refactor: move aimbat source to src directory

.github/workflows/build.yml

@@ -20,6 +20,7 @@ jobs:
         python-version:
           - "3.12"
           - "3.13"
+          - "3.14"
 
     steps:
       - uses: actions/checkout@v4
@@ -35,7 +36,7 @@ jobs:
         run: |
           uv build
       - name: Upload build artifacts
-        if: ${{ matrix.python-version == '3.13' && github.event.workflow_run.conclusion == 'success'}}
+        if: ${{ matrix.python-version == '3.14' && github.event.workflow_run.conclusion == 'success'}}
         uses: actions/upload-artifact@v4
         with:
           name: packages

.github/workflows/run-tests.yml

@@ -8,7 +8,7 @@ jobs:
     strategy:
       matrix:
         os: [ubuntu-latest, windows-latest, macos-latest]
-        python-version: ["3.12", "3.13"]
+        python-version: ["3.12", "3.13", "3.14"]
 
     steps:
       - uses: awalsh128/cache-apt-pkgs-action@latest
@@ -30,7 +30,7 @@ jobs:
           uv sync --locked --all-extras --no-group docs
           uv run black . --check --diff --color
           uv run ruff check
-          uv run py.test --mpl --mypy --cov=aimbat --cov-append --cov-report=term-missing  --junitxml=junit.xml
+          uv run py.test --mpl --mypy --cov src --cov-append --cov-report=term-missing  --junitxml=junit.xml
 
       - name: Store coverage results as artifacts
         uses: actions/upload-artifact@v4

Makefile

@@ -40,10 +40,10 @@ test-tutorial: check-uv ## Check if the tutorial notebook runs error-free.
 	uv run py.test --nbmake docs/examples/tutorial.ipynb
 
 tests: check-uv mypy test-tutorial ## Run all tests with pytest.
-	uv run pytest --cov=aimbat --cov-report=term-missing --cov-report=html --mpl
+	uv run pytest --cov-report=term-missing --cov-report=html --mpl
 
 mypy: check-uv ## Run typing tests with pytest.
-	uv run pytest --mypy -m mypy aimbat tests
+	uv run pytest --mypy -m mypy src tests
 
 docs: check-uv install ## Build html docs.
 	uv run mkdocs build
@@ -52,7 +52,7 @@ docs-export: check-uv install ## Export installed package information to docs/re
 	uv export --only=docs -o docs/requirements.txt
 
 live-docs: check-uv install ## Live build html docs. They are served on http://localhost:8000
-	uv run mkdocs serve -w README.md -w aimbat
+	uv run mkdocs serve -w README.md -w src
 
 notebook: check-uv install ## Run a jupyter notebook in the uv environment
 	uv run jupyter-lab

flake.nix

@@ -26,9 +26,9 @@
             nativeBuildInputs = with pkgs; [
               uv
               ruff
-              python312
+              (python314.withPackages (ps: with ps; [tox]))
               python313
-              python313Packages.tox
+              python312
               gnumake
               sqlitebrowser
             ];
@@ -39,7 +39,7 @@
                   stdenv.cc.cc.lib
                   zlib
                   zstd
-                  xorg.libX11
+                  libX11
                   libGL
                   glib
                   libxkbcommon
@@ -48,6 +48,9 @@
                   dbus
                   wayland
                 ]}:$LD_LIBRARY_PATH
+                export UV_PYTHON=$(which python3.14)
+                export UV_NO_MANAGED_PYTHON=true
+                [ ! -d .venv ] && uv venv --system-site-packages
                 uv sync --locked --all-extras
                 VENV=.venv
                 export MPLBACKEND=QtAgg

mkdocs.yml

@@ -1,5 +1,5 @@
 site_name: AIMBAT
-copyright: Copyright © 2024-2025 Simon Lloyd
+copyright: Copyright © 2024-2026 Simon Lloyd
 
 # Repository
 repo_name: pysmo/aimbat

pyproject.toml

@@ -6,7 +6,7 @@ authors = [
     { name = "Xiaoting Lou", email = "xlou@u.northwestern.edu" },
     { name = "Simon M. Lloyd", email = "simon@slloyd.net" },
 ]
-requires-python = ">=3.12,<3.14"
+requires-python = ">=3.12,<3.15"
 readme = "README.md"
 license = "GPL-3.0-or-later"
 classifiers = [
@@ -80,11 +80,9 @@ exclude = [
     "docs",
 ]
 
