15da1a14607a28fee09f6
   md5: 755b096086851e1193f3b10347415d7c
diff --git a/pixi.toml b/pixi.toml
index 0520d9a0cbb..2643f1827f5 100644
--- a/pixi.toml
+++ b/pixi.toml
@@ -101,3 +101,5 @@ r-rcpptoml = ">=0.2.3,<0.3"
 r-doparallel = ">=1.0.17,<2"
 r-reticulate = ">=1.45.0,<2"
 r-readr = ">=2.2.0,<3"
+cdo = ">=2.5.0,<3"
+r-stars = ">=0.7_1,<0.8"

From fc55b75a99757d6491d603d15075e29bb41a1eca Mon Sep 17 00:00:00 2001
From: Alexey Shiklomanov <alexey.shiklomanov@gmail.com>
Date: Fri, 3 Apr 2026 10:54:30 -0400
Subject: [PATCH 15/75] workflow runs with outputs concatenated

...but we reset to initial conditions every time.
---
 .../sipnet-restart-workflow/02-run-sipnet.R   | 36 ++++++++++++++-----
 .../sipnet-restart-workflow/03-plot-outputs.R | 25 +++++++++++++
 2 files changed, 52 insertions(+), 9 deletions(-)
 create mode 100644 modules/data.land/inst/sipnet-restart-workflow/03-plot-outputs.R

diff --git a/modules/data.land/inst/sipnet-restart-workflow/02-run-sipnet.R b/modules/data.land/inst/sipnet-restart-workflow/02-run-sipnet.R
index 6b59709410f..bc3327bed22 100644
--- a/modules/data.land/inst/sipnet-restart-workflow/02-run-sipnet.R
+++ b/modules/data.land/inst/sipnet-restart-workflow/02-run-sipnet.R
@@ -87,18 +87,21 @@ segments <- tibble::tibble(
   start_date = c(start_date, crop_cycles[["date"]]),
   end_date = c(crop_cycles[["date"]] - 1, end_date)
 ) |>
-  dplyr::mutate(segment_id = dplyr::row_number())
+  dplyr::mutate(
+    segment_id = sprintf("%03d", dplyr::row_number()),
+    segment_dir = file.path(outdir, paste0("segment_", segment_id))
+  )
 
 ################################################################################
 
 for (isegment in seq_len(nrow(segments))) {
   message("Running segment ", isegment)
   segment <- segments[isegment, ]
-  segment_id <- sprintf("%03d", isegment)
+  segment_id <- segment[["segment_id"]]
   dstart <- segment[["start_date"]]
   dend <- segment[["end_date"]]
 
-  segment_dir <- file.path(outdir, paste0("segment_", segment_id))
+  segment_dir <- segment[["segment_dir"]]
   if (dir.exists(segment_dir)) {
     unlink(segment_dir, recursive = TRUE)
   }
@@ -128,14 +131,15 @@ for (isegment in seq_len(nrow(segments))) {
     overwrite = TRUE
   )
 
+  runid <- "1"
   # Segment-specific settings
   segment_outdir <- file.path(segment_dir, "out")
   dir.create(segment_outdir, showWarnings = FALSE, recursive = TRUE)
-  segment_outdir_withid <- file.path(segment_outdir, segment_id)
+  segment_outdir_withid <- file.path(segment_outdir, runid)
   # Don't need to create the outdir here because it is created by write.configs
   segment_rundir <- file.path(segment_dir, "run")
   dir.create(segment_rundir, showWarnings = FALSE, recursive = TRUE)
-  segment_rundir_withid <- file.path(segment_rundir, segment_id)
+  segment_rundir_withid <- file.path(segment_rundir, runid)
   dir.create(segment_rundir_withid, showWarnings = FALSE, recursive = TRUE)
 
   segment_settings <- settings
@@ -156,7 +160,7 @@ for (isegment in seq_len(nrow(segments))) {
   segment_settings[[c("model", "restart_out")]] <- restart_out
 
   # Write runs file
-  writeLines(segment_id, file.path(segment_rundir, "runs.txt"))
+  writeLines(runid, file.path(segment_rundir, "runs.txt"))
 
   # TODO: Logic to get the trait values corresponding to the segment's PFT.
   # 1. Cross-reference crop_code against PFT
@@ -167,7 +171,7 @@ for (isegment in seq_len(nrow(segments))) {
     defaults = settings[["pfts"]],
     trait.values = segment_traits,
     settings = segment_settings,
-    run.id = segment_id
+    run.id = runid
   )
 
   runs <- PEcAn.workflow::start_model_runs(segment_settings, write = FALSE)
@@ -183,5 +187,19 @@ for (isegment in seq_len(nrow(segments))) {
   )
 }
 
-# TODO: Post processing. Combine all the segments together and return output in
-# PEcAn standard.
+# TODO: Concatenate the NetCDF files. This is annoyingly hard in R (unless I use `stars`?)
+
+segment_ncfiles <- lapply(
+  segments[["segment_dir"]],
+  \(x) list.files(
+    file.path(x, "out", "1"),
+    pattern = "\\d+\\.nc",
+    full.names = TRUE
+  )
+) |>
+  do.call(what = c)
+
+segment_files_byyear <- split(segment_ncfiles, factor(basename(segment_ncfiles)))
+combined_outdir <- fs::dir_create(fs::path(outdir_root, "out"))
+names(segment_files_byyear) <- fs::path(combined_outdir, names(segment_files_byyear))
+results <- purrr::imap(segment_files_byyear, PEcAn.SIPNET::mergeNC)
diff --git a/modules/data.land/inst/sipnet-restart-workflow/03-plot-outputs.R b/modules/data.land/inst/sipnet-restart-workflow/03-plot-outputs.R
new file mode 100644
index 00000000000..0884f1a12bd
--- /dev/null
+++ b/modules/data.land/inst/sipnet-restart-workflow/03-plot-outputs.R
@@ -0,0 +1,25 @@
+#!/usr/bin/env Rscript
+
+config <- config::get(file = "modules/data.land/inst/sipnet-restart-workflow/config.yml")
+
+outdir <- file.path(config$outdir_root, "out")
+ncfiles <- list.files(outdir, full.names = TRUE)
+nc <- ncdf4::nc_open(ncfiles[[1]])
+
+results <- PEcAn.utils::read.output(
+  ncfiles = ncfiles,
+  variables = c("NPP", "GPP", "NEE", "LAI", "AGB", "TotSoilCarb"),
+  dataframe = TRUE
+)
+
+library(ggplot2)
+results |>
+  tidyr::pivot_longer(
+    -c("posix", "year"),
+    names_to = "variable",
+    values_to = "value"
+  ) |>
+  ggplot() +
+  aes(x = posix, y = value) +
+  geom_line() +
+  facet_wrap(vars(variable), scales = "free")

From c33de6c4ecad31f39430f703d7e5b25abc9d7de6 Mon Sep 17 00:00:00 2001
From: Alexey Shiklomanov <alexey.shiklomanov@gmail.com>
Date: Fri, 3 Apr 2026 11:00:58 -0400
Subject: [PATCH 16/75] fix syntax for model restarts

---
 .../data.land/inst/sipnet-restart-workflow/02-run-sipnet.R | 7 +++++--
 1 file changed, 5 insertions(+), 2 deletions(-)

diff --git a/modules/data.land/inst/sipnet-restart-workflow/02-run-sipnet.R b/modules/data.land/inst/sipnet-restart-workflow/02-run-sipnet.R
index bc3327bed22..f1cd1f16fa6 100644
--- a/modules/data.land/inst/sipnet-restart-workflow/02-run-sipnet.R
+++ b/modules/data.land/inst/sipnet-restart-workflow/02-run-sipnet.R
@@ -150,14 +150,17 @@ for (isegment in seq_len(nrow(segments))) {
   segment_settings[[c("run", "end.date")]] <- dend
   segment_settings[[c("run", "inputs", "met", "path")]] <- met_segment_file
   segment_settings[[c("run", "inputs", "events")]] <- list(path = segment_eventfile)
+  if (is.null(segment_settings[[c("model", "options")]])) {
+    segment_settings[[c("model", "options")]] <- list()
+  }
 
   if (isegment > 1) {
     # For isegment > 1, we restart from the *previous* segment's restart.out
-    segment_settings[[c("model", "restart_in")]] <- restart_out
+    segment_settings[[c("model", "options", "RESTART_IN")]] <- restart_out
   }
   # ...and now, define a new restart.out for *this* segment
   restart_out <- file.path(segment_dir, "restart.out")
-  segment_settings[[c("model", "restart_out")]] <- restart_out
+  segment_settings[[c("model", "options", "RESTART_OUT")]] <- restart_out
 
   # Write runs file
   writeLines(runid, file.path(segment_rundir, "runs.txt"))

From a68f8cd14ad2781b2a63c0a4e5f1b80f633e630f Mon Sep 17 00:00:00 2001
From: Alexey Shiklomanov <alexey.shiklomanov@gmail.com>
Date: Fri, 3 Apr 2026 15:28:05 -0400
Subject: [PATCH 17/75] working restart workflow

---
 base/remote/R/check_model_run.R               |  4 +-
 .../sipnet-restart-workflow/02-run-sipnet.R   | 26 +++++-
 .../sipnet-restart-workflow/03-plot-outputs.R | 30 ++++++-
 .../inst/sipnet-restart-workflow/91-debug.R   | 83 +++++++++++++++++++
 .../inst/sipnet-restart-workflow/config.yml   |  2 +
 5 files changed, 135 insertions(+), 10 deletions(-)
 create mode 100644 modules/data.land/inst/sipnet-restart-workflow/91-debug.R

diff --git a/base/remote/R/check_model_run.R b/base/remote/R/check_model_run.R
index c74184d7f01..2c733d875e5 100644
--- a/base/remote/R/check_model_run.R
+++ b/base/remote/R/check_model_run.R
@@ -10,9 +10,9 @@ check_model_run <- function(out, stop.on.error = TRUE) {
     success <- FALSE
     msg <- paste0("Model run aborted with the following error:\n", out)
     if (stop.on.error) {
-      PEcAn.logger::logger.severe(msg)
+      PEcAn.logger::logger.severe(msg, wrap = FALSE)
     } else {
-      PEcAn.logger::logger.error(msg)
+      PEcAn.logger::logger.error(msg, wrap = FALSE)
     }
   } else {
     success <- TRUE
diff --git a/modules/data.land/inst/sipnet-restart-workflow/02-run-sipnet.R b/modules/data.land/inst/sipnet-restart-workflow/02-run-sipnet.R
index f1cd1f16fa6..afc5b5a8f4b 100644
--- a/modules/data.land/inst/sipnet-restart-workflow/02-run-sipnet.R
+++ b/modules/data.land/inst/sipnet-restart-workflow/02-run-sipnet.R
@@ -34,8 +34,16 @@ met <- file.path(
 )
 stopifnot(file.exists(met))
 
+icfile <- file.path(
+  config[["ic_dir"]],
+  site_id,
+  glue::glue("IC_site_{site_id}_1.nc")
+)
+stopifnot(file.exists(icfile))
+
 ################################################################################
-outdir <- fs::path(outdir_root, "segments") |> fs::dir_create()
+outdir <- fs::path(outdir_root, "segments")
+unlink(outdir, recursive = TRUE)
 
 settings <- PEcAn.settings::as.Settings(list(
   outdir = file.path(outdir, "out"),
@@ -48,7 +56,13 @@ settings <- PEcAn.settings::as.Settings(list(
   model = list(
     type = "SIPNET",
     binary = binary,
-    revision = "v2"
+    revision = "v2",
+    options = list(
+      GDD = 0,
+      NITROGEN_CYCLE = 0,
+      ANAEROBIC = 0,
+      LITTER_POOL = 1
+    )
   ),
   run = list(
     site = list(
@@ -59,7 +73,10 @@ settings <- PEcAn.settings::as.Settings(list(
     ),
     start.date = start_date,
     end.date = end_date,
-    inputs = list(met = list(path = met))
+    inputs = list(
+      met = list(path = met),
+      poolinitcond = list(path = icfile)
+    )
   ),
   host = list(
     name = "localhost"
@@ -89,7 +106,7 @@ segments <- tibble::tibble(
 ) |>
   dplyr::mutate(
     segment_id = sprintf("%03d", dplyr::row_number()),
-    segment_dir = file.path(outdir, paste0("segment_", segment_id))
+    segment_dir = file.path(fs::path_abs(outdir), paste0("segment_", segment_id))
   )
 
 ################################################################################
@@ -139,6 +156,7 @@ for (isegment in seq_len(nrow(segments))) {
   # Don't need to create the outdir here because it is created by write.configs
   segment_rundir <- file.path(segment_dir, "run")
   dir.create(segment_rundir, showWarnings = FALSE, recursive = TRUE)
+  file.create(file.path(segment_rundir, "README.txt"))
   segment_rundir_withid <- file.path(segment_rundir, runid)
   dir.create(segment_rundir_withid, showWarnings = FALSE, recursive = TRUE)
 
diff --git a/modules/data.land/inst/sipnet-restart-workflow/03-plot-outputs.R b/modules/data.land/inst/sipnet-restart-workflow/03-plot-outputs.R
index 0884f1a12bd..f1822f4277c 100644
--- a/modules/data.land/inst/sipnet-restart-workflow/03-plot-outputs.R
+++ b/modules/data.land/inst/sipnet-restart-workflow/03-plot-outputs.R
@@ -6,14 +6,27 @@ outdir <- file.path(config$outdir_root, "out")
 ncfiles <- list.files(outdir, full.names = TRUE)
 nc <- ncdf4::nc_open(ncfiles[[1]])
 
+outdir_root <- config[["outdir_root"]]
+events_json_file <- fs::path(outdir_root, "events.json")
+events <- jsonlite::read_json(events_json_file, simplifyVector = FALSE)
+
+events_df <- dplyr::bind_rows(events[[1]][["events"]]) |>
+  dplyr::mutate(date = as.Date(.data$date)) |>
+  dplyr::filter(.data$event_type != "irrigation") |>
+  dplyr::arrange(.data$date)
+
+events_df |>
+  dplyr::select("event_type":"crop_code")
+
 results <- PEcAn.utils::read.output(
   ncfiles = ncfiles,
-  variables = c("NPP", "GPP", "NEE", "LAI", "AGB", "TotSoilCarb"),
+  variables = c("NEE", "LAI", "AGB", "TotSoilCarb"),
   dataframe = TRUE
-)
+) |>
+  dplyr::as_tibble()
 
 library(ggplot2)
-results |>
+plt <- results |>
   tidyr::pivot_longer(
     -c("posix", "year"),
     names_to = "variable",
@@ -22,4 +35,13 @@ results |>
   ggplot() +
   aes(x = posix, y = value) +
   geom_line() +
-  facet_wrap(vars(variable), scales = "free")
+  geom_vline(
+    aes(xintercept = date, color = event_type),
+    data = events_df,
+    linetype = "dashed"
+  ) +
+  facet_wrap(vars(variable), scales = "free") +
+  theme_bw() +
+  theme(legend.position = "bottom")
+
+ggsave("~/Pictures/restarts.png", plt, width = 12, height = 9, units = "in")
diff --git a/modules/data.land/inst/sipnet-restart-workflow/91-debug.R b/modules/data.land/inst/sipnet-restart-workflow/91-debug.R
new file mode 100644
index 00000000000..f748910ff84
--- /dev/null
+++ b/modules/data.land/inst/sipnet-restart-workflow/91-debug.R
@@ -0,0 +1,83 @@
+#!/usr/bin/env Rscript
+
+library(dplyr)
+library(ggplot2)
+library(readr)
+
+sipnet_out_file <- "modules/data.land/inst/sipnet-restart-workflow/_test/segments/segment_001/out/1/sipnet.out"
+
+skip_n <- 0
+sipnet_output <- tryCatch({
+  utils::read.table(sipnet_out_file, header = TRUE, skip = skip_n, sep = "")
+}, error = function(err) {
+  PEcAn.logger::logger.warn(
+    "Failed to read using `read.table`. ",
+    "Trying to parse output manually."
+  )
+  raw_lines <- readLines(sipnet_out_file)
+  raw_header <- raw_lines[[1 + skip_n]]
+  raw_body <- tail(raw_lines, -(1 + skip_n))
+  # SIPNET output is right-aligned with the column names in the header.
+  # We use this to figure out where the numbers end if there are no spaces.
+  token_matches <- gregexpr("\\S+", raw_header, perl = TRUE)
+  proc_header <- regmatches(raw_header, token_matches)[[1]]
+  col_ends <- token_matches[[1]] + attr(token_matches[[1]], "match.length") - 1
+  col_starts <- c(1, head(col_ends, -1) + 1)
+  col_widths <- col_ends - col_starts + 1
+  result <- read.fwf(
+    textConnection(raw_body),
+    widths = col_widths,
+    col.names = proc_header,
+    na.strings = c("nan", "-nan")
+  )
+  result[] <- lapply(result, as.numeric)
+  result
+})
+
+dat <- as_tibble(sipnet_output) |>
+  mutate(
+    date = PEcAn.SIPNET:::sipnet2datetime(year, day, time),
+    .before = 0
+  )
+
+head(dat, 20)
+
+dwide <- dat |>
+  select(-c("year", "day", "time")) |>
+  tidyr::pivot_longer(
+    -"date",
+    names_to = "variable",
+    values_to = "value"
+  )
+
+dwide |>
+  # filter(date < "2016-07-15") |>
+  # filter(date < "2016-06-11") |>
+  ggplot() +
+  aes(x = date, y = value) +
+  geom_line() +
+  facet_wrap(vars(variable), scales = "free")
+
+ggsave("~/Pictures/bad-segment-early.png")
+
+# Find first NA
+first_na_index <- which(rowSums(is.na(dat)) > 0)[1]
+start_row <- pmax(1, first_na_index - 10)
+end_row   <- pmin(nrow(dat), first_na_index + 10)
+result <- dat |>
+  slice(start_row:end_row)
+
+print(dat, n = Inf)
+
+dat |>
+  dplyr::filter(is.na(litter))
+
+tail(dat, 30) |> dplyr::glimpse()
+
+ncfile <- "modules/data.land/inst/sipnet-restart-workflow/_test/segments/segment_001/out/1/2016.nc"
+vnames <- c("")
+dnc <- PEcAn.utils::read.output(ncfiles = ncfile, dataframe = TRUE) |>
+  as_tibble()
+nc <- ncdf4::nc_open(ncfile)
+names(nc$var)
+time <- ncdf4::ncvar_get(nc, "time")
diff --git a/modules/data.land/inst/sipnet-restart-workflow/config.yml b/modules/data.land/inst/sipnet-restart-workflow/config.yml
index 032e814ae3d..39be52d49c5 100644
--- a/modules/data.land/inst/sipnet-restart-workflow/config.yml
+++ b/modules/data.land/inst/sipnet-restart-workflow/config.yml
@@ -7,6 +7,7 @@ default:
   dp_path: "/projectnb/dietzelab/ccmmf/management/irrigation/design_points.csv"
   sipnet_binary: "/projectnb/dietzelab/ccmmf/usr/ashiklom/pecan/sipnet/sipnet"
   met_dir: "/projectnb/dietzelab/ccmmf/ensemble/ERA5_SIPNET"
+  ic_dir: "/projectnb/dietzelab/ccmmf/ensemble/IC_files"
   planting_events_dir: "/projectnb/dietzelab/ccmmf/management/event_files"
   mslsp_path: "/projectnb/dietzelab/ccmmf/management/phenology/matched_landiq_mslsp_v4.1"
 
@@ -16,5 +17,6 @@ ashiklom:
   dp_path: !expr path.expand("~/data/design_points.csv")
   sipnet_binary: !expr normalizePath("../_helpers/sipnet/sipnet.master", mustWork = TRUE)
   met_dir: !expr path.expand("~/data/ERA5-site-processed")
+  ic_dir: !expr path.expand("~/data/IC-site")
   planting_events_dir: !expr path.expand("~/data/event-files/planting")
   mslsp_path: !expr path.expand("~/data/matched_landiq_mslsp_v4.1")

From 964b1741ac8453fb19ea11a34a72be13e1a6af59 Mon Sep 17 00:00:00 2001
From: Alexey Shiklomanov <alexey.shiklomanov@gmail.com>
Date: Sat, 4 Apr 2026 13:54:19 -0400
Subject: [PATCH 18/75] WIP PFT configuration

---
 .../sipnet-restart-workflow/02-run-sipnet.R   | 61 ++++++++++++++++---
 .../inst/sipnet-restart-workflow/config.yml   |  2 +
 2 files changed, 53 insertions(+), 10 deletions(-)

diff --git a/modules/data.land/inst/sipnet-restart-workflow/02-run-sipnet.R b/modules/data.land/inst/sipnet-restart-workflow/02-run-sipnet.R
index afc5b5a8f4b..274dad34c78 100644
--- a/modules/data.land/inst/sipnet-restart-workflow/02-run-sipnet.R
+++ b/modules/data.land/inst/sipnet-restart-workflow/02-run-sipnet.R
@@ -19,6 +19,29 @@ site_lon <- dp_data[["lon"]]
 events_json_file <- fs::path(outdir_root, "events.json")
 events <- jsonlite::read_json(events_json_file, simplifyVector = FALSE)
 
+# Determine initial PFT
+events_df <- events |>
+  purrr::pluck(1, "events") |>
+  dplyr::bind_rows() |>
+  dplyr::arrange(.data$date)
+
+crop2pft <- function(crop_code) {
+  # crop_code <- c("F1", "R1", "G2", "F16")
+  cls <- substr(crop_code, 1, 1)
+  dplyr::case_when(
+    cls == "D" ~ "temperate.deciduous",
+    cls == "F" ~ "annual_crop",
+    cls == "G" ~ "grassland",
+    cls == "P" ~ "grassland",
+    cls == "R" ~ "grassland",
+    is.na(crop_code) ~ "soil",
+    TRUE ~ "UNKNOWN_PFT"
+  )
+}
+
+# Before first planting event, assume soil
+initial_pft <- "soil"
+
 all_dates <- events |>
   purrr::pluck(1, "events") |>
   purrr::map_chr("date") |>
@@ -41,18 +64,31 @@ icfile <- file.path(
 )
 stopifnot(file.exists(icfile))
 
+pft_dir <- config[["pft_dir"]]
+stopifnot(dir.exists(pft_dir))
+
 ################################################################################
 outdir <- fs::path(outdir_root, "segments")
 unlink(outdir, recursive = TRUE)
 
+pfts <- c("temperate.deciduous", "grass", "annual_crop") |>
+  purrr::map(~list(
+    name = .x,
+    posterior.files = file.path(pft_dir, .x, "post.distns.Rdata"),
+    outdir = paste0(file.path(pft_dir, .x), "/")
+  )) |>
+  c(list(list(name = "soil", outdir = file.path(pft_dir, "soil/"))))
+
+settings_outdir <- file.path(outdir, "out")
+dir.create(settings_outdir, showWarnings = FALSE, recursive = TRUE)
+settings_rundir <- file.path(outdir, "run")
+dir.create(settings_rundir, showWarnings = FALSE, recursive = TRUE)
+
 settings <- PEcAn.settings::as.Settings(list(
-  outdir = file.path(outdir, "out"),
-  rundir = file.path(outdir, "run"),
-  modeloutdir = file.path(outdir, "out"),
-  pfts = list(list(
-    name = "grassland",
-    constants = list(num = 1)
-  )),
+  outdir = settings_outdir,
+  modeloutdir = settings_outdir,
+  rundir = settings_rundir,
+  pfts = pfts,
   model = list(
     type = "SIPNET",
     binary = binary,
@@ -69,7 +105,10 @@ settings <- PEcAn.settings::as.Settings(list(
       id = site_id,
       name = site_id,
       lat = site_lat,
-      lon = site_lon
+      lon = site_lon,
+      site.pft = list(
+        soil = "soil"
+      )
     ),
     start.date = start_date,
     end.date = end_date,
@@ -102,11 +141,13 @@ site_events_common[["events"]] <- NULL
 # Get segments
 segments <- tibble::tibble(
   start_date = c(start_date, crop_cycles[["date"]]),
-  end_date = c(crop_cycles[["date"]] - 1, end_date)
+  end_date = c(crop_cycles[["date"]] - 1, end_date),
+  crop_code = c(NA_character_, crop_cycles[["crop_code"]])
 ) |>
   dplyr::mutate(
+    pft = crop2pft(.data$crop_code),
     segment_id = sprintf("%03d", dplyr::row_number()),
-    segment_dir = file.path(fs::path_abs(outdir), paste0("segment_", segment_id))
+    segment_dir = file.path(fs::path_abs(outdir), paste0("segment_", .data$segment_id))
   )
 
 ################################################################################
diff --git a/modules/data.land/inst/sipnet-restart-workflow/config.yml b/modules/data.land/inst/sipnet-restart-workflow/config.yml
index 39be52d49c5..d83f56178ac 100644
--- a/modules/data.land/inst/sipnet-restart-workflow/config.yml
+++ b/modules/data.land/inst/sipnet-restart-workflow/config.yml
@@ -10,6 +10,7 @@ default:
   ic_dir: "/projectnb/dietzelab/ccmmf/ensemble/IC_files"
   planting_events_dir: "/projectnb/dietzelab/ccmmf/management/event_files"
   mslsp_path: "/projectnb/dietzelab/ccmmf/management/phenology/matched_landiq_mslsp_v4.1"
+  pft_dir: "..."
 
 ashiklom:
   irrigation_path: !expr path.expand("~/data/irrigation-events-out/irrigation_10000.parquet")
@@ -20,3 +21,4 @@ ashiklom:
   ic_dir: !expr path.expand("~/data/IC-site")
   planting_events_dir: !expr path.expand("~/data/event-files/planting")
   mslsp_path: !expr path.expand("~/data/matched_landiq_mslsp_v4.1")
+  pft_dir: !expr path.expand("~/data/pfts")

From 0cf878288e99bb304c3d1afc62dc4bbce6af4df5 Mon Sep 17 00:00:00 2001
From: Alexey Shiklomanov <alexey.shiklomanov@gmail.com>
Date: Sun, 5 Apr 2026 13:32:59 -0400
Subject: [PATCH 19/75] ensemble restart workflow

---
 models/sipnet/R/split_inputs.SIPNET.R         |  82 +++-
 models/sipnet/R/write.configs.SIPNET.R        |   4 +-
 .../sipnet-restart-workflow/02-run-sipnet.R   | 365 +++++++++---------
 .../inst/sipnet-restart-workflow/81-utils.R   |  33 ++
 .../inst/sipnet-restart-workflow/config.yml   |   1 +
 .../R/generate_joint_ensemble_design.R        |   4 +-
 6 files changed, 306 insertions(+), 183 deletions(-)
 create mode 100644 modules/data.land/inst/sipnet-restart-workflow/81-utils.R

diff --git a/models/sipnet/R/split_inputs.SIPNET.R b/models/sipnet/R/split_inputs.SIPNET.R
index 56aa09f786d..c58af889e89 100644
--- a/models/sipnet/R/split_inputs.SIPNET.R
+++ b/models/sipnet/R/split_inputs.SIPNET.R
@@ -1,6 +1,74 @@
+#!/usr/bin/env Rscript
+
+#' @export
+split_inputs.SIPNET <- function(start.time, stop.time, inputs, overwrite = FALSE, outpath = NULL) {
+  result <- inputs
+  if ("met" %in% names(inputs)) {
+    result[["met"]][["path"]] <- split_sipnet_met(
+      start.time,
+      stop.time,
+      inputs$met$path,
+      overwrite = overwrite,
+      outpath = outpath
+    )
+  }
+
+  if ("events" %in% names(inputs)) {
+    result[["events"]][["path"]] <- split_sipnet_events(
+      start.time,
+      stop.time,
+      inputs$events$path,
+      overwrite = overwrite,
+      outpath = outpath
+    )
+  }
+  result
+}
+
+split_sipnet_events <- function(start.time, stop.time, eventfile, overwrite = FALSE, outpath = FALSE) {
+  # Read events.in
+  # eventfile <- sipnet_eventfile
+  # start.time <- dstart
+  # stop.time <- dend
+  prefix <- sub(".in", "", basename(eventfile), fixed = TRUE)
+  outpath <- outpath %||% dirname(eventfile)
+  dir.create(outpath, recursive = TRUE, showWarnings = FALSE)
+
+  #Changing the name of the files, so it would contain the name of the hour as well.
+  formatted_start <- strftime(start.time)
+  formatted_stop <- strftime(stop.time)
+  outfile <- file.path(outpath, paste0(prefix, ".", formatted_start, "-", formatted_stop, ".in"))
+  names(outfile) <- paste(start.time, "-", stop.time)
+
+  if (file.exists(outfile) && !overwrite) {
+    PEcAn.logger::logger.warn(
+      outfile,
+      " already exists and overwrite is FALSE, so keeping existing file."
+    )
+    return(outfile)
+  }
+
+  # We can't use `read.table` or similar here because events file rows have
+  # different numbers of columns depending on event type. Instead, we just
+  # filter based on the event date, which is always the first two columns (year
+  # and doy).
+  events_in_raw <- readLines(eventfile)
+  events_in_list <- strsplit(events_in_raw, "[[:space:]]+")
+  years_in <- vapply(events_in_list, \(x) as.integer(x[[1]]), integer(1))
+  doys_in <- vapply(events_in_list, \(x) as.integer(x[[2]]), integer(1))
+  # Not using sipnet2datetime here because it returns times with time zones,
+  # which could cause subtle timezone-related bugs
+  dates_in <- as.Date(sprintf("%d-01-01", years_in)) + doys_in
+  idx_keep <- (dates_in >= start.time) & (dates_in <= stop.time)
+  if (length(idx_keep) == 0) {
+    PEcAn.logger::logger.warn("No events to keep, so `events.in` will be empty")
+  }
+  events_out_str <- events_in_raw[idx_keep]
+  writeLines(events_out_str, outfile)
+  invisible(outfile)
+}
+
 ## split clim file into smaller time units to use in KF
-##' @title split_inputs.SIPNET
-##' @name  split_inputs.SIPNET
 ##' @author Mike Dietze and Ann Raiho
 ##' 
 ##' @param start.time start date and time for each SDA ensemble
@@ -14,9 +82,7 @@
 ##' @importFrom rlang .data
 ##' @importFrom dplyr %>%
 ##' @export
-split_inputs.SIPNET <- function(start.time, stop.time, inputs, overwrite = FALSE, outpath = NULL) {
-  #### Get met paths
-  met <- inputs
+split_sipnet_met <- function(start.time, stop.time, met, overwrite = FALSE, outpath = NULL) {
   path <- dirname(met)
   prefix <- sub(".clim", "", basename(met), fixed = TRUE)
   if(is.null(outpath)){
@@ -33,7 +99,11 @@ split_inputs.SIPNET <- function(start.time, stop.time, inputs, overwrite = FALSE
   formatted_stop <- gsub(' ',"_", as.character(stop.time))
   file <- paste0(outpath, "/", prefix, ".", formatted_start, "-", formatted_stop, ".clim")
   
-  if(file.exists(file) & !overwrite){
+  if(file.exists(file) && !overwrite){
+    PEcAn.logger::logger.warn(
+      file,
+      " already exists and overwrite is FALSE, so keeping existing file."
+    )
     return(file)
   }
 
diff --git a/models/sipnet/R/write.configs.SIPNET.R b/models/sipnet/R/write.configs.SIPNET.R
index 80ab6a2c830..9ea25e4753d 100755
--- a/models/sipnet/R/write.configs.SIPNET.R
+++ b/models/sipnet/R/write.configs.SIPNET.R
@@ -124,7 +124,7 @@ write.config.SIPNET <- function(defaults, trait.values, settings, run.id, inputs
     }
   }
   PEcAn.logger::logger.info(paste0("Writing SIPNET configs with input ", template.clim))
-  
+
   # find out where to write run/ouput
   rundir <- file.path(settings$host$rundir, as.character(run.id))
   outdir <- file.path(settings$host$outdir, as.character(run.id))
@@ -132,7 +132,7 @@ write.config.SIPNET <- function(defaults, trait.values, settings, run.id, inputs
     rundir <- file.path(settings$rundir, as.character(run.id))
     outdir <- file.path(settings$modeloutdir, as.character(run.id))
   }
-  
+
   # create launch script (which will create symlink)
   if (!is.null(settings$model$jobtemplate) && file.exists(settings$model$jobtemplate)) {
     jobsh <- readLines(con = settings$model$jobtemplate, n = -1)
diff --git a/modules/data.land/inst/sipnet-restart-workflow/02-run-sipnet.R b/modules/data.land/inst/sipnet-restart-workflow/02-run-sipnet.R
index 274dad34c78..357f218bc63 100644
--- a/modules/data.land/inst/sipnet-restart-workflow/02-run-sipnet.R
+++ b/modules/data.land/inst/sipnet-restart-workflow/02-run-sipnet.R
@@ -1,47 +1,34 @@
 #!/usr/bin/env Rscript
 
-devtools::load_all("modules/data.land")
+library(PEcAn.data.land)
+# devtools::load_all("modules/data.land")
 devtools::load_all("models/sipnet")
 
+source("modules/data.land/inst/sipnet-restart-workflow/81-utils.R")
+
 config <- config::get(file = "modules/data.land/inst/sipnet-restart-workflow/config.yml")
 
 outdir_root <- config[["outdir_root"]]
+# Cleanup some existing files to have a clean start
+list.files(outdir_root, full.names = TRUE) |>
+  grepv(pattern = "events.json", invert = TRUE, fixed = TRUE) |>
+  unlink(recursive = TRUE)
 
 binary <- config[["sipnet_binary"]]
 stopifnot(file.exists(binary))
 
+n_ensemble <- config[["n_ensemble"]]
+
 site_id <- config[["site_id"]]
 dp_data <- read.csv(config[["dp_path"]]) |>
   dplyr::filter(.data$id == .env$site_id)
 site_lat <- dp_data[["lat"]]
 site_lon <- dp_data[["lon"]]
 
-events_json_file <- fs::path(outdir_root, "events.json")
+events_json_file <- file.path(outdir_root, "events.json")
+sipnet_eventfile <- PEcAn.SIPNET::write.events.SIPNET(events_json_file, outdir_root)
 events <- jsonlite::read_json(events_json_file, simplifyVector = FALSE)
 
-# Determine initial PFT
-events_df <- events |>
-  purrr::pluck(1, "events") |>
-  dplyr::bind_rows() |>
-  dplyr::arrange(.data$date)
-
-crop2pft <- function(crop_code) {
-  # crop_code <- c("F1", "R1", "G2", "F16")
-  cls <- substr(crop_code, 1, 1)
-  dplyr::case_when(
-    cls == "D" ~ "temperate.deciduous",
-    cls == "F" ~ "annual_crop",
-    cls == "G" ~ "grassland",
-    cls == "P" ~ "grassland",
-    cls == "R" ~ "grassland",
-    is.na(crop_code) ~ "soil",
-    TRUE ~ "UNKNOWN_PFT"
-  )
-}
-
-# Before first planting event, assume soil
-initial_pft <- "soil"
-
 all_dates <- events |>
   purrr::pluck(1, "events") |>
   purrr::map_chr("date") |>
@@ -50,26 +37,22 @@ all_dates <- events |>
 start_date <- min(all_dates)
 end_date <- max(all_dates)
 
