From 185c8f4806ec8de00797e4342f0f06f636301125 Mon Sep 17 00:00:00 2001 From: Simon Lloyd Date: Sun, 15 Feb 2026 19:51:55 +0000 Subject: [PATCH] refactor: move aimbat source to src directory --- .github/workflows/build.yml | 3 +- .github/workflows/run-tests.yml | 4 +- Makefile | 6 +- flake.lock | 12 +- flake.nix | 9 +- mkdocs.yml | 2 +- pyproject.toml | 13 +- {aimbat => src/aimbat}/__init__.py | 0 {aimbat => src/aimbat}/app.py | 1 - {aimbat => src/aimbat}/cli/__init__.py | 0 {aimbat => src/aimbat}/cli/common.py | 0 {aimbat => src/aimbat}/cli/data.py | 0 {aimbat => src/aimbat}/cli/event.py | 0 {aimbat => src/aimbat}/cli/iccs.py | 34 +- {aimbat => src/aimbat}/cli/project.py | 0 {aimbat => src/aimbat}/cli/seismogram.py | 0 {aimbat => src/aimbat}/cli/snapshot.py | 0 {aimbat => src/aimbat}/cli/station.py | 0 {aimbat => src/aimbat}/cli/utils/__init__.py | 1 - {aimbat => src/aimbat}/cli/utils/app.py | 0 .../aimbat}/cli/utils/sampledata.py | 0 {aimbat => src/aimbat}/config.py | 14 +- {aimbat => src/aimbat}/lib/__init__.py | 0 {aimbat => src/aimbat}/lib/common.py | 0 {aimbat => src/aimbat}/lib/data.py | 0 {aimbat => src/aimbat}/lib/db.py | 1 - {aimbat => src/aimbat}/lib/event.py | 0 {aimbat => src/aimbat}/lib/iccs.py | 32 +- {aimbat => src/aimbat}/lib/io/__init__.py | 0 {aimbat => src/aimbat}/lib/io/_io.py | 0 {aimbat => src/aimbat}/lib/io/_sac.py | 0 {aimbat => src/aimbat}/lib/models.py | 0 {aimbat => src/aimbat}/lib/project.py | 8 +- {aimbat => src/aimbat}/lib/seismogram.py | 0 {aimbat => src/aimbat}/lib/snapshot.py | 0 {aimbat => src/aimbat}/lib/station.py | 0 {aimbat => src/aimbat}/lib/typing.py | 0 {aimbat => src/aimbat}/lib/utils/__init__.py | 0 {aimbat => src/aimbat}/lib/utils/checkdata.py | 0 {aimbat => src/aimbat}/lib/utils/json.py | 0 .../aimbat}/lib/utils/sampledata.py | 0 {aimbat => src/aimbat}/logger.py | 0 tests/test_app.py | 28 +- tests/test_data.py | 17 +- tests/test_event.py | 77 +- tests/test_project.py | 13 +- tests/test_seismogram.py | 116 +- tests/test_settings.py | 5 +- tests/test_snapshot.py | 43 +- tests/test_station.py | 50 +- tests/test_utils.py | 43 +- tox.ini | 13 +- uv.lock | 1996 +++++++++++------ 53 files changed, 1630 insertions(+), 911 deletions(-) rename {aimbat => src/aimbat}/__init__.py (100%) rename {aimbat => src/aimbat}/app.py (99%) rename {aimbat => src/aimbat}/cli/__init__.py (100%) rename {aimbat => src/aimbat}/cli/common.py (100%) rename {aimbat => src/aimbat}/cli/data.py (100%) rename {aimbat => src/aimbat}/cli/event.py (100%) rename {aimbat => src/aimbat}/cli/iccs.py (84%) rename {aimbat => src/aimbat}/cli/project.py (100%) rename {aimbat => src/aimbat}/cli/seismogram.py (100%) rename {aimbat => src/aimbat}/cli/snapshot.py (100%) rename {aimbat => src/aimbat}/cli/station.py (100%) rename {aimbat => src/aimbat}/cli/utils/__init__.py (98%) rename {aimbat => src/aimbat}/cli/utils/app.py (100%) rename {aimbat => src/aimbat}/cli/utils/sampledata.py (100%) rename {aimbat => src/aimbat}/config.py (91%) rename {aimbat => src/aimbat}/lib/__init__.py (100%) rename {aimbat => src/aimbat}/lib/common.py (100%) rename {aimbat => src/aimbat}/lib/data.py (100%) rename {aimbat => src/aimbat}/lib/db.py (99%) rename {aimbat => src/aimbat}/lib/event.py (100%) rename {aimbat => src/aimbat}/lib/iccs.py (77%) rename {aimbat => src/aimbat}/lib/io/__init__.py (100%) rename {aimbat => src/aimbat}/lib/io/_io.py (100%) rename {aimbat => src/aimbat}/lib/io/_sac.py (100%) rename {aimbat => src/aimbat}/lib/models.py (100%) rename {aimbat => src/aimbat}/lib/project.py (97%) rename {aimbat => src/aimbat}/lib/seismogram.py (100%) rename {aimbat => src/aimbat}/lib/snapshot.py (100%) rename {aimbat => src/aimbat}/lib/station.py (100%) rename {aimbat => src/aimbat}/lib/typing.py (100%) rename {aimbat => src/aimbat}/lib/utils/__init__.py (100%) rename {aimbat => src/aimbat}/lib/utils/checkdata.py (100%) rename {aimbat => src/aimbat}/lib/utils/json.py (100%) rename {aimbat => src/aimbat}/lib/utils/sampledata.py (100%) rename {aimbat => src/aimbat}/logger.py (100%) diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml index e9648543..0517e8ac 100644 --- a/.github/workflows/build.yml +++ b/.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 diff --git a/.github/workflows/run-tests.yml b/.github/workflows/run-tests.yml index 70556112..6f0efd3e 100644 --- a/.github/workflows/run-tests.yml +++ b/.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 diff --git a/Makefile b/Makefile index b8836515..c4925a81 100644 --- a/Makefile +++ b/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 diff --git a/flake.lock b/flake.lock index d89e5822..3ffa88a5 100644 --- a/flake.lock +++ b/flake.lock @@ -42,11 +42,11 @@ "nixpkgs": "nixpkgs" }, "locked": { - "lastModified": 1752054764, - "narHash": "sha256-Ob/HuUhANoDs+nvYqyTKrkcPXf4ZgXoqMTQoCK0RFgQ=", + "lastModified": 1762090880, + "narHash": "sha256-fbRQzIGPkjZa83MowjbD2ALaJf9y6KMDdJBQMKFeY/8=", "owner": "nix-community", "repo": "nixgl", - "rev": "a8e1ce7d49a149ed70df676785b07f63288f53c5", + "rev": "b6105297e6f0cd041670c3e8628394d4ee247ed5", "type": "github" }, "original": { @@ -72,11 +72,11 @@ }, "nixpkgs_2": { "locked": { - "lastModified": 1759036355, - "narHash": "sha256-0m27AKv6ka+q270dw48KflE0LwQYrO7Fm4/2//KCVWg=", + "lastModified": 1771008912, + "narHash": "sha256-gf2AmWVTs8lEq7z/3ZAsgnZDhWIckkb+ZnAo5RzSxJg=", "owner": "nixos", "repo": "nixpkgs", - "rev": "e9f00bd893984bc8ce46c895c3bf7cac95331127", + "rev": "a82ccc39b39b621151d6732718e3e250109076fa", "type": "github" }, "original": { diff --git a/flake.nix b/flake.nix index a3d208c2..ace814e1 100644 --- a/flake.nix +++ b/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 diff --git a/mkdocs.yml b/mkdocs.yml index b0414435..a3e6a96f 100644 --- a/mkdocs.yml +++ b/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 diff --git a/pyproject.toml b/pyproject.toml index f25e94fb..dbdaff93 100644 --- a/pyproject.toml +++ b/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] diff --git a/aimbat/__init__.py b/src/aimbat/__init__.py similarity index 100% rename from aimbat/__init__.py rename to src/aimbat/__init__.py diff --git a/aimbat/app.py b/src/aimbat/app.py similarity index 99% rename from aimbat/app.py rename to src/aimbat/app.py index eb480b83..c0bc6dc2 100644 --- a/aimbat/app.py +++ b/src/aimbat/app.py @@ -22,7 +22,6 @@ from rich.console import Console import sys - try: __version__ = str(metadata.version("aimbat")) except Exception: diff --git a/aimbat/cli/__init__.py b/src/aimbat/cli/__init__.py similarity index 100% rename from aimbat/cli/__init__.py