+
 [tool.hatch.build.targets.wheel]
-exclude = [
-    "tests",
-    "docs",
-]
+packages = ["src/aimbat"]
 
 [build-system]
 requires = ["hatchling"]
@@ -95,16 +93,20 @@ build-backend = "hatchling.build"
 # xvfb_height = 1080
 testpaths = [
   "tests",
+  "src",
 ]
 mpl-generate-summary = "html"
 mpl-use-full-test-name = true
 
 [tool.mypy]
+mypy_path = "src"
 namespace_packages = true
 disallow_untyped_defs = true
 warn_unused_ignores = true
 warn_redundant_casts = true
 
+[tool.coverage.run]
+source = ["src"]
 [tool.coverage.report]
 exclude_also = [
     "def __repr__",
@@ -126,6 +128,7 @@ exclude_also = [
 target-version = [
     "py312",
     "py313",
+    "py314",
 ]
 
 [tool.ruff]

aimbat/app.py → src/aimbat/app.py

@@ -22,7 +22,6 @@
 from rich.console import Console
 import sys
 
-
 try:
     __version__ = str(metadata.version("aimbat"))
 except Exception:

aimbat/cli/iccs.py → src/aimbat/cli/iccs.py

@@ -12,8 +12,8 @@
 @Parameter(name="*")
 @dataclass
 class IccsPlotParameters:
-    pad: bool = True
-    "Add extra padding to the time window for plotting."
+    context: bool = True
+    "Plot seismograms with extra context instead of the short tapered ones used for cross-correlation."
     all: bool = False
     "Include all seismograms in the plot, even if not used in stack."
 
@@ -30,58 +30,58 @@ def _run_iccs(autoflip: bool = False, autoselect: bool = False) -> None:
 
 
 @simple_exception
-def _plot_stack(padded: bool, all: bool) -> None:
+def _plot_stack(context: bool, all: bool) -> None:
     from aimbat.lib.db import engine
     from aimbat.lib.iccs import create_iccs_instance, plot_stack
     from sqlmodel import Session
 
     with Session(engine) as session:
         iccs = create_iccs_instance(session)
-        plot_stack(iccs, padded, all)
+        plot_stack(iccs, context, all)
 
 
 @simple_exception
-def _plot_seismograms(padded: bool, all: bool) -> None:
+def _plot_seismograms(context: bool, all: bool) -> None:
     from aimbat.lib.db import engine
     from aimbat.lib.iccs import create_iccs_instance, plot_seismograms
     from sqlmodel import Session
 
     with Session(engine) as session:
         iccs = create_iccs_instance(session)
-        plot_seismograms(iccs, padded, all)
+        plot_seismograms(iccs, context, all)
 
 
 @simple_exception
-def _update_pick(padded: bool, all: bool, use_seismogram_image: bool) -> None:
+def _update_pick(context: bool, all: bool, use_seismogram_image: bool) -> None:
     from aimbat.lib.db import engine
     from aimbat.lib.iccs import create_iccs_instance, update_pick
     from sqlmodel import Session
 
     with Session(engine) as session:
         iccs = create_iccs_instance(session)
-        update_pick(session, iccs, padded, all, use_seismogram_image)
+        update_pick(session, iccs, context, all, use_seismogram_image)
 
 
 @simple_exception
-def _update_timewindow(padded: bool, all: bool, use_seismogram_image: bool) -> None:
+def _update_timewindow(context: bool, all: bool, use_seismogram_image: bool) -> None:
     from aimbat.lib.db import engine
     from aimbat.lib.iccs import create_iccs_instance, update_timewindow
     from sqlmodel import Session
 
     with Session(engine) as session:
         iccs = create_iccs_instance(session)
-        update_timewindow(session, iccs, padded, all, use_seismogram_image)
+        update_timewindow(session, iccs, context, all, use_seismogram_image)
 