-met <- file.path(
-  config[["met_dir"]],
-  site_id,
-  "ERA5.1.2016-01-01.2024-12-31.clim"
-)
-stopifnot(file.exists(met))
 
-icfile <- file.path(
-  config[["ic_dir"]],
-  site_id,
-  glue::glue("IC_site_{site_id}_1.nc")
-)
-stopifnot(file.exists(icfile))
+met <- file.path(config[["met_dir"]], site_id) |>
+  list.files("ERA5\\..*\\.clim", full.names = TRUE) |>
+  as.list()
+names(met) <- paste0("path", seq_along(met))
+
+icfile <- file.path(config[["ic_dir"]], site_id) |>
+  list.files("IC_site_.*\\.nc", full.names = TRUE) |>
+  as.list()
+names(icfile) <- paste0("path", seq_along(icfile))
 
 pft_dir <- config[["pft_dir"]]
 stopifnot(dir.exists(pft_dir))
 
 ################################################################################
-outdir <- fs::path(outdir_root, "segments")
-unlink(outdir, recursive = TRUE)
+outdir <- fs::path_abs(file.path(outdir_root, "output"))
 
 pfts <- c("temperate.deciduous", "grass", "annual_crop") |>
   purrr::map(~list(
@@ -78,17 +61,39 @@ pfts <- c("temperate.deciduous", "grass", "annual_crop") |>
     outdir = paste0(file.path(pft_dir, .x), "/")
   )) |>
   c(list(list(name = "soil", outdir = file.path(pft_dir, "soil/"))))
+names(pfts) <- rep("pft", length(pfts))
 
 settings_outdir <- file.path(outdir, "out")
 dir.create(settings_outdir, showWarnings = FALSE, recursive = TRUE)
 settings_rundir <- file.path(outdir, "run")
 dir.create(settings_rundir, showWarnings = FALSE, recursive = TRUE)
 
-settings <- PEcAn.settings::as.Settings(list(
-  outdir = settings_outdir,
+ensemble_settings <- list(
+  size = n_ensemble,
+  variable = "LAI",
+  variable = "SoilMoist",
+  variable = "GPP",
+  variable = "SoilResp",
+  variable = "AGB",
+  variable = "NEE",
+  samplingspace = list(
+    parameters = list(method = "uniform"),
+    events = list(method = "sampling"),
+    met = list(method = "sampling"),
+    poolinitcond = list(method = "sampling"),
+    # leaf_phenology = list(method = "sampling")
+    NULL
+  ),
+  start.year = lubridate::year(start_date),
+  end.year = lubridate::year(end_date)
+)
+
+settings_raw <- PEcAn.settings::as.Settings(list(
+  outdir = outdir_root,
   modeloutdir = settings_outdir,
   rundir = settings_rundir,
   pfts = pfts,
+  ensemble = ensemble_settings,
   model = list(
     type = "SIPNET",
     binary = binary,
@@ -114,154 +119,168 @@ settings <- PEcAn.settings::as.Settings(list(
     end.date = end_date,
     inputs = list(
       met = list(path = met),
-      poolinitcond = list(path = icfile)
+      poolinitcond = list(path = icfile),
+      events = list(path = sipnet_eventfile)
     )
   ),
   host = list(
     name = "localhost"
   )
 ))
+# Get parameter samples for all relevant PFTs
+sens_design <- PEcAn.uncertainty::generate_joint_ensemble_design(
+  settings_raw,
+  settings_raw$ensemble$size
+)
 
-crop_cycles <- events_to_crop_cycle_starts(events_json_file)
-# Empty example
-# crop_cycles <- tibble::tibble(
-#   site_id = character(0),
-#   date = as.Date(NULL),
-#   crop_code = character(0)
-# )
-
-# TODO: Iterate over events
-site_events_obj <- events[[1]]
-
-site_id <- site_events_obj[["site_id"]]
-site_events_list <- site_events_obj[["events"]]
-site_events_common <- site_events_obj
-site_events_common[["events"]] <- NULL
-
-# Get segments
-segments <- tibble::tibble(
-  start_date = c(start_date, crop_cycles[["date"]]),
-  end_date = c(crop_cycles[["date"]] - 1, end_date),
-  crop_code = c(NA_character_, crop_cycles[["crop_code"]])
-) |>
-  dplyr::mutate(
-    pft = crop2pft(.data$crop_code),
-    segment_id = sprintf("%03d", dplyr::row_number()),
-    segment_dir = file.path(fs::path_abs(outdir), paste0("segment_", .data$segment_id))
-  )
+settings <- PEcAn.workflow::runModule.run.write.configs(
+  settings_raw,
+  input_design = sens_design$X
+)
+
+inputs_runs <- file.path(settings$outdir, "runs_manifest.csv") |>
+  read.csv() |>
+  cbind(sens_design[["X"]])
+
+write.csv(inputs_runs, file = file.path(settings$outdir, "inputs_runs.csv"))
 
 ################################################################################
+# Begin loop
+for (irun in seq_len(nrow(inputs_runs))) {
+  # irun <- 1
+  run_row <- inputs_runs[irun, ]
+  run_id <- run_row[["run_id"]]
+  run_dir <- file.path(settings$rundir, run_id)
+  run_outdir <- file.path(settings$modeloutdir, run_id)
+  run_settings <- subset_paths(settings, run_row)
+
+  ens_samples_file <- file.path(
+    run_settings$outdir,
+    sprintf("ensemble.samples.%s.Rdata", run_settings$ensemble$ensemble.id)
+  )
+  stopifnot(file.exists(ens_samples_file))
+  ensemble_samples <- PEcAn.utils::load_local(ens_samples_file)[["ens.samples"]]
+  run_traits <- lapply(ensemble_samples, \(dat) dat[run_row[["param"]], ])
+
+  # TODO: Different runs might have different events.json files. But for now,
+  # this is hard coded to a single set of events.
+  run_events_json <- events_json_file
+  crop_cycles <- events_to_crop_cycle_starts(run_events_json)
+
+  # Get segments
+  segments <- data.frame(
+    start_date = c(run_settings$run$start.date, crop_cycles[["date"]]),
+    end_date = c(crop_cycles[["date"]] - 1, run_settings$run$end.date),
+    crop_code = c(NA_character_, crop_cycles[["crop_code"]])
+  )
+  segments[["pft"]] <- crop2pft(segments[["crop_code"]])
+  segments[["segment_id"]] <- sprintf("%03d", seq_len(nrow(segments)))
+  segments[["segment_dir"]] <- file.path(
+    run_dir,
+    "segments",
+    sprintf("segment_%s", segments[["segment_id"]])
+  )
+
+  segment_root <- file.path()
 
-for (isegment in seq_len(nrow(segments))) {
-  message("Running segment ", isegment)
-  segment <- segments[isegment, ]
-  segment_id <- segment[["segment_id"]]
-  dstart <- segment[["start_date"]]
-  dend <- segment[["end_date"]]
+  for (isegment in seq_len(nrow(segments))) {
+    # isegment <- 1
+    segment <- segments[isegment, ]
+    segment_id <- segment[["segment_id"]]
+    dstart <- segment[["start_date"]]
+    dend <- segment[["end_date"]]
+    segment_dir <- segment[["segment_dir"]]
+
+    runid_dummy <- "1"
 
-  segment_dir <- segment[["segment_dir"]]
-  if (dir.exists(segment_dir)) {
     unlink(segment_dir, recursive = TRUE)
-  }
-  dir.create(segment_dir, showWarnings = FALSE, recursive = TRUE)
-
-  # Filter events to relevant dates
-  events_sub <- site_events_list |>
-    purrr::keep(~as.Date(.x[["date"]]) >= dstart) |>
-    purrr::keep(~as.Date(.x[["date"]]) <= dend)
-
-  # Segment-separated events file
-  eventfile <- file.path(segment_dir, "events.json")
-  segment_event_obj <- list(c(site_events_common, events = list(events_sub)))
-  jsonlite::write_json(segment_event_obj, eventfile, auto_unbox = TRUE, pretty = TRUE)
-
-  segment_eventfile <- PEcAn.SIPNET::write.events.SIPNET(eventfile, segment_dir)
-
-  metpath <- settings[[c("run", "inputs", "met", "path")]]
-
-  # Subset the met to only the dates in this segment. SIPNET does not respect
-  # start/end date, only the dates in the .clim file.
-  met_segment_file <- split_inputs.SIPNET(
-    dstart,
-    dend,
-    metpath,
-    outpath = segment_dir,
-    overwrite = TRUE
-  )
+    dir.create(segment_dir, showWarnings = FALSE, recursive = TRUE)
+
+    segment_inputs <- split_inputs.SIPNET(
+      dstart,
+      dend,
+      run_settings$run$inputs,
+      overwrite = TRUE,
+      outpath = segment_dir
+    )
 
-  runid <- "1"
-  # Segment-specific settings
-  segment_outdir <- file.path(segment_dir, "out")
-  dir.create(segment_outdir, showWarnings = FALSE, recursive = TRUE)
-  segment_outdir_withid <- file.path(segment_outdir, runid)
-  # Don't need to create the outdir here because it is created by write.configs
-  segment_rundir <- file.path(segment_dir, "run")
-  dir.create(segment_rundir, showWarnings = FALSE, recursive = TRUE)
-  file.create(file.path(segment_rundir, "README.txt"))
-  segment_rundir_withid <- file.path(segment_rundir, runid)
-  dir.create(segment_rundir_withid, showWarnings = FALSE, recursive = TRUE)
-
-  segment_settings <- settings
-  segment_settings[["outdir"]] <- segment_outdir
-  segment_settings[["modeloutdir"]] <- segment_outdir
-  segment_settings[["rundir"]] <- segment_rundir
-  segment_settings[[c("run", "start.date")]] <- dstart
-  segment_settings[[c("run", "end.date")]] <- dend
-  segment_settings[[c("run", "inputs", "met", "path")]] <- met_segment_file
-  segment_settings[[c("run", "inputs", "events")]] <- list(path = segment_eventfile)
-  if (is.null(segment_settings[[c("model", "options")]])) {
-    segment_settings[[c("model", "options")]] <- list()
-  }
+    # Segment-specific settings
+    segment_outdir <- file.path(segment_dir, "out")
+    dir.create(segment_outdir, showWarnings = FALSE, recursive = TRUE)
+    segment_rundir <- file.path(segment_dir, "run")
+    dir.create(segment_rundir, showWarnings = FALSE, recursive = TRUE)
+    file.create(file.path(segment_rundir, "README.txt"))
+
+    segment_rundir_withid <- file.path(segment_rundir, runid_dummy)
+    dir.create(segment_rundir_withid, showWarnings = FALSE, recursive = TRUE)
+    segment_outdir_withid <- file.path(segment_outdir, runid_dummy)
+    dir.create(segment_outdir_withid, showWarnings = FALSE, recursive = TRUE)
+
+    segment_settings <- run_settings
+    segment_settings[["outdir"]] <- segment_outdir
+    segment_settings[["modeloutdir"]] <- segment_outdir
+    segment_settings[["rundir"]] <- segment_rundir
+    segment_settings[[c("run", "start.date")]] <- dstart
+    segment_settings[[c("run", "end.date")]] <- dend
+    segment_settings[[c("run", "inputs")]] <- segment_inputs
+    segment_settings
+    if (is.null(segment_settings[[c("model", "options")]])) {
+      segment_settings[[c("model", "options")]] <- list()
+    }
+
+    if (isegment > 1) {
+      # For isegment > 1, we restart from the *previous* segment's restart.out
+      segment_settings[[c("model", "options", "RESTART_IN")]] <- restart_out
+    }
+    # ...and now, define a new restart.out for *this* segment
+    restart_out <- file.path(segment_rundir, "restart.out")
+    segment_settings[[c("model", "options", "RESTART_OUT")]] <- restart_out
+
+    segment_traits <- run_traits[[segment[["pft"]]]]
+
+    # Write dummy runs file
+    writeLines(runid_dummy, file.path(segment_rundir, "runs.txt"))
+
+    config <- PEcAn.SIPNET::write.config.SIPNET(
+      defaults = segment_settings[["pfts"]],
+      trait.values = segment_traits,
+      settings = segment_settings,
+      run.id = runid_dummy
+    )
 
-  if (isegment > 1) {
-    # For isegment > 1, we restart from the *previous* segment's restart.out
-    segment_settings[[c("model", "options", "RESTART_IN")]] <- restart_out
+    runs <- PEcAn.workflow::start_model_runs(segment_settings, write = FALSE)
+
+    model2netcdf.SIPNET(
+      outdir = segment_outdir_withid,
+      sitelat = segment_settings[[c("run", "site", "lat")]],
+      sitelon = segment_settings[[c("run", "site", "lon")]],
+      start_date = dstart,
+      end_date = dend,
+      revision = segment_settings[[c("model", "revision")]],
+      overwrite = TRUE
+    )
   }
-  # ...and now, define a new restart.out for *this* segment
-  restart_out <- file.path(segment_dir, "restart.out")
-  segment_settings[[c("model", "options", "RESTART_OUT")]] <- restart_out
-
-  # Write runs file
-  writeLines(runid, file.path(segment_rundir, "runs.txt"))
-
-  # TODO: Logic to get the trait values corresponding to the segment's PFT.
-  # 1. Cross-reference crop_code against PFT
-  # 2. Get traits from PFT posterior file.
-  segment_traits <- list(list())
-
-  config <- PEcAn.SIPNET::write.config.SIPNET(
-    defaults = settings[["pfts"]],
-    trait.values = segment_traits,
-    settings = segment_settings,
-    run.id = runid
-  )
 
-  runs <- PEcAn.workflow::start_model_runs(segment_settings, write = FALSE)
+  segment_ncfiles <- lapply(
+    segments[["segment_dir"]],
+    \(x) {
+      list.files(
+        file.path(x, "out", "1"),
+        pattern = "\\d+\\.nc",
+        full.names = TRUE
+      )
+    }
+  ) |>
+    do.call(what = c)
 
-  model2netcdf.SIPNET(
-    outdir = segment_outdir_withid,
-    sitelat = segment_settings[[c("run", "site", "lat")]],
-    sitelon = segment_settings[[c("run", "site", "lon")]],
-    start_date = dstart,
-    end_date = dend,
-    revision = segment_settings[[c("model", "revision")]],
-    overwrite = TRUE
+  segment_files_byyear <- split(
+    segment_ncfiles,
+    factor(basename(segment_ncfiles))
   )
-}
-
-# TODO: Concatenate the NetCDF files. This is annoyingly hard in R (unless I use `stars`?)
-
-segment_ncfiles <- lapply(
-  segments[["segment_dir"]],
-  \(x) list.files(
-    file.path(x, "out", "1"),
-    pattern = "\\d+\\.nc",
-    full.names = TRUE
+  segment_outfiles <- file.path(run_outdir, names(segment_files_byyear))
+  results <- purrr::map2(
+    segment_files_byyear,
+    segment_outfiles,
+    PEcAn.SIPNET::mergeNC
   )
-) |>
-  do.call(what = c)
-
-segment_files_byyear <- split(segment_ncfiles, factor(basename(segment_ncfiles)))
-combined_outdir <- fs::dir_create(fs::path(outdir_root, "out"))
-names(segment_files_byyear) <- fs::path(combined_outdir, names(segment_files_byyear))
-results <- purrr::imap(segment_files_byyear, PEcAn.SIPNET::mergeNC)
+}
diff --git a/modules/data.land/inst/sipnet-restart-workflow/81-utils.R b/modules/data.land/inst/sipnet-restart-workflow/81-utils.R
new file mode 100644
index 00000000000..558abf94542
--- /dev/null
+++ b/modules/data.land/inst/sipnet-restart-workflow/81-utils.R
@@ -0,0 +1,33 @@
+#' settings for whole run with many paths per input ->
+#' settings for one ensemble member with one path per input
+#'
+#' @param settings single-site settings object (not Multisettings)
+#' @param inputs named list of input indices (one row of the sample design)
+subset_paths <- function(settings, path_nums) {
+  for (input in names(path_nums)) {
+    if (!(input %in% names(settings$run$inputs))) {
+      next
+    }
+    path_idx <- path_nums[[input]]
+    all_paths <- settings$run$inputs[[input]]$path
+    if (path_idx > length(all_paths)) {
+      PEcAn.logger::logger.severe("No path at input ", sQuote(input), " index ", path_idx)
+    }
+    settings$run$inputs[[input]]$path <- all_paths[[path_idx]]
+  }
+  settings
+}
+
+crop2pft <- function(crop_code) {
+  # crop_code <- c("F1", "R1", "G2", "F16")
+  cls <- substr(crop_code, 1, 1)
+  dplyr::case_when(
+    cls == "D" ~ "temperate.deciduous",
+    cls == "F" ~ "annual_crop",
+    cls == "G" ~ "grass",
+    cls == "P" ~ "grass",
+    cls == "R" ~ "grass",
+    is.na(crop_code) ~ "soil",
+    TRUE ~ "UNKNOWN_PFT"
+  )
+}
diff --git a/modules/data.land/inst/sipnet-restart-workflow/config.yml b/modules/data.land/inst/sipnet-restart-workflow/config.yml
index d83f56178ac..bc2614cd962 100644
--- a/modules/data.land/inst/sipnet-restart-workflow/config.yml
+++ b/modules/data.land/inst/sipnet-restart-workflow/config.yml
@@ -11,6 +11,7 @@ default:
   planting_events_dir: "/projectnb/dietzelab/ccmmf/management/event_files"
   mslsp_path: "/projectnb/dietzelab/ccmmf/management/phenology/matched_landiq_mslsp_v4.1"
   pft_dir: "..."
+  n_ensemble: 3
 
 ashiklom:
   irrigation_path: !expr path.expand("~/data/irrigation-events-out/irrigation_10000.parquet")
diff --git a/modules/uncertainty/R/generate_joint_ensemble_design.R b/modules/uncertainty/R/generate_joint_ensemble_design.R
index c94b0525127..e3faeb2656e 100644
--- a/modules/uncertainty/R/generate_joint_ensemble_design.R
+++ b/modules/uncertainty/R/generate_joint_ensemble_design.R
@@ -58,7 +58,7 @@ generate_joint_ensemble_design <- function(settings,
   if (sobol) {
     ensemble_size <- as.numeric(ensemble_size) * 2
   }
-  ens.sample.method <- settings$ensemble$samplingspace$parameters$method
+  ens.sample.method <- settings$ensemble$samplingspace$parameters$method %||% "uniform"
   design_list <- list()
   sampled_inputs <- list()
   posterior.files <- settings$pfts %>%
@@ -119,4 +119,4 @@ generate_joint_ensemble_design <- function(settings,
   # list includes additional info beyond just X that's required by the function that 
   # does the sobol index calculations, but not required to do the runs themselves.
   return(list(X = design_matrix))
-}
\ No newline at end of file
+}

From 3cc91715b74b4fe0803119a3557fca4cf5ef97ba Mon Sep 17 00:00:00 2001
From: Alexey Shiklomanov <alexey.shiklomanov@gmail.com>
Date: Sun, 5 Apr 2026 13:34:49 -0400
Subject: [PATCH 20/75] move to root workflows dir

---
 .../sipnet-restart-workflow/01-prepare-events.R               | 2 +-
 .../sipnet-restart-workflow/02-run-sipnet.R                   | 4 ++--
 .../sipnet-restart-workflow/03-plot-outputs.R                 | 0
 .../inst => workflows}/sipnet-restart-workflow/81-utils.R     | 0
 .../inst => workflows}/sipnet-restart-workflow/91-debug.R     | 0
 .../inst => workflows}/sipnet-restart-workflow/config.yml     | 0
 6 files changed, 3 insertions(+), 3 deletions(-)
 rename {modules/data.land/inst => workflows}/sipnet-restart-workflow/01-prepare-events.R (97%)
 rename {modules/data.land/inst => workflows}/sipnet-restart-workflow/02-run-sipnet.R (98%)
 rename {modules/data.land/inst => workflows}/sipnet-restart-workflow/03-plot-outputs.R (100%)
 rename {modules/data.land/inst => workflows}/sipnet-restart-workflow/81-utils.R (100%)
 rename {modules/data.land/inst => workflows}/sipnet-restart-workflow/91-debug.R (100%)
 rename {modules/data.land/inst => workflows}/sipnet-restart-workflow/config.yml (100%)

diff --git a/modules/data.land/inst/sipnet-restart-workflow/01-prepare-events.R b/workflows/sipnet-restart-workflow/01-prepare-events.R
similarity index 97%
rename from modules/data.land/inst/sipnet-restart-workflow/01-prepare-events.R
rename to workflows/sipnet-restart-workflow/01-prepare-events.R
index 724bc75064c..2e7bebe0fe5 100644
--- a/modules/data.land/inst/sipnet-restart-workflow/01-prepare-events.R
+++ b/workflows/sipnet-restart-workflow/01-prepare-events.R
@@ -1,6 +1,6 @@
 #!/usr/bin/env Rscript
 
-config <- config::get(file = "modules/data.land/inst/sipnet-restart-workflow/config.yml")
+config <- config::get(file = "workflows/sipnet-restart-workflow/config.yml")
 
 # Pick a parcel from irrigation
 pid <- config[["parcel_id"]]
diff --git a/modules/data.land/inst/sipnet-restart-workflow/02-run-sipnet.R b/workflows/sipnet-restart-workflow/02-run-sipnet.R
similarity index 98%
rename from modules/data.land/inst/sipnet-restart-workflow/02-run-sipnet.R
rename to workflows/sipnet-restart-workflow/02-run-sipnet.R
index 357f218bc63..561300dc9e9 100644
--- a/modules/data.land/inst/sipnet-restart-workflow/02-run-sipnet.R
+++ b/workflows/sipnet-restart-workflow/02-run-sipnet.R
@@ -4,9 +4,9 @@ library(PEcAn.data.land)
 # devtools::load_all("modules/data.land")
 devtools::load_all("models/sipnet")
 
-source("modules/data.land/inst/sipnet-restart-workflow/81-utils.R")
+source("workflows/sipnet-restart-workflow/81-utils.R")
 
-config <- config::get(file = "modules/data.land/inst/sipnet-restart-workflow/config.yml")
+config <- config::get(file = "workflows/sipnet-restart-workflow/config.yml")
 
 outdir_root <- config[["outdir_root"]]
 # Cleanup some existing files to have a clean start
diff --git a/modules/data.land/inst/sipnet-restart-workflow/03-plot-outputs.R b/workflows/sipnet-restart-workflow/03-plot-outputs.R
similarity index 100%
rename from modules/data.land/inst/sipnet-restart-workflow/03-plot-outputs.R
rename to workflows/sipnet-restart-workflow/03-plot-outputs.R
diff --git a/modules/data.land/inst/sipnet-restart-workflow/81-utils.R b/workflows/sipnet-restart-workflow/81-utils.R
similarity index 100%
rename from modules/data.land/inst/sipnet-restart-workflow/81-utils.R
rename to workflows/sipnet-restart-workflow/81-utils.R
diff --git a/modules/data.land/inst/sipnet-restart-workflow/91-debug.R b/workflows/sipnet-restart-workflow/91-debug.R
similarity index 100%
rename from modules/data.land/inst/sipnet-restart-workflow/91-debug.R
rename to workflows/sipnet-restart-workflow/91-debug.R
diff --git a/modules/data.land/inst/sipnet-restart-workflow/config.yml b/workflows/sipnet-restart-workflow/config.yml
similarity index 100%
rename from modules/data.land/inst/sipnet-restart-workflow/config.yml
rename to workflows/sipnet-restart-workflow/config.yml

From 5e8a404d83f8173cf841f9f8e2eeb8d3909a1879 Mon Sep 17 00:00:00 2001
From: Alexey Shiklomanov <alexey.shiklomanov@gmail.com>
Date: Sun, 5 Apr 2026 14:13:45 -0400
Subject: [PATCH 21/75] refactor settings creation into own file

---
 .../02-prepare-settings.R                     | 116 ++++++++++++++
 .../{02-run-sipnet.R => 03-run-sipnet.R}      | 141 ++----------------
 .../{03-plot-outputs.R => 04-plot-outputs.R}  |   0
 workflows/sipnet-restart-workflow/config.yml  |   2 +-
 4 files changed, 130 insertions(+), 129 deletions(-)
 create mode 100644 workflows/sipnet-restart-workflow/02-prepare-settings.R
 rename workflows/sipnet-restart-workflow/{02-run-sipnet.R => 03-run-sipnet.R} (56%)
 rename workflows/sipnet-restart-workflow/{03-plot-outputs.R => 04-plot-outputs.R} (100%)

diff --git a/workflows/sipnet-restart-workflow/02-prepare-settings.R b/workflows/sipnet-restart-workflow/02-prepare-settings.R
new file mode 100644
index 00000000000..b562ba3906d
--- /dev/null
+++ b/workflows/sipnet-restart-workflow/02-prepare-settings.R
@@ -0,0 +1,116 @@
+#!/usr/bin/env Rscript
+
+config <- config::get(file = "workflows/sipnet-restart-workflow/config.yml")
+outdir_root <- config[["outdir_root"]]
+
+outdir <- normalizePath(file.path(outdir_root, "output"))
+modeloutdir <- file.path(outdir, "out")
+dir.create(modeloutdir, showWarnings = FALSE, recursive = TRUE)
+settings_rundir <- file.path(outdir, "run")
+dir.create(settings_rundir, showWarnings = FALSE, recursive = TRUE)
+
+binary <- config[["sipnet_binary"]]
+stopifnot(file.exists(binary))
+
+n_ensemble <- config[["n_ensemble"]]
+
+site_id <- config[["site_id"]]
+
+dp_data <- read.csv(config[["dp_path"]]) |>
+  dplyr::filter(.data$id == .env$site_id)
+site_lat <- dp_data[["lat"]]
+site_lon <- dp_data[["lon"]]
+
+events_json_file <- file.path(outdir_root, "events.json")
+sipnet_eventfile <- PEcAn.SIPNET::write.events.SIPNET(events_json_file, outdir_root)
+events <- jsonlite::read_json(events_json_file, simplifyVector = FALSE)
+
+all_dates <- events |>
+  purrr::pluck(1, "events") |>
+  purrr::map_chr("date") |>
+  as.Date()
+
+start_date <- min(all_dates)
+end_date <- max(all_dates)
+
+metfiles <- file.path(config[["met_dir"]], site_id) |>
+  list.files("ERA5\\..*\\.clim", full.names = TRUE) |>
+  as.list()
+names(metfiles) <- paste0("path", seq_along(metfiles))
+
+icfiles <- file.path(config[["ic_dir"]], site_id) |>
+  list.files("IC_site_.*\\.nc", full.names = TRUE) |>
+  as.list()
+names(icfiles) <- paste0("path", seq_along(icfiles))
+
+pft_dir <- config[["pft_dir"]]
+stopifnot(dir.exists(pft_dir))
+
+pfts <- c("temperate.deciduous", "grass", "annual_crop") |>
+  purrr::map(~list(
+    name = .x,
+    posterior.files = file.path(pft_dir, .x, "post.distns.Rdata"),
+    outdir = paste0(file.path(pft_dir, .x), "/")
+  )) |>
+  c(list(list(name = "soil", outdir = file.path(pft_dir, "soil/"))))
+names(pfts) <- rep("pft", length(pfts))
+
+ensemble_settings <- list(
+  size = n_ensemble,
+  variable = "LAI",
+  variable = "SoilMoist",
+  variable = "GPP",
+  variable = "SoilResp",
+  variable = "AGB",
+  variable = "NEE",
+  samplingspace = list(
+    parameters = list(method = "uniform"),
+    events = list(method = "sampling"),
+    met = list(method = "sampling"),
+    poolinitcond = list(method = "sampling")
+  ),
+  start.year = lubridate::year(start_date),
+  end.year = lubridate::year(end_date)
+)
+
+settings_raw <- PEcAn.settings::as.Settings(list(
+  outdir = outdir,
+  modeloutdir = modeloutdir,
+  rundir = settings_rundir,
+  pfts = pfts,
+  ensemble = ensemble_settings,
+  model = list(
+    type = "SIPNET",
+    binary = binary,
+    revision = "v2",
+    options = list(
+      GDD = 0,
+      NITROGEN_CYCLE = 0,
+      ANAEROBIC = 0,
+      LITTER_POOL = 1
+    )
+  ),
+  run = list(
+    site = list(
+      id = site_id,
+      name = site_id,
+      lat = site_lat,
+      lon = site_lon,
+      site.pft = list(
+        soil = "soil"
+      )
+    ),
+    start.date = start_date,
+    end.date = end_date,
+    inputs = list(
+      met = list(path = metfiles),
+      poolinitcond = list(path = icfiles),
+      events = list(path = sipnet_eventfile)
+    )
+  ),
+  host = list(
+    name = "localhost"
+  )
+))
+
+PEcAn.settings::write.settings(settings_raw, "settings.xml", outdir_root)
diff --git a/workflows/sipnet-restart-workflow/02-run-sipnet.R b/workflows/sipnet-restart-workflow/03-run-sipnet.R
similarity index 56%
rename from workflows/sipnet-restart-workflow/02-run-sipnet.R
rename to workflows/sipnet-restart-workflow/03-run-sipnet.R
index 561300dc9e9..bee1a2adc33 100644
--- a/workflows/sipnet-restart-workflow/02-run-sipnet.R
+++ b/workflows/sipnet-restart-workflow/03-run-sipnet.R
@@ -1,132 +1,22 @@
 #!/usr/bin/env Rscript
 
-library(PEcAn.data.land)
-# devtools::load_all("modules/data.land")
-devtools::load_all("models/sipnet")
+if (FALSE) {
+  devtools::install("models/sipnet", upgrade = FALSE)
+  devtools::install("modules/data.land", upgrade = FALSE)
+}
 
 source("workflows/sipnet-restart-workflow/81-utils.R")
 
 config <- config::get(file = "workflows/sipnet-restart-workflow/config.yml")
 
 outdir_root <- config[["outdir_root"]]
-# Cleanup some existing files to have a clean start
-list.files(outdir_root, full.names = TRUE) |>
-  grepv(pattern = "events.json", invert = TRUE, fixed = TRUE) |>
-  unlink(recursive = TRUE)
-
-binary <- config[["sipnet_binary"]]
-stopifnot(file.exists(binary))
-
-n_ensemble <- config[["n_ensemble"]]
-
-site_id <- config[["site_id"]]
-dp_data <- read.csv(config[["dp_path"]]) |>
-  dplyr::filter(.data$id == .env$site_id)
-site_lat <- dp_data[["lat"]]
-site_lon <- dp_data[["lon"]]
 
 events_json_file <- file.path(outdir_root, "events.json")
-sipnet_eventfile <- PEcAn.SIPNET::write.events.SIPNET(events_json_file, outdir_root)
-events <- jsonlite::read_json(events_json_file, simplifyVector = FALSE)
-
-all_dates <- events |>
-  purrr::pluck(1, "events") |>
-  purrr::map_chr("date") |>
-  as.Date()
-
-start_date <- min(all_dates)
-end_date <- max(all_dates)
-
-
-met <- file.path(config[["met_dir"]], site_id) |>
-  list.files("ERA5\\..*\\.clim", full.names = TRUE) |>
-  as.list()
-names(met) <- paste0("path", seq_along(met))
-
-icfile <- file.path(config[["ic_dir"]], site_id) |>
-  list.files("IC_site_.*\\.nc", full.names = TRUE) |>
-  as.list()
-names(icfile) <- paste0("path", seq_along(icfile))
-
-pft_dir <- config[["pft_dir"]]
-stopifnot(dir.exists(pft_dir))
 
-################################################################################
-outdir <- fs::path_abs(file.path(outdir_root, "output"))
+settings_raw <- PEcAn.settings::read.settings(file.path(outdir_root, "settings.xml"))
+unlink(settings_raw$outdir, recursive = TRUE)
+dir.create(settings_raw$outdir, recursive = TRUE, showWarnings = FALSE)
 
-pfts <- c("temperate.deciduous", "grass", "annual_crop") |>
-  purrr::map(~list(
-    name = .x,
-    posterior.files = file.path(pft_dir, .x, "post.distns.Rdata"),
-    outdir = paste0(file.path(pft_dir, .x), "/")
-  )) |>
-  c(list(list(name = "soil", outdir = file.path(pft_dir, "soil/"))))
-names(pfts) <- rep("pft", length(pfts))
-
-settings_outdir <- file.path(outdir, "out")
-dir.create(settings_outdir, showWarnings = FALSE, recursive = TRUE)
-settings_rundir <- file.path(outdir, "run")
-dir.create(settings_rundir, showWarnings = FALSE, recursive = TRUE)
-
-ensemble_settings <- list(
-  size = n_ensemble,
-  variable = "LAI",
-  variable = "SoilMoist",
-  variable = "GPP",
-  variable = "SoilResp",
-  variable = "AGB",
-  variable = "NEE",
-  samplingspace = list(
-    parameters = list(method = "uniform"),
-    events = list(method = "sampling"),
-    met = list(method = "sampling"),
-    poolinitcond = list(method = "sampling"),
-    # leaf_phenology = list(method = "sampling")
-    NULL
-  ),
-  start.year = lubridate::year(start_date),
-  end.year = lubridate::year(end_date)
-)
-
-settings_raw <- PEcAn.settings::as.Settings(list(
-  outdir = outdir_root,
-  modeloutdir = settings_outdir,
-  rundir = settings_rundir,
-  pfts = pfts,
-  ensemble = ensemble_settings,
-  model = list(
-    type = "SIPNET",
-    binary = binary,
-    revision = "v2",
-    options = list(
-      GDD = 0,
-      NITROGEN_CYCLE = 0,
-      ANAEROBIC = 0,
-      LITTER_POOL = 1
-    )
-  ),
-  run = list(
-    site = list(
-      id = site_id,
-      name = site_id,
-      lat = site_lat,
-      lon = site_lon,
-      site.pft = list(
-        soil = "soil"
-      )
-    ),
-    start.date = start_date,
-    end.date = end_date,
-    inputs = list(
-      met = list(path = met),
-      poolinitcond = list(path = icfile),
-      events = list(path = sipnet_eventfile)
-    )
-  ),
-  host = list(
-    name = "localhost"
-  )
-))
 # Get parameter samples for all relevant PFTs
 sens_design <- PEcAn.uncertainty::generate_joint_ensemble_design(
   settings_raw,
@@ -144,14 +34,12 @@ inputs_runs <- file.path(settings$outdir, "runs_manifest.csv") |>
 
 write.csv(inputs_runs, file = file.path(settings$outdir, "inputs_runs.csv"))
 