rename to src/aimbat/cli/__init__.py diff --git a/aimbat/cli/common.py b/src/aimbat/cli/common.py similarity index 100% rename from aimbat/cli/common.py rename to src/aimbat/cli/common.py diff --git a/aimbat/cli/data.py b/src/aimbat/cli/data.py similarity index 100% rename from aimbat/cli/data.py rename to src/aimbat/cli/data.py diff --git a/aimbat/cli/event.py b/src/aimbat/cli/event.py similarity index 100% rename from aimbat/cli/event.py rename to src/aimbat/cli/event.py diff --git a/aimbat/cli/iccs.py b/src/aimbat/cli/iccs.py similarity index 84% rename from aimbat/cli/iccs.py rename to src/aimbat/cli/iccs.py index 70e9eba0..019d28fd 100644 --- a/aimbat/cli/iccs.py +++ b/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__": diff --git a/aimbat/cli/project.py b/src/aimbat/cli/project.py similarity index 100% rename from aimbat/cli/project.py rename to src/aimbat/cli/project.py diff --git a/aimbat/cli/seismogram.py b/src/aimbat/cli/seismogram.py similarity index 100% rename from aimbat/cli/seismogram.py rename to src/aimbat/cli/seismogram.py diff --git a/aimbat/cli/snapshot.py b/src/aimbat/cli/snapshot.py similarity index 100% rename from aimbat/cli/snapshot.py rename to src/aimbat/cli/snapshot.py diff --git a/aimbat/cli/station.py b/src/aimbat/cli/station.py similarity index 100% rename from aimbat/cli/station.py rename to src/aimbat/cli/station.py diff --git a/aimbat/cli/utils/__init__.py b/src/aimbat/cli/utils/__init__.py similarity index 98% rename from aimbat/cli/utils/__init__.py rename to src/aimbat/cli/utils/__init__.py index c5cf6a4f..668eb685 100644 --- a/aimbat/cli/utils/__init__.py +++ b/src/aimbat/cli/utils/__init__.py @@ -2,5 +2,4 @@ from .app import app - __all__ = ["app"] diff --git a/aimbat/cli/utils/app.py b/src/aimbat/cli/utils/app.py similarity index 100% rename from aimbat/cli/utils/app.py rename to src/aimbat/cli/utils/app.py diff --git a/aimbat/cli/utils/sampledata.py b/src/aimbat/cli/utils/sampledata.py similarity index 100% rename from aimbat/cli/utils/sampledata.py rename to src/aimbat/cli/utils/sampledata.py diff --git a/aimbat/config.py b/src/aimbat/config.py similarity index 91% rename from aimbat/config.py rename to src/aimbat/config.py index a96d9256..52bc89b7 100644 --- a/aimbat/config.py +++ b/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.", diff --git a/aimbat/lib/__init__.py b/src/aimbat/lib/__init__.py similarity index 100% rename from aimbat/lib/__init__.py rename to src/aimbat/lib/__init__.py diff --git a/aimbat/lib/common.py b/src/aimbat/lib/common.py similarity index 100% rename from aimbat/lib/common.py rename to src/aimbat/lib/common.py diff --git a/aimbat/lib/data.py b/src/aimbat/lib/data.py similarity index 100% rename from aimbat/lib/data.py rename to src/aimbat/lib/data.py diff --git a/aimbat/lib/db.py b/src/aimbat/lib/db.py similarity index 99% rename from aimbat/lib/db.py rename to src/aimbat/lib/db.py index c70f1fa9..fd800338 100644 --- a/aimbat/lib/db.py +++ b/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.""" diff --git a/aimbat/lib/event.py b/src/aimbat/lib/event.py similarity index 100% rename from aimbat/lib/event.py rename to src/aimbat/lib/event.py diff --git a/aimbat/lib/iccs.py b/src/aimbat/lib/iccs.py similarity index 77% rename from aimbat/lib/iccs.py