 
 @simple_exception
-def _update_min_ccnorm(padded: bool, all: bool) -> None:
+def _update_min_ccnorm(context: bool, all: bool) -> None:
     from aimbat.lib.db import engine
     from aimbat.lib.iccs import create_iccs_instance, update_min_ccnorm
     from sqlmodel import Session
 
     with Session(engine) as session:
         iccs = create_iccs_instance(session)
-        update_min_ccnorm(session, iccs, padded, all)
+        update_min_ccnorm(session, iccs, context, all)
 
 
 app = App(name="iccs", help=__doc__, help_format="markdown")
@@ -125,7 +125,7 @@ def cli_iccs_plot_stack(
     iccs_parameters = iccs_parameters or IccsPlotParameters()
     global_parameters = global_parameters or GlobalParameters()
 
-    _plot_stack(iccs_parameters.pad, iccs_parameters.all)
+    _plot_stack(iccs_parameters.context, iccs_parameters.all)
 
 
 @plot.command(name="image")
@@ -143,7 +143,7 @@ def cli_iccs_plot_seismograms(
     iccs_parameters = iccs_parameters or IccsPlotParameters()
     global_parameters = global_parameters or GlobalParameters()
 
-    _plot_seismograms(iccs_parameters.pad, iccs_parameters.all)
+    _plot_seismograms(iccs_parameters.context, iccs_parameters.all)
 
 
 @update.command(name="pick")
@@ -163,7 +163,7 @@ def cli_iccs_update_pick(
     global_parameters = global_parameters or GlobalParameters()
 
     _update_pick(
-        iccs_parameters.pad,
+        iccs_parameters.context,
         iccs_parameters.all,
         use_seismogram_image,
     )
@@ -186,7 +186,7 @@ def cli_iccs_update_timewindow(
     global_parameters = global_parameters or GlobalParameters()
 
     _update_timewindow(
-        iccs_parameters.pad,
+        iccs_parameters.context,
         iccs_parameters.all,
         use_seismogram_image,
     )
@@ -203,7 +203,7 @@ def cli_iccs_update_min_ccnorm(
     iccs_parameters = iccs_parameters or IccsPlotParameters()
     global_parameters = global_parameters or GlobalParameters()
 
-    _update_min_ccnorm(iccs_parameters.pad, iccs_parameters.all)
+    _update_min_ccnorm(iccs_parameters.context, iccs_parameters.all)
 
 
 if __name__ == "__main__":

aimbat/cli/utils/__init__.py → src/aimbat/cli/utils/__init__.py

@@ -2,5 +2,4 @@
 
 from .app import app
 
-
 __all__ = ["app"]

aimbat/config.py → src/aimbat/config.py

@@ -30,28 +30,28 @@ class Settings(BaseSettings):
     """Enable debug logging."""
 
     window_pre: timedelta = Field(
-        default=ICCS_DEFAULTS.WINDOW_PRE,
+        default=ICCS_DEFAULTS.window_pre,
         lt=0,
         description="Initial relative begin time of window.",
     )
     """Initial relative begin time of window."""
 
     window_post: timedelta = Field(
-        default=ICCS_DEFAULTS.WINDOW_POST,
+        default=ICCS_DEFAULTS.window_post,
         ge=0,
         description="Initial relative end time of window.",
     )
     """Initial relative end time of window."""
 
-    window_padding: timedelta = Field(
-        default=ICCS_DEFAULTS.PLOT_PADDING,
+    context_width: timedelta = Field(
+        default=ICCS_DEFAULTS.context_width,
         gt=0,
-        description="Padding around time window.",
+        description="Context padding to apply before and after the time window.",
     )
-    """Padding around time window."""
+    """Context padding to apply before and after the time window."""
 
     min_ccnorm: float | np.floating = Field(
-        default=ICCS_DEFAULTS.MIN_CCNORM,
+        default=ICCS_DEFAULTS.min_ccnorm,
         ge=0,
         le=1,
         description="Initial minimum cross correlation coefficient.",

aimbat/lib/db.py → src/aimbat/lib/db.py

@@ -3,6 +3,5 @@
 from sqlmodel import create_engine
 from aimbat.config import settings
 
-
 engine = create_engine(url=settings.db_url, echo=False)
 """AIMBAT database engine."""