-################################################################################
 # Begin loop
 for (irun in seq_len(nrow(inputs_runs))) {
-  # irun <- 1
   run_row <- inputs_runs[irun, ]
   run_id <- run_row[["run_id"]]
   run_dir <- file.path(settings$rundir, run_id)
-  run_outdir <- file.path(settings$modeloutdir, run_id)
+  run_modeloutdir <- file.path(settings$modeloutdir, run_id)
   run_settings <- subset_paths(settings, run_row)
 
   ens_samples_file <- file.path(
@@ -165,12 +53,12 @@ for (irun in seq_len(nrow(inputs_runs))) {
   # TODO: Different runs might have different events.json files. But for now,
   # this is hard coded to a single set of events.
   run_events_json <- events_json_file
-  crop_cycles <- events_to_crop_cycle_starts(run_events_json)
+  crop_cycles <- PEcAn.data.land::events_to_crop_cycle_starts(run_events_json)
 
   # Get segments
   segments <- data.frame(
-    start_date = c(run_settings$run$start.date, crop_cycles[["date"]]),
-    end_date = c(crop_cycles[["date"]] - 1, run_settings$run$end.date),
+    start_date = c(as.Date(run_settings$run$start.date), crop_cycles[["date"]]),
+    end_date = c(crop_cycles[["date"]] - 1, as.Date(run_settings$run$end.date)),
     crop_code = c(NA_character_, crop_cycles[["crop_code"]])
   )
   segments[["pft"]] <- crop2pft(segments[["crop_code"]])
@@ -181,10 +69,7 @@ for (irun in seq_len(nrow(inputs_runs))) {
     sprintf("segment_%s", segments[["segment_id"]])
   )
 
-  segment_root <- file.path()
-
   for (isegment in seq_len(nrow(segments))) {
-    # isegment <- 1
     segment <- segments[isegment, ]
     segment_id <- segment[["segment_id"]]
     dstart <- segment[["start_date"]]
@@ -196,7 +81,7 @@ for (irun in seq_len(nrow(inputs_runs))) {
     unlink(segment_dir, recursive = TRUE)
     dir.create(segment_dir, showWarnings = FALSE, recursive = TRUE)
 
-    segment_inputs <- split_inputs.SIPNET(
+    segment_inputs <- PEcAn.SIPNET::split_inputs.SIPNET(
       dstart,
       dend,
       run_settings$run$inputs,
@@ -277,7 +162,7 @@ for (irun in seq_len(nrow(inputs_runs))) {
     segment_ncfiles,
     factor(basename(segment_ncfiles))
   )
-  segment_outfiles <- file.path(run_outdir, names(segment_files_byyear))
+  segment_outfiles <- file.path(run_modeloutdir, names(segment_files_byyear))
   results <- purrr::map2(
     segment_files_byyear,
     segment_outfiles,
diff --git a/workflows/sipnet-restart-workflow/03-plot-outputs.R b/workflows/sipnet-restart-workflow/04-plot-outputs.R
similarity index 100%
rename from workflows/sipnet-restart-workflow/03-plot-outputs.R
rename to workflows/sipnet-restart-workflow/04-plot-outputs.R
diff --git a/workflows/sipnet-restart-workflow/config.yml b/workflows/sipnet-restart-workflow/config.yml
index bc2614cd962..d2f8659e651 100644
--- a/workflows/sipnet-restart-workflow/config.yml
+++ b/workflows/sipnet-restart-workflow/config.yml
@@ -1,7 +1,7 @@
 default:
   parcel_id: 39011
   site_id: "cf1c223d4e408116"
-  outdir_root: "modules/data.land/inst/sipnet-restart-workflow/_test"
+  outdir_root: "workflows/sipnet-restart-workflow/_test"
   irrigation_path: "/projectnb/dietzelab/ccmmf/usr/ashiklom/event-outputs/irrigation_10000.parquet"
   parcel_path: "/projectnb/dietzelab/ccmmf/LandIQ-harmonized-v4.1/parcels.gpkg"
   dp_path: "/projectnb/dietzelab/ccmmf/management/irrigation/design_points.csv"

From f0b07c7b9fe988ff8a54025d22369ca1fcdfab8d Mon Sep 17 00:00:00 2001
From: Alexey Shiklomanov <alexey.shiklomanov@gmail.com>
Date: Sun, 5 Apr 2026 14:28:22 -0400
Subject: [PATCH 22/75] pull run_sipnet_segmented into own function

---
 .../sipnet-restart-workflow/03-run-sipnet.R   | 132 +----------------
 workflows/sipnet-restart-workflow/81-utils.R  | 137 ++++++++++++++++++
 2 files changed, 138 insertions(+), 131 deletions(-)

diff --git a/workflows/sipnet-restart-workflow/03-run-sipnet.R b/workflows/sipnet-restart-workflow/03-run-sipnet.R
index bee1a2adc33..483dba03ef1 100644
--- a/workflows/sipnet-restart-workflow/03-run-sipnet.R
+++ b/workflows/sipnet-restart-workflow/03-run-sipnet.R
@@ -37,135 +37,5 @@ write.csv(inputs_runs, file = file.path(settings$outdir, "inputs_runs.csv"))
 # Begin loop
 for (irun in seq_len(nrow(inputs_runs))) {
   run_row <- inputs_runs[irun, ]
-  run_id <- run_row[["run_id"]]
-  run_dir <- file.path(settings$rundir, run_id)
-  run_modeloutdir <- file.path(settings$modeloutdir, run_id)
-  run_settings <- subset_paths(settings, run_row)
-
-  ens_samples_file <- file.path(
-    run_settings$outdir,
-    sprintf("ensemble.samples.%s.Rdata", run_settings$ensemble$ensemble.id)
-  )
-  stopifnot(file.exists(ens_samples_file))
-  ensemble_samples <- PEcAn.utils::load_local(ens_samples_file)[["ens.samples"]]
-  run_traits <- lapply(ensemble_samples, \(dat) dat[run_row[["param"]], ])
-
-  # TODO: Different runs might have different events.json files. But for now,
-  # this is hard coded to a single set of events.
-  run_events_json <- events_json_file
-  crop_cycles <- PEcAn.data.land::events_to_crop_cycle_starts(run_events_json)
-
-  # Get segments
-  segments <- data.frame(
-    start_date = c(as.Date(run_settings$run$start.date), crop_cycles[["date"]]),
-    end_date = c(crop_cycles[["date"]] - 1, as.Date(run_settings$run$end.date)),
-    crop_code = c(NA_character_, crop_cycles[["crop_code"]])
-  )
-  segments[["pft"]] <- crop2pft(segments[["crop_code"]])
-  segments[["segment_id"]] <- sprintf("%03d", seq_len(nrow(segments)))
-  segments[["segment_dir"]] <- file.path(
-    run_dir,
-    "segments",
-    sprintf("segment_%s", segments[["segment_id"]])
-  )
-
-  for (isegment in seq_len(nrow(segments))) {
-    segment <- segments[isegment, ]
-    segment_id <- segment[["segment_id"]]
-    dstart <- segment[["start_date"]]
-    dend <- segment[["end_date"]]
-    segment_dir <- segment[["segment_dir"]]
-
-    runid_dummy <- "1"
-
-    unlink(segment_dir, recursive = TRUE)
-    dir.create(segment_dir, showWarnings = FALSE, recursive = TRUE)
-
-    segment_inputs <- PEcAn.SIPNET::split_inputs.SIPNET(
-      dstart,
-      dend,
-      run_settings$run$inputs,
-      overwrite = TRUE,
-      outpath = segment_dir
-    )
-
-    # Segment-specific settings
-    segment_outdir <- file.path(segment_dir, "out")
-    dir.create(segment_outdir, showWarnings = FALSE, recursive = TRUE)
-    segment_rundir <- file.path(segment_dir, "run")
-    dir.create(segment_rundir, showWarnings = FALSE, recursive = TRUE)
-    file.create(file.path(segment_rundir, "README.txt"))
-
-    segment_rundir_withid <- file.path(segment_rundir, runid_dummy)
-    dir.create(segment_rundir_withid, showWarnings = FALSE, recursive = TRUE)
-    segment_outdir_withid <- file.path(segment_outdir, runid_dummy)
-    dir.create(segment_outdir_withid, showWarnings = FALSE, recursive = TRUE)
-
-    segment_settings <- run_settings
-    segment_settings[["outdir"]] <- segment_outdir
-    segment_settings[["modeloutdir"]] <- segment_outdir
-    segment_settings[["rundir"]] <- segment_rundir
-    segment_settings[[c("run", "start.date")]] <- dstart
-    segment_settings[[c("run", "end.date")]] <- dend
-    segment_settings[[c("run", "inputs")]] <- segment_inputs
-    segment_settings
-    if (is.null(segment_settings[[c("model", "options")]])) {
-      segment_settings[[c("model", "options")]] <- list()
-    }
-
-    if (isegment > 1) {
-      # For isegment > 1, we restart from the *previous* segment's restart.out
-      segment_settings[[c("model", "options", "RESTART_IN")]] <- restart_out
-    }
-    # ...and now, define a new restart.out for *this* segment
-    restart_out <- file.path(segment_rundir, "restart.out")
-    segment_settings[[c("model", "options", "RESTART_OUT")]] <- restart_out
-
-    segment_traits <- run_traits[[segment[["pft"]]]]
-
-    # Write dummy runs file
-    writeLines(runid_dummy, file.path(segment_rundir, "runs.txt"))
-
-    config <- PEcAn.SIPNET::write.config.SIPNET(
-      defaults = segment_settings[["pfts"]],
-      trait.values = segment_traits,
-      settings = segment_settings,
-      run.id = runid_dummy
-    )
-
-    runs <- PEcAn.workflow::start_model_runs(segment_settings, write = FALSE)
-
-    model2netcdf.SIPNET(
-      outdir = segment_outdir_withid,
-      sitelat = segment_settings[[c("run", "site", "lat")]],
-      sitelon = segment_settings[[c("run", "site", "lon")]],
-      start_date = dstart,
-      end_date = dend,
-      revision = segment_settings[[c("model", "revision")]],
-      overwrite = TRUE
-    )
-  }
-
-  segment_ncfiles <- lapply(
-    segments[["segment_dir"]],
-    \(x) {
-      list.files(
-        file.path(x, "out", "1"),
-        pattern = "\\d+\\.nc",
-        full.names = TRUE
-      )
-    }
-  ) |>
-    do.call(what = c)
-
-  segment_files_byyear <- split(
-    segment_ncfiles,
-    factor(basename(segment_ncfiles))
-  )
-  segment_outfiles <- file.path(run_modeloutdir, names(segment_files_byyear))
-  results <- purrr::map2(
-    segment_files_byyear,
-    segment_outfiles,
-    PEcAn.SIPNET::mergeNC
-  )
+  run_sipnet_segmented(settings, run_row, events_json_file)
 }
diff --git a/workflows/sipnet-restart-workflow/81-utils.R b/workflows/sipnet-restart-workflow/81-utils.R
index 558abf94542..d9e150edf7d 100644
--- a/workflows/sipnet-restart-workflow/81-utils.R
+++ b/workflows/sipnet-restart-workflow/81-utils.R
@@ -31,3 +31,140 @@ crop2pft <- function(crop_code) {
     TRUE ~ "UNKNOWN_PFT"
   )
 }
+
+run_sipnet_segmented <- function(
+  settings,
+  run_row,
+  events_json_file,
+  crop2pft = crop2pft
+) {
+  run_id <- run_row[["run_id"]]
+  run_dir <- file.path(settings$rundir, run_id)
+  run_modeloutdir <- file.path(settings$modeloutdir, run_id)
+  run_settings <- subset_paths(settings, run_row)
+
+  ens_samples_file <- file.path(
+    run_settings$outdir,
+    sprintf("ensemble.samples.%s.Rdata", run_settings$ensemble$ensemble.id)
+  )
+  stopifnot(file.exists(ens_samples_file))
+  ensemble_samples <- PEcAn.utils::load_local(ens_samples_file)[["ens.samples"]]
+  run_traits <- lapply(ensemble_samples, \(dat) dat[run_row[["param"]], ])
+
+  # TODO: Store this in settings or something?
+  crop_cycles <- PEcAn.data.land::events_to_crop_cycle_starts(events_json_file)
+
+  # Get segments
+  segments <- data.frame(
+    start_date = c(as.Date(run_settings$run$start.date), crop_cycles[["date"]]),
+    end_date = c(crop_cycles[["date"]] - 1, as.Date(run_settings$run$end.date)),
+    crop_code = c(NA_character_, crop_cycles[["crop_code"]])
+  )
+  segments[["pft"]] <- crop2pft(segments[["crop_code"]])
+  segments[["segment_id"]] <- sprintf("%03d", seq_len(nrow(segments)))
+  segment_rootdir <- file.path(file.path(run_dir, "segments"))
+  segments[["segment_dir"]] <- file.path(
+    segment_rootdir,
+    sprintf("segment_%s", segments[["segment_id"]])
+  )
+
+  for (isegment in seq_len(nrow(segments))) {
+    segment <- segments[isegment, ]
+    dstart <- segment[["start_date"]]
+    dend <- segment[["end_date"]]
+    segment_dir <- segment[["segment_dir"]]
+
+    unlink(segment_dir, recursive = TRUE)
+    dir.create(segment_dir, showWarnings = FALSE, recursive = TRUE)
+
+    runid_dummy <- "1"
+
+    segment_inputs <- PEcAn.SIPNET::split_inputs.SIPNET(
+      dstart,
+      dend,
+      run_settings$run$inputs,
+      overwrite = TRUE,
+      outpath = segment_dir
+    )
+
+    # Segment-specific settings
+    segment_outdir <- file.path(segment_dir, "out")
+    dir.create(segment_outdir, showWarnings = FALSE, recursive = TRUE)
+    segment_rundir <- file.path(segment_dir, "run")
+    dir.create(segment_rundir, showWarnings = FALSE, recursive = TRUE)
+    file.create(file.path(segment_rundir, "README.txt"))
+
+    segment_rundir_withid <- file.path(segment_rundir, runid_dummy)
+    dir.create(segment_rundir_withid, showWarnings = FALSE, recursive = TRUE)
+    segment_outdir_withid <- file.path(segment_outdir, runid_dummy)
+    dir.create(segment_outdir_withid, showWarnings = FALSE, recursive = TRUE)
+
+    segment_settings <- run_settings
+    segment_settings[["outdir"]] <- segment_outdir
+    segment_settings[["modeloutdir"]] <- segment_outdir
+    segment_settings[["rundir"]] <- segment_rundir
+    segment_settings[[c("run", "start.date")]] <- dstart
+    segment_settings[[c("run", "end.date")]] <- dend
+    segment_settings[[c("run", "inputs")]] <- segment_inputs
+    segment_settings
+    if (is.null(segment_settings[[c("model", "options")]])) {
+      segment_settings[[c("model", "options")]] <- list()
+    }
+
+    if (isegment > 1) {
+      # For isegment > 1, we restart from the *previous* segment's restart.out
+      segment_settings[[c("model", "options", "RESTART_IN")]] <- restart_out
+    }
+    # ...and now, define a new restart.out for *this* segment
+    restart_out <- file.path(segment_rundir, "restart.out")
+    segment_settings[[c("model", "options", "RESTART_OUT")]] <- restart_out
+
+    segment_traits <- run_traits[[segment[["pft"]]]]
+
+    # Write dummy runs file
+    writeLines(runid_dummy, file.path(segment_rundir, "runs.txt"))
+
+    PEcAn.SIPNET::write.config.SIPNET(
+      defaults = segment_settings[["pfts"]],
+      trait.values = segment_traits,
+      settings = segment_settings,
+      run.id = runid_dummy
+    )
+
+    PEcAn.workflow::start_model_runs(segment_settings, write = FALSE)
+
+    PEcAn.SIPNET::model2netcdf.SIPNET(
+      outdir = segment_outdir_withid,
+      sitelat = segment_settings[[c("run", "site", "lat")]],
+      sitelon = segment_settings[[c("run", "site", "lon")]],
+      start_date = dstart,
+      end_date = dend,
+      revision = segment_settings[[c("model", "revision")]],
+      overwrite = TRUE
+    )
+  }
+
+  segment_ncfiles <- lapply(
+    segments[["segment_dir"]],
+    \(x) {
+      list.files(
+        file.path(x, "out", "1"),
+        pattern = "\\d+\\.nc",
+        full.names = TRUE
+      )
+    }
+  ) |>
+    do.call(what = c)
+
+  segment_files_byyear <- split(
+    segment_ncfiles,
+    factor(basename(segment_ncfiles))
+  )
+  segment_outfiles <- file.path(run_modeloutdir, names(segment_files_byyear))
+  results <- purrr::map2(
+    segment_files_byyear,
+    segment_outfiles,
+    PEcAn.SIPNET::mergeNC
+  )
+  results
+}

From 0df2bbc9fe7bd912ab7103cfddeea851097ffd6e Mon Sep 17 00:00:00 2001
From: Alexey Shiklomanov <alexey.shiklomanov@gmail.com>
Date: Sun, 5 Apr 2026 14:37:16 -0400
Subject: [PATCH 23/75] update plotting code

---
 .../sipnet-restart-workflow/04-plot-outputs.R | 40 ++++++++++---------
 1 file changed, 22 insertions(+), 18 deletions(-)

diff --git a/workflows/sipnet-restart-workflow/04-plot-outputs.R b/workflows/sipnet-restart-workflow/04-plot-outputs.R
index f1822f4277c..683c728d2f5 100644
--- a/workflows/sipnet-restart-workflow/04-plot-outputs.R
+++ b/workflows/sipnet-restart-workflow/04-plot-outputs.R
@@ -1,10 +1,8 @@
 #!/usr/bin/env Rscript
 
-config <- config::get(file = "modules/data.land/inst/sipnet-restart-workflow/config.yml")
+library(ggplot2)
 
-outdir <- file.path(config$outdir_root, "out")
-ncfiles <- list.files(outdir, full.names = TRUE)
-nc <- ncdf4::nc_open(ncfiles[[1]])
+config <- config::get(file = "workflows/sipnet-restart-workflow/config.yml")
 
 outdir_root <- config[["outdir_root"]]
 events_json_file <- fs::path(outdir_root, "events.json")
@@ -15,33 +13,39 @@ events_df <- dplyr::bind_rows(events[[1]][["events"]]) |>
   dplyr::filter(.data$event_type != "irrigation") |>
   dplyr::arrange(.data$date)
 
-events_df |>
-  dplyr::select("event_type":"crop_code")
+modeloutdir <- file.path(config$outdir_root, "output", "out")
+runids <- list.files(modeloutdir)
+
+read_output <- function(modeloutdir, runid) {
+  PEcAn.utils::read.output(
+    runid,
+    file.path(modeloutdir, runid),
+    variables = c("NEE", "LAI", "AGB", "TotSoilCarb"),
+    dataframe = TRUE
+  ) |>
+    dplyr::mutate(run_id = .env$runid) |>
+    dplyr::as_tibble()
+}
 
-results <- PEcAn.utils::read.output(
-  ncfiles = ncfiles,
-  variables = c("NEE", "LAI", "AGB", "TotSoilCarb"),
-  dataframe = TRUE
-) |>
-  dplyr::as_tibble()
+results <- purrr::map(runids, read_output, modeloutdir = modeloutdir) |>
+  dplyr::bind_rows()
 
-library(ggplot2)
 plt <- results |>
   tidyr::pivot_longer(
-    -c("posix", "year"),
+    -c("posix", "year", "run_id"),
     names_to = "variable",
     values_to = "value"
   ) |>
   ggplot() +
-  aes(x = posix, y = value) +
+  aes(x = posix, y = value, color = run_id) +
   geom_line() +
   geom_vline(
-    aes(xintercept = date, color = event_type),
-    data = events_df,
-    linetype = "dashed"
+    aes(xintercept = date, linetype = event_type),
+    data = events_df
   ) +
   facet_wrap(vars(variable), scales = "free") +
   theme_bw() +
   theme(legend.position = "bottom")
+plt
 
 ggsave("~/Pictures/restarts.png", plt, width = 12, height = 9, units = "in")

From 2b4bf9ede1a0ae04f607ed82b8e81d8472cb2ee5 Mon Sep 17 00:00:00 2001
From: Alexey Shiklomanov <alexey.shiklomanov@gmail.com>
Date: Sun, 5 Apr 2026 15:50:33 -0400
Subject: [PATCH 24/75] support event ensembles

---
 .../01-prepare-events.R                       | 82 ++++++++++++++-----
 .../02-prepare-settings.R                     | 17 +++-
 .../sipnet-restart-workflow/03-run-sipnet.R   | 11 +--
 .../sipnet-restart-workflow/04-plot-outputs.R |  8 +-
 .../{81-utils.R => utils.R}                   | 35 ++++++--
 5 files changed, 115 insertions(+), 38 deletions(-)
 rename workflows/sipnet-restart-workflow/{81-utils.R => utils.R} (82%)

diff --git a/workflows/sipnet-restart-workflow/01-prepare-events.R b/workflows/sipnet-restart-workflow/01-prepare-events.R
index 2e7bebe0fe5..03659d183b6 100644
--- a/workflows/sipnet-restart-workflow/01-prepare-events.R
+++ b/workflows/sipnet-restart-workflow/01-prepare-events.R
@@ -23,9 +23,10 @@ if (is.null(site_id)) {
 }
 
 # Make the events.json
-planting <- fs::dir_ls(
+planting <- list.files(
   config[["planting_events_dir"]],
-  regexp = "planting_statewide_.*\\.parquet"
+  "planting_statewide_.*\\.parquet",
+  full.names = TRUE
 ) |>
   arrow::open_dataset() |>
   dplyr::collect() |>
@@ -33,9 +34,6 @@ planting <- fs::dir_ls(
   dplyr::mutate(date = as.Date(.data$date)) |>
   tibble::as_tibble()
 
-code_pft_mapping <- planting |>
-  dplyr::distinct(crop_code = .data$code, .data$PFT)
-
 planting_events <- planting |>
   dplyr::select(
     "site_id", "event_type", "date",
@@ -78,22 +76,27 @@ end_date <- max(harvest_events$date)
 
 irrigation_path <- config[["irrigation_path"]]
 
-irrigation_events <- arrow::open_dataset(irrigation_path) |>
-  dplyr::filter(
-    .data$parcel_id == .env$pid,
-    .data$ens_id == "irr_ens_001"
-  ) |>
-  dplyr::select(-"ens_id") |>
+irrigation_events_raw <- arrow::open_dataset(irrigation_path) |>
+  dplyr::filter(.data$parcel_id == .env$pid) |>
   dplyr::collect() |>
-  tibble::as_tibble() |>
+  tibble::as_tibble()
+
+# Irrigation events include uncertainty ensembles, so we process them
+# accordingly.
+irrigation_events_all <- irrigation_events_raw |>
   dplyr::filter(.data$date <= .env$end_date) |>
   dplyr::mutate(
     event_type = "irrigation",
-    site_id = as.character(.data$parcel_id),
-    .keep = "unused"
+    site_id = as.character(.data$parcel_id)
   ) |>
+  dplyr::select(-c("parcel_id")) |>
   dplyr::relocate("site_id", "event_type", "date")
 
+irrigation_events_list <- split(
+  dplyr::select(irrigation_events_all, -"ens_id"),
+  irrigation_events_all[["ens_id"]]
+)
+
 make_event_list <- function(df) {
   df2list <- function(df) {
     as.list(df) |> purrr::list_transpose()
@@ -105,11 +108,46 @@ make_event_list <- function(df) {
 
 planting_n <- make_event_list(planting_events)
 harvest_n <- make_event_list(harvest_events)
-irrigation_n <- make_event_list(irrigation_events)
-all_events <- dplyr::bind_rows(planting_n, harvest_n, irrigation_n) |>
-  dplyr::summarize(events = list(purrr::list_c(.data$events)), .by = "site_id") |>
-  dplyr::mutate(pecan_events_version = "0.1.1", .before = "site_id")
-
-outdir_root <- fs::dir_create(config[["outdir_root"]])
-events_json_file <- fs::path(outdir_root, "events.json")
-jsonlite::write_json(all_events, events_json_file, pretty = TRUE, auto_unbox = TRUE)
+irrigation_n_list <- purrr::map(irrigation_events_list, make_event_list)
+
+make_all_events <- function(...) {
+  dplyr::bind_rows(...) |>
+    dplyr::summarize(events = list(purrr::list_c(.data$events)), .by = "site_id") |>
+    dplyr::mutate(pecan_events_version = "0.1.1", .before = "site_id")
+}
+
+# NOTE: This only works if we each event type has either 1 ensemble or the same
+# number of ensembles. For varying names of ensembles, we need a more
+# sophisticated strategy.
+all_events_list <- purrr::pmap(
+  list(list(planting_n), list(harvest_n), irrigation_n_list),
+  make_all_events
+)
+
+outdir_root <- config[["outdir_root"]]
+events_dir <- file.path(outdir_root, "events")
+dir.create(events_dir, showWarnings = FALSE, recursive = TRUE)
+
+names(all_events_list) <- file.path(
+  events_dir,
+  paste0(gsub("^irr_", "event_", names(irrigation_events_list)), ".json")
+)
+
+purrr::iwalk(
+  all_events_list,
+  jsonlite::write_json,
+  pretty = TRUE,
+  auto_unbox = TRUE
+)
+
+# NOTE: Right now, `write.events.SIPNET` has no way to customize the filename,
+# only the output directory. So we have to create a bunch of individual
+# directories here, with each one containing one SIPNET event file (but
+# possibly for multiple sites).
+sipnet_event_dirs <- gsub("\\.json$", ".sipnet", names(all_events_list))
+
+purrr::walk2(
+  names(all_events_list),
+  sipnet_event_dirs,
+  PEcAn.SIPNET::write.events.SIPNET
+)
diff --git a/workflows/sipnet-restart-workflow/02-prepare-settings.R b/workflows/sipnet-restart-workflow/02-prepare-settings.R
index b562ba3906d..8b973ed5e1e 100644
--- a/workflows/sipnet-restart-workflow/02-prepare-settings.R
+++ b/workflows/sipnet-restart-workflow/02-prepare-settings.R
@@ -21,9 +21,15 @@ dp_data <- read.csv(config[["dp_path"]]) |>
 site_lat <- dp_data[["lat"]]
 site_lon <- dp_data[["lon"]]
 
-events_json_file <- file.path(outdir_root, "events.json")
-sipnet_eventfile <- PEcAn.SIPNET::write.events.SIPNET(events_json_file, outdir_root)
-events <- jsonlite::read_json(events_json_file, simplifyVector = FALSE)
+events_dir <- file.path(outdir_root, "events")
+events_files <- list.files(events_dir, recursive = TRUE, full.names = TRUE)
+events_json_files <- as.list(grepv(".*\\.json$", events_files))
+names(events_json_files) <- paste0("path", seq_along(events_json_files))
+sipnet_eventfiles <- as.list(grepv(".*\\.sipnet/events-.*\\.in", events_files))
+names(sipnet_eventfiles) <- paste0("path", seq_along(sipnet_eventfiles))
+
+# HACK: Get the start and end date from the limits of the first event file.
+events <- jsonlite::read_json(events_json_files[[1]], simplifyVector = FALSE)
 
 all_dates <- events |>
   purrr::pluck(1, "events") |>
@@ -105,7 +111,10 @@ settings_raw <- PEcAn.settings::as.Settings(list(
     inputs = list(
       met = list(path = metfiles),
       poolinitcond = list(path = icfiles),
-      events = list(path = sipnet_eventfile)
+      events = list(
+        path = sipnet_eventfiles,
+        source = events_json_files
+      )
     )
   ),
   host = list(
diff --git a/workflows/sipnet-restart-workflow/03-run-sipnet.R b/workflows/sipnet-restart-workflow/03-run-sipnet.R
index 483dba03ef1..be37c28d7b4 100644
--- a/workflows/sipnet-restart-workflow/03-run-sipnet.R
+++ b/workflows/sipnet-restart-workflow/03-run-sipnet.R
@@ -5,15 +5,15 @@ if (FALSE) {
   devtools::install("modules/data.land", upgrade = FALSE)
 }
 
-source("workflows/sipnet-restart-workflow/81-utils.R")
+source("workflows/sipnet-restart-workflow/utils.R")
 
 config <- config::get(file = "workflows/sipnet-restart-workflow/config.yml")
 
 outdir_root <- config[["outdir_root"]]
 
-events_json_file <- file.path(outdir_root, "events.json")
-
 settings_raw <- PEcAn.settings::read.settings(file.path(outdir_root, "settings.xml"))
+
+# Delete existing outdir so we always start fresh
 unlink(settings_raw$outdir, recursive = TRUE)
 dir.create(settings_raw$outdir, recursive = TRUE, showWarnings = FALSE)
 
@@ -34,8 +34,9 @@ inputs_runs <- file.path(settings$outdir, "runs_manifest.csv") |>
 
 write.csv(inputs_runs, file = file.path(settings$outdir, "inputs_runs.csv"))
 
-# Begin loop
+# Loop over runs. Within each run, loop over segments. Individual runs should
+# be naively parallelizable and therefore suitable for `clustermq`, etc.
 for (irun in seq_len(nrow(inputs_runs))) {
   run_row <- inputs_runs[irun, ]
-  run_sipnet_segmented(settings, run_row, events_json_file)
+  run_sipnet_segmented(settings, run_row)
 }
diff --git a/workflows/sipnet-restart-workflow/04-plot-outputs.R b/workflows/sipnet-restart-workflow/04-plot-outputs.R
index 683c728d2f5..2539c2f47d8 100644
--- a/workflows/sipnet-restart-workflow/04-plot-outputs.R
+++ b/workflows/sipnet-restart-workflow/04-plot-outputs.R
@@ -48,4 +48,10 @@ plt <- results |>
   theme(legend.position = "bottom")
 plt
 
-ggsave("~/Pictures/restarts.png", plt, width = 12, height = 9, units = "in")
+ggsave(
+  file.path(outdir_root, "restarts.png"),
+  plt,
+  width = 12,
+  height = 9,
+  units = "in"
+)
diff --git a/workflows/sipnet-restart-workflow/81-utils.R b/workflows/sipnet-restart-workflow/utils.R
similarity index 82%
rename from workflows/sipnet-restart-workflow/81-utils.R
rename to workflows/sipnet-restart-workflow/utils.R
index d9e150edf7d..ba62ac0f5dc 100644
--- a/workflows/sipnet-restart-workflow/81-utils.R
+++ b/workflows/sipnet-restart-workflow/utils.R
@@ -5,7 +5,7 @@
 #' @param inputs named list of input indices (one row of the sample design)
 subset_paths <- function(settings, path_nums) {
   for (input in names(path_nums)) {
-    if (!(input %in% names(settings$run$inputs))) {
+    if (!is.list(settings$run$inputs[[input]])) {
       next
     }
     path_idx <- path_nums[[input]]
@@ -14,11 +14,32 @@ subset_paths <- function(settings, path_nums) {
       PEcAn.logger::logger.severe("No path at input ", sQuote(input), " index ", path_idx)
     }
     settings$run$inputs[[input]]$path <- all_paths[[path_idx]]
+    # If we define a list of `source`s, also try to subset that (if the lengths
+    # match). This is especially useful for processing events (because we store
+    # the original JSON path in the `source`).
+    if (!is.list(settings$run$inputs[[input]]$source)) {
+      next
+    }
+    all_source_paths <- settings$run$inputs[[input]]$source
+    n_source <- length(all_source_paths)
+    n_path <- length(all_paths)
+    if (n_source != n_path) {
+      PEcAn.logger::logger.warn(sprintf(
+        paste(
+          "For input %s, number of paths (%d) ",
+          "is not equal to number of sources (%d). ",
+          "Assuming these are different things and therefore leaving sources as is."
+        ),
+        input, n_path, n_source
+      ))
+      next
+    }
+    settings$run$inputs[[input]]$source <- all_source_paths[[path_idx]]
   }
   settings
 }
 
-crop2pft <- function(crop_code) {
+crop2pft_example <- function(crop_code) {
   # crop_code <- c("F1", "R1", "G2", "F16")
   cls <- substr(crop_code, 1, 1)
   dplyr::case_when(
@@ -35,8 +56,7 @@ crop2pft <- function(crop_code) {
 run_sipnet_segmented <- function(
   settings,
   run_row,
-  events_json_file,
-  crop2pft = crop2pft
+  crop2pft = crop2pft_example
 ) {
   run_id <- run_row[["run_id"]]
   run_dir <- file.path(settings$rundir, run_id)
@@ -51,8 +71,9 @@ run_sipnet_segmented <- function(
   ensemble_samples <- PEcAn.utils::load_local(ens_samples_file)[["ens.samples"]]
   run_traits <- lapply(ensemble_samples, \(dat) dat[run_row[["param"]], ])
 
-  # TODO: Store this in settings or something?
-  crop_cycles <- PEcAn.data.land::events_to_crop_cycle_starts(events_json_file)
+  crop_cycles <- PEcAn.data.land::events_to_crop_cycle_starts(
+    run_settings$run$inputs$events$source
+  )
 
   # Get segments
   segments <- data.frame(
@@ -144,6 +165,7 @@ run_sipnet_segmented <- function(
     )
   }
 
+  # Get the list of all segment output NetCDFs
   segment_ncfiles <- lapply(
     segments[["segment_dir"]],
     \(x) {
@@ -156,6 +178,7 @@ run_sipnet_segmented <- function(
   ) |>
     do.call(what = c)
 
+  # ...and concatenate them together into annual NetCDFs.
   segment_files_byyear <- split(
     segment_ncfiles,
     factor(basename(segment_ncfiles))

From e3cf5fbd70c3f624bdbcc649a85b6d99d2a339eb Mon Sep 17 00:00:00 2001
From: Alexey Shiklomanov <alexey.shiklomanov@gmail.com>
Date: Sun, 5 Apr 2026 15:57:47 -0400
Subject: [PATCH 25/75] add README

---
 workflows/sipnet-restart-workflow/README.md | 19 +++++++++++++++++++
 1 file changed, 19 insertions(+)
 create mode 100644 workflows/sipnet-restart-workflow/README.md

diff --git a/workflows/sipnet-restart-workflow/README.md b/workflows/sipnet-restart-workflow/README.md
new file mode 100644
index 00000000000..13df30fac36
--- /dev/null
+++ b/workflows/sipnet-restart-workflow/README.md
@@ -0,0 +1,19 @@
+# SIPNET restart workflow for events
+
+This is a demonstration of a workaround for running SIPNET with event files that include crop changes/rotations.
+
+## Execution
+
+1. Install PEcAn locally (`make install`, etc.).
+2. Inspect the `config.yml` and add/modify paths or other values as needed.
+3. Run the numbered R scripts in order.
+
+## Organization
+
+- `config.yml` --- Configuration file for use with the [`config`](https://rstudio.github.io/config/index.html) package. Mostly used for setting machine-specific paths to various inputs. This is pre-populated with inputs for @ashiklom 's local machine and the BU GEO cluster (under the `default` profile).
+
+- `01-prepare-events.R` --- Read raw events data (in parquet format) and write out ensembles of PEcAn `event.json` files and SIPNET-specific versions thereof
+- `02-prepare-settings.R` --- Generate a PEcAn `settings.xml` file populated with machine-specific paths and appropriate configurations.
+- `03-run-sipnet.R` --- Run the workflow sequentially.
+    - Almost all of the functionality is implemented in `utils.R`.
+- `04-plot-outputs.R` --- Load outputs (using `PEcAn.utils::read.output`) and visualize