rename to src/aimbat/lib/iccs.py index 30894a70..97734a8f 100644 --- a/aimbat/lib/iccs.py +++ b/src/aimbat/lib/iccs.py @@ -33,7 +33,7 @@ def create_iccs_instance(session: Session) -> ICCS: window_pre=active_event.parameters.window_pre, window_post=active_event.parameters.window_post, min_ccnorm=active_event.parameters.min_ccnorm, - plot_padding=settings.window_padding, + context_width=settings.context_width, ) @@ -54,59 +54,59 @@ def run_iccs(session: Session, iccs: ICCS, autoflip: bool, autoselect: bool) -> session.commit() -def plot_stack(iccs: ICCS, padded: bool, all: bool) -> None: +def plot_stack(iccs: ICCS, context: bool, all: bool) -> None: """Plot the ICCS stack. Parameters: iccs: ICCS instance. - padded: Whether to pad the stack. + context: Whether to use seismograms with extra context. all: Whether to plot all seismograms. """ logger.info("Plotting ICCS stack for active event.") - _plot_stack(iccs, padded, all) + _plot_stack(iccs, context, all) -def plot_seismograms(iccs: ICCS, padded: bool, all: bool) -> None: +def plot_seismograms(iccs: ICCS, context: bool, all: bool) -> None: """Plot the ICCS seismograms as an image. Parameters: iccs: ICCS instance. - padded: Whether to pad the seismograms. + context: Whether to use seismograms with extra context. all: Whether to plot all seismograms. """ logger.info("Plotting ICCS seismograms for active event.") - _plot_seismograms(iccs, padded, all) + _plot_seismograms(iccs, context, all) def update_pick( - session: Session, iccs: ICCS, padded: bool, all: bool, use_seismogram_image: bool + session: Session, iccs: ICCS, context: bool, all: bool, use_seismogram_image: bool ) -> None: """Update the pick for the active event. Parameters: iccs: ICCS instance. - padded: Whether to pad the seismograms. + context: Whether to use seismograms with extra context. all: Whether to plot all seismograms. use_seismogram_image: Whether to use the seismogram image to update pick. """ logger.info("Updating pick for active event.") - _update_pick(iccs, padded, all, use_seismogram_image) + _update_pick(iccs, context, all, use_seismogram_image) session.commit() def update_timewindow( - session: Session, iccs: ICCS, padded: bool, all: bool, use_seismogram_image: bool + session: Session, iccs: ICCS, context: bool, all: bool, use_seismogram_image: bool ) -> None: """Update the time window for the active event. Parameters: iccs: ICCS instance. - padded: Whether to pad the seismograms. + context: Whether to use seismograms with extra context. all: Whether to plot all seismograms. use_seismogram_image: Whether to use the seismogram image to update pick. """ @@ -114,7 +114,7 @@ def update_timewindow( logger.info("Updating time window for active event.") logger.debug(f"Current {iccs.window_pre = }, {iccs.window_post = }.") - _update_timewindow(iccs, padded, all, use_seismogram_image) + _update_timewindow(iccs, context, all, use_seismogram_image) logger.debug(f"Updated {iccs.window_pre = }, {iccs.window_post = }.") active_event = event.get_active_event(session) @@ -123,19 +123,19 @@ def update_timewindow( session.commit() -def update_min_ccnorm(session: Session, iccs: ICCS, padded: bool, all: bool) -> None: +def update_min_ccnorm(session: Session, iccs: ICCS, context: bool, all: bool) -> None: """Update the