From 15052977e3bcc407269a864a4ca1389f649eff3c Mon Sep 17 00:00:00 2001
From: Alexey Shiklomanov <alexey.shiklomanov@gmail.com>
Date: Thu, 9 Apr 2026 16:14:10 -0400
Subject: [PATCH 26/75] sipnet: make sure trait.values is a list

---
 models/sipnet/R/write.configs.SIPNET.R | 7 +++++++
 1 file changed, 7 insertions(+)

diff --git a/models/sipnet/R/write.configs.SIPNET.R b/models/sipnet/R/write.configs.SIPNET.R
index 9ea25e4753d..cd5b1cac9e0 100755
--- a/models/sipnet/R/write.configs.SIPNET.R
+++ b/models/sipnet/R/write.configs.SIPNET.R
@@ -78,6 +78,13 @@
 write.config.SIPNET <- function(defaults, trait.values, settings, run.id, inputs = NULL, IC = NULL,
                                 restart = NULL, spinup = NULL) {
 
+  if (!is.list(trait.values)) {
+    PEcAn.logger::logger.severe(paste0(
+      "Even though SIPNET only takes one PFT at a time, ",
+      "`trait.values` must be a list with names corresponding to PFTs."
+    ))
+  }
+
   rev_raw <- settings$model$revision
   legacy_v1 <- c("102319", "136", "r136", "ssr", "git")
   if (is.null(rev_raw) || rev_raw %in% legacy_v1) {

From f33d822b89b5e4f9e6fc95384eab1829931b8014 Mon Sep 17 00:00:00 2001
From: Alexey Shiklomanov <alexey.shiklomanov@gmail.com>
Date: Thu, 9 Apr 2026 16:37:00 -0400
Subject: [PATCH 27/75] sipnet: coerce start/end time to datetime

in split inputs. otherwise, data.frame subsetting doesn't work (but only
raises an error), which ultimately leads to empty files.
---
 models/sipnet/R/split_inputs.SIPNET.R | 20 ++++++++++++++++++++
 1 file changed, 20 insertions(+)

diff --git a/models/sipnet/R/split_inputs.SIPNET.R b/models/sipnet/R/split_inputs.SIPNET.R
index c58af889e89..407cc48b61b 100644
--- a/models/sipnet/R/split_inputs.SIPNET.R
+++ b/models/sipnet/R/split_inputs.SIPNET.R
@@ -83,6 +83,8 @@ split_sipnet_events <- function(start.time, stop.time, eventfile, overwrite = FA
 ##' @importFrom dplyr %>%
 ##' @export
 split_sipnet_met <- function(start.time, stop.time, met, overwrite = FALSE, outpath = NULL) {
+  start.time <- coerce_to_datetime(start.time)
+  stop.time <- coerce_to_datetime(stop.time)
   path <- dirname(met)
   prefix <- sub(".clim", "", basename(met), fixed = TRUE)
   if(is.null(outpath)){
@@ -130,3 +132,21 @@ split_sipnet_met <- function(start.time, stop.time, met, overwrite = FALSE, outp
   #settings$run$inputs$met$path <- file
   return(file)
 } # split_inputs.SIPNET
+
+coerce_to_datetime <- function(x) {
+  if (inherits(x, "POSIXt")) {
+    return(x)
+  }
+  xname <- deparse(substitute(x))
+  if (!inherits(x, "Date")) {
+    PEcAn.logger::logger.severe(
+      "Invalid ", xname, " : ", x,
+      " (class: ", class(x), ")"
+    )
+  }
+  PEcAn.logger::logger.warn(paste0(
+    xname, " is a date, but this function expects a datetime. ",
+    "Coercing to datetime by setting to midnight UTC."
+  ))
+  as.POSIXct(x)
+}

From 0e4cb639151890f71518ae8dbd23cdc12c3bdd9b Mon Sep 17 00:00:00 2001
From: Alexey Shiklomanov <alexey.shiklomanov@gmail.com>
Date: Thu, 9 Apr 2026 16:38:54 -0400
Subject: [PATCH 28/75] use real harvest events

---
 .../sipnet-restart-workflow/01-prepare-events.R | 17 ++++++++++-------
 1 file changed, 10 insertions(+), 7 deletions(-)

diff --git a/workflows/sipnet-restart-workflow/01-prepare-events.R b/workflows/sipnet-restart-workflow/01-prepare-events.R
index 03659d183b6..ffb83c4aa2d 100644
--- a/workflows/sipnet-restart-workflow/01-prepare-events.R
+++ b/workflows/sipnet-restart-workflow/01-prepare-events.R
@@ -32,6 +32,8 @@ planting <- list.files(
   dplyr::collect() |>
   dplyr::filter(.data$site_id == as.character(.env$pid)) |>
   dplyr::mutate(date = as.Date(.data$date)) |>
+  # Start no earlier than 2016 because our met doesn't go back before 2015
+  dplyr::filter(date >= as.Date("2016-01-01")) |>
   tibble::as_tibble()
 
 planting_events <- planting |>
@@ -61,14 +63,15 @@ phenology <- fs::dir_ls(mslsp_path, glob = "*.parquet") |>
   )
 
 # Dummy values for testing
-harvest_events <- phenology |>
-  dplyr::mutate(
-    event_type = "harvest",
-    site_id = as.character(.data$parcel_id),
-    frac_above_removed_0to1 = 0.85
-  ) |>
+harvest_dir <- config[["harvest_events_dir"]]
+pidc <- as.character(pid)
+harvest_events <- list.files(harvest_dir, "*.parquet", full.names = TRUE) |>
+  arrow::open_dataset() |>
+  dplyr::filter(.data$site_id == .env$pidc) |>
+  dplyr::collect() |>
+  tibble::as_tibble() |>
   dplyr::select(
-    "site_id", "event_type", "date" = mslsp_OGMn, "frac_above_removed_0to1"
+    "site_id", "event_type", "date", dplyr::starts_with("frac_")
   )
 
 start_date <- min(planting$date)

From d155df7f28a386f065a8554966e213db25796781 Mon Sep 17 00:00:00 2001
From: Alexey Shiklomanov <alexey.shiklomanov@gmail.com>
Date: Thu, 9 Apr 2026 16:39:16 -0400
Subject: [PATCH 29/75] allow prepare-events to work without irrigation

---
 .../01-prepare-events.R                        | 18 +++++++++++++-----
 1 file changed, 13 insertions(+), 5 deletions(-)

diff --git a/workflows/sipnet-restart-workflow/01-prepare-events.R b/workflows/sipnet-restart-workflow/01-prepare-events.R
index ffb83c4aa2d..e740a3b6a66 100644
--- a/workflows/sipnet-restart-workflow/01-prepare-events.R
+++ b/workflows/sipnet-restart-workflow/01-prepare-events.R
@@ -122,19 +122,27 @@ make_all_events <- function(...) {
 # NOTE: This only works if we each event type has either 1 ensemble or the same
 # number of ensembles. For varying names of ensembles, we need a more
 # sophisticated strategy.
-all_events_list <- purrr::pmap(
-  list(list(planting_n), list(harvest_n), irrigation_n_list),
-  make_all_events
+pmap_args <- c(
+  if (length(planting_n) > 0) list(list(planting_n)),
+  if (length(harvest_n) > 0) list(list(harvest_n)),
+  if (length(irrigation_n_list) > 0) irrigation_n_list
 )
+all_events_list <- purrr::pmap(pmap_args, make_all_events)
 
 outdir_root <- config[["outdir_root"]]
 events_dir <- file.path(outdir_root, "events")
+unlink(events_dir, recursive = TRUE)
 dir.create(events_dir, showWarnings = FALSE, recursive = TRUE)
 
 names(all_events_list) <- file.path(
-  events_dir,
-  paste0(gsub("^irr_", "event_", names(irrigation_events_list)), ".json")
+  events_dir, paste0("event_", seq_along(all_events_list), ".json")
 )
+if (length(irrigation_events_list) > 0) {
+  names(all_events_list) <- file.path(
+    events_dir,
+    paste0(gsub("^irr_", "event_", names(irrigation_events_list)), ".json")
+  )
+}
 
 purrr::iwalk(
   all_events_list,

From cb5cc1cfb6a39a4432ebd71a1140535ffd2c049f Mon Sep 17 00:00:00 2001
From: Alexey Shiklomanov <alexey.shiklomanov@gmail.com>
Date: Thu, 9 Apr 2026 16:39:37 -0400
Subject: [PATCH 30/75] update met paths to use xxN_yy.yE -type naming

---
 workflows/sipnet-restart-workflow/02-prepare-settings.R | 8 +++++++-
 1 file changed, 7 insertions(+), 1 deletion(-)

diff --git a/workflows/sipnet-restart-workflow/02-prepare-settings.R b/workflows/sipnet-restart-workflow/02-prepare-settings.R
index 8b973ed5e1e..e393bb12a4f 100644
--- a/workflows/sipnet-restart-workflow/02-prepare-settings.R
+++ b/workflows/sipnet-restart-workflow/02-prepare-settings.R
@@ -39,9 +39,15 @@ all_dates <- events |>
 start_date <- min(all_dates)
 end_date <- max(all_dates)
 
-metfiles <- file.path(config[["met_dir"]], site_id) |>
+met_dir <- sprintf(
+  "%sN_%sW",
+  format(round(abs(site_lat) * 2) / 2, nsmall = 0, drop0trailing = TRUE),
+  format(round(abs(site_lon) * 2) / 2, nsmall = 0, drop0trailing = TRUE)
+)
+metfiles <- file.path(config[["met_dir"]], met_dir) |>
   list.files("ERA5\\..*\\.clim", full.names = TRUE) |>
   as.list()
+stopifnot(length(metfiles) > 0)
 names(metfiles) <- paste0("path", seq_along(metfiles))
 
 icfiles <- file.path(config[["ic_dir"]], site_id) |>

From 22bc879b038d618af483fba21a94460a59d50c3a Mon Sep 17 00:00:00 2001
From: Alexey Shiklomanov <alexey.shiklomanov@gmail.com>
Date: Thu, 9 Apr 2026 16:40:13 -0400
Subject: [PATCH 31/75] put all settings logic into prepare-settings

---
 .../02-prepare-settings.R                     | 23 +++++++++-
 .../sipnet-restart-workflow/03-run-sipnet.R   | 46 +++++++------------
 2 files changed, 38 insertions(+), 31 deletions(-)

diff --git a/workflows/sipnet-restart-workflow/02-prepare-settings.R b/workflows/sipnet-restart-workflow/02-prepare-settings.R
index e393bb12a4f..b7854c97487 100644
--- a/workflows/sipnet-restart-workflow/02-prepare-settings.R
+++ b/workflows/sipnet-restart-workflow/02-prepare-settings.R
@@ -128,4 +128,25 @@ settings_raw <- PEcAn.settings::as.Settings(list(
   )
 ))
 
-PEcAn.settings::write.settings(settings_raw, "settings.xml", outdir_root)
+# Delete existing outdir so we always start fresh
+unlink(settings_raw$outdir, recursive = TRUE)
+dir.create(settings_raw$outdir, recursive = TRUE, showWarnings = FALSE)
+
+# Get parameter samples for all relevant PFTs
+sens_design <- PEcAn.uncertainty::generate_joint_ensemble_design(
+  settings_raw,
+  settings_raw$ensemble$size
+)
+
+settings <- PEcAn.workflow::runModule.run.write.configs(
+  settings_raw,
+  input_design = sens_design$X
+)
+
+inputs_runs <- file.path(settings$outdir, "runs_manifest.csv") |>
+  read.csv() |>
+  cbind(sens_design[["X"]])
+
+write.csv(inputs_runs, file = file.path(settings$outdir, "inputs_runs.csv"))
+
+PEcAn.settings::write.settings(settings, "settings.xml", outdir_root)
diff --git a/workflows/sipnet-restart-workflow/03-run-sipnet.R b/workflows/sipnet-restart-workflow/03-run-sipnet.R
index be37c28d7b4..066e78c1f3a 100644
--- a/workflows/sipnet-restart-workflow/03-run-sipnet.R
+++ b/workflows/sipnet-restart-workflow/03-run-sipnet.R
@@ -5,38 +5,24 @@ if (FALSE) {
   devtools::install("modules/data.land", upgrade = FALSE)
 }
 
-source("workflows/sipnet-restart-workflow/utils.R")
-
 config <- config::get(file = "workflows/sipnet-restart-workflow/config.yml")
 
-outdir_root <- config[["outdir_root"]]
-
-settings_raw <- PEcAn.settings::read.settings(file.path(outdir_root, "settings.xml"))
-
-# Delete existing outdir so we always start fresh
-unlink(settings_raw$outdir, recursive = TRUE)
-dir.create(settings_raw$outdir, recursive = TRUE, showWarnings = FALSE)
-
-# Get parameter samples for all relevant PFTs
-sens_design <- PEcAn.uncertainty::generate_joint_ensemble_design(
-  settings_raw,
-  settings_raw$ensemble$size
-)
+do_run_sipnet_segmented <- function(irun) {
+  source("workflows/sipnet-restart-workflow/utils.R", local = TRUE)
+  config <- config::get(file = "workflows/sipnet-restart-workflow/config.yml")
+  settings <- PEcAn.settings::read.settings(file.path(config[["outdir_root"]], "settings.xml"))
+  inputs_runs <- read.csv(file.path(settings$outdir, "inputs_runs.csv"))
+  run_sipnet_segmented(settings, inputs_runs[irun, ])  # nolint
+}
 
-settings <- PEcAn.workflow::runModule.run.write.configs(
-  settings_raw,
-  input_design = sens_design$X
+# Run in parallel using crew
+nworkers <- pmin(config[["n_ensemble"]], parallel::detectCores())
+controller <- crew::crew_controller_local(workers = nworkers)
+crew_results <- controller$map(
+  command = do_run_sipnet_segmented(irun),
+  iterate = list(irun = seq_len(config[["n_ensemble"]])),
+  data = list(settings = settings, do_run_sipnet_segmented = do_run_sipnet_segmented)
 )
 
-inputs_runs <- file.path(settings$outdir, "runs_manifest.csv") |>
-  read.csv() |>
-  cbind(sens_design[["X"]])
-
-write.csv(inputs_runs, file = file.path(settings$outdir, "inputs_runs.csv"))
-
-# Loop over runs. Within each run, loop over segments. Individual runs should
-# be naively parallelizable and therefore suitable for `clustermq`, etc.
-for (irun in seq_len(nrow(inputs_runs))) {
-  run_row <- inputs_runs[irun, ]
-  run_sipnet_segmented(settings, run_row)
-}
+# Or, to run sequentially:
+# for (i in seq_len(config[["n_ensemble"]])) do_run_sipnet_segmented(i)   # nolint

From d1d825242a3806ff89da1e0e3ae7f7c191a14090 Mon Sep 17 00:00:00 2001
From: Alexey Shiklomanov <alexey.shiklomanov@gmail.com>
Date: Thu, 9 Apr 2026 16:41:00 -0400
Subject: [PATCH 32/75] better plotting

---
 .../sipnet-restart-workflow/04-plot-outputs.R | 24 ++++++++++++++++---
 1 file changed, 21 insertions(+), 3 deletions(-)

diff --git a/workflows/sipnet-restart-workflow/04-plot-outputs.R b/workflows/sipnet-restart-workflow/04-plot-outputs.R
index 2539c2f47d8..2c595b66c9f 100644
--- a/workflows/sipnet-restart-workflow/04-plot-outputs.R
+++ b/workflows/sipnet-restart-workflow/04-plot-outputs.R
@@ -5,7 +5,11 @@ library(ggplot2)
 config <- config::get(file = "workflows/sipnet-restart-workflow/config.yml")
 
 outdir_root <- config[["outdir_root"]]
-events_json_file <- fs::path(outdir_root, "events.json")
+
+settings <- PEcAn.settings::read.settings(file.path(outdir_root, "settings.xml"))
+events_json_file <- settings |>
+  purrr::chuck("run", "inputs", "events", "source", "path1")
+
 events <- jsonlite::read_json(events_json_file, simplifyVector = FALSE)
 
 events_df <- dplyr::bind_rows(events[[1]][["events"]]) |>
@@ -20,7 +24,8 @@ read_output <- function(modeloutdir, runid) {
   PEcAn.utils::read.output(
     runid,
     file.path(modeloutdir, runid),
-    variables = c("NEE", "LAI", "AGB", "TotSoilCarb"),
+    variables = c("NEE", "LAI", "AGB", "TotSoilCarb", "leaf_carbon_content", "litter_carbon_content"),
+    # variables = NULL,
     dataframe = TRUE
   ) |>
     dplyr::mutate(run_id = .env$runid) |>
@@ -43,6 +48,7 @@ plt <- results |>
     aes(xintercept = date, linetype = event_type),
     data = events_df
   ) +
+  scale_linetype_manual(values = c("planting" = "dotted", "harvest" = "dashed")) +
   facet_wrap(vars(variable), scales = "free") +
   theme_bw() +
   theme(legend.position = "bottom")
@@ -51,7 +57,19 @@ plt
 ggsave(
   file.path(outdir_root, "restarts.png"),
   plt,
-  width = 12,
+  width = 14.5,
   height = 9,
   units = "in"
 )
+
+zoomed <- plt +
+  xlim(
+    lubridate::ymd_h("2017-10-01T00"),
+    lubridate::ymd_h("2017-10-17T01")
+  )
+zoomed
+ggsave(
+  file.path(outdir_root, "zoomed.png"),
+  zoomed,
+  width = 14.5, height = 9, units = "in"
+)

From 4f9781ce85f311eb51a14e9a16ae6b0990dba336 Mon Sep 17 00:00:00 2001
From: Alexey Shiklomanov <alexey.shiklomanov@gmail.com>
Date: Thu, 9 Apr 2026 16:41:20 -0400
Subject: [PATCH 33/75] bugfix handling of trait.values

it must be a list!
---
 workflows/sipnet-restart-workflow/utils.R | 10 ++++++++--
 1 file changed, 8 insertions(+), 2 deletions(-)

diff --git a/workflows/sipnet-restart-workflow/utils.R b/workflows/sipnet-restart-workflow/utils.R
index ba62ac0f5dc..f39b07bb3f9 100644
--- a/workflows/sipnet-restart-workflow/utils.R
+++ b/workflows/sipnet-restart-workflow/utils.R
@@ -43,6 +43,8 @@ crop2pft_example <- function(crop_code) {
   # crop_code <- c("F1", "R1", "G2", "F16")
   cls <- substr(crop_code, 1, 1)
   dplyr::case_when(
+    crop_code == "P1" ~ "annual_crop",
+    crop_code == "G2" ~ "annual_crop",
     cls == "D" ~ "temperate.deciduous",
     cls == "F" ~ "annual_crop",
     cls == "G" ~ "grass",
@@ -127,7 +129,6 @@ run_sipnet_segmented <- function(
     segment_settings[[c("run", "start.date")]] <- dstart
     segment_settings[[c("run", "end.date")]] <- dend
     segment_settings[[c("run", "inputs")]] <- segment_inputs
-    segment_settings
     if (is.null(segment_settings[[c("model", "options")]])) {
       segment_settings[[c("model", "options")]] <- list()
     }
@@ -140,7 +141,12 @@ run_sipnet_segmented <- function(
     restart_out <- file.path(segment_rundir, "restart.out")
     segment_settings[[c("model", "options", "RESTART_OUT")]] <- restart_out
 
-    segment_traits <- run_traits[[segment[["pft"]]]]
+    # trait.values must be a list of pfts, even though SIPNET takes only one
+    # PFT as input. However, we can pass soil params through a "soil" PFT.
+    # Here, if the segment PFT is soil, that's what we send. If the segment PFT
+    # is anything else, we send that *and* the soil params.
+    choose_pft <- unique(c(segment[["pft"]], "soil"))
+    segment_traits <- run_traits[choose_pft]
 
     # Write dummy runs file
     writeLines(runid_dummy, file.path(segment_rundir, "runs.txt"))

From 2c9521d9ffcda86b1aa98d7000a5c1ba7ee2d386 Mon Sep 17 00:00:00 2001
From: Alexey Shiklomanov <alexey.shiklomanov@gmail.com>
Date: Thu, 9 Apr 2026 16:41:41 -0400
Subject: [PATCH 34/75] pixi updates + script to find winter crops

---
 pixi.lock                                     | 939 +++++++++---------
 .../92-find-winter-crop.R                     |  40 +
 2 files changed, 506 insertions(+), 473 deletions(-)
 create mode 100644 workflows/sipnet-restart-workflow/92-find-winter-crop.R

diff --git a/pixi.lock b/pixi.lock
index 3e0ca16fa62..7c0c3bfb476 100644
--- a/pixi.lock
+++ b/pixi.lock
@@ -9,8 +9,7 @@ environments:
       linux-64:
       - conda: https://conda.anaconda.org/conda-forge/linux-64/_openmp_mutex-4.5-20_gnu.conda
       - conda: https://conda.anaconda.org/conda-forge/noarch/_r-mutex-1.0.1-anacondar_1.tar.bz2
-      - conda: https://conda.anaconda.org/conda-forge/linux-64/air-0.8.2-hb17b654_0.conda
-      - conda: https://conda.anaconda.org/conda-forge/linux-64/attr-2.5.2-hb03c661_1.conda
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/air-0.8.2-hb17b654_1.conda
       - conda: https://conda.anaconda.org/conda-forge/linux-64/aws-c-auth-0.9.3-hef928c7_0.conda
       - conda: https://conda.anaconda.org/conda-forge/linux-64/aws-c-cal-0.9.13-h2c9d079_1.conda
       - conda: https://conda.anaconda.org/conda-forge/linux-64/aws-c-common-0.12.6-hb03c661_0.conda
@@ -29,17 +28,17 @@ environments:
       - conda: https://conda.anaconda.org/conda-forge/linux-64/azure-storage-blobs-cpp-12.16.0-hdd73cc9_1.conda
       - conda: https://conda.anaconda.org/conda-forge/linux-64/azure-storage-common-cpp-12.12.0-ha7a2c86_1.conda
       - conda: https://conda.anaconda.org/conda-forge/linux-64/azure-storage-files-datalake-cpp-12.14.0-h52c5a47_1.conda
-      - conda: https://conda.anaconda.org/conda-forge/linux-64/binutils_impl_linux-64-2.45.1-default_hfdba357_101.conda
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/binutils_impl_linux-64-2.45.1-default_hfdba357_102.conda
       - conda: https://conda.anaconda.org/conda-forge/linux-64/blosc-1.21.6-he440d0b_1.conda
       - conda: https://conda.anaconda.org/conda-forge/linux-64/bwidget-1.10.1-ha770c72_1.conda
       - conda: https://conda.anaconda.org/conda-forge/linux-64/bzip2-1.0.8-hda65f42_9.conda
       - conda: https://conda.anaconda.org/conda-forge/linux-64/c-ares-1.34.6-hb03c661_0.conda
       - conda: https://conda.anaconda.org/conda-forge/noarch/ca-certificates-2026.2.25-hbd8a1cb_0.conda
       - conda: https://conda.anaconda.org/conda-forge/linux-64/cairo-1.18.4-he90730b_1.conda
-      - conda: https://conda.anaconda.org/conda-forge/linux-64/cdo-2.5.0-hbf53078_5.conda
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/cdo-2.5.0-h54830fc_7.conda
       - conda: https://conda.anaconda.org/conda-forge/linux-64/curl-8.19.0-hcf29cc6_0.conda
-      - conda: https://conda.anaconda.org/conda-forge/linux-64/eccodes-2.46.0-h83bc92c_0.conda
-      - conda: https://conda.anaconda.org/conda-forge/linux-64/expat-2.7.4-hecca717_0.conda
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   license_family: BSD
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   - libgfortran
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   license_family: MIT
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   size: 144010
   timestamp: 1719014356708
+- conda: https://conda.anaconda.org/conda-forge/linux-64/freetype-2.14.3-ha770c72_0.conda
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-  - libexpat >=2.7.4,<3.0a0
-  - libfreetype >=2.14.2
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   - libstdcxx >=14
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   - libgfortran
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   - libstdcxx >=14
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   license_family: BSD
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   license_family: GPL
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+  - liblapacke 3.11.0   6*_openblas
+  - libcblas   3.11.0   6*_openblas
   - mkl <2026
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-  - libcblas   3.11.0   5*_openblas
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-  - liblapacke 3.11.0   5*_openblas
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-  - blas 2.305   openblas
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+  - expat 2.7.5.*
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   license_family: MIT
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-  - libzlib >=1.3.1,<2.0a0
+  - libzlib >=1.3.2,<2.0a0
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+  - freetype >=2.14.3
   license: GPL-2.0-only OR FTL
-  size: 386316
-  timestamp: 1772757193822
+  size: 384575
+  timestamp: 1774298162622
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-  md5: 8aa8205bf4e18885c25149c3d391ed39
+- conda: https://conda.anaconda.org/conda-forge/linux-64/libgdal-core-3.12.3-he63569f_3.conda
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-  - lerc >=4.0.0,<5.0a0
-  - libarchive >=3.8.5,<3.9.0a0
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   - libspatialite >=5.1.0,<5.2.0a0
-  - libsqlite >=3.51.2,<4.0a0
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   - libxml2
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   - muparser >=2.3.5,<2.4.0a0
-  - openssl >=3.5.5,<4.0a0
+  - openssl >=3.5.6,<4.0a0
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   - zstd >=1.5.7,<1.6.0a0
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+  - libgdal 3.12.3.*
   license: MIT
   license_family: MIT
-  size: 12954415
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+  size: 12920201
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 - conda: https://conda.anaconda.org/conda-forge/linux-64/libgfortran-15.2.0-h69a702a_18.conda
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-- conda: https://conda.anaconda.org/conda-forge/linux-64/liblapack-3.11.0-5_h47877c9_openblas.conda
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-  md5: b38076eb5c8e40d0106beda6f95d7609
+- conda: https://conda.anaconda.org/conda-forge/linux-64/liblapack-3.11.0-6_h47877c9_openblas.conda
+  build_number: 6
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+  - libblas 3.11.0 6_h4a7cf45_openblas
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-  - blas 2.305   openblas
-  - liblapacke 3.11.0   5*_openblas
-  - libcblas   3.11.0   5*_openblas
+  - blas 2.306   openblas
+  - liblapacke 3.11.0   6*_openblas
+  - libcblas   3.11.0   6*_openblas
   license: BSD-3-Clause
   license_family: BSD
-  size: 18200
-  timestamp: 1765818857876
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 - conda: https://conda.anaconda.org/conda-forge/linux-64/liblzma-5.8.2-hb03c661_0.conda
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-- conda: https://conda.anaconda.org/conda-forge/linux-64/libnetcdf-4.9.3-nompi_hbf2fc22_104.conda
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+- conda: https://conda.anaconda.org/conda-forge/linux-64/libnetcdf-4.10.0-nompi_hb6f1874_103.conda
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   - libaec >=1.1.5,<2.0a0
-  - libcurl >=8.18.0,<9.0a0
+  - libcurl >=8.19.0,<9.0a0
   - libgcc >=14
   - libstdcxx >=14
   - libxml2
   - libxml2-16 >=2.14.6
   - libzip >=1.11.2,<2.0a0
-  - libzlib >=1.3.1,<2.0a0
+  - libzlib >=1.3.2,<2.0a0
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   - zstd >=1.5.7,<1.6.0a0
   license: MIT
   license_family: MIT
-  size: 870788
-  timestamp: 1770718321021
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 - conda: https://conda.anaconda.org/conda-forge/linux-64/libnghttp2-1.68.1-h877daf1_0.conda
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-- conda: https://conda.anaconda.org/conda-forge/linux-64/libopenblas-0.3.30-pthreads_h94d23a6_4.conda
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-  md5: be43915efc66345cccb3c310b6ed0374
+- conda: https://conda.anaconda.org/conda-forge/linux-64/libopenblas-0.3.32-pthreads_h94d23a6_0.conda
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   - libgcc >=14
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   constrains:
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+  - openblas >=0.3.32,<0.3.33.0a0
   license: BSD-3-Clause
   license_family: BSD
-  size: 5927939
-  timestamp: 1763114673331
+  size: 5928890
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 - conda: https://conda.anaconda.org/conda-forge/linux-64/libopengl-1.7.0-ha4b6fd6_2.conda
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   timestamp: 1770434436295
-- conda: https://conda.anaconda.org/conda-forge/linux-64/libpng-1.6.55-h421ea60_0.conda
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-  md5: 5f13ffc7d30ffec87864e678df9957b4
+- conda: https://conda.anaconda.org/conda-forge/linux-64/libpng-1.6.57-h421ea60_0.conda
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-  - libzlib >=1.3.1,<2.0a0
+  - libgcc >=14
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   license: zlib-acknowledgement
-  size: 317669
-  timestamp: 1770691470744
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 - conda: https://conda.anaconda.org/conda-forge/linux-64/libprotobuf-6.31.1-h49aed37_4.conda
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   timestamp: 1768735071295
-- conda: https://conda.anaconda.org/conda-forge/linux-64/libuuid-2.41.3-h5347b49_0.conda
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-  md5: db409b7c1720428638e7c0d509d3e1b5
+- conda: https://conda.anaconda.org/conda-forge/linux-64/libuuid-2.42-h5347b49_0.conda
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+  md5: 38ffe67b78c9d4de527be8315e5ada2c
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   - libgcc >=14
   license: BSD-3-Clause
   license_family: BSD
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-  timestamp: 1766271528534
+  size: 40297
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 - conda: https://conda.anaconda.org/conda-forge/linux-64/libuv-1.51.0-hb03c661_1.conda
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   timestamp: 1730442108429
-- conda: https://conda.anaconda.org/conda-forge/linux-64/libzlib-1.3.1-hb9d3cd8_2.conda
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-  md5: edb0dca6bc32e4f4789199455a1dbeb8
+- conda: https://conda.anaconda.org/conda-forge/linux-64/libzlib-1.3.2-h25fd6f3_2.conda
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-  - libgcc >=13
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-  - zlib 1.3.1 *_2
+  - zlib 1.3.2 *_2
   license: Zlib
   license_family: Other
-  size: 60963
-  timestamp: 1727963148474
+  size: 63629
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 - conda: https://conda.anaconda.org/conda-forge/linux-64/lz4-c-1.10.0-h5888daf_1.conda
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   timestamp: 1753889274283
-- conda: https://conda.anaconda.org/conda-forge/linux-64/magics-4.16.0-h637ef6b_3.conda
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-  md5: de519f1c69a8e0963fb52ab9deff9999
+- conda: https://conda.anaconda.org/conda-forge/linux-64/magics-4.16.0-h1a1f456_4.conda
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-  - magics-python
-  - pango >=1.56.4,<2.0a0
-  - proj >=9.7.0,<9.8.0a0
-  - simplejson
+  - freetype
+  - pango
   - xorg-xorgproto
+  - cairo
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+  - libnetcdf
   - zlib
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   constrains:
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   license: Apache-2.0
-  license_family: Apache
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+  license_family: APACHE
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 - conda: https://conda.anaconda.org/conda-forge/noarch/magics-python-1.5.8-pyhd8ed1ab_1.conda
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-- conda: https://conda.anaconda.org/conda-forge/linux-64/openssl-3.6.1-h35e630c_1.conda
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-  md5: f61eb8cd60ff9057122a3d338b99c00f
+- conda: https://conda.anaconda.org/conda-forge/linux-64/openssl-3.6.2-h35e630c_0.conda
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   - ca-certificates
   - libgcc >=14
   license: Apache-2.0
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   timestamp: 1768247825733
-- conda: https://conda.anaconda.org/conda-forge/linux-64/pandoc-3.9.0.1-ha770c72_0.conda
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+- conda: https://conda.anaconda.org/conda-forge/linux-64/pango-1.56.4-hda50119_1.conda
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-  - libpng >=1.6.49,<1.7.0a0
-  - libzlib >=1.3.1,<2.0a0
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   license: LGPL-2.1-or-later
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-- conda: https://conda.anaconda.org/conda-forge/linux-64/python-3.14.3-he1279bd_1_cp314t.conda
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+- conda: https://conda.anaconda.org/conda-forge/linux-64/python-3.14.4-hf9ea5aa_0_cp314t.conda
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+  timestamp: 1773974259444
 - conda: https://conda.anaconda.org/conda-forge/noarch/r-urlchecker-1.0.1-r45hc72bb7e_4.conda
   sha256: 3c1ac479352099400b82b866db5a49b6c2f9802451e5ecf42385abaf4db73f4f
   md5: d8603dd91958a841382fdced991aba9a
@@ -5630,9 +5624,9 @@ packages:
   license_family: MIT
   size: 10399678
   timestamp: 1760099076903
-- conda: https://conda.anaconda.org/conda-forge/linux-64/r-vctrs-0.7.1-r45h3697838_0.conda
-  sha256: 25033570039c1a0ff96356fc4f867c268fc299b379a5e4e4f41ba1263cdce162
-  md5: f6e3a62834212f3a44fa4a0a97fedcde
+- conda: https://conda.anaconda.org/conda-forge/linux-64/r-vctrs-0.7.2-r45h3697838_0.conda
+  sha256: 36c857e7ca159d01f7bd295d6b09edb716fd5948a44e3d761e24bddbc17bc2e1
+  md5: fc66ffed8a4bd9176dd17d2eec7bcca7
   depends:
   - __glibc >=2.17,<3.0.a0
   - libgcc >=14
@@ -5644,8 +5638,8 @@ packages:
   - r-rlang >=1.0.6
   license: MIT
   license_family: MIT
-  size: 1393729
-  timestamp: 1769235449223
+  size: 1393433
+  timestamp: 1774123916873
 - conda: https://conda.anaconda.org/conda-forge/noarch/r-viridislite-0.4.3-r45hc72bb7e_0.conda
   sha256: b9ec9606562f0f6bdefc237bbc6163eb1cb022f9d699c80771bc84af0ae37269
   md5: bcadc0a3726e2191e51449f67fa5e0a9
@@ -5668,9 +5662,9 @@ packages:
   license_family: MIT
   size: 3724506
   timestamp: 1757566751580
-- conda: https://conda.anaconda.org/conda-forge/linux-64/r-vroom-1.7.0-r45h3697838_0.conda
-  sha256: 71b7da0c90cbcc0430f34a30a38b71c754bc6fa90dbf955438be2db3021c693f
-  md5: e43318d3f2be7d5adf0c06d79520ac8f
+- conda: https://conda.anaconda.org/conda-forge/linux-64/r-vroom-1.7.1-r45h3697838_0.conda
+  sha256: c322b1115a9e066505deb292ab38c76ad9d2a983c8269c82e89229dbf6bf5494
+  md5: 8e45deb7cb8502dda9073be1a5e664df
   depends:
   - __glibc >=2.17,<3.0.a0
   - libgcc >=14
@@ -5692,8 +5686,8 @@ packages:
   - r-withr
   license: MIT
   license_family: MIT
-  size: 935533
-  timestamp: 1769540679531
+  size: 934319
+  timestamp: 1774940641597
 - conda: https://conda.anaconda.org/conda-forge/noarch/r-waldo-0.6.2-r45hc72bb7e_1.conda
   sha256: 57eb80cb919524dde77b4c19f257ac9b327aba900e28298d990fa622f30b6f09
   md5: 86406bcc46061e27fe7ec24f73eb6676
@@ -5741,9 +5735,9 @@ packages:
   license_family: MIT
   size: 1723697
   timestamp: 1766049716560
-- conda: https://conda.anaconda.org/conda-forge/linux-64/r-xfun-0.56-r45h3697838_0.conda
-  sha256: ed1c5ea8936a6f775ae4331926a5ced5979b40aa2a19cecf95d46fb215a55aed
-  md5: 1141e09b09648c582b353895bed4b934
+- conda: https://conda.anaconda.org/conda-forge/linux-64/r-xfun-0.57-r45h3697838_0.conda
+  sha256: 29e388ad6532d694f84407f97adb1043ef2d92c25b01affaeed19a6487ad4cba
+  md5: 5016c4e6a78579e1fd3156d2894b474f
   depends:
   - __glibc >=2.17,<3.0.a0
   - libgcc >=14
@@ -5751,8 +5745,8 @@ packages:
   - r-base >=4.5,<4.6.0a0
   license: MIT
   license_family: MIT
-  size: 594506
-  timestamp: 1768794446551
+  size: 597036
+  timestamp: 1774807163423
 - conda: https://conda.anaconda.org/conda-forge/linux-64/r-xml-3.99_0.22-r45hf705907_0.conda
   sha256: b8baf74e5bae3bcb8ca66d53595c59251a6fb937df23047dd869056e448bf726
   md5: c39ff975e024c2af2b2828e0147239d3
@@ -6126,17 +6120,16 @@ packages:
   license_family: MOZILLA
   size: 311150
   timestamp: 1772476812121
-- conda: https://conda.anaconda.org/conda-forge/linux-64/zlib-1.3.1-hb9d3cd8_2.conda
-  sha256: 5d7c0e5f0005f74112a34a7425179f4eb6e73c92f5d109e6af4ddeca407c92ab
-  md5: c9f075ab2f33b3bbee9e62d4ad0a6cd8
+- conda: https://conda.anaconda.org/conda-forge/linux-64/zlib-1.3.2-h25fd6f3_2.conda
+  sha256: 245c9ee8d688e23661b95e3c6dd7272ca936fabc03d423cdb3cdee1bbcf9f2f2
+  md5: c2a01a08fc991620a74b32420e97868a
   depends:
   - __glibc >=2.17,<3.0.a0
-  - libgcc >=13
-  - libzlib 1.3.1 hb9d3cd8_2
+  - libzlib 1.3.2 h25fd6f3_2
   license: Zlib
   license_family: Other
-  size: 92286
-  timestamp: 1727963153079
+  size: 95931
+  timestamp: 1774072620848
 - conda: https://conda.anaconda.org/conda-forge/linux-64/zstd-1.5.7-hb78ec9c_6.conda
   sha256: 68f0206ca6e98fea941e5717cec780ed2873ffabc0e1ed34428c061e2c6268c7
   md5: 4a13eeac0b5c8e5b8ab496e6c4ddd829
diff --git a/workflows/sipnet-restart-workflow/92-find-winter-crop.R b/workflows/sipnet-restart-workflow/92-find-winter-crop.R
new file mode 100644
index 00000000000..71f6b40bdea
--- /dev/null
+++ b/workflows/sipnet-restart-workflow/92-find-winter-crop.R
@@ -0,0 +1,40 @@
+#!/usr/bin/env Rscript
+
+config <- config::get(file = "workflows/sipnet-restart-workflow/config.yml")
+
+planting <- list.files(
+  config[["planting_events_dir"]],
+  "planting_statewide_.*\\.parquet",
+  full.names = TRUE
+) |>
+  arrow::open_dataset() |>
+  dplyr::collect() |>
+  dplyr::mutate(date = as.Date(.data$date)) |>
+  tibble::as_tibble()
+
+planting |>
+  dplyr::filter(lubridate::month(date) >= 11) |>
+  dplyr::arrange(date) |>
+  print(n = 30)
+
+pid <- "101007"  # hay
+
+pid <- "106453" # hay --> row --> hay
+pid <- "10726" # woody
+pid <- "154989" # woody --> hay --> row --> hay
+
+planting_site <- planting |>
+  dplyr::filter(.data$site_id == .env$pid)
+harvest <- list.files(
+  config[["harvest_events_dir"]],
+  ".*\\.parquet",
+  full.names = TRUE
+) |>
+  arrow::open_dataset() |>
+  dplyr::filter(.data$site_id == .env$pid) |>
+  dplyr::collect() |>
+  dplyr::mutate(date = as.Date(.data$date)) |>
+  dplyr::as_tibble()
+events <- dplyr::bind_rows(planting_site, harvest) |>
+  dplyr::arrange(.data$date)
+events

From 959ed7b743c2729e5248d5f9c4ebca194aaea0eb Mon Sep 17 00:00:00 2001
From: Alexey Shiklomanov <alexey.shiklomanov@gmail.com>
Date: Thu, 9 Apr 2026 16:50:17 -0400
Subject: [PATCH 35/75] better variable list handling in plots

---
 .../sipnet-restart-workflow/04-plot-outputs.R   | 17 ++++++++++++-----
 1 file changed, 12 insertions(+), 5 deletions(-)

diff --git a/workflows/sipnet-restart-workflow/04-plot-outputs.R b/workflows/sipnet-restart-workflow/04-plot-outputs.R
index 2c595b66c9f..eabf14dd56d 100644
--- a/workflows/sipnet-restart-workflow/04-plot-outputs.R
+++ b/workflows/sipnet-restart-workflow/04-plot-outputs.R
@@ -20,21 +20,28 @@ events_df <- dplyr::bind_rows(events[[1]][["events"]]) |>
 modeloutdir <- file.path(config$outdir_root, "output", "out")
 runids <- list.files(modeloutdir)
 
-read_output <- function(modeloutdir, runid) {
+vars_some <- c("NEE", "LAI", "AGB", "TotSoilCarb", "leaf_carbon_content", "litter_carbon_content")
+vars_more <- c(
+  "GPP", "NPP", "TotalResp", "AutoResp", "HeteroResp", "SoilResp", "NEE", "AbvGrndWood",
+  "leaf_carbon_content", "TotLivBiom", "TotSoilCarb", "Qle", "Transp", "SoilMoist", "SoilMoistFrac",
+  "litter_carbon_content", "LAI", "fine_root_carbon_content", "coarse_root_carbon_content",
+  "AGB", "GWBI"
+  # "mineral_N", "soil_organic_N", "litter_N", "N2O_flux", "N_leaching", "N_fixation", "N_uptake", "CH4_flux", "SWE"
+)
+
+read_output <- function(modeloutdir, runid, variables = vars_some) {
   PEcAn.utils::read.output(
     runid,
     file.path(modeloutdir, runid),
-    variables = c("NEE", "LAI", "AGB", "TotSoilCarb", "leaf_carbon_content", "litter_carbon_content"),
-    # variables = NULL,
+    variables = variables,
     dataframe = TRUE
   ) |>
     dplyr::mutate(run_id = .env$runid) |>
     dplyr::as_tibble()
 }
 
-results <- purrr::map(runids, read_output, modeloutdir = modeloutdir) |>
+results <- purrr::map(runids, read_output, modeloutdir = modeloutdir, variables = vars_more) |>
   dplyr::bind_rows()
-
 plt <- results |>
   tidyr::pivot_longer(
     -c("posix", "year", "run_id"),

From f2d384d843e8da3e600eaad6881f24e167d25148 Mon Sep 17 00:00:00 2001
From: Alexey Shiklomanov <alexey.shiklomanov@gmail.com>
Date: Thu, 9 Apr 2026 17:28:06 -0400
Subject: [PATCH 36/75] fix start/end handling & interaction with segments

---
 .../data.land/R/events_to_crop_cycle_starts.R |  1 +
 .../01-prepare-events.R                       | 38 +++++++++++--------
 .../02-prepare-settings.R                     | 16 +++++---
 workflows/sipnet-restart-workflow/utils.R     | 22 +++++------
 4 files changed, 45 insertions(+), 32 deletions(-)

diff --git a/modules/data.land/R/events_to_crop_cycle_starts.R b/modules/data.land/R/events_to_crop_cycle_starts.R
index c9a64ebd1c4..65dbaed77f1 100644
--- a/modules/data.land/R/events_to_crop_cycle_starts.R
+++ b/modules/data.land/R/events_to_crop_cycle_starts.R
@@ -48,5 +48,6 @@ find_crop_changes <- function(event_df) {
     dplyr::mutate(crop_cycle_id = dplyr::consecutive_id(.data$site_id, .data$crop_code)) |>
     dplyr::group_by(.data$site_id, .data$crop_cycle_id) |>
     dplyr::slice_min(.data$date) |>
+    dplyr::ungroup() |>
     dplyr::select("site_id", "date", "crop_code")
 }
diff --git a/workflows/sipnet-restart-workflow/01-prepare-events.R b/workflows/sipnet-restart-workflow/01-prepare-events.R
index e740a3b6a66..7992c51224d 100644
--- a/workflows/sipnet-restart-workflow/01-prepare-events.R
+++ b/workflows/sipnet-restart-workflow/01-prepare-events.R
@@ -36,6 +36,9 @@ planting <- list.files(
   dplyr::filter(date >= as.Date("2016-01-01")) |>
   tibble::as_tibble()
 
+# Start date is the first planting (after 2016)
+start_date <- min(planting$date)
+
 planting_events <- planting |>
   dplyr::select(
     "site_id", "event_type", "date",
@@ -50,31 +53,33 @@ planting_events <- planting |>
     "coarse_root_n_kg_m2" = "N_COARSEROOT"
   )
 
-# Harvest
-mslsp_path <- config[["mslsp_path"]]
-phenology <- fs::dir_ls(mslsp_path, glob = "*.parquet") |>
-  arrow::open_dataset() |>
-  dplyr::filter(.data$parcel_id == .env$pid, !is.na(.data$mslsp_cycle)) |>
-  dplyr::collect() |>
-  tibble::as_tibble() |>
-  dplyr::arrange(.data$year, .data$mslsp_cycle) |>
-  dplyr::relocate(
-    "year", "mslsp_cycle", dplyr::starts_with("landiq_"),
-  )
+# Phenology is not currently used...
+# mslsp_path <- config[["mslsp_path"]]
+# phenology <- fs::dir_ls(mslsp_path, glob = "*.parquet") |>
+#   arrow::open_dataset() |>
+#   dplyr::filter(.data$parcel_id == .env$pid, !is.na(.data$mslsp_cycle)) |>
+#   dplyr::collect() |>
+#   tibble::as_tibble() |>
+#   dplyr::arrange(.data$year, .data$mslsp_cycle) |>
+#   dplyr::relocate(
+#     "year", "mslsp_cycle", dplyr::starts_with("landiq_"),
+#   )
 
-# Dummy values for testing
 harvest_dir <- config[["harvest_events_dir"]]
 pidc <- as.character(pid)
 harvest_events <- list.files(harvest_dir, "*.parquet", full.names = TRUE) |>
   arrow::open_dataset() |>
-  dplyr::filter(.data$site_id == .env$pidc) |>
+  dplyr::filter(
+    .data$site_id == .env$pidc,
+    .data$date >= .env$start_date
+  ) |>
   dplyr::collect() |>
   tibble::as_tibble() |>
   dplyr::select(
     "site_id", "event_type", "date", dplyr::starts_with("frac_")
   )
 
-start_date <- min(planting$date)
+# End with the final harvest
 end_date <- max(harvest_events$date)
 
 irrigation_path <- config[["irrigation_path"]]
@@ -87,7 +92,10 @@ irrigation_events_raw <- arrow::open_dataset(irrigation_path) |>
 # Irrigation events include uncertainty ensembles, so we process them
 # accordingly.
 irrigation_events_all <- irrigation_events_raw |>
-  dplyr::filter(.data$date <= .env$end_date) |>
+  dplyr::filter(
+    .data$date >= .env$start_date,
+    .data$date <= .env$end_date
+  ) |>
   dplyr::mutate(
     event_type = "irrigation",
     site_id = as.character(.data$parcel_id)
diff --git a/workflows/sipnet-restart-workflow/02-prepare-settings.R b/workflows/sipnet-restart-workflow/02-prepare-settings.R
index b7854c97487..bda1b93c49b 100644
--- a/workflows/sipnet-restart-workflow/02-prepare-settings.R
+++ b/workflows/sipnet-restart-workflow/02-prepare-settings.R
@@ -28,16 +28,22 @@ names(events_json_files) <- paste0("path", seq_along(events_json_files))
 sipnet_eventfiles <- as.list(grepv(".*\\.sipnet/events-.*\\.in", events_files))
 names(sipnet_eventfiles) <- paste0("path", seq_along(sipnet_eventfiles))
 
-# HACK: Get the start and end date from the limits of the first event file.
+# NOTE: We start from the first planting (after 2016) and end at the last harvest
 events <- jsonlite::read_json(events_json_files[[1]], simplifyVector = FALSE)
 
-all_dates <- events |>
-  purrr::pluck(1, "events") |>
+planting_dates <- events |>
+  purrr::chuck(1, "events") |>
+  purrr::keep(\(x) x$event_type == "planting") |>
   purrr::map_chr("date") |>
   as.Date()
+start_date <- min(planting_dates)
 
-start_date <- min(all_dates)
-end_date <- max(all_dates)
+harvest_dates <- events |>
+  purrr::pluck(1, "events") |>
+  purrr::keep(\(x) x$event_type == "harvest") |>
+  purrr::map_chr("date") |>
+  as.Date()
+end_date <- max(harvest_dates)
 
 met_dir <- sprintf(
   "%sN_%sW",
diff --git a/workflows/sipnet-restart-workflow/utils.R b/workflows/sipnet-restart-workflow/utils.R
index f39b07bb3f9..f29cc4eaa07 100644
--- a/workflows/sipnet-restart-workflow/utils.R
+++ b/workflows/sipnet-restart-workflow/utils.R
@@ -75,21 +75,19 @@ run_sipnet_segmented <- function(
 
   crop_cycles <- PEcAn.data.land::events_to_crop_cycle_starts(
     run_settings$run$inputs$events$source
-  )
+  ) |>
+    dplyr::ungroup()
 
   # Get segments
-  segments <- data.frame(
-    start_date = c(as.Date(run_settings$run$start.date), crop_cycles[["date"]]),
-    end_date = c(crop_cycles[["date"]] - 1, as.Date(run_settings$run$end.date)),
-    crop_code = c(NA_character_, crop_cycles[["crop_code"]])
-  )
-  segments[["pft"]] <- crop2pft(segments[["crop_code"]])
-  segments[["segment_id"]] <- sprintf("%03d", seq_len(nrow(segments)))
   segment_rootdir <- file.path(file.path(run_dir, "segments"))
-  segments[["segment_dir"]] <- file.path(
-    segment_rootdir,
-    sprintf("segment_%s", segments[["segment_id"]])
-  )
+  segments <- crop_cycles |>
+    dplyr::rename(start_date = "date") |>
+    dplyr::mutate(
+      end_date = dplyr::lead(.data$start_date - 1, default = as.Date(run_settings$run$end.date)),
+      pft = crop2pft(.data$crop_code),
+      segment_id = sprintf("%03d", dplyr::row_number()),
+      segment_dir = file.path(segment_rootdir, sprintf("segment_%s", .data$segment_id))
+    )
 
   for (isegment in seq_len(nrow(segments))) {
     segment <- segments[isegment, ]

From 9a378cbede656a3b31fef284f92d328bb2518e34 Mon Sep 17 00:00:00 2001
From: Alexey Shiklomanov <alexey.shiklomanov@gmail.com>
Date: Fri, 10 Apr 2026 12:58:05 -0400
Subject: [PATCH 37/75] simplify crew config

---
 workflows/sipnet-restart-workflow/03-run-sipnet.R | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/workflows/sipnet-restart-workflow/03-run-sipnet.R b/workflows/sipnet-restart-workflow/03-run-sipnet.R
index 066e78c1f3a..066f469c76e 100644
--- a/workflows/sipnet-restart-workflow/03-run-sipnet.R
+++ b/workflows/sipnet-restart-workflow/03-run-sipnet.R
@@ -21,7 +21,7 @@ controller <- crew::crew_controller_local(workers = nworkers)
 crew_results <- controller$map(
   command = do_run_sipnet_segmented(irun),
   iterate = list(irun = seq_len(config[["n_ensemble"]])),
-  data = list(settings = settings, do_run_sipnet_segmented = do_run_sipnet_segmented)
+  data = list(do_run_sipnet_segmented = do_run_sipnet_segmented)
 )
 
 # Or, to run sequentially:

From 67b10394fc65617958b65359e1a189341ff0d491 Mon Sep 17 00:00:00 2001
From: Alexey Shiklomanov <alexey.shiklomanov@gmail.com>
Date: Fri, 10 Apr 2026 16:47:07 -0400
Subject: [PATCH 38/75] add `combine_sipnet_out`; document new split funcs

---
 models/sipnet/NAMESPACE                  |  2 +-
 models/sipnet/R/combine_sipnet_out.R     | 30 ++++++++++++++
 models/sipnet/R/model2netcdf.SIPNET.R    | 33 +---------------
 models/sipnet/R/read_sipnet_out.R        | 40 +++++++++++++++++++
 models/sipnet/R/split_inputs.SIPNET.R    | 50 ++++++++++++++++--------
 models/sipnet/man/combine_sipnet_out.Rd  | 24 ++++++++++++
 models/sipnet/man/read_restart.SIPNET.Rd | 13 ------
 models/sipnet/man/read_sipnet_out.Rd     | 17 ++++++++
 models/sipnet/man/split_inputs.SIPNET.Rd | 26 +++++++-----
 models/sipnet/man/split_sipnet_events.Rd | 28 +++++++++++++
 models/sipnet/man/split_sipnet_met.Rd    | 28 +++++++++++++
 11 files changed, 220 insertions(+), 71 deletions(-)
 create mode 100644 models/sipnet/R/combine_sipnet_out.R
 create mode 100644 models/sipnet/R/read_sipnet_out.R
 create mode 100644 models/sipnet/man/combine_sipnet_out.Rd
 create mode 100644 models/sipnet/man/read_sipnet_out.Rd
 create mode 100644 models/sipnet/man/split_sipnet_events.Rd
 create mode 100644 models/sipnet/man/split_sipnet_met.Rd

diff --git a/models/sipnet/NAMESPACE b/models/sipnet/NAMESPACE
index efa0bc19570..f9f6ca518e8 100644
--- a/models/sipnet/NAMESPACE
+++ b/models/sipnet/NAMESPACE
@@ -1,5 +1,6 @@
 # Generated by roxygen2: do not edit by hand
 
+export(combine_sipnet_out)
 export(mergeNC)
 export(met2model.SIPNET)
 export(model2netcdf.SIPNET)
@@ -13,4 +14,3 @@ export(write.events.SIPNET)
 export(write_restart.SIPNET)
 importFrom(dplyr,"%>%")
 importFrom(rlang,"%||%")
-importFrom(rlang,.data)
diff --git a/models/sipnet/R/combine_sipnet_out.R b/models/sipnet/R/combine_sipnet_out.R
new file mode 100644
index 00000000000..5093c25d8de
--- /dev/null
+++ b/models/sipnet/R/combine_sipnet_out.R
@@ -0,0 +1,30 @@
+#!/usr/bin/env Rscript
+
+#' Combine a bunch of `sipnet.out` files into a single file
+#'
+#' @param directory Parent directory to search for `sipnet.out` files. You must
+#' provide either this or an explicit vector of `files`.
+#' @param outfile File to which combined `sipnet.out` will be written
+#' @param files (optional) Explicit vector of paths to `sipnet.out` files to
+#' combine. Note that files need not be named `sipnet.out`, but they must be
+#' readable with [read_sipnet_out()].
+#'
+#' @return `outfile` (path to output file), invisibly
+#' @export
+combine_sipnet_out <- function(directory, outfile, files = NULL) {
+  if (missing(directory) && is.null(files)) {
+    PEcAn.logger::logger.severe("Must provide either `directory` or `files`")
+  }
+  if (is.null(files)) {
+    files <- sort(list.files(directory, "sipnet\\.out", full.names = TRUE, recursive = TRUE))
+  }
+  if (!(length(files) > 0)) {
+    PEcAn.logger::logger.severe("No files provided; nothing to combine.")
+  }
+  flist <- lapply(files, read_sipnet_out)
+  combined <- do.call(rbind.data.frame, flist)
+  # Mimic the SIPNET fixed-width right-aligned format
+  combined_fwf <- format(combined, justify = "right")
+  write.table(combined_fwf, outfile, row.names = FALSE, col.names = TRUE, quote = FALSE, sep = "  ")
+  invisible(outfile)
+}
diff --git a/models/sipnet/R/model2netcdf.SIPNET.R b/models/sipnet/R/model2netcdf.SIPNET.R
index b7793b4f2b7..2353f3500c6 100644
--- a/models/sipnet/R/model2netcdf.SIPNET.R
+++ b/models/sipnet/R/model2netcdf.SIPNET.R
@@ -60,38 +60,7 @@ model2netcdf.SIPNET <- function(outdir, sitelat, sitelon, start_date, end_date,
                                 overwrite = FALSE, conflict = FALSE) {
   ### Read in model output in SIPNET format
   sipnet_out_file <- file.path(outdir, prefix)
-  # SIPNET v1 had a "Notes" comment line before the header; v2 removed it.
-  # if the first line starts with "year", there is no Notes line.
-  first_line <- readLines(sipnet_out_file, n = 1)
-  skip_n <- if (grepl("^year", first_line)) 0 else 1
-  # Temporary workaround until
-  # https://github.com/PecanProject/sipnet/issues/304 is resolved.
-  sipnet_output <- tryCatch({
-    utils::read.table(sipnet_out_file, header = TRUE, skip = skip_n, sep = "")
-  }, error = function(err) {
-    PEcAn.logger::logger.warn(
-      "Failed to read using `read.table`. ",
-      "Trying to parse output manually."
-    )
-    raw_lines <- readLines(sipnet_out_file)
-    raw_header <- raw_lines[[1 + skip_n]]
-    raw_body <- tail(raw_lines, -(1 + skip_n))
-    # SIPNET output is right-aligned with the column names in the header.
-    # We use this to figure out where the numbers end if there are no spaces.
-    token_matches <- gregexpr("\\S+", raw_header, perl = TRUE)
-    proc_header <- regmatches(raw_header, token_matches)[[1]]
-    col_ends <- token_matches[[1]] + attr(token_matches[[1]], "match.length") - 1
-    col_starts <- c(1, head(col_ends, -1) + 1)
-    col_widths <- col_ends - col_starts + 1
-    result <- read.fwf(
-      textConnection(raw_body),
-      widths = col_widths,
-      col.names = proc_header,
-      na.strings = c("nan", "-nan")
-    )
-    result[] <- lapply(result, as.numeric)
-    result
-  })
+  sipnet_output <- read_sipnet_out(sipnet_output)
   #sipnet_output_dims <- dim(sipnet_output)
   
   ### Determine number of years and output timestep
diff --git a/models/sipnet/R/read_sipnet_out.R b/models/sipnet/R/read_sipnet_out.R
new file mode 100644
index 00000000000..810a0d68b5b
--- /dev/null
+++ b/models/sipnet/R/read_sipnet_out.R
@@ -0,0 +1,40 @@
+#' Read `sipnet.out` file to `data.frame`
+#'
+#' @param sipnet_out_file Path to `sipnet.out` file
+#'
+#' @return `data.frame` of SIPNET output
+read_sipnet_out <- function(sipnet_out_file) {
+  # SIPNET v1 had a "Notes" comment line before the header; v2 removed it.
+  # if the first line starts with "year", there is no Notes line.
+  first_line <- readLines(sipnet_out_file, n = 1)
+  skip_n <- if (grepl("^year", first_line)) 0 else 1
+  # Temporary workaround until
+  # https://github.com/PecanProject/sipnet/issues/304 is resolved.
+  sipnet_output <- tryCatch({
+    utils::read.table(sipnet_out_file, header = TRUE, skip = skip_n, sep = "")
+  }, error = function(err) {
+    PEcAn.logger::logger.warn(
+      "Failed to read using `read.table`. ",
+      "Trying to parse output manually."
+    )
+    raw_lines <- readLines(sipnet_out_file)
+    raw_header <- raw_lines[[1 + skip_n]]
+    raw_body <- tail(raw_lines, -(1 + skip_n))
+    # SIPNET output is right-aligned with the column names in the header.
+    # We use this to figure out where the numbers end if there are no spaces.
+    token_matches <- gregexpr("\\S+", raw_header, perl = TRUE)
+    proc_header <- regmatches(raw_header, token_matches)[[1]]
+    col_ends <- token_matches[[1]] + attr(token_matches[[1]], "match.length") - 1
+    col_starts <- c(1, head(col_ends, -1) + 1)
+    col_widths <- col_ends - col_starts + 1
+    result <- read.fwf(
+      textConnection(raw_body),
+      widths = col_widths,
+      col.names = proc_header,
+      na.strings = c("nan", "-nan")
+    )
+    result[] <- lapply(result, as.numeric)
+    result
+  })
+  sipnet_output
+}
diff --git a/models/sipnet/R/split_inputs.SIPNET.R b/models/sipnet/R/split_inputs.SIPNET.R
index 407cc48b61b..9dc9f5be3ad 100644
--- a/models/sipnet/R/split_inputs.SIPNET.R
+++ b/models/sipnet/R/split_inputs.SIPNET.R
@@ -1,5 +1,25 @@
 #!/usr/bin/env Rscript
 
+#' Split SIPNET inputs into multiple files based on start and end time
+#'
+#' Subset each SIPNET input file and write a new file containing values `>=
+#' start.time` and `<= end.time` (note: `end.time` is inclusive!)
+#'
+#' NOTE that sipnet met files contain dates _and_ times, while sipnet event
+#' files contain only dates. Comparing a datetime to a date will coerce the
+#' date to midnight UTC.
+#'
+#' @param start.time Start date or datetime for splitting
+#' @param stop.time End date or datetime for splitting
+#' @param inputs Named `inputs` list as provided by PEcAn `settings`. Must have
+#' structure like:
+#' `list(met = list(path = "path/to/sipnet.clim"), events = list(path = "path/to/events.in"), ...)`
+#'
+#' @inheritParams split_sipnet_met
+#' @author Alexey Shiklomanov
+#'
+#' @return Modified `inputs` list with all `path` entries replaced with new
+#' paths (suitable for inserting back into `settings$run$inputs`).
 #' @export
 split_inputs.SIPNET <- function(start.time, stop.time, inputs, overwrite = FALSE, outpath = NULL) {
   result <- inputs
@@ -25,11 +45,12 @@ split_inputs.SIPNET <- function(start.time, stop.time, inputs, overwrite = FALSE
   result
 }
 
+#' Split sipnet `events.in` files according to start and stop date
+#'
+#' @param eventfile Path to `events.in` file.
+#' @inheritParams split_inputs.SIPNET
 split_sipnet_events <- function(start.time, stop.time, eventfile, overwrite = FALSE, outpath = FALSE) {
   # Read events.in
-  # eventfile <- sipnet_eventfile
-  # start.time <- dstart
-  # stop.time <- dend
   prefix <- sub(".in", "", basename(eventfile), fixed = TRUE)
   outpath <- outpath %||% dirname(eventfile)
   dir.create(outpath, recursive = TRUE, showWarnings = FALSE)
@@ -58,7 +79,7 @@ split_sipnet_events <- function(start.time, stop.time, eventfile, overwrite = FA
   doys_in <- vapply(events_in_list, \(x) as.integer(x[[2]]), integer(1))
   # Not using sipnet2datetime here because it returns times with time zones,
   # which could cause subtle timezone-related bugs
-  dates_in <- as.Date(sprintf("%d-01-01", years_in)) + doys_in
+  dates_in <- as.Date(sprintf("%d-01-01", years_in)) + (doys_in - 1)
   idx_keep <- (dates_in >= start.time) & (dates_in <= stop.time)
   if (length(idx_keep) == 0) {
     PEcAn.logger::logger.warn("No events to keep, so `events.in` will be empty")
@@ -68,20 +89,17 @@ split_sipnet_events <- function(start.time, stop.time, eventfile, overwrite = FA
   invisible(outfile)
 }
 
-## split clim file into smaller time units to use in KF
-##' @author Mike Dietze and Ann Raiho
-##' 
+##' split sipnet clim file based on start and end time
+##'
+##' @author Mike Dietze, Ann Raiho, Alexey Shiklomanov
+##'
 ##' @param start.time start date and time for each SDA ensemble
 ##' @param stop.time stop date and time for each SDA ensemble
-##' @param inputs list of model inputs to use in write.configs.SIPNET
-##' @param overwrite Default FALSE
-##' @param outpath if specified, write output to a new directory. Default NULL writes back to the directory being read
-##' @description Splits climate met for SIPNET
-##' 
-##' @return file split up climate file
-##' @importFrom rlang .data
-##' @importFrom dplyr %>%
-##' @export
+##' @param met path to sipnet clim file to be split 
+##' @param overwrite if `TRUE`, overwrite existing target file (Default `FALSE`)
+##' @param outpath if specified, write output to a new directory. Default `NULL` writes back to the directory being read
+##'
+##' @return path to split up climate file
 split_sipnet_met <- function(start.time, stop.time, met, overwrite = FALSE, outpath = NULL) {
   start.time <- coerce_to_datetime(start.time)
   stop.time <- coerce_to_datetime(stop.time)
diff --git a/models/sipnet/man/combine_sipnet_out.Rd b/models/sipnet/man/combine_sipnet_out.Rd
new file mode 100644
index 00000000000..4fedd52cded
--- /dev/null
+++ b/models/sipnet/man/combine_sipnet_out.Rd
@@ -0,0 +1,24 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/combine_sipnet_out.R
+\name{combine_sipnet_out}
+\alias{combine_sipnet_out}
+\title{Combine a bunch of \code{sipnet.out} files into a single file}
+\usage{
+combine_sipnet_out(directory, outfile, files = NULL)
+}
+\arguments{
+\item{directory}{Parent directory to search for \code{sipnet.out} files. You must
+provide either this or an explicit vector of \code{files}.}
+
+\item{outfile}{File to which combined \code{sipnet.out} will be written}
+
+\item{files}{(optional) Explicit vector of paths to \code{sipnet.out} files to
+combine. Note that files need not be named \code{sipnet.out}, but they must be
+readable with \code{\link[=read_sipnet_out]{read_sipnet_out()}}.}
+}
+\value{
+\code{outfile} (path to output file), invisibly
+}
+\description{
+Combine a bunch of \code{sipnet.out} files into a single file
+}
diff --git a/models/sipnet/man/read_restart.SIPNET.Rd b/models/sipnet/man/read_restart.SIPNET.Rd
index 7bb8f4553e6..6bbc4d07fdb 100644
--- a/models/sipnet/man/read_restart.SIPNET.Rd
+++ b/models/sipnet/man/read_restart.SIPNET.Rd
@@ -6,19 +6,6 @@
 \usage{
 read_restart.SIPNET(outdir, runid, stop.time, settings, var.names, params)
 }
-\arguments{
-\item{outdir}{Output directory}
-
-\item{runid}{Run ID}
-
-\item{stop.time}{Year that is being read}
-
-\item{settings}{PEcAn settings object}
-
-\item{var.names}{Variable names to be extracted}
-
-\item{params}{Any parameters required for state calculations}
-}
 \value{
 X.vec      vector of forecasts
 }
diff --git a/models/sipnet/man/read_sipnet_out.Rd b/models/sipnet/man/read_sipnet_out.Rd
new file mode 100644
index 00000000000..be533af4c89
--- /dev/null
+++ b/models/sipnet/man/read_sipnet_out.Rd
@@ -0,0 +1,17 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/read_sipnet_out.R
+\name{read_sipnet_out}
+\alias{read_sipnet_out}
+\title{Read \code{sipnet.out} file to \code{data.frame}}
+\usage{
+read_sipnet_out(sipnet_out_file)
+}
+\arguments{
+\item{sipnet_out_file}{Path to \code{sipnet.out} file}
+}
+\value{
+\code{data.frame} of SIPNET output
+}
+\description{
+Read \code{sipnet.out} file to \code{data.frame}
+}
diff --git a/models/sipnet/man/split_inputs.SIPNET.Rd b/models/sipnet/man/split_inputs.SIPNET.Rd
index 96fc565c94d..80fe14fa63a 100644
--- a/models/sipnet/man/split_inputs.SIPNET.Rd
+++ b/models/sipnet/man/split_inputs.SIPNET.Rd
@@ -2,7 +2,7 @@
 % Please edit documentation in R/split_inputs.SIPNET.R
 \name{split_inputs.SIPNET}
 \alias{split_inputs.SIPNET}
-\title{split_inputs.SIPNET}
+\title{Split SIPNET inputs into multiple files based on start and end time}
 \usage{
 split_inputs.SIPNET(
   start.time,
@@ -13,22 +13,30 @@ split_inputs.SIPNET(
 )
 }
 \arguments{
-\item{start.time}{start date and time for each SDA ensemble}
+\item{start.time}{Start date or datetime for splitting}
 
-\item{stop.time}{stop date and time for each SDA ensemble}
+\item{stop.time}{End date or datetime for splitting}
 
-\item{inputs}{list of model inputs to use in write.configs.SIPNET}
+\item{inputs}{Named \code{inputs} list as provided by PEcAn \code{settings}. Must have
+structure like:
+\code{list(met = list(path = "path/to/sipnet.clim"), events = list(path = "path/to/events.in"), ...)}}
 
-\item{overwrite}{Default FALSE}
+\item{overwrite}{if \code{TRUE}, overwrite existing target file (Default \code{FALSE})}
 