minimum cross correlation coefficient for the active event. Parameters: iccs: ICCS instance. - padded: Whether to pad the seismograms. + context: Whether to use seismograms with extra context. all: Whether to plot all seismograms. """ logger.info("Updating minimum cross correlation coefficient for active event.") logger.debug(f"Current {iccs.min_ccnorm = }.") - _update_min_ccnorm(iccs, padded, all) + _update_min_ccnorm(iccs, context, all) logger.debug(f"Updated {iccs.min_ccnorm = }.") active_event = event.get_active_event(session) diff --git a/aimbat/lib/io/__init__.py b/src/aimbat/lib/io/__init__.py similarity index 100% rename from aimbat/lib/io/__init__.py rename to src/aimbat/lib/io/__init__.py diff --git a/aimbat/lib/io/_io.py b/src/aimbat/lib/io/_io.py similarity index 100% rename from aimbat/lib/io/_io.py rename to src/aimbat/lib/io/_io.py diff --git a/aimbat/lib/io/_sac.py b/src/aimbat/lib/io/_sac.py similarity index 100% rename from aimbat/lib/io/_sac.py rename to src/aimbat/lib/io/_sac.py diff --git a/aimbat/lib/models.py b/src/aimbat/lib/models.py similarity index 100% rename from aimbat/lib/models.py rename to src/aimbat/lib/models.py diff --git a/aimbat/lib/project.py b/src/aimbat/lib/project.py similarity index 97% rename from aimbat/lib/project.py rename to src/aimbat/lib/project.py index 0d62eb1a..345165ee 100644 --- a/aimbat/lib/project.py +++ b/src/aimbat/lib/project.py @@ -62,9 +62,7 @@ def create_project() -> None: # This trigger ensures that only one event can be active at a time with engine.connect() as connection: - connection.execute( - text( - """CREATE TRIGGER single_active_event + connection.execute(text("""CREATE TRIGGER single_active_event BEFORE UPDATE ON aimbatevent FOR EACH ROW WHEN NEW.active = TRUE @@ -72,9 +70,7 @@ def create_project() -> None: UPDATE aimbatevent SET active = NULL WHERE active = TRUE AND id != NEW.id; END; - """ - ) - ) + """)) def delete_project() -> None: diff --git a/aimbat/lib/seismogram.py b/src/aimbat/lib/seismogram.py similarity index 100% rename from aimbat/lib/seismogram.py rename to src/aimbat/lib/seismogram.py diff --git a/aimbat/lib/snapshot.py b/src/aimbat/lib/snapshot.py similarity index 100% rename from aimbat/lib/snapshot.py rename to src/aimbat/lib/snapshot.py diff --git a/aimbat/lib/station.py b/src/aimbat/lib/station.py similarity index 100% rename from aimbat/lib/station.py rename to src/aimbat/lib/station.py diff --git a/aimbat/lib/typing.py b/src/aimbat/lib/typing.py similarity index 100% rename from aimbat/lib/typing.py rename to src/aimbat/lib/typing.py diff --git a/aimbat/lib/utils/__init__.py b/src/aimbat/lib/utils/__init__.py similarity index 100% rename from aimbat/lib/utils/__init__.py rename to src/aimbat/lib/utils/__init__.py diff --git a/aimbat/lib/utils/checkdata.py b/src/aimbat/lib/utils/checkdata.py similarity index 100% rename from aimbat/lib/utils/checkdata.py rename to src/aimbat/lib/utils/checkdata.py diff --git a/aimbat/lib/utils/json.py b/src/aimbat/lib/utils/json.py similarity index 100% rename from aimbat/lib/utils/json.py rename to src/aimbat/lib/utils/json.py diff --git a/aimbat/lib/utils/sampledata.py b/src/aimbat/lib/utils/sampledata.py similarity index 100% rename from aimbat/lib/utils/sampledata.py rename to src/aimbat/lib/utils/sampledata.py