-\item{outpath}{if specified, write output to a new directory. Default NULL writes back to the directory being read}
+\item{outpath}{if specified, write output to a new directory. Default \code{NULL} writes back to the directory being read}
 }
 \value{
-file split up climate file
+Modified \code{inputs} list with all \code{path} entries replaced with new
+paths (suitable for inserting back into \code{settings$run$inputs}).
 }
 \description{
-Splits climate met for SIPNET
+Subset each SIPNET input file and write a new file containing values \verb{>= start.time} and \verb{<= end.time} (note: \code{end.time} is inclusive!)
+}
+\details{
+NOTE that sipnet met files contain dates \emph{and} times, while sipnet event
+files contain only dates. Comparing a datetime to a date will coerce the
+date to midnight UTC.
 }
 \author{
-Mike Dietze and Ann Raiho
+Alexey Shiklomanov
 }
diff --git a/models/sipnet/man/split_sipnet_events.Rd b/models/sipnet/man/split_sipnet_events.Rd
new file mode 100644
index 00000000000..6bb609546f2
--- /dev/null
+++ b/models/sipnet/man/split_sipnet_events.Rd
@@ -0,0 +1,28 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/split_inputs.SIPNET.R
+\name{split_sipnet_events}
+\alias{split_sipnet_events}
+\title{Split sipnet \code{events.in} files according to start and stop date}
+\usage{
+split_sipnet_events(
+  start.time,
+  stop.time,
+  eventfile,
+  overwrite = FALSE,
+  outpath = FALSE
+)
+}
+\arguments{
+\item{start.time}{Start date or datetime for splitting}
+
+\item{stop.time}{End date or datetime for splitting}
+
+\item{eventfile}{Path to \code{events.in} file.}
+
+\item{overwrite}{if \code{TRUE}, overwrite existing target file (Default \code{FALSE})}
+
+\item{outpath}{if specified, write output to a new directory. Default \code{NULL} writes back to the directory being read}
+}
+\description{
+Split sipnet \code{events.in} files according to start and stop date
+}
diff --git a/models/sipnet/man/split_sipnet_met.Rd b/models/sipnet/man/split_sipnet_met.Rd
new file mode 100644
index 00000000000..2d714d75f51
--- /dev/null
+++ b/models/sipnet/man/split_sipnet_met.Rd
@@ -0,0 +1,28 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/split_inputs.SIPNET.R
+\name{split_sipnet_met}
+\alias{split_sipnet_met}
+\title{split sipnet clim file based on start and end time}
+\usage{
+split_sipnet_met(start.time, stop.time, met, overwrite = FALSE, outpath = NULL)
+}
+\arguments{
+\item{start.time}{start date and time for each SDA ensemble}
+
+\item{stop.time}{stop date and time for each SDA ensemble}
+
+\item{met}{path to sipnet clim file to be split}
+
+\item{overwrite}{if \code{TRUE}, overwrite existing target file (Default \code{FALSE})}
+
+\item{outpath}{if specified, write output to a new directory. Default \code{NULL} writes back to the directory being read}
+}
+\value{
+path to split up climate file
+}
+\description{
+split sipnet clim file based on start and end time
+}
+\author{
+Mike Dietze, Ann Raiho, Alexey Shiklomanov
+}

From df8f712c9d1886a7b55c4f83c3b3b76353b669e4 Mon Sep 17 00:00:00 2001
From: Alexey Shiklomanov <alexey.shiklomanov@gmail.com>
Date: Fri, 10 Apr 2026 17:17:45 -0400
Subject: [PATCH 39/75] write new job.sh instead of actually doing runs

---
 .../sipnet-restart-workflow/03-run-sipnet.R   | 25 ++----
 workflows/sipnet-restart-workflow/utils.R     | 76 ++++++++++---------
 2 files changed, 49 insertions(+), 52 deletions(-)

diff --git a/workflows/sipnet-restart-workflow/03-run-sipnet.R b/workflows/sipnet-restart-workflow/03-run-sipnet.R
index 066f469c76e..376b4e1b41b 100644
--- a/workflows/sipnet-restart-workflow/03-run-sipnet.R
+++ b/workflows/sipnet-restart-workflow/03-run-sipnet.R
@@ -7,22 +7,13 @@ if (FALSE) {
 
 config <- config::get(file = "workflows/sipnet-restart-workflow/config.yml")
 
-do_run_sipnet_segmented <- function(irun) {
-  source("workflows/sipnet-restart-workflow/utils.R", local = TRUE)
-  config <- config::get(file = "workflows/sipnet-restart-workflow/config.yml")
-  settings <- PEcAn.settings::read.settings(file.path(config[["outdir_root"]], "settings.xml"))
-  inputs_runs <- read.csv(file.path(settings$outdir, "inputs_runs.csv"))
-  run_sipnet_segmented(settings, inputs_runs[irun, ])  # nolint
-}
+settings <- PEcAn.settings::read.settings(file.path(config[["outdir_root"]], "settings.xml"))
+inputs_runs <- read.csv(file.path(settings$outdir, "inputs_runs.csv"))
+
+source("workflows/sipnet-restart-workflow/utils.R")
 
-# Run in parallel using crew
-nworkers <- pmin(config[["n_ensemble"]], parallel::detectCores())
-controller <- crew::crew_controller_local(workers = nworkers)
-crew_results <- controller$map(
-  command = do_run_sipnet_segmented(irun),
-  iterate = list(irun = seq_len(config[["n_ensemble"]])),
-  data = list(do_run_sipnet_segmented = do_run_sipnet_segmented)
-)
+for (i in seq_len(nrow(inputs_runs))) {
+  run_sipnet_segmented(settings, inputs_runs[i, ], replace_and_link = TRUE)
+}
 
-# Or, to run sequentially:
-# for (i in seq_len(config[["n_ensemble"]])) do_run_sipnet_segmented(i)   # nolint
+PEcAn.workflow::runModule_start_model_runs(settings)
diff --git a/workflows/sipnet-restart-workflow/utils.R b/workflows/sipnet-restart-workflow/utils.R
index f29cc4eaa07..0a9d7561ad3 100644
--- a/workflows/sipnet-restart-workflow/utils.R
+++ b/workflows/sipnet-restart-workflow/utils.R
@@ -58,7 +58,8 @@ crop2pft_example <- function(crop_code) {
 run_sipnet_segmented <- function(
   settings,
   run_row,
-  crop2pft = crop2pft_example
+  crop2pft = crop2pft_example,
+  replace_and_link = FALSE
 ) {
   run_id <- run_row[["run_id"]]
   run_dir <- file.path(settings$rundir, run_id)
@@ -89,6 +90,8 @@ run_sipnet_segmented <- function(
       segment_dir = file.path(segment_rootdir, sprintf("segment_%s", .data$segment_id))
     )
 
+  jobsh_files <- character()
+
   for (isegment in seq_len(nrow(segments))) {
     segment <- segments[isegment, ]
     dstart <- segment[["start_date"]]
@@ -156,42 +159,45 @@ run_sipnet_segmented <- function(
       run.id = runid_dummy
     )
 
-    PEcAn.workflow::start_model_runs(segment_settings, write = FALSE)
+    segment_jobsh <- file.path(segment_settings$rundir, runid_dummy, "job.sh")
+    stopifnot(file.exists(segment_jobsh))
+    jobsh_files <- c(jobsh_files, segment_jobsh)
+  }
 
-    PEcAn.SIPNET::model2netcdf.SIPNET(
-      outdir = segment_outdir_withid,
-      sitelat = segment_settings[[c("run", "site", "lat")]],
-      sitelon = segment_settings[[c("run", "site", "lon")]],
-      start_date = dstart,
-      end_date = dend,
-      revision = segment_settings[[c("model", "revision")]],
-      overwrite = TRUE
+  # Now, get the run's jobsh file
+  run_jobsh <- file.path(run_dir, "job.sh")
+  target_sipnet_out <- file.path(run_modeloutdir, "sipnet.out")
+  segmented_jobsh_file <- file.path(run_dir, "job_segmented.sh")
+  segmented_jobsh_lines <- c(
+    "#!/usr/bin/env bash",
+    "",
+    "# Redirect output",
+    "exec 3>&1",
+    paste("exec &>", shQuote(file.path(run_modeloutdir, "logfile.txt"))),
+    "",
+    "# Run model segments",
+    paste("bash", jobsh_files),
+    "",
+    "# Concatenate sipnet out files",
+    sprintf(
+      "Rscript -e \"PEcAn.SIPNET::combine_sipnet_out(directory = %s, outfile = %s)\"",
+      shQuote(segment_rootdir),
+      shQuote(target_sipnet_out)
     )
+  )
+  writeLines(segmented_jobsh_lines, segmented_jobsh_file)
+  if (replace_and_link) {
+    run_jobsh_backup <- file.path(run_dir, "job_original.sh")
+    file.rename(run_jobsh, run_jobsh_backup)
+    file.symlink(segmented_jobsh_file, run_jobsh)
+    Sys.chmod(run_jobsh, mode = "0755")
   }
+  invisible(segmented_jobsh_file)
+}
 
-  # Get the list of all segment output NetCDFs
-  segment_ncfiles <- lapply(
-    segments[["segment_dir"]],
-    \(x) {
-      list.files(
-        file.path(x, "out", "1"),
-        pattern = "\\d+\\.nc",
-        full.names = TRUE
-      )
-    }
-  ) |>
-    do.call(what = c)
-
-  # ...and concatenate them together into annual NetCDFs.
-  segment_files_byyear <- split(
-    segment_ncfiles,
-    factor(basename(segment_ncfiles))
-  )
-  segment_outfiles <- file.path(run_modeloutdir, names(segment_files_byyear))
-  results <- purrr::map2(
-    segment_files_byyear,
-    segment_outfiles,
-    PEcAn.SIPNET::mergeNC
-  )
-  results
+if (FALSE) {
+  for (fname in jobsh_files) {
+    print(fname)
+    system2("bash", fname)
+  }
 }

From b7fac24f7cc5cbca6aa3043e6c7bb9c54b93a975 Mon Sep 17 00:00:00 2001
From: Alexey Shiklomanov <alexey.shiklomanov@gmail.com>
Date: Fri, 10 Apr 2026 17:54:03 -0400
Subject: [PATCH 40/75] bugfix model2netcdf.sipnet

---
 models/sipnet/R/model2netcdf.SIPNET.R | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/models/sipnet/R/model2netcdf.SIPNET.R b/models/sipnet/R/model2netcdf.SIPNET.R
index 2353f3500c6..57c99878a52 100644
--- a/models/sipnet/R/model2netcdf.SIPNET.R
+++ b/models/sipnet/R/model2netcdf.SIPNET.R
@@ -60,7 +60,7 @@ model2netcdf.SIPNET <- function(outdir, sitelat, sitelon, start_date, end_date,
                                 overwrite = FALSE, conflict = FALSE) {
   ### Read in model output in SIPNET format
   sipnet_out_file <- file.path(outdir, prefix)
-  sipnet_output <- read_sipnet_out(sipnet_output)
+  sipnet_output <- read_sipnet_out(sipnet_out_file)
   #sipnet_output_dims <- dim(sipnet_output)
   
   ### Determine number of years and output timestep

From 546ee44fc6f8eadcdde29e64d072870ae2b4668d Mon Sep 17 00:00:00 2001
From: Alexey Shiklomanov <alexey.shiklomanov@gmail.com>
Date: Fri, 10 Apr 2026 17:54:26 -0400
Subject: [PATCH 41/75] complete more pecanic workflow

---
 .../02-prepare-settings.R                     | 19 +-------
 .../sipnet-restart-workflow/03-run-sipnet.R   | 19 +++++---
 workflows/sipnet-restart-workflow/utils.R     | 46 +++++++++++++++----
 3 files changed, 50 insertions(+), 34 deletions(-)

diff --git a/workflows/sipnet-restart-workflow/02-prepare-settings.R b/workflows/sipnet-restart-workflow/02-prepare-settings.R
index bda1b93c49b..7910b9695d0 100644
--- a/workflows/sipnet-restart-workflow/02-prepare-settings.R
+++ b/workflows/sipnet-restart-workflow/02-prepare-settings.R
@@ -138,21 +138,4 @@ settings_raw <- PEcAn.settings::as.Settings(list(
 unlink(settings_raw$outdir, recursive = TRUE)
 dir.create(settings_raw$outdir, recursive = TRUE, showWarnings = FALSE)
 
-# Get parameter samples for all relevant PFTs
-sens_design <- PEcAn.uncertainty::generate_joint_ensemble_design(
-  settings_raw,
-  settings_raw$ensemble$size
-)
-
-settings <- PEcAn.workflow::runModule.run.write.configs(
-  settings_raw,
-  input_design = sens_design$X
-)
-
-inputs_runs <- file.path(settings$outdir, "runs_manifest.csv") |>
-  read.csv() |>
-  cbind(sens_design[["X"]])
-
-write.csv(inputs_runs, file = file.path(settings$outdir, "inputs_runs.csv"))
-
-PEcAn.settings::write.settings(settings, "settings.xml", outdir_root)
+PEcAn.settings::write.settings(settings_raw, "settings.xml", outdir_root)
diff --git a/workflows/sipnet-restart-workflow/03-run-sipnet.R b/workflows/sipnet-restart-workflow/03-run-sipnet.R
index 376b4e1b41b..534ad4512f2 100644
--- a/workflows/sipnet-restart-workflow/03-run-sipnet.R
+++ b/workflows/sipnet-restart-workflow/03-run-sipnet.R
@@ -7,13 +7,20 @@ if (FALSE) {
 
 config <- config::get(file = "workflows/sipnet-restart-workflow/config.yml")
 
-settings <- PEcAn.settings::read.settings(file.path(config[["outdir_root"]], "settings.xml"))
-inputs_runs <- read.csv(file.path(settings$outdir, "inputs_runs.csv"))
+settings_raw <- PEcAn.settings::read.settings(file.path(config[["outdir_root"]], "settings.xml"))
 
-source("workflows/sipnet-restart-workflow/utils.R")
+sens_design <- PEcAn.uncertainty::generate_joint_ensemble_design(
+  settings_raw,
+  settings_raw$ensemble$size
+)
+write.csv(sens_design$X, file.path(settings_raw$outdir, "input_design.csv"))
 
-for (i in seq_len(nrow(inputs_runs))) {
-  run_sipnet_segmented(settings, inputs_runs[i, ], replace_and_link = TRUE)
-}
+settings <- PEcAn.workflow::runModule.run.write.configs(
+  settings_raw,
+  input_design = sens_design$X
+)
+
+source("workflows/sipnet-restart-workflow/utils.R")
+jobfiles <- write_segmented_configs.SIPNET(settings, sens_design$X)
 
 PEcAn.workflow::runModule_start_model_runs(settings)
diff --git a/workflows/sipnet-restart-workflow/utils.R b/workflows/sipnet-restart-workflow/utils.R
index 0a9d7561ad3..8e43e8d4f9f 100644
--- a/workflows/sipnet-restart-workflow/utils.R
+++ b/workflows/sipnet-restart-workflow/utils.R
@@ -55,11 +55,29 @@ crop2pft_example <- function(crop_code) {
   )
 }
 
-run_sipnet_segmented <- function(
+write_segmented_configs.SIPNET <- function(settings, input_design = NULL, ...) {
+  manifest_file <- file.path(settings$outdir, "runs_manifest.csv")
+  if (!file.exists(manifest_file)) {
+    PEcAn.logger::logger.severe("Could not find manifest file: ", manifest_file)
+  }
+  inputs_runs <- read.csv(manifest_file)
+  if (!is.null(input_design)) {
+    inputs_runs <- cbind.data.frame(inputs_runs, input_design)
+  }
+
+  new_jobfiles <- character()
+
+  for (i in seq_along(nrow(inputs_runs))) {
+    new_jobfiles[[i]] <- write_segment_configs(settings, inputs_runs[i, ], ...)
+  }
+  invisible(new_jobfiles)
+}
+
+write_segment_configs <- function(
   settings,
   run_row,
   crop2pft = crop2pft_example,
-  replace_and_link = FALSE
+  replace_and_link = TRUE
 ) {
   run_id <- run_row[["run_id"]]
   run_dir <- file.path(settings$rundir, run_id)
@@ -72,7 +90,8 @@ run_sipnet_segmented <- function(
   )
   stopifnot(file.exists(ens_samples_file))
   ensemble_samples <- PEcAn.utils::load_local(ens_samples_file)[["ens.samples"]]
-  run_traits <- lapply(ensemble_samples, \(dat) dat[run_row[["param"]], ])
+  i_param <- run_row[["param"]] %||% 1
+  run_traits <- lapply(ensemble_samples, \(dat) dat[i_param, ])
 
   crop_cycles <- PEcAn.data.land::events_to_crop_cycle_starts(
     run_settings$run$inputs$events$source
@@ -183,6 +202,20 @@ run_sipnet_segmented <- function(
       "Rscript -e \"PEcAn.SIPNET::combine_sipnet_out(directory = %s, outfile = %s)\"",
       shQuote(segment_rootdir),
       shQuote(target_sipnet_out)
+    ),
+    "",
+    "# Convert output to PEcAn standard",
+    sprintf(
+      "Rscript -e \"PEcAn.SIPNET::model2netcdf.SIPNET(%s)\"",
+      paste(
+        sprintf("outdir = %s", shQuote(run_modeloutdir)),
+        sprintf("sitelat = %s", as.character(settings$run$site$lat)),
+        sprintf("sitelon = %s", as.character(settings$run$site$lon)),
+        sprintf("start_date = %s", shQuote(settings$run$start.date)),
+        sprintf("end_date = %s", shQuote(settings$run$end.date)),
+        sprintf("revision = %s", shQuote(settings$model$revision)),
+        sep = ", "
+      )
     )
   )
   writeLines(segmented_jobsh_lines, segmented_jobsh_file)
@@ -194,10 +227,3 @@ run_sipnet_segmented <- function(
   }
   invisible(segmented_jobsh_file)
 }
-
-if (FALSE) {
-  for (fname in jobsh_files) {
-    print(fname)
-    system2("bash", fname)
-  }
-}

From c0317a45680eb7905898de922af471ea41299cd5 Mon Sep 17 00:00:00 2001
From: Alexey Shiklomanov <alexey.shiklomanov@gmail.com>
Date: Sat, 11 Apr 2026 08:22:31 -0400
Subject: [PATCH 42/75] grepv --> grep(..., values = TRUE)

Co-authored-by: Akash B V <www.divinehome12@gmail.com>
---
 workflows/sipnet-restart-workflow/02-prepare-settings.R | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/workflows/sipnet-restart-workflow/02-prepare-settings.R b/workflows/sipnet-restart-workflow/02-prepare-settings.R
index 7910b9695d0..73c1fd5f8b3 100644
--- a/workflows/sipnet-restart-workflow/02-prepare-settings.R
+++ b/workflows/sipnet-restart-workflow/02-prepare-settings.R
@@ -23,9 +23,9 @@ site_lon <- dp_data[["lon"]]
 
 events_dir <- file.path(outdir_root, "events")
 events_files <- list.files(events_dir, recursive = TRUE, full.names = TRUE)
-events_json_files <- as.list(grepv(".*\\.json$", events_files))
+events_json_files <- as.list(grep(".*\\.json$", events_files, value = TRUE))
 names(events_json_files) <- paste0("path", seq_along(events_json_files))
-sipnet_eventfiles <- as.list(grepv(".*\\.sipnet/events-.*\\.in", events_files))
+sipnet_eventfiles <- as.list(grep(".*\\.sipnet/events-.*\\.in", events_files, value = TRUE))
 names(sipnet_eventfiles) <- paste0("path", seq_along(sipnet_eventfiles))
 
 # NOTE: We start from the first planting (after 2016) and end at the last harvest

From 390e5d88f78a69b349fdc939c3f926f557832c2d Mon Sep 17 00:00:00 2001
From: Alexey Shiklomanov <alexey.shiklomanov@gmail.com>
Date: Sat, 11 Apr 2026 08:23:07 -0400
Subject: [PATCH 43/75] bugfix: seq_along --> seq_len

Co-authored-by: Akash B V <www.divinehome12@gmail.com>
---
 workflows/sipnet-restart-workflow/utils.R | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/workflows/sipnet-restart-workflow/utils.R b/workflows/sipnet-restart-workflow/utils.R
index 8e43e8d4f9f..9e16b4b3037 100644
--- a/workflows/sipnet-restart-workflow/utils.R
+++ b/workflows/sipnet-restart-workflow/utils.R
@@ -67,7 +67,7 @@ write_segmented_configs.SIPNET <- function(settings, input_design = NULL, ...) {
 
   new_jobfiles <- character()
 
-  for (i in seq_along(nrow(inputs_runs))) {
+  for (i in seq_len(nrow(inputs_runs))) {
     new_jobfiles[[i]] <- write_segment_configs(settings, inputs_runs[i, ], ...)
   }
   invisible(new_jobfiles)

From ea4ca660d906739b9662e3bf0863d12de7357421 Mon Sep 17 00:00:00 2001
From: Alexey Shiklomanov <alexey.shiklomanov@gmail.com>
Date: Sat, 11 Apr 2026 08:35:06 -0400
Subject: [PATCH 44/75] typo extra file.path

Co-authored-by: Akash B V <www.divinehome12@gmail.com>
---
 workflows/sipnet-restart-workflow/utils.R | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/workflows/sipnet-restart-workflow/utils.R b/workflows/sipnet-restart-workflow/utils.R
index 9e16b4b3037..00c30d2cb79 100644
--- a/workflows/sipnet-restart-workflow/utils.R
+++ b/workflows/sipnet-restart-workflow/utils.R
@@ -99,7 +99,7 @@ write_segment_configs <- function(
     dplyr::ungroup()
 
   # Get segments
-  segment_rootdir <- file.path(file.path(run_dir, "segments"))
+  segment_rootdir <- file.path(run_dir, "segments")
   segments <- crop_cycles |>
     dplyr::rename(start_date = "date") |>
     dplyr::mutate(

From dc4e8bbbefe15dba9495c31b10c4c60382b48c75 Mon Sep 17 00:00:00 2001
From: Alexey Shiklomanov <alexey.shiklomanov@gmail.com>
Date: Fri, 17 Apr 2026 09:28:14 -0400
Subject: [PATCH 45/75] More robust segment logic

Allows for run start.date to be earlier than the first planting (in
which case, add a "spin-up" segment), or after the first planting (in
which case, clip the segments accordingly).
---
 workflows/sipnet-restart-workflow/utils.R | 65 +++++++++++++++++++----
 1 file changed, 54 insertions(+), 11 deletions(-)

diff --git a/workflows/sipnet-restart-workflow/utils.R b/workflows/sipnet-restart-workflow/utils.R
index 00c30d2cb79..c07a80fb8ff 100644
--- a/workflows/sipnet-restart-workflow/utils.R
+++ b/workflows/sipnet-restart-workflow/utils.R
@@ -73,6 +73,58 @@ write_segmented_configs.SIPNET <- function(settings, input_design = NULL, ...) {
   invisible(new_jobfiles)
 }
 
+segment_dataframe <- function(run_settings) {
+  events_json <- run_settings$run$inputs$events$source
+  stopifnot(file.exists(events_json))
+
+  crop_cycles <- PEcAn.data.land::events_to_crop_cycle_starts(events_json) |>
+    dplyr::ungroup()
+
+  run_start <- as.Date(run_settings$run$start.date)
+  run_end <- as.Date(run_settings$run$end.date)
+
+  # First, build segment data.frame just from the crop cycles. Note that we
+  # already include the run end date (lead(..., default = run_end)).
+  segments <- crop_cycles |>
+    dplyr::rename(start_date = "date") |>
+    dplyr::mutate(
+      end_date = dplyr::lead(.data$start_date - 1, default = run_end),
+    )
+
+  # If we start *before* the first planting, add a segment for that.
+  if (run_start < min(segments[["start_date"]])) {
+    first_segment <- tibble::tibble(
+      crop_cycle_id = 0,
+      site_id = segments[["site_id"]][[1]],
+      start_date = run_start,
+      end_date = segments[["start_date"]][[1]] - 1,
+      crop_code = NA_character_
+    )
+    segments <- dplyr::bind_rows(first_segment, segments)
+  }
+
+  # If the run start is *after* the first planting, clip to the start date.
+  if (run_start > min(segments[["start_date"]])) {
+    segments <- segments |>
+      dplyr::filter(
+        .data$start_date >= .env$run_start,
+        # Also clip the end date to avoid edge cases where run_start == end_date
+        .data$end_date > .env$run_start
+      )
+    if (nrow(segments) < 1) {
+      PEcAn.logger::logger.severe(
+        "Filtering resulted in no segments. ",
+        "This is an invalid state; check settings and events.json."
+      )
+    }
+    segments[1, "start_date"] <- run_start
+  }
+
+  segments |>
+    dplyr::arrange(.data$start_date) |>
+    dplyr::mutate(segment_id = sprintf("%03d", dplyr::row_number()))
+}
+
 write_segment_configs <- function(
   settings,
   run_row,
@@ -83,6 +135,7 @@ write_segment_configs <- function(
   run_dir <- file.path(settings$rundir, run_id)
   run_modeloutdir <- file.path(settings$modeloutdir, run_id)
   run_settings <- subset_paths(settings, run_row)
+  segment_rootdir <- file.path(run_dir, "segments")
 
   ens_samples_file <- file.path(
     run_settings$outdir,
@@ -93,19 +146,9 @@ write_segment_configs <- function(
   i_param <- run_row[["param"]] %||% 1
   run_traits <- lapply(ensemble_samples, \(dat) dat[i_param, ])
 
-  crop_cycles <- PEcAn.data.land::events_to_crop_cycle_starts(
-    run_settings$run$inputs$events$source
-  ) |>
-    dplyr::ungroup()
-
-  # Get segments
-  segment_rootdir <- file.path(run_dir, "segments")
-  segments <- crop_cycles |>
-    dplyr::rename(start_date = "date") |>
+  segments <- segment_dataframe(run_settings) |>
     dplyr::mutate(
-      end_date = dplyr::lead(.data$start_date - 1, default = as.Date(run_settings$run$end.date)),
       pft = crop2pft(.data$crop_code),
-      segment_id = sprintf("%03d", dplyr::row_number()),
       segment_dir = file.path(segment_rootdir, sprintf("segment_%s", .data$segment_id))
     )
 

From 8ab19bdcbe7a3da0ec949f6755abea2b2c860f78 Mon Sep 17 00:00:00 2001
From: Alexey Shiklomanov <alexey.shiklomanov@gmail.com>
Date: Fri, 17 Apr 2026 09:37:16 -0400
Subject: [PATCH 46/75] crop -> crop_code in tests

---
 .../tests/testthat/test-events_to_crop_cycle_starts.R     | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/modules/data.land/tests/testthat/test-events_to_crop_cycle_starts.R b/modules/data.land/tests/testthat/test-events_to_crop_cycle_starts.R
index 19c92de805b..4a00cd0c0c9 100644
--- a/modules/data.land/tests/testthat/test-events_to_crop_cycle_starts.R
+++ b/modules/data.land/tests/testthat/test-events_to_crop_cycle_starts.R
@@ -1,6 +1,6 @@
 test_that("non-planting events are ignored", {
   dat <- dplyr::tribble(
-    ~site_id, ~date, ~event_type, ~crop,
+    ~site_id, ~date, ~event_type, ~crop_code,
     "a", "2016-01-01", "planting", "almond",
     "a", "2016-05-01", "irrigation", NA_character_,
     "a", "2017-01-01", "planting", "almond",
@@ -14,7 +14,7 @@ test_that("non-planting events are ignored", {
 
 test_that("nonconsecutive runs of the same crop counted separately", {
   dat <- dplyr::tribble(
-    ~site_id, ~date, ~event_type, ~crop,
+    ~site_id, ~date, ~event_type, ~crop_code,
     "b", "2016-03-01", "planting", "tomato",
     "b", "2017-03-05", "planting", "tomato",
     "b", "2018-04-15", "planting", "potato",
@@ -27,7 +27,7 @@ test_that("nonconsecutive runs of the same crop counted separately", {
 
 test_that("sites are counted separately", {
   dat <- dplyr::tribble(
-    ~site_id, ~date, ~event_type, ~crop,
+    ~site_id, ~date, ~event_type, ~crop_code,
     "a", "2016-03-01", "planting", "grape",
     "b", "2016-03-01", "planting", "grape",
     "c", "2023-03-01", "planting", "grape",
@@ -45,5 +45,5 @@ test_that("reads from JSON", {
   )
   res <- events_to_crop_cycle_starts(path)
   expect_equal(res$date, "2022-02-19")
-  expect_equal(res$crop, "EX1")
+  expect_equal(res$crop_code, "EX1")
 })

From 7f03d0464d79b27548431c1b3b1257c5d6156090 Mon Sep 17 00:00:00 2001
From: Alexey Shiklomanov <alexey.shiklomanov@gmail.com>
Date: Fri, 17 Apr 2026 09:40:40 -0400
Subject: [PATCH 47/75] outpath should be NULL, not FALSE

---
 models/sipnet/R/split_inputs.SIPNET.R    | 2 +-
 models/sipnet/man/split_sipnet_events.Rd | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/models/sipnet/R/split_inputs.SIPNET.R b/models/sipnet/R/split_inputs.SIPNET.R
index 9dc9f5be3ad..4b95724779c 100644
--- a/models/sipnet/R/split_inputs.SIPNET.R
+++ b/models/sipnet/R/split_inputs.SIPNET.R
@@ -49,7 +49,7 @@ split_inputs.SIPNET <- function(start.time, stop.time, inputs, overwrite = FALSE
 #'
 #' @param eventfile Path to `events.in` file.
 #' @inheritParams split_inputs.SIPNET
-split_sipnet_events <- function(start.time, stop.time, eventfile, overwrite = FALSE, outpath = FALSE) {
+split_sipnet_events <- function(start.time, stop.time, eventfile, overwrite = FALSE, outpath = NULL) {
   # Read events.in
   prefix <- sub(".in", "", basename(eventfile), fixed = TRUE)
   outpath <- outpath %||% dirname(eventfile)
diff --git a/models/sipnet/man/split_sipnet_events.Rd b/models/sipnet/man/split_sipnet_events.Rd
index 6bb609546f2..2ebdba2091c 100644
--- a/models/sipnet/man/split_sipnet_events.Rd
+++ b/models/sipnet/man/split_sipnet_events.Rd
@@ -9,7 +9,7 @@ split_sipnet_events(
   stop.time,
   eventfile,
   overwrite = FALSE,
-  outpath = FALSE
+  outpath = NULL
 )
 }
 \arguments{

From 10eec01d741b07d7cca92a868c15d04f26e47639 Mon Sep 17 00:00:00 2001
From: Alexey Shiklomanov <alexey.shiklomanov@gmail.com>
Date: Fri, 17 Apr 2026 09:51:14 -0400
Subject: [PATCH 48/75] better docs + warnings for sipnet trait.values

---
 models/sipnet/R/write.configs.SIPNET.R   | 16 ++++++++++++++--
 models/sipnet/man/write.config.SIPNET.Rd |  4 +++-
 2 files changed, 17 insertions(+), 3 deletions(-)

diff --git a/models/sipnet/R/write.configs.SIPNET.R b/models/sipnet/R/write.configs.SIPNET.R
index cd5b1cac9e0..1956ad3519a 100755
--- a/models/sipnet/R/write.configs.SIPNET.R
+++ b/models/sipnet/R/write.configs.SIPNET.R
@@ -64,8 +64,10 @@
 #'
 #' @param defaults nested list of named constant parameter values. The
 #' structure is `list(list(constants = list(trait1 = <value>, trait2 = <value>, ...)))`.
-#' Only `defaults[[1]]$constants` is used; all other elements are silently ignored. 
-#' @param trait.values vector of samples for a given trait
+#' Only `defaults[[1]]$constants` is used; all other elements are silently ignored.
+#' @param trait.values named list of trait values for each PFT. SIPNET can
+#'  handle only one vegetation PFT, and an optional "soil" PFT for soil constants.
+#'  `trait.values` that do not fit this format will throw a warning.
 #' @param settings PEcAn settings object
 #' @param run.id run ID
 #' @param inputs list of model inputs
@@ -85,6 +87,16 @@ write.config.SIPNET <- function(defaults, trait.values, settings, run.id, inputs
     ))
   }
 
+  if (
+    (length(trait.values) > 2) ||
+      (length(trait.values) == 2 && !("soil" %in% names(trait.values)))
+  ) {
+    PEcAn.logger::logger.warn(paste0(
+      "SIPNET can only handle one vegetation PFT and one optional soil PFT. ",
+      "Passing multiple vegetation PFTs may lead to unexpected behavior."
+    ))
+  }
+
   rev_raw <- settings$model$revision
   legacy_v1 <- c("102319", "136", "r136", "ssr", "git")
   if (is.null(rev_raw) || rev_raw %in% legacy_v1) {
diff --git a/models/sipnet/man/write.config.SIPNET.Rd b/models/sipnet/man/write.config.SIPNET.Rd
index b241757e2b6..37ef098e459 100644
--- a/models/sipnet/man/write.config.SIPNET.Rd
+++ b/models/sipnet/man/write.config.SIPNET.Rd
@@ -20,7 +20,9 @@ write.config.SIPNET(
 structure is \verb{list(list(constants = list(trait1 = <value>, trait2 = <value>, ...)))}.
 Only \code{defaults[[1]]$constants} is used; all other elements are silently ignored.}
 
-\item{trait.values}{vector of samples for a given trait}
+\item{trait.values}{named list of trait values for each PFT. SIPNET can
+handle only one vegetation PFT, and an optional "soil" PFT for soil constants.
+\code{trait.values} that do not fit this format will throw a warning.}
 
 \item{settings}{PEcAn settings object}
 

From c31c63bc1806203ae17316d5076d0d325f19aab1 Mon Sep 17 00:00:00 2001
From: Alexey Shiklomanov <alexey.shiklomanov@gmail.com>
Date: Fri, 17 Apr 2026 09:55:32 -0400
Subject: [PATCH 49/75] comment about file sorting

---
 models/sipnet/R/combine_sipnet_out.R | 6 ++++++
 1 file changed, 6 insertions(+)

diff --git a/models/sipnet/R/combine_sipnet_out.R b/models/sipnet/R/combine_sipnet_out.R
index 5093c25d8de..8465ae5ad8f 100644
--- a/models/sipnet/R/combine_sipnet_out.R
+++ b/models/sipnet/R/combine_sipnet_out.R
@@ -16,6 +16,12 @@ combine_sipnet_out <- function(directory, outfile, files = NULL) {
     PEcAn.logger::logger.severe("Must provide either `directory` or `files`")
   }
   if (is.null(files)) {
+    # NOTE that this expects file paths (including parent directories) to be
+    # lexicographically sorted. For the common case of segmented SIPNET runs,
+    # the parent directories are named `segment_001`, `segment_002`, etc., so
+    # this will work automatically.
+    # If you don't want to make this assumption, or have a custom sort order,
+    # pass `files` directly to this function.
     files <- sort(list.files(directory, "sipnet\\.out", full.names = TRUE, recursive = TRUE))
   }
   if (!(length(files) > 0)) {