diff --git a/aimbat/logger.py b/src/aimbat/logger.py similarity index 100% rename from aimbat/logger.py rename to src/aimbat/logger.py diff --git a/tests/test_app.py b/tests/test_app.py index d011087f..77832dff 100644 --- a/tests/test_app.py +++ b/tests/test_app.py @@ -11,19 +11,35 @@ def mock_raise(*args: list[Any], **kwargs: dict[str, Any]) -> None: raise Exception -def test_cli(capsys: pytest.CaptureFixture, monkeypatch: pytest.MonkeyPatch) -> None: - """Test aimbat cli without any subcommands.""" +def test_cli_usage(capsys: pytest.CaptureFixture) -> None: + """Test aimbat cli help output.""" from aimbat import app - app.app([]) - assert "Usage" in capsys.readouterr().out + with pytest.raises(SystemExit) as excinfo: + app.app(["--help"]) + + assert excinfo.value.code == 0 + + captured = capsys.readouterr() + assert "Usage" in captured.out + + +def test_cli_version( + capsys: pytest.CaptureFixture, monkeypatch: pytest.MonkeyPatch +) -> None: + """Test aimbat cli version flag.""" + from aimbat import app monkeypatch.setattr(metadata, "version", mock_return_str) reload(app) - app.app("--version") + with pytest.raises(SystemExit) as excinfo: + app.app(["--version"]) + assert excinfo.value.code == 0 assert "1.2.3" in capsys.readouterr().out monkeypatch.setattr(metadata, "version", mock_raise) reload(app) - app.app("--version") + with pytest.raises(SystemExit) as excinfo: + app.app(["--version"]) + assert excinfo.value.code == 0 assert "unknown" in capsys.readouterr().out diff --git a/tests/test_data.py b/tests/test_data.py index 5aabd35d..89156b80 100644 --- a/tests/test_data.py +++ b/tests/test_data.py @@ -40,7 +40,10 @@ def test_cli_data_add( ) -> None: sac_file_good_as_string = str(sac_file_good) - app(["data", "add", "--no-progress", sac_file_good_as_string]) + with pytest.raises(SystemExit) as excinfo: + app(["data", "add", "--no-progress", sac_file_good_as_string]) + + assert excinfo.value.code == 0 session = fixture_session_with_project seismogram_filename = session.exec(select(AimbatDataSource.sourcename)).one() @@ -100,7 +103,11 @@ def test_cli_data_list( ) -> None: cmd = ["data", "list"] cmd.extend(cli_args) - app(cmd) + with pytest.raises(SystemExit) as excinfo: + app(cmd) + + assert excinfo.value.code == 0 + captured = capsys.readouterr() assert expected in captured.out @@ -124,7 +131,11 @@ def test_cli_dump_data( fixture_session_with_data: Session, capsys: pytest.CaptureFixture, ) -> None: - app(["data", "dump"]) + with pytest.raises(SystemExit) as excinfo: + app(["data", "dump"]) + + assert excinfo.value.code == 0 + captured = capsys.readouterr() loaded_json = json.loads(captured.out) assert isinstance(loaded_json, list) diff --git a/tests/test_event.py b/tests/test_event.py index 1fc53a7e..6c88939a 100644 --- a/tests/test_event.py +++ b/tests/test_event.py @@ -49,7 +49,11 @@ def test_cli_delete_event_by_id(self, session: Session) -> None: aimbat_event = self.get_random_event(session) id = aimbat_event.id - app(["event", "delete", str(id)]) + with pytest.raises(SystemExit) as excinfo: + app(["event", "delete", str(id)]) + + assert excinfo.value.code == 0 + session.flush() assert ( session.exec(select(AimbatEvent).where(AimbatEvent.id == id)).one_or_none() @@ -60,18 +64,26 @@ def