From d6555db706cc7eac35dd613982e2e4f06ca209b0 Mon Sep 17 00:00:00 2001
From: Alexey Shiklomanov <alexey.shiklomanov@gmail.com>
Date: Fri, 17 Apr 2026 10:11:12 -0400
Subject: [PATCH 50/75] warn on non-alternating harvest-planting cycles

---
 .../data.land/R/events_to_crop_cycle_starts.R | 24 ++++++++++++++++---
 1 file changed, 21 insertions(+), 3 deletions(-)

diff --git a/modules/data.land/R/events_to_crop_cycle_starts.R b/modules/data.land/R/events_to_crop_cycle_starts.R
index 65dbaed77f1..f17982cb8c3 100644
--- a/modules/data.land/R/events_to_crop_cycle_starts.R
+++ b/modules/data.land/R/events_to_crop_cycle_starts.R
@@ -31,12 +31,30 @@
 #' events_to_crop_cycle_starts(evts)
 #' }
 events_to_crop_cycle_starts <- function(event_json) {
-  jsonlite::read_json(event_json) |>
+  event_df <- jsonlite::read_json(event_json) |>
     dplyr::bind_rows() |>
     dplyr::mutate(events = purrr::map(.data$events, as.data.frame)) |>
-    tidyr::unnest(.data$events) |>
+    tidyr::unnest("events") |>
+    dplyr::filter(event_type %in% c("planting", "harvest")) |>
     dplyr::mutate(date = as.Date(.data$date)) |>
-    find_crop_changes()
+    dplyr::arrange(.data$date)
+  # We should always have alternating planting-harvest-planting-harvest cycles.
+  # If we don't, raise a warning.
+  dup_events <- event_df |>
+    dplyr::filter(
+      (.data$event_type == dplyr::lag(.data$event_type)) |
+        (.data$event_type == dplyr::lead(.data$event_type))
+    ) |>
+    dplyr::select("site_id", "date", "event_type", "crop_code")
+  if ((ndup <- nrow(dup_events)) > 0) {
+    dfdump <- paste("# ", capture.output(print(dup_events)), collapse = "\n")
+    PEcAn.logger::logger.warn(
+      "Detected", ndup, "instances of non-alternating harvest-planting cycles:",
+      "\n", dfdump,
+      wrap = FALSE
+    )
+  }
+  find_crop_changes(event_df)
 }
 
 # helper for events_to_crop_cyle_starts,

From 2173db96bcadc2a8d223a492f24db131fb0efcad Mon Sep 17 00:00:00 2001
From: Alexey Shiklomanov <alexey.shiklomanov@gmail.com>
Date: Fri, 17 Apr 2026 10:14:10 -0400
Subject: [PATCH 51/75] remove pixi and WIP files

---
 pixi.lock                                     | 6142 -----------------
 pixi.toml                                     |  105 -
 workflows/sipnet-restart-workflow/91-debug.R  |   83 -
 .../92-find-winter-crop.R                     |   40 -
 4 files changed, 6370 deletions(-)
 delete mode 100644 pixi.lock
 delete mode 100644 pixi.toml
 delete mode 100644 workflows/sipnet-restart-workflow/91-debug.R
 delete mode 100644 workflows/sipnet-restart-workflow/92-find-winter-crop.R

diff --git a/pixi.lock b/pixi.lock
deleted file mode 100644
index 7c0c3bfb476..00000000000
--- a/pixi.lock
+++ /dev/null
@@ -1,6142 +0,0 @@
-version: 6
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-    options:
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-    packages:
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-      - conda: https://conda.anaconda.org/conda-forge/linux-64/air-0.8.2-hb17b654_1.conda
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-      - conda: https://conda.anaconda.org/conda-forge/linux-64/aws-c-cal-0.9.13-h2c9d079_1.conda
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-      - conda: https://conda.anaconda.org/conda-forge/linux-64/aws-c-compression-0.3.1-h8b1a151_9.conda
-      - conda: https://conda.anaconda.org/conda-forge/linux-64/aws-c-event-stream-0.5.7-h28f887f_1.conda
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-  license_family: BSD
-  size: 601375
-  timestamp: 1764777111296
diff --git a/pixi.toml b/pixi.toml
deleted file mode 100644
index 2643f1827f5..00000000000
--- a/pixi.toml
+++ /dev/null
@@ -1,105 +0,0 @@
-[workspace]
-authors = ["Alexey Shiklomanov <alexey.shiklomanov@gmail.com>"]
-channels = ["conda-forge"]
-name = "cimis-et-complete"
-platforms = ["linux-64"]
-version = "0.1.0"
-
-[tasks]
-[tasks.pak]
-args = [{arg = "pkg"}]
-cmd = 'Rscript -e "pak::pak(\"{{ pkg }}\")"'
-
-[tasks.rdinst]
-args = [{arg = "path"}]
-cmd = 'Rscript -e "devtools::install(\"{{ path }}\", upgrade = FALSE)"'
-
-[tasks.rdoc]
-args = [{arg = "path"}]
-cmd = 'Rscript -e "devtools::document(\"{{ path }}\")"'
-
-[tasks.inst_local]
-depends-on = [
-  {task = "rdinst", args = ["base/logger"]},
-  {task = "rdinst", args = ["base/utils"]},
-  {task = "rdinst", args = ["base/remote"]},
-  {task = "rdinst", args = ["base/db"]},
-  {task = "rdinst", args = ["modules/data.land"]},
-  {task = "rdinst", args = ["modules/data.atmosphere"]},
-  {task = "rdinst", args = ["models/sipnet"]},
-  {task = "rdinst", args = ["base/settings"]}
-]
-
-[tasks.targets]
-args = [{arg = "tar_project", default = "small"}]
-cmd = "TAR_PROJECT={{ tar_project }} Rscript -e 'targets::tar_make()'"
-
-[tasks.outdated]
-args = [{arg = "tar_project", default = "small"}]
-cmd = "TAR_PROJECT={{ tar_project }} Rscript -e 'targets::tar_outdated()'"
-
-[tasks.target_build]
-depends-on = [
-  {task = "rdinst", args = ["modules/data.land"]},
-  {task = "targets"}
-]
-
-[dependencies]
-r = ">=4"
-r-roxygen2 = "==7.3.3"
-r-abind = ">=1.4.5"
-r-arrow = "*"
-r-coda = "*"
-r-curl = "*"
-r-dbplyr = ">=2.4.0"
-r-devtools = "*"
-r-dplyr = ">=1.1.2"
-r-dplR = "*"
-r-foreach = "*"
-r-fs = "*"
-r-future = "*"
-r-furrr = "*"
-r-httr = "*"
-r-httr2 = "*"
-r-jsonlite = "*"
-r-lubridate = "*"
-r-magrittr = "*"
-r-nanoarrow = "*"
-r-ncdf4 = ">=1.15"
-r-purrr = "*"
-r-rlang = "*"
-r-sf = "*"
-r-stringi = "*"
-r-stringr = "*"
-r-terra = "*"
-r-testthat = "*"
-r-tibble = "*"
-r-tidyr = "*"
-r-tidyselect = "*"
-r-withr = "*"
-r-xml = ">=3.98"
-r-dbi = "*"
-r-glue = "*"
-"r-R.utils" = "*"
-r-units = "*"
-r-urltools = "*"
-r-languageserver = ">=0.3.17,<0.4"
-r-targets = ">=1.12.0,<2"
-r-here = ">=1.0.2,<2"
-r-tarchetypes = ">=0.14.0,<0.15"
-r-ggplot2 = ">=4.0.2,<5"
-r-mirai = ">=2.6.1,<3"
-r-clustermq = ">=0.9.8,<0.10"
-r-crew = ">=1.3.0,<2"
-"r-crew.cluster" = ">=0.4.0,<0.5"
-air = ">=0.8.2,<0.9"
-r-visnetwork = ">=2.1.4,<3"
-r-pak = "*"
-r-jsonvalidate = ">=1.5.0,<2"
-r-rjags = ">=4_17,<5"
-r-rcpptoml = ">=0.2.3,<0.3"
-r-doparallel = ">=1.0.17,<2"
-r-reticulate = ">=1.45.0,<2"
-r-readr = ">=2.2.0,<3"
-cdo = ">=2.5.0,<3"
-r-stars = ">=0.7_1,<0.8"
diff --git a/workflows/sipnet-restart-workflow/91-debug.R b/workflows/sipnet-restart-workflow/91-debug.R
deleted file mode 100644
index f748910ff84..00000000000
--- a/workflows/sipnet-restart-workflow/91-debug.R
+++ /dev/null
@@ -1,83 +0,0 @@
-#!/usr/bin/env Rscript
-
-library(dplyr)
-library(ggplot2)
-library(readr)
-
-sipnet_out_file <- "modules/data.land/inst/sipnet-restart-workflow/_test/segments/segment_001/out/1/sipnet.out"
-
-skip_n <- 0
-sipnet_output <- tryCatch({
-  utils::read.table(sipnet_out_file, header = TRUE, skip = skip_n, sep = "")
-}, error = function(err) {
-  PEcAn.logger::logger.warn(
-    "Failed to read using `read.table`. ",
-    "Trying to parse output manually."
-  )
-  raw_lines <- readLines(sipnet_out_file)
-  raw_header <- raw_lines[[1 + skip_n]]
-  raw_body <- tail(raw_lines, -(1 + skip_n))
-  # SIPNET output is right-aligned with the column names in the header.
-  # We use this to figure out where the numbers end if there are no spaces.
-  token_matches <- gregexpr("\\S+", raw_header, perl = TRUE)
-  proc_header <- regmatches(raw_header, token_matches)[[1]]
-  col_ends <- token_matches[[1]] + attr(token_matches[[1]], "match.length") - 1
-  col_starts <- c(1, head(col_ends, -1) + 1)
-  col_widths <- col_ends - col_starts + 1
-  result <- read.fwf(
-    textConnection(raw_body),
-    widths = col_widths,
-    col.names = proc_header,
-    na.strings = c("nan", "-nan")
-  )
-  result[] <- lapply(result, as.numeric)
-  result
-})
-
-dat <- as_tibble(sipnet_output) |>
-  mutate(
-    date = PEcAn.SIPNET:::sipnet2datetime(year, day, time),
-    .before = 0
-  )
-
-head(dat, 20)
-
-dwide <- dat |>
-  select(-c("year", "day", "time")) |>
-  tidyr::pivot_longer(
-    -"date",
-    names_to = "variable",
-    values_to = "value"
-  )
-
-dwide |>
-  # filter(date < "2016-07-15") |>
-  # filter(date < "2016-06-11") |>
-  ggplot() +
-  aes(x = date, y = value) +
-  geom_line() +
-  facet_wrap(vars(variable), scales = "free")
-
-ggsave("~/Pictures/bad-segment-early.png")
-
-# Find first NA
-first_na_index <- which(rowSums(is.na(dat)) > 0)[1]
-start_row <- pmax(1, first_na_index - 10)
-end_row   <- pmin(nrow(dat), first_na_index + 10)
-result <- dat |>
-  slice(start_row:end_row)
-
-print(dat, n = Inf)
-
-dat |>
-  dplyr::filter(is.na(litter))
-
-tail(dat, 30) |> dplyr::glimpse()
-
-ncfile <- "modules/data.land/inst/sipnet-restart-workflow/_test/segments/segment_001/out/1/2016.nc"
-vnames <- c("")
-dnc <- PEcAn.utils::read.output(ncfiles = ncfile, dataframe = TRUE) |>
-  as_tibble()
-nc <- ncdf4::nc_open(ncfile)
-names(nc$var)
-time <- ncdf4::ncvar_get(nc, "time")
diff --git a/workflows/sipnet-restart-workflow/92-find-winter-crop.R b/workflows/sipnet-restart-workflow/92-find-winter-crop.R
deleted file mode 100644
index 71f6b40bdea..00000000000
--- a/workflows/sipnet-restart-workflow/92-find-winter-crop.R
+++ /dev/null
@@ -1,40 +0,0 @@
-#!/usr/bin/env Rscript
-
-config <- config::get(file = "workflows/sipnet-restart-workflow/config.yml")
-
-planting <- list.files(
-  config[["planting_events_dir"]],
-  "planting_statewide_.*\\.parquet",
-  full.names = TRUE
-) |>
-  arrow::open_dataset() |>
-  dplyr::collect() |>
-  dplyr::mutate(date = as.Date(.data$date)) |>
-  tibble::as_tibble()
-
-planting |>
-  dplyr::filter(lubridate::month(date) >= 11) |>
-  dplyr::arrange(date) |>
-  print(n = 30)
-
-pid <- "101007"  # hay
-
-pid <- "106453" # hay --> row --> hay
-pid <- "10726" # woody
-pid <- "154989" # woody --> hay --> row --> hay
-
-planting_site <- planting |>
-  dplyr::filter(.data$site_id == .env$pid)
-harvest <- list.files(
-  config[["harvest_events_dir"]],
-  ".*\\.parquet",
-  full.names = TRUE
-) |>
-  arrow::open_dataset() |>
-  dplyr::filter(.data$site_id == .env$pid) |>
-  dplyr::collect() |>
-  dplyr::mutate(date = as.Date(.data$date)) |>
-  dplyr::as_tibble()
-events <- dplyr::bind_rows(planting_site, harvest) |>
-  dplyr::arrange(.data$date)
-events

From 11fa8634a2f10c3eaef994de7f251c8dadd2cb59 Mon Sep 17 00:00:00 2001
From: Alexey Shiklomanov <alexey.shiklomanov@gmail.com>
Date: Fri, 17 Apr 2026 10:25:37 -0400
Subject: [PATCH 52/75] better combine_sipnet_out docs

---
 models/sipnet/R/combine_sipnet_out.R    | 6 +++---
 models/sipnet/man/combine_sipnet_out.Rd | 6 +++---
 2 files changed, 6 insertions(+), 6 deletions(-)

diff --git a/models/sipnet/R/combine_sipnet_out.R b/models/sipnet/R/combine_sipnet_out.R
index 8465ae5ad8f..18c8b5f57e2 100644
--- a/models/sipnet/R/combine_sipnet_out.R
+++ b/models/sipnet/R/combine_sipnet_out.R
@@ -5,9 +5,9 @@
 #' @param directory Parent directory to search for `sipnet.out` files. You must
 #' provide either this or an explicit vector of `files`.
 #' @param outfile File to which combined `sipnet.out` will be written
-#' @param files (optional) Explicit vector of paths to `sipnet.out` files to
-#' combine. Note that files need not be named `sipnet.out`, but they must be
-#' readable with [read_sipnet_out()].
+#' @param files Optional vector of paths to files to combine. All must be
+#' readable with [read_sipnet_out()]. If `NULL` (default), looks for files
+#' named `sipnet.out` in `directory` and its subdirectories, recursively.
 #'
 #' @return `outfile` (path to output file), invisibly
 #' @export
diff --git a/models/sipnet/man/combine_sipnet_out.Rd b/models/sipnet/man/combine_sipnet_out.Rd
index 4fedd52cded..85358b569ff 100644
--- a/models/sipnet/man/combine_sipnet_out.Rd
+++ b/models/sipnet/man/combine_sipnet_out.Rd
@@ -12,9 +12,9 @@ provide either this or an explicit vector of \code{files}.}
 
 \item{outfile}{File to which combined \code{sipnet.out} will be written}
 
-\item{files}{(optional) Explicit vector of paths to \code{sipnet.out} files to
-combine. Note that files need not be named \code{sipnet.out}, but they must be
-readable with \code{\link[=read_sipnet_out]{read_sipnet_out()}}.}
+\item{files}{Optional vector of paths to files to combine. All must be
+readable with \code{\link[=read_sipnet_out]{read_sipnet_out()}}. If \code{NULL} (default), looks for files
+named \code{sipnet.out} in \code{directory} and its subdirectories, recursively.}
 }
 \value{
 \code{outfile} (path to output file), invisibly

From 2ce339ec8ff96a55d740b02625c0900405461108 Mon Sep 17 00:00:00 2001
From: Alexey Shiklomanov <alexey.shiklomanov@gmail.com>
Date: Fri, 17 Apr 2026 10:36:58 -0400
Subject: [PATCH 53/75] add todo for crop2pft

---
 workflows/sipnet-restart-workflow/utils.R | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/workflows/sipnet-restart-workflow/utils.R b/workflows/sipnet-restart-workflow/utils.R
index c07a80fb8ff..b6fc4c868f9 100644
--- a/workflows/sipnet-restart-workflow/utils.R
+++ b/workflows/sipnet-restart-workflow/utils.R
@@ -39,8 +39,10 @@ subset_paths <- function(settings, path_nums) {
   settings
 }
 
+# TODO: We need a better, consistent implementation of this. However, this is
+# OK as an example of a function that implements the capabilities needed for
+# `write_segment_configs`.
 crop2pft_example <- function(crop_code) {
-  # crop_code <- c("F1", "R1", "G2", "F16")
   cls <- substr(crop_code, 1, 1)
   dplyr::case_when(
     crop_code == "P1" ~ "annual_crop",

From 3843f1220eaaadbf857b6f0d972a8445fefe22ff Mon Sep 17 00:00:00 2001
From: Alexey Shiklomanov <alexey.shiklomanov@gmail.com>
Date: Fri, 17 Apr 2026 10:38:17 -0400
Subject: [PATCH 54/75] option to force reruns of segments (default=FALSE)

if true, recursively delete segment folders for each segment.
---
 workflows/sipnet-restart-workflow/utils.R | 7 +++++--
 1 file changed, 5 insertions(+), 2 deletions(-)

diff --git a/workflows/sipnet-restart-workflow/utils.R b/workflows/sipnet-restart-workflow/utils.R
index b6fc4c868f9..8e06808ff39 100644
--- a/workflows/sipnet-restart-workflow/utils.R
+++ b/workflows/sipnet-restart-workflow/utils.R
@@ -131,7 +131,8 @@ write_segment_configs <- function(
   settings,
   run_row,
   crop2pft = crop2pft_example,
-  replace_and_link = TRUE
+  replace_and_link = TRUE,
+  force_rerun = FALSE
 ) {
   run_id <- run_row[["run_id"]]
   run_dir <- file.path(settings$rundir, run_id)
@@ -162,7 +163,9 @@ write_segment_configs <- function(
     dend <- segment[["end_date"]]
     segment_dir <- segment[["segment_dir"]]
 
-    unlink(segment_dir, recursive = TRUE)
+    if (force_rerun) {
+      unlink(segment_dir, recursive = TRUE)
+    }
     dir.create(segment_dir, showWarnings = FALSE, recursive = TRUE)
 
     runid_dummy <- "1"

From 275678608ecf60122baa5dd8b64e906c33b9e3dd Mon Sep 17 00:00:00 2001
From: Alexey Shiklomanov <alexey.shiklomanov@gmail.com>
Date: Fri, 17 Apr 2026 11:15:21 -0400
Subject: [PATCH 55/75] set pft_dir for BU SCC

---
 workflows/sipnet-restart-workflow/config.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/workflows/sipnet-restart-workflow/config.yml b/workflows/sipnet-restart-workflow/config.yml
index d2f8659e651..0b0032960d8 100644
--- a/workflows/sipnet-restart-workflow/config.yml
+++ b/workflows/sipnet-restart-workflow/config.yml
@@ -10,7 +10,7 @@ default:
   ic_dir: "/projectnb/dietzelab/ccmmf/ensemble/IC_files"
   planting_events_dir: "/projectnb/dietzelab/ccmmf/management/event_files"
   mslsp_path: "/projectnb/dietzelab/ccmmf/management/phenology/matched_landiq_mslsp_v4.1"
-  pft_dir: "..."
+  pft_dir: "/projectnb/dietzelab/ccmmf/ensemble/pfts"
   n_ensemble: 3
 
 ashiklom:

From 3ea3b2bb3e001ef2d76746b3cd3507ffd8479726 Mon Sep 17 00:00:00 2001
From: Alexey Shiklomanov <alexey.shiklomanov@gmail.com>
Date: Fri, 17 Apr 2026 12:15:02 -0400
Subject: [PATCH 56/75] drop "sipnet only takes one PFT" from warning

---
 models/sipnet/R/write.configs.SIPNET.R | 5 ++---
 1 file changed, 2 insertions(+), 3 deletions(-)

diff --git a/models/sipnet/R/write.configs.SIPNET.R b/models/sipnet/R/write.configs.SIPNET.R
index ef38c05e228..9212f2ce8cf 100755
--- a/models/sipnet/R/write.configs.SIPNET.R
+++ b/models/sipnet/R/write.configs.SIPNET.R
@@ -81,10 +81,9 @@ write.config.SIPNET <- function(defaults, trait.values, settings, run.id, inputs
                                 restart = NULL, spinup = NULL) {
 
   if (!is.list(trait.values)) {
-    PEcAn.logger::logger.severe(paste0(
-      "Even though SIPNET only takes one PFT at a time, ",
+    PEcAn.logger::logger.severe(
       "`trait.values` must be a list with names corresponding to PFTs."
-    ))
+    )
   }
 
   if (

From 53f251626029634d6a20f887fc2cf82218152347 Mon Sep 17 00:00:00 2001
From: Alexey Shiklomanov <alexey.shiklomanov@gmail.com>
Date: Fri, 17 Apr 2026 12:17:10 -0400
Subject: [PATCH 57/75] update sipnet configs docs

---
 models/sipnet/R/split_inputs.SIPNET.R | 6 +++---
 models/sipnet/man/split_sipnet_met.Rd | 8 ++++----
 2 files changed, 7 insertions(+), 7 deletions(-)

diff --git a/models/sipnet/R/split_inputs.SIPNET.R b/models/sipnet/R/split_inputs.SIPNET.R
index 4b95724779c..a83d6955922 100644
--- a/models/sipnet/R/split_inputs.SIPNET.R
+++ b/models/sipnet/R/split_inputs.SIPNET.R
@@ -89,12 +89,12 @@ split_sipnet_events <- function(start.time, stop.time, eventfile, overwrite = FA
   invisible(outfile)
 }
 
-##' split sipnet clim file based on start and end time
+##' Extract subset of a sipnet clim file based on start and end time
 ##'
 ##' @author Mike Dietze, Ann Raiho, Alexey Shiklomanov
 ##'
-##' @param start.time start date and time for each SDA ensemble
-##' @param stop.time stop date and time for each SDA ensemble
+##' @param start.time start date and time at which to start extraction
+##' @param stop.time stop date and time at which to stop extraction
 ##' @param met path to sipnet clim file to be split 
 ##' @param overwrite if `TRUE`, overwrite existing target file (Default `FALSE`)
 ##' @param outpath if specified, write output to a new directory. Default `NULL` writes back to the directory being read
diff --git a/models/sipnet/man/split_sipnet_met.Rd b/models/sipnet/man/split_sipnet_met.Rd
index 2d714d75f51..daf39a5ed30 100644
--- a/models/sipnet/man/split_sipnet_met.Rd
+++ b/models/sipnet/man/split_sipnet_met.Rd
@@ -2,14 +2,14 @@
 % Please edit documentation in R/split_inputs.SIPNET.R
 \name{split_sipnet_met}
 \alias{split_sipnet_met}
-\title{split sipnet clim file based on start and end time}
+\title{Extract subset of a sipnet clim file based on start and end time}
 \usage{
 split_sipnet_met(start.time, stop.time, met, overwrite = FALSE, outpath = NULL)
 }
 \arguments{
-\item{start.time}{start date and time for each SDA ensemble}
+\item{start.time}{start date and time at which to start extraction}
 
-\item{stop.time}{stop date and time for each SDA ensemble}
+\item{stop.time}{stop date and time at which to stop extraction}
 
 \item{met}{path to sipnet clim file to be split}
 
@@ -21,7 +21,7 @@ split_sipnet_met(start.time, stop.time, met, overwrite = FALSE, outpath = NULL)
 path to split up climate file
 }
 \description{
-split sipnet clim file based on start and end time
+Extract subset of a sipnet clim file based on start and end time
 }
 \author{
 Mike Dietze, Ann Raiho, Alexey Shiklomanov

From 0b3ac45e17d0d1943505f6065dda716c1bfad20a Mon Sep 17 00:00:00 2001
From: Alexey Shiklomanov <alexey.shiklomanov@gmail.com>
Date: Fri, 17 Apr 2026 13:07:21 -0400
Subject: [PATCH 58/75] split inputs consistently is < end.time, not <=

---
 models/sipnet/R/split_inputs.SIPNET.R     | 6 +++---
 models/sipnet/man/split_inputs.SIPNET.Rd  | 2 +-
 workflows/sipnet-restart-workflow/utils.R | 4 +++-
 3 files changed, 7 insertions(+), 5 deletions(-)

diff --git a/models/sipnet/R/split_inputs.SIPNET.R b/models/sipnet/R/split_inputs.SIPNET.R
index a83d6955922..45530d02c93 100644
--- a/models/sipnet/R/split_inputs.SIPNET.R
+++ b/models/sipnet/R/split_inputs.SIPNET.R
@@ -3,7 +3,7 @@
 #' Split SIPNET inputs into multiple files based on start and end time
 #'
 #' Subset each SIPNET input file and write a new file containing values `>=
-#' start.time` and `<= end.time` (note: `end.time` is inclusive!)
+#' start.time` and `< end.time` (note: end time is *not* inclusive)
 #'
 #' NOTE that sipnet met files contain dates _and_ times, while sipnet event
 #' files contain only dates. Comparing a datetime to a date will coerce the
@@ -80,7 +80,7 @@ split_sipnet_events <- function(start.time, stop.time, eventfile, overwrite = FA
   # Not using sipnet2datetime here because it returns times with time zones,
   # which could cause subtle timezone-related bugs
   dates_in <- as.Date(sprintf("%d-01-01", years_in)) + (doys_in - 1)
-  idx_keep <- (dates_in >= start.time) & (dates_in <= stop.time)
+  idx_keep <- (dates_in >= start.time) & (dates_in < stop.time)
   if (length(idx_keep) == 0) {
     PEcAn.logger::logger.warn("No events to keep, so `events.in` will be empty")
   }
@@ -95,7 +95,7 @@ split_sipnet_events <- function(start.time, stop.time, eventfile, overwrite = FA
 ##'
 ##' @param start.time start date and time at which to start extraction
 ##' @param stop.time stop date and time at which to stop extraction
-##' @param met path to sipnet clim file to be split 
+##' @param met path to sipnet clim file to be split
 ##' @param overwrite if `TRUE`, overwrite existing target file (Default `FALSE`)
 ##' @param outpath if specified, write output to a new directory. Default `NULL` writes back to the directory being read
 ##'
diff --git a/models/sipnet/man/split_inputs.SIPNET.Rd b/models/sipnet/man/split_inputs.SIPNET.Rd
index 80fe14fa63a..cef939824b3 100644
--- a/models/sipnet/man/split_inputs.SIPNET.Rd
+++ b/models/sipnet/man/split_inputs.SIPNET.Rd
@@ -30,7 +30,7 @@ Modified \code{inputs} list with all \code{path} entries replaced with new
 paths (suitable for inserting back into \code{settings$run$inputs}).
 }
 \description{
-Subset each SIPNET input file and write a new file containing values \verb{>= start.time} and \verb{<= end.time} (note: \code{end.time} is inclusive!)
+Subset each SIPNET input file and write a new file containing values \verb{>= start.time} and \verb{< end.time} (note: end time is \emph{not} inclusive)
 }
 \details{
 NOTE that sipnet met files contain dates \emph{and} times, while sipnet event
diff --git a/workflows/sipnet-restart-workflow/utils.R b/workflows/sipnet-restart-workflow/utils.R
index 8e06808ff39..ae27a3f732e 100644
--- a/workflows/sipnet-restart-workflow/utils.R
+++ b/workflows/sipnet-restart-workflow/utils.R
@@ -172,7 +172,9 @@ write_segment_configs <- function(
 
     segment_inputs <- PEcAn.SIPNET::split_inputs.SIPNET(
       dstart,
-      dend,
+      # NOTE: In split_inputs, end.time is *not* inclusive.
+      # But `dend` *is* inclusive. So `+1` as a workaround here.
+      (dend + 1),
       run_settings$run$inputs,
       overwrite = TRUE,
       outpath = segment_dir

From 3ab8def831f640b1c23ec838b0c157682a68c190 Mon Sep 17 00:00:00 2001
From: Alexey Shiklomanov <alexey.shiklomanov@gmail.com>
Date: Fri, 17 Apr 2026 13:17:14 -0400
Subject: [PATCH 59/75] downgrade datetime coercion message to debug

---
 models/sipnet/R/split_inputs.SIPNET.R | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/models/sipnet/R/split_inputs.SIPNET.R b/models/sipnet/R/split_inputs.SIPNET.R
index 45530d02c93..d76b84672ab 100644
--- a/models/sipnet/R/split_inputs.SIPNET.R
+++ b/models/sipnet/R/split_inputs.SIPNET.R
@@ -162,9 +162,9 @@ coerce_to_datetime <- function(x) {
       " (class: ", class(x), ")"
     )
   }
-  PEcAn.logger::logger.warn(paste0(
-    xname, " is a date, but this function expects a datetime. ",
+  PEcAn.logger::logger.debg(
+    xname, "is a date, but this function expects a datetime.",
     "Coercing to datetime by setting to midnight UTC."
-  ))
-  as.POSIXct(x)
+  )
+  as.POSIXct(x, tz = "UTC")
 }

From 691e7d5c3636cb55fb01d102e3e0eee8eca43f43 Mon Sep 17 00:00:00 2001
From: Alexey Shiklomanov <alexey.shiklomanov@gmail.com>
Date: Fri, 17 Apr 2026 13:52:40 -0400
Subject: [PATCH 60/75] change inputs -> results to avoid confusion

---
 models/sipnet/R/split_inputs.SIPNET.R | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/models/sipnet/R/split_inputs.SIPNET.R b/models/sipnet/R/split_inputs.SIPNET.R
index d76b84672ab..7fd5540f5ab 100644
--- a/models/sipnet/R/split_inputs.SIPNET.R
+++ b/models/sipnet/R/split_inputs.SIPNET.R
@@ -23,21 +23,21 @@
 #' @export
 split_inputs.SIPNET <- function(start.time, stop.time, inputs, overwrite = FALSE, outpath = NULL) {
   result <- inputs
-  if ("met" %in% names(inputs)) {
+  if ("met" %in% names(result)) {
     result[["met"]][["path"]] <- split_sipnet_met(
       start.time,
       stop.time,
-      inputs$met$path,
+      result$met$path,
       overwrite = overwrite,
       outpath = outpath
     )
   }
 
-  if ("events" %in% names(inputs)) {
+  if ("events" %in% names(result)) {
     result[["events"]][["path"]] <- split_sipnet_events(
       start.time,
       stop.time,
-      inputs$events$path,
+      result$events$path,
       overwrite = overwrite,
       outpath = outpath
     )

From 617b2fe23525ddc1c7ef0693e377fede8607fe45 Mon Sep 17 00:00:00 2001
From: Alexey Shiklomanov <alexey.shiklomanov@gmail.com>
Date: Fri, 17 Apr 2026 14:02:37 -0400
Subject: [PATCH 61/75] various R CMD check fixes

---
 models/sipnet/R/combine_sipnet_out.R     |  2 +-
 models/sipnet/R/model2netcdf.SIPNET.R    |  1 +
 models/sipnet/R/read_sipnet_out.R        |  6 +++---
 models/sipnet/R/split_inputs.SIPNET.R    |  2 +-
 models/sipnet/man/read_restart.SIPNET.Rd | 13 +++++++++++++
 5 files changed, 19 insertions(+), 5 deletions(-)

diff --git a/models/sipnet/R/combine_sipnet_out.R b/models/sipnet/R/combine_sipnet_out.R
index 18c8b5f57e2..3728867d64c 100644
--- a/models/sipnet/R/combine_sipnet_out.R
+++ b/models/sipnet/R/combine_sipnet_out.R
@@ -31,6 +31,6 @@ combine_sipnet_out <- function(directory, outfile, files = NULL) {
   combined <- do.call(rbind.data.frame, flist)
   # Mimic the SIPNET fixed-width right-aligned format
   combined_fwf <- format(combined, justify = "right")
-  write.table(combined_fwf, outfile, row.names = FALSE, col.names = TRUE, quote = FALSE, sep = "  ")
+  utils::write.table(combined_fwf, outfile, row.names = FALSE, col.names = TRUE, quote = FALSE, sep = "  ")
   invisible(outfile)
 }
diff --git a/models/sipnet/R/model2netcdf.SIPNET.R b/models/sipnet/R/model2netcdf.SIPNET.R
index 1befa6e775d..46e5c5d2040 100644
--- a/models/sipnet/R/model2netcdf.SIPNET.R
+++ b/models/sipnet/R/model2netcdf.SIPNET.R
@@ -13,6 +13,7 @@
 #' }
 #' @export mergeNC
 #' @name mergeNC
+#' @importfrom rlang .data
 #' @source https://github.com/RS-eco/processNC/blob/main/R/mergeNC.R
 mergeNC <- function(
     ##title<< Aggregate data in netCDF files
diff --git a/models/sipnet/R/read_sipnet_out.R b/models/sipnet/R/read_sipnet_out.R
index 810a0d68b5b..457a965803c 100644
--- a/models/sipnet/R/read_sipnet_out.R
+++ b/models/sipnet/R/read_sipnet_out.R
@@ -19,15 +19,15 @@ read_sipnet_out <- function(sipnet_out_file) {
     )
     raw_lines <- readLines(sipnet_out_file)
     raw_header <- raw_lines[[1 + skip_n]]
-    raw_body <- tail(raw_lines, -(1 + skip_n))
+    raw_body <- utils::tail(raw_lines, -(1 + skip_n))
     # SIPNET output is right-aligned with the column names in the header.
     # We use this to figure out where the numbers end if there are no spaces.
     token_matches <- gregexpr("\\S+", raw_header, perl = TRUE)
     proc_header <- regmatches(raw_header, token_matches)[[1]]
     col_ends <- token_matches[[1]] + attr(token_matches[[1]], "match.length") - 1
-    col_starts <- c(1, head(col_ends, -1) + 1)
+    col_starts <- c(1, utils::head(col_ends, -1) + 1)
     col_widths <- col_ends - col_starts + 1
-    result <- read.fwf(
+    result <- utils::read.fwf(
       textConnection(raw_body),
       widths = col_widths,
       col.names = proc_header,
diff --git a/models/sipnet/R/split_inputs.SIPNET.R b/models/sipnet/R/split_inputs.SIPNET.R
index 7fd5540f5ab..a71dc270fc7 100644
--- a/models/sipnet/R/split_inputs.SIPNET.R
+++ b/models/sipnet/R/split_inputs.SIPNET.R
@@ -162,7 +162,7 @@ coerce_to_datetime <- function(x) {
       " (class: ", class(x), ")"
     )
   }
-  PEcAn.logger::logger.debg(
+  PEcAn.logger::logger.debug(
     xname, "is a date, but this function expects a datetime.",
     "Coercing to datetime by setting to midnight UTC."
   )
diff --git a/models/sipnet/man/read_restart.SIPNET.Rd b/models/sipnet/man/read_restart.SIPNET.Rd
index 6bbc4d07fdb..7bb8f4553e6 100644
--- a/models/sipnet/man/read_restart.SIPNET.Rd
+++ b/models/sipnet/man/read_restart.SIPNET.Rd
@@ -6,6 +6,19 @@
 \usage{
 read_restart.SIPNET(outdir, runid, stop.time, settings, var.names, params)
 }
+\arguments{
+\item{outdir}{Output directory}
+
+\item{runid}{Run ID}
+
+\item{stop.time}{Year that is being read}
+
+\item{settings}{PEcAn settings object}
+
+\item{var.names}{Variable names to be extracted}
+
+\item{params}{Any parameters required for state calculations}
+}
 \value{
 X.vec      vector of forecasts
 }

From e49e7e8d062c37ad7eb3610bdff87c9d74929a3c Mon Sep 17 00:00:00 2001
From: Alexey Shiklomanov <alexey.shiklomanov@gmail.com>
Date: Fri, 17 Apr 2026 14:02:50 -0400
Subject: [PATCH 62/75] fix split inputs tests with new structure

---
 models/sipnet/tests/testthat/test-split_inputs.SIPNET.R | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/models/sipnet/tests/testthat/test-split_inputs.SIPNET.R b/models/sipnet/tests/testthat/test-split_inputs.SIPNET.R
index 2abcee8c253..b7b7c7fd453 100644
--- a/models/sipnet/tests/testthat/test-split_inputs.SIPNET.R
+++ b/models/sipnet/tests/testthat/test-split_inputs.SIPNET.R
@@ -14,7 +14,7 @@ test_that("split_inputs", {
     start.time = dates,
     stop.time = c(dates[-1], as.Date("2006-01-01")), # Stop just _before_ these dates
     MoreArgs = list(
-      inputs = climfile,
+      inputs = list(met = list(path = climfile)),
       outpath = outdir
     )
   )

From 79952c42fa303077ef856982389c4eb90efdf4cd Mon Sep 17 00:00:00 2001
From: Alexey Shiklomanov <alexey.shiklomanov@gmail.com>
Date: Fri, 17 Apr 2026 14:03:03 -0400
Subject: [PATCH 63/75] fix events_to_crop_cycle_starts tests

Based on the actual JSON contents.
---
 .../tests/testthat/test-events_to_crop_cycle_starts.R         | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/modules/data.land/tests/testthat/test-events_to_crop_cycle_starts.R b/modules/data.land/tests/testthat/test-events_to_crop_cycle_starts.R
index 4a00cd0c0c9..4b4fe97f6a5 100644
--- a/modules/data.land/tests/testthat/test-events_to_crop_cycle_starts.R
+++ b/modules/data.land/tests/testthat/test-events_to_crop_cycle_starts.R
@@ -44,6 +44,6 @@ test_that("reads from JSON", {
     package = "PEcAn.data.land"
   )
   res <- events_to_crop_cycle_starts(path)
-  expect_equal(res$date, "2022-02-19")
-  expect_equal(res$crop_code, "EX1")
+  expect_equal(res$date, as.Date("2022-02-19"))
+  expect_equal(res$crop_code, "Mo17")
 })

From 3f6ea0d8212fb5fb53fb02c665cbbf6e0d941a9c Mon Sep 17 00:00:00 2001
From: Alexey Shiklomanov <alexey.shiklomanov@gmail.com>
Date: Fri, 17 Apr 2026 14:20:54 -0400
Subject: [PATCH 64/75] fix sipnet split_input tests

---
 models/sipnet/R/split_inputs.SIPNET.R         |  4 +--
 .../tests/testthat/test-split_inputs.SIPNET.R | 25 +++++++++++++++----
 2 files changed, 22 insertions(+), 7 deletions(-)

diff --git a/models/sipnet/R/split_inputs.SIPNET.R b/models/sipnet/R/split_inputs.SIPNET.R
index a71dc270fc7..6e40bf9fe56 100644
--- a/models/sipnet/R/split_inputs.SIPNET.R
+++ b/models/sipnet/R/split_inputs.SIPNET.R
@@ -158,8 +158,8 @@ coerce_to_datetime <- function(x) {
   xname <- deparse(substitute(x))
   if (!inherits(x, "Date")) {
     PEcAn.logger::logger.severe(
-      "Invalid ", xname, " : ", x,
-      " (class: ", class(x), ")"
+      "Invalid", xname, ":", x,
+      "(class:", class(x), ")"
     )
   }
   PEcAn.logger::logger.debug(
diff --git a/models/sipnet/tests/testthat/test-split_inputs.SIPNET.R b/models/sipnet/tests/testthat/test-split_inputs.SIPNET.R
index b7b7c7fd453..59de46292ca 100644
--- a/models/sipnet/tests/testthat/test-split_inputs.SIPNET.R
+++ b/models/sipnet/tests/testthat/test-split_inputs.SIPNET.R
@@ -9,7 +9,7 @@ test_that("split_inputs", {
     by = "2 years"
   )
 
-  clim_split <- mapply(
+  clim_split_list <- mapply(
     split_inputs.SIPNET,
     start.time = dates,
     stop.time = c(dates[-1], as.Date("2006-01-01")), # Stop just _before_ these dates
@@ -18,6 +18,7 @@ test_that("split_inputs", {
       outpath = outdir
     )
   )
+  clim_split <- vapply(clim_split_list, \(x) x$path, character(1))
 
   # all steps processed
   expect_length(clim_split, 4)
@@ -30,20 +31,34 @@ test_that("split_inputs", {
     read.table(climfile),
     clim_split |>
       lapply(read.table) |>
-      do.call(what = "rbind")
+      c(make.row.names = FALSE) |>
+      do.call(what = rbind)
   )
 })
 
-test_that("v2 clim format", {
+test_that("split_inputs insists on start/end time being dates", {
   outdir <- withr::local_tempdir()
   climfile <- file.path("data", "niwot_1999_v2.clim")
 
-  clim_split <- split_inputs.SIPNET(
+  expect_error(split_inputs.SIPNET(
     start.time = "1999-01-01",
     stop.time = "1999-04-01",
-    inputs = climfile,
+    inputs = list(met = list(path = climfile)),
+    outpath = outdir
+  ), "Invalid start.time")
+})
+
+test_that("v2 clim format", {
+  outdir <- withr::local_tempdir()
+  climfile <- file.path("data", "niwot_1999_v2.clim")
+
+  clim_split_list <- split_inputs.SIPNET(
+    start.time = as.Date("1999-01-01"),
+    stop.time = as.Date("1999-04-01"),
+    inputs = list(met = list(path = climfile)),
     outpath = outdir
   )
+  clim_split <- vapply(clim_split_list, \(x) x$path, character(1))
   expect_length(clim_split, 1)
   expect_length(readLines(clim_split), 90 * 2) # Jan-March 2x/day
   expect_equal(ncol(read.table(clim_split, nrows = 1)), 12)

From 464acf7d99712360b0457c8d954c3da92bc22370 Mon Sep 17 00:00:00 2001
From: Alexey Shiklomanov <alexey.shiklomanov@gmail.com>
Date: Fri, 17 Apr 2026 14:22:07 -0400
Subject: [PATCH 65/75] more rcheck fixes

---
 models/sipnet/NAMESPACE               | 1 +
 models/sipnet/R/model2netcdf.SIPNET.R | 2 +-
 2 files changed, 2 insertions(+), 1 deletion(-)

diff --git a/models/sipnet/NAMESPACE b/models/sipnet/NAMESPACE
index f9f6ca518e8..376a4eb12cb 100644
--- a/models/sipnet/NAMESPACE
+++ b/models/sipnet/NAMESPACE
@@ -14,3 +14,4 @@ export(write.events.SIPNET)
 export(write_restart.SIPNET)
 importFrom(dplyr,"%>%")
 importFrom(rlang,"%||%")
+importFrom(rlang,.data)
diff --git a/models/sipnet/R/model2netcdf.SIPNET.R b/models/sipnet/R/model2netcdf.SIPNET.R
index 46e5c5d2040..9ea15e48d15 100644
--- a/models/sipnet/R/model2netcdf.SIPNET.R
+++ b/models/sipnet/R/model2netcdf.SIPNET.R
@@ -13,7 +13,7 @@
 #' }
 #' @export mergeNC
 #' @name mergeNC
-#' @importfrom rlang .data
+#' @importFrom rlang .data
 #' @source https://github.com/RS-eco/processNC/blob/main/R/mergeNC.R
 mergeNC <- function(
     ##title<< Aggregate data in netCDF files

From 7456de0594e22708a19cec6382d0477496d8cd30 Mon Sep 17 00:00:00 2001
From: Alexey Shiklomanov <alexey.shiklomanov@gmail.com>
Date: Fri, 17 Apr 2026 14:22:20 -0400
Subject: [PATCH 66/75] revert setting default ensemble method

---
 modules/uncertainty/R/generate_joint_ensemble_design.R | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/modules/uncertainty/R/generate_joint_ensemble_design.R b/modules/uncertainty/R/generate_joint_ensemble_design.R
index e3faeb2656e..470a9688033 100644
--- a/modules/uncertainty/R/generate_joint_ensemble_design.R
+++ b/modules/uncertainty/R/generate_joint_ensemble_design.R
@@ -58,7 +58,7 @@ generate_joint_ensemble_design <- function(settings,
   if (sobol) {
     ensemble_size <- as.numeric(ensemble_size) * 2
   }
-  ens.sample.method <- settings$ensemble$samplingspace$parameters$method %||% "uniform"
+  ens.sample.method <- settings$ensemble$samplingspace$parameters$method
   design_list <- list()
   sampled_inputs <- list()
   posterior.files <- settings$pfts %>%

From a40d0b2edff8d4ba8abd10a34448630b007dca5a Mon Sep 17 00:00:00 2001
From: Alexey Shiklomanov <alexey.shiklomanov@gmail.com>
Date: Fri, 17 Apr 2026 14:46:52 -0400
Subject: [PATCH 67/75] add tests for splitting sipnet events

---
 .../tests/testthat/data/events-39011.in       | 123 ++++++++++++++++++
 .../tests/testthat/test-split_inputs.SIPNET.R |  32 ++++-
 2 files changed, 154 insertions(+), 1 deletion(-)
 create mode 100644 models/sipnet/tests/testthat/data/events-39011.in

diff --git a/models/sipnet/tests/testthat/data/events-39011.in b/models/sipnet/tests/testthat/data/events-39011.in
new file mode 100644
index 00000000000..badfb845b58
--- /dev/null
+++ b/models/sipnet/tests/testthat/data/events-39011.in
@@ -0,0 +1,123 @@
+2016  161  irrig  9.65252 0
+2016  205  irrig  9.64896 0
+2016  256  irrig  9.58199 0
+2017  163  irrig  9.53059 0
+2017  205  irrig  9.55854 0
+2017  256  irrig  9.63501 0
+2018  159  irrig  9.6026 0
+2018  164  plant  17.7 5.31 3.54 8.85
+2018  164  irrig  55.26454 0
+2018  243  irrig  46.66387 0
+2018  304 harv   0.85 0 0.15 1
+2019  159  plant  32.4 9.72 6.48 16.2
+2019  165  irrig  6.32198 0
+2019  172  irrig  6.12285 0
+2019  179  irrig  6.02169 0
+2019  186  irrig  6.15909 0
+2019  193  irrig  6.18148 0
+2019  200  irrig  6.43141 0
+2019  207  irrig  6.28203 0
+2019  214  irrig  6.25072 0
+2019  221  irrig  5.97653 0
+2019  228  irrig  5.91664 0
+2019  236  irrig  6.41118 0
+2019  244  irrig  6.37572 0
+2019  253  irrig  6.11432 0
+2019  264  irrig  6.04351 0
+2019  277  irrig  6.03546 0
+2019  288 harv   0.85 0 0.15 1
+2019  292  irrig  5.91671 0
+2019  306  irrig  5.95993 0
+2019  324  irrig  5.96982 0
+2020  7  irrig  5.74717 0
+2020  32  irrig  5.85457 0
+2020  47  irrig  5.69725 0
+2020  59  irrig  5.9169 0
+2020  80  irrig  6.06453 0
+2020  93  irrig  6.16762 0
+2020  108  irrig  5.9422 0
+2020  116  irrig  5.71009 0
+2020  123  irrig  5.85222 0
+2020  130  irrig  5.90922 0
+2020  138  irrig  6.23485 0
+2020  146  irrig  6.19786 0
+2020  151  plant  28.4 8.52 5.68 14.2
+2020  153  irrig  5.93207 0
+2020  160  irrig  6.19921 0
+2020  167  irrig  5.84346 0
+2020  174  irrig  6.35657 0
+2020  181  irrig  6.36321 0
+2020  188  irrig  6.20552 0
+2020  195  irrig  6.38482 0
+2020  202  irrig  5.93723 0
+2020  209  irrig  5.86775 0
+2020  216  irrig  6.36583 0
+2020  223  irrig  5.72889 0
+2020  230  irrig  5.83106 0
+2020  238  irrig  6.01655 0
+2020  246  irrig  5.75161 0
+2020  256  irrig  6.17723 0
+2020  268  irrig  5.92472 0
+2020  282  irrig  5.93119 0
+2020  297  irrig  5.81343 0
+2020  299 harv   0.85 0 0.15 1
+2020  316  irrig  5.97592 0
+2020  336  irrig  5.85369 0
+2020  364  irrig  5.95409 0
+2021  17  irrig  5.73476 0
+2021  56  irrig  6.14175 0
+2021  69  irrig  5.97068 0
+2021  86  irrig  6.08402 0
+2021  95  irrig  5.72843 0
+2021  104  irrig  6.01936 0
+2021  112  irrig  6.07443 0
+2021  120  irrig  5.83634 0
+2021  127  irrig  6.4189 0
+2021  133  irrig  5.72954 0
+2021  140  irrig  5.94605 0
+2021  147  irrig  6.13868 0
+2021  153  plant  29.8 8.94 5.96 14.9
+2021  154  irrig  6.48331 0
+2021  161  irrig  5.98042 0
+2021  168  irrig  6.44376 0
+2021  174  irrig  5.69915 0
+2021  181  irrig  6.42743 0
+2021  188  irrig  6.45644 0
+2021  194  irrig  5.82907 0
+2021  201  irrig  6.3062 0
+2021  208  irrig  6.45553 0
+2021  215  irrig  6.4415 0
+2021  222  irrig  6.04692 0
+2021  229  irrig  5.97619 0
+2021  237  irrig  5.85328 0
+2021  245  irrig  6.13553 0
+2021  253  irrig  5.71006 0
+2021  263  irrig  5.74335 0
+2021  275  irrig  5.8088 0
+2021  286 harv   0.85 0 0.15 1
+2021  289  irrig  5.82425 0
+2021  320  irrig  5.82727 0
+2021  360  irrig  5.6906 0
+2022  19  irrig  5.96617 0
+2022  27  plant  4.3 1.29 0.86 2.15
+2022  177 harv   0.85 0 0.15 1
+2022  194  plant  13.6 4.08 2.72 6.8
+2022  240  irrig  39.32469 0
+2022  267 harv   0.85 0 0.15 1
+2023  162  plant  31.8 9.54 6.36 15.9
+2023  166  irrig  6.38402 0
+2023  173  irrig  5.78955 0
+2023  181  irrig  6.49648 0
+2023  188  irrig  6.47614 0
+2023  195  irrig  6.10943 0
+2023  202  irrig  6.24171 0
+2023  209  irrig  6.21757 0
+2023  216  irrig  5.91485 0
+2023  224  irrig  6.5025 0
+2023  232  irrig  6.26688 0
+2023  240  irrig  6.02302 0
+2023  249  irrig  5.83862 0
+2023  259  irrig  6.00448 0
+2023  271  irrig  5.7135 0
+2023  285  irrig  5.93296 0
+2023  286 harv   0.85 0 0.15 1
diff --git a/models/sipnet/tests/testthat/test-split_inputs.SIPNET.R b/models/sipnet/tests/testthat/test-split_inputs.SIPNET.R
index 59de46292ca..db09a03bfa8 100644
--- a/models/sipnet/tests/testthat/test-split_inputs.SIPNET.R
+++ b/models/sipnet/tests/testthat/test-split_inputs.SIPNET.R
@@ -18,7 +18,7 @@ test_that("split_inputs", {
       outpath = outdir
     )
   )
-  clim_split <- vapply(clim_split_list, \(x) x$path, character(1))
+  clim_split <- vapply(clim_split_list, `[[`, character(1), "path")
 
   # all steps processed
   expect_length(clim_split, 4)
@@ -63,3 +63,33 @@ test_that("v2 clim format", {
   expect_length(readLines(clim_split), 90 * 2) # Jan-March 2x/day
   expect_equal(ncol(read.table(clim_split, nrows = 1)), 12)
 })
+
+test_that("splitting event files", {
+  outdir <- withr::local_tempdir()
+  eventfile <- file.path("data", "events-39011.in")
+  dates <- seq(
+    from = as.Date("2016-01-01"),
+    to = as.Date("2024-01-01"),
+    by = "6 months"
+  )
+
+  inputs <- mapply(
+    split_inputs.SIPNET,
+    start.time = head(dates, -1),
+    stop.time = tail(dates, -1),
+    MoreArgs = list(
+      inputs = list(events = list(path = eventfile)),
+      outpath = outdir
+    )
+  )
+
+  new_events <- vapply(inputs, `[[`, character(1), "path")
+  expect_true(length(new_events) == (length(dates) - 1))
+  expect_true(all(file.exists(new_events)))
+
+  original <- readLines(eventfile)
+  combined <- lapply(new_events, readLines) |>
+    do.call(what = c) |>
+    unname()
+  expect_equal(original, combined)
+})

From 0abbbf738d04db312561bd3ba44b4876d5877b05 Mon Sep 17 00:00:00 2001
From: Alexey Shiklomanov <alexey.shiklomanov@gmail.com>
Date: Fri, 17 Apr 2026 15:38:51 -0400
Subject: [PATCH 68/75] fix: write_events.SIPNET actually sorts by date

---
 models/sipnet/R/write.events.SIPNET.R         | 14 +++++---
 .../tests/testthat/test-write.events.SIPNET.R | 32 +++++++++++++++++++
 2 files changed, 41 insertions(+), 5 deletions(-)

diff --git a/models/sipnet/R/write.events.SIPNET.R b/models/sipnet/R/write.events.SIPNET.R
index 1afc0f43620..06477ebadcc 100644
--- a/models/sipnet/R/write.events.SIPNET.R
+++ b/models/sipnet/R/write.events.SIPNET.R
@@ -77,12 +77,16 @@ write.events.SIPNET <- function(events_json, outdir) {
         dates <- as.Date(vapply(evs, function(e) as.character(e$date), character(1)))
         years <- as.integer(format(dates, "%Y"))
         days <- as.integer(format(dates, "%j"))
+        # Sort everything first; then just loop normally
         ord <- order(dates)
-        lines <- character(length(ord))
-        for (i in ord) {
-            e <- evs[[i]]
-            year <- years[[i]]
-            day <- days[[i]]
+        evs_sorted <- evs[ord]
+        days_sorted <- days[ord]
+        years_sorted <- years[ord]
+        lines <- character(length(evs))
+        for (i in seq_along(evs)) {
+            e <- evs_sorted[[i]]
+            year <- years_sorted[[i]]
+            day <- days_sorted[[i]]
             type <- e$event_type
             if (type == "tillage") {
                 f <- if (is.null(e$tillage_eff_0to1)) 0 else e$tillage_eff_0to1
diff --git a/models/sipnet/tests/testthat/test-write.events.SIPNET.R b/models/sipnet/tests/testthat/test-write.events.SIPNET.R
index f792a1fcc09..92a98433611 100644
--- a/models/sipnet/tests/testthat/test-write.events.SIPNET.R
+++ b/models/sipnet/tests/testthat/test-write.events.SIPNET.R
@@ -39,3 +39,35 @@ testthat::test_that("write.events.SIPNET handles multi-site events.json (one fil
     testthat::expect_true(startsWith(norm(got2[1]), "2022 60 plant"))
     testthat::expect_true(startsWith(norm(tail(got2, 1)), "2022 69 irrig"))
 })
+
+testthat::test_that("events are sorted by date", {
+    ev_json1 <- system.file(file.path("events_fixtures", "events_site1.json"),
+        package = "PEcAn.data.land"
+    )
+    outdir <- withr::local_tempdir()
+    events_orig <- jsonlite::read_json(ev_json1)
+    # Shuffle the events
+    n_events <- length(events_orig[[1]]$events)
+    withr::with_seed(8675309, {
+      idx <- sample(n_events)
+    })
+    events_shuffled <- events_orig
+    events_shuffled[[1]]$events <- events_shuffled[[1]]$events[idx]
+    shuffled_file <- file.path(outdir, "events.json")
+    jsonlite::write_json(events_shuffled, shuffled_file, auto_unbox = TRUE)
+    files <- write.events.SIPNET(shuffled_file, outdir)
+    expect_length(files, 1)
+    got <- readLines(files[1])
+    expected <- c(
+        "2022  35  till  0.2",
+        "2022  40  till  0.1",
+        "2022  40  irrig  5 1",
+        "2022  40  fert   0 0 10",
+        "2022  50  plant  10 3 2 5",
+        "2022  250 harv   0.1 0 0 0"
+    )
+    # Three events in the middle have the same dates, so they won't sort
+    # reliably. Just check that the first and last two events are correct.
+    expect_equal(norm(head(got, 1)), norm(head(expected, 1)))
+    expect_equal(norm(tail(got, 2)), norm(tail(expected, 2)))
+})

From f061e0923c9385f02283371c00e7f9cd3eecfc50 Mon Sep 17 00:00:00 2001
From: Alexey Shiklomanov <alexey.shiklomanov@gmail.com>
Date: Fri, 17 Apr 2026 15:49:56 -0400
Subject: [PATCH 69/75] continue runs to end of year

---
 .../02-prepare-settings.R                     |  4 ++-
 .../sipnet-restart-workflow/04-plot-outputs.R | 28 +++++++++----------
 2 files changed, 17 insertions(+), 15 deletions(-)

diff --git a/workflows/sipnet-restart-workflow/02-prepare-settings.R b/workflows/sipnet-restart-workflow/02-prepare-settings.R
index 73c1fd5f8b3..f2a64bf2546 100644
--- a/workflows/sipnet-restart-workflow/02-prepare-settings.R
+++ b/workflows/sipnet-restart-workflow/02-prepare-settings.R
@@ -43,7 +43,9 @@ harvest_dates <- events |>
   purrr::keep(\(x) x$event_type == "harvest") |>
   purrr::map_chr("date") |>
   as.Date()
-end_date <- max(harvest_dates)
+
+# Run through the end of the year post harvest
+end_date <- lubridate::make_date(lubridate::year(max(harvest_dates)), 12, 31)
 
 met_dir <- sprintf(
   "%sN_%sW",
diff --git a/workflows/sipnet-restart-workflow/04-plot-outputs.R b/workflows/sipnet-restart-workflow/04-plot-outputs.R
index eabf14dd56d..8e0268de184 100644
--- a/workflows/sipnet-restart-workflow/04-plot-outputs.R
+++ b/workflows/sipnet-restart-workflow/04-plot-outputs.R
@@ -59,24 +59,24 @@ plt <- results |>
   facet_wrap(vars(variable), scales = "free") +
   theme_bw() +
   theme(legend.position = "bottom")
-plt
+if (interactive()) plt
 
 ggsave(
   file.path(outdir_root, "restarts.png"),
   plt,
-  width = 14.5,
-  height = 9,
+  width = 18.5,
+  height = 13,
   units = "in"
 )
 
-zoomed <- plt +
-  xlim(
-    lubridate::ymd_h("2017-10-01T00"),
-    lubridate::ymd_h("2017-10-17T01")
-  )
-zoomed
-ggsave(
-  file.path(outdir_root, "zoomed.png"),
-  zoomed,
-  width = 14.5, height = 9, units = "in"
-)
+# zoomed <- plt +
+#   xlim(
+#     lubridate::ymd_h("2017-10-01T00"),
+#     lubridate::ymd_h("2017-10-17T01")
+#   )
+# zoomed
+# ggsave(
+#   file.path(outdir_root, "zoomed.png"),
+#   zoomed,
+#   width = 14.5, height = 9, units = "in"
+# )

From 6554a6b06340e3081d1f1053226b02ff4f00f5f6 Mon Sep 17 00:00:00 2001
From: Alexey Shiklomanov <alexey.shiklomanov@gmail.com>
Date: Fri, 17 Apr 2026 15:56:36 -0400
Subject: [PATCH 70/75] !(length > 0) --> length == 0

---
 models/sipnet/R/combine_sipnet_out.R | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/models/sipnet/R/combine_sipnet_out.R b/models/sipnet/R/combine_sipnet_out.R
index 3728867d64c..8b73b1bef1c 100644
--- a/models/sipnet/R/combine_sipnet_out.R
+++ b/models/sipnet/R/combine_sipnet_out.R
@@ -24,7 +24,7 @@ combine_sipnet_out <- function(directory, outfile, files = NULL) {
     # pass `files` directly to this function.
     files <- sort(list.files(directory, "sipnet\\.out", full.names = TRUE, recursive = TRUE))
   }
-  if (!(length(files) > 0)) {
+  if (length(files) == 0) {
     PEcAn.logger::logger.severe("No files provided; nothing to combine.")
   }
   flist <- lapply(files, read_sipnet_out)

From d5c359e264fa4aa84accb8269b45bfd3d25cbaaa Mon Sep 17 00:00:00 2001
From: Alexey Shiklomanov <alexey.shiklomanov@gmail.com>
Date: Fri, 17 Apr 2026 16:00:01 -0400
Subject: [PATCH 71/75] run in whole-year chunks

start jan 1 of first planting year

end dec 31 of last harvest year
---
 workflows/sipnet-restart-workflow/02-prepare-settings.R | 6 ++++--
 1 file changed, 4 insertions(+), 2 deletions(-)

diff --git a/workflows/sipnet-restart-workflow/02-prepare-settings.R b/workflows/sipnet-restart-workflow/02-prepare-settings.R
index f2a64bf2546..9e46fb23b62 100644
--- a/workflows/sipnet-restart-workflow/02-prepare-settings.R
+++ b/workflows/sipnet-restart-workflow/02-prepare-settings.R
@@ -36,7 +36,6 @@ planting_dates <- events |>
   purrr::keep(\(x) x$event_type == "planting") |>
   purrr::map_chr("date") |>
   as.Date()
-start_date <- min(planting_dates)
 
 harvest_dates <- events |>
   purrr::pluck(1, "events") |>
@@ -44,7 +43,10 @@ harvest_dates <- events |>
   purrr::map_chr("date") |>
   as.Date()
 
-# Run through the end of the year post harvest
+# Start Jan 1 of the year of the first planting
+start_date <- lubridate::make_date(lubridate::year(min(planting_dates)), 1, 1)
+
+# End Dec 31 of the year of the last harvest
 end_date <- lubridate::make_date(lubridate::year(max(harvest_dates)), 12, 31)
 
 met_dir <- sprintf(

From 453fc3b769048cd9c7ed085e97e3dcf397ba4c43 Mon Sep 17 00:00:00 2001
From: Alexey Shiklomanov <alexey.shiklomanov@gmail.com>
Date: Fri, 17 Apr 2026 16:15:09 -0400
Subject: [PATCH 72/75] generate dependencies (unrelated - data.atmosphere)

---
 docker/depends/pecan_package_dependencies.csv | 2 --
 1 file changed, 2 deletions(-)

diff --git a/docker/depends/pecan_package_dependencies.csv b/docker/depends/pecan_package_dependencies.csv
index 32a5c8d7003..539867d4bd7 100644
--- a/docker/depends/pecan_package_dependencies.csv
+++ b/docker/depends/pecan_package_dependencies.csv
@@ -489,7 +489,6 @@
 "rcrossref","*","base/db","Suggests",FALSE
 "readr","*","models/ldndc","Imports",FALSE
 "readr","*","modules/assim.sequential","Suggests",FALSE
-"REddyProc","*","modules/data.atmosphere","Imports",FALSE
 "redland","*","modules/data.land","Suggests",FALSE
 "reshape","*","modules/data.remote","Suggests",FALSE
 "reshape2","*","base/visualization","Imports",FALSE
@@ -684,7 +683,6 @@
 "tools","*","modules/allometry","Imports",FALSE
 "traits","*","modules/data.land","Suggests",FALSE
 "TruncatedNormal",">= 2.2","modules/assim.batch","Imports",FALSE
-"truncnorm","*","modules/data.atmosphere","Imports",FALSE
 "units","*","base/db","Imports",FALSE
 "units","*","modules/benchmark","Imports",FALSE
 "units","*","modules/data.atmosphere","Imports",FALSE

From 77022811302c14f63557e90f61634f344bddd0af Mon Sep 17 00:00:00 2001
From: Alexey Shiklomanov <alexey.shiklomanov@gmail.com>
Date: Fri, 17 Apr 2026 16:20:38 -0400
Subject: [PATCH 73/75] remove warning for duplicate harvest/planting

https://github.com/PecanProject/pecan/pull/3919#discussion_r3102871967
---
 .../data.land/R/events_to_crop_cycle_starts.R | 22 +++----------------
 1 file changed, 3 insertions(+), 19 deletions(-)

diff --git a/modules/data.land/R/events_to_crop_cycle_starts.R b/modules/data.land/R/events_to_crop_cycle_starts.R
index f17982cb8c3..dec6d04f71e 100644
--- a/modules/data.land/R/events_to_crop_cycle_starts.R
+++ b/modules/data.land/R/events_to_crop_cycle_starts.R
@@ -31,30 +31,14 @@
 #' events_to_crop_cycle_starts(evts)
 #' }
 events_to_crop_cycle_starts <- function(event_json) {
-  event_df <- jsonlite::read_json(event_json) |>
+  jsonlite::read_json(event_json) |>
     dplyr::bind_rows() |>
     dplyr::mutate(events = purrr::map(.data$events, as.data.frame)) |>
     tidyr::unnest("events") |>
     dplyr::filter(event_type %in% c("planting", "harvest")) |>
     dplyr::mutate(date = as.Date(.data$date)) |>
-    dplyr::arrange(.data$date)
-  # We should always have alternating planting-harvest-planting-harvest cycles.
-  # If we don't, raise a warning.
-  dup_events <- event_df |>
-    dplyr::filter(
-      (.data$event_type == dplyr::lag(.data$event_type)) |
-        (.data$event_type == dplyr::lead(.data$event_type))
-    ) |>
-    dplyr::select("site_id", "date", "event_type", "crop_code")
-  if ((ndup <- nrow(dup_events)) > 0) {
-    dfdump <- paste("# ", capture.output(print(dup_events)), collapse = "\n")
-    PEcAn.logger::logger.warn(
-      "Detected", ndup, "instances of non-alternating harvest-planting cycles:",
-      "\n", dfdump,
-      wrap = FALSE
-    )
-  }
-  find_crop_changes(event_df)
+    dplyr::arrange(.data$date) |>
+    find_crop_changes()
 }
 
 # helper for events_to_crop_cyle_starts,

From a5dae4867828ae26b97383fe78fcd0fc59861a3d Mon Sep 17 00:00:00 2001
From: Alexey Shiklomanov <alexey.shiklomanov@gmail.com>
Date: Fri, 17 Apr 2026 16:39:08 -0400
Subject: [PATCH 74/75] Revert temp changes to data.atmosphere DESCRIPTION

This reverts commit 67e055dabf938f23441b805be9c7ec6397ffe0b4.
---
 docker/depends/pecan_package_dependencies.csv | 2 ++
 modules/data.atmosphere/DESCRIPTION           | 2 ++
 2 files changed, 4 insertions(+)

diff --git a/docker/depends/pecan_package_dependencies.csv b/docker/depends/pecan_package_dependencies.csv
index 539867d4bd7..32a5c8d7003 100644
--- a/docker/depends/pecan_package_dependencies.csv
+++ b/docker/depends/pecan_package_dependencies.csv
@@ -489,6 +489,7 @@
 "rcrossref","*","base/db","Suggests",FALSE
 "readr","*","models/ldndc","Imports",FALSE
 "readr","*","modules/assim.sequential","Suggests",FALSE
+"REddyProc","*","modules/data.atmosphere","Imports",FALSE
 "redland","*","modules/data.land","Suggests",FALSE
 "reshape","*","modules/data.remote","Suggests",FALSE
 "reshape2","*","base/visualization","Imports",FALSE
@@ -683,6 +684,7 @@
 "tools","*","modules/allometry","Imports",FALSE
 "traits","*","modules/data.land","Suggests",FALSE
 "TruncatedNormal",">= 2.2","modules/assim.batch","Imports",FALSE
+"truncnorm","*","modules/data.atmosphere","Imports",FALSE
 "units","*","base/db","Imports",FALSE
 "units","*","modules/benchmark","Imports",FALSE
 "units","*","modules/data.atmosphere","Imports",FALSE
diff --git a/modules/data.atmosphere/DESCRIPTION b/modules/data.atmosphere/DESCRIPTION
index 9729b1757f0..9c978a6fd37 100644
--- a/modules/data.atmosphere/DESCRIPTION
+++ b/modules/data.atmosphere/DESCRIPTION
@@ -47,6 +47,7 @@ Imports:
     PEcAn.utils,
     purrr (>= 0.2.3),
     raster,
+    REddyProc,
     reshape2,
     rlang (>= 0.2.0),
     sf,
@@ -57,6 +58,7 @@ Imports:
     tibble,
     tidyr,
     tidyselect,
+    truncnorm,
     units,
     utils,
     XML (>= 3.98-1.4),

From 81e49dc5a0af79c72c1d3d5111cb4ac5ff81722e Mon Sep 17 00:00:00 2001
From: Alexey Shiklomanov <alexey.shiklomanov@gmail.com>
Date: Fri, 17 Apr 2026 16:54:59 -0400
Subject: [PATCH 75/75] .data predicate in crop cycle starts

---
 modules/data.land/R/events_to_crop_cycle_starts.R | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/modules/data.land/R/events_to_crop_cycle_starts.R b/modules/data.land/R/events_to_crop_cycle_starts.R
index dec6d04f71e..371a7f80599 100644
--- a/modules/data.land/R/events_to_crop_cycle_starts.R
+++ b/modules/data.land/R/events_to_crop_cycle_starts.R
@@ -35,7 +35,7 @@ events_to_crop_cycle_starts <- function(event_json) {
     dplyr::bind_rows() |>
     dplyr::mutate(events = purrr::map(.data$events, as.data.frame)) |>
     tidyr::unnest("events") |>
-    dplyr::filter(event_type %in% c("planting", "harvest")) |>
+    dplyr::filter(.data$event_type %in% c("planting", "harvest")) |>
     dplyr::mutate(date = as.Date(.data$date)) |>
     dplyr::arrange(.data$date) |>
     find_crop_changes()