test_cli_delete_event_by_id_with_wrong_id(self, session: Session) -> None: from aimbat.app import app from uuid import uuid4 + settings.debug = False + id = uuid4() - with pytest.raises(NoResultFound): + with pytest.raises(SystemExit) as excinfo: app(["event", "delete", str(id)]) + assert excinfo.value.code == 1 + def test_cli_delete_event_by_string(self, session: Session) -> None: from aimbat.app import app aimbat_event = random.choice(list(session.exec(select(AimbatEvent)))) id = aimbat_event.id - app(["event", "delete", str(id)[:5]]) + with pytest.raises(SystemExit) as excinfo: + app(["event", "delete", str(id)[:5]]) + + assert excinfo.value.code == 0 + session.flush() assert ( session.exec(select(AimbatEvent).where(AimbatEvent.id == id)).one_or_none() @@ -131,7 +143,10 @@ def test_cli_event_activate(self, session: Session) -> None: event = self.get_random_event(session) assert event.active is None - app(["event", "activate", str(event.id)]) + with pytest.raises(SystemExit) as excinfo: + app(["event", "activate", str(event.id)]) + + assert excinfo.value.code == 0 session.refresh(event) assert event.active is True @@ -143,7 +158,10 @@ def test_cli_event_activate_with_str_id(self, session: Session) -> None: assert event.active is None short_uuid = str(event.id)[:6] - app(["event", "activate", short_uuid]) + with pytest.raises(SystemExit) as excinfo: + app(["event", "activate", short_uuid]) + + assert excinfo.value.code == 0 session.refresh(event) assert event.active is True @@ -240,10 +258,17 @@ def test_cli_get_event_parameter( from aimbat.app import app _ = self.activate_random_event(session) - app(["event", "get", "completed"]) + + with pytest.raises(SystemExit) as excinfo: + app(["event", "get", "completed"]) + + assert excinfo.value.code == 0 assert "False" in capsys.readouterr().out - app(["event", "get", "window_post"]) + with pytest.raises(SystemExit) as excinfo: + app(["event", "get", "window_post"]) + + assert excinfo.value.code == 0 assert f"{settings.window_post.total_seconds()}s" in capsys.readouterr().out @@ -251,8 +276,13 @@ class TestCliEvent(TestEventBase): def test_cli_usage(self, capsys: pytest.CaptureFixture) -> None: from aimbat.app import app - app(["event"]) - assert "Usage" in capsys.readouterr().out + with pytest.raises(SystemExit) as excinfo: + app(["event", "--help"]) + + assert excinfo.value.code == 0 + + captured = capsys.readouterr() + assert "Usage" in captured.out def test_cli_set_event_parameter( self, session: Session, capsys: pytest.CaptureFixture @@ -260,10 +290,22 @@ def test_cli_set_event_parameter( from aimbat.app import app _ = self.activate_random_event(session) - app(["event", "get", "completed"]) + + with pytest.raises(SystemExit) as excinfo: + app(["event", "get", "completed"]) + + assert excinfo.value.code == 0 assert "False" in capsys.readouterr().out - app(["event", "set", "completed", "True"]) - app(["event", "get", "completed"]) + + with pytest.raises(SystemExit) as excinfo: + app(["event", "set", "completed", "True"]) + + assert excinfo.value.code == 0 + + with pytest.raises(SystemExit) as excinfo: + app(["event", "get", "completed"]) + + assert excinfo.value.code == 0 assert "True" in capsys.readouterr().out def test_cli_event_list( @@ -273,7 +315,10 @@ def test_cli_event_list( ) -> None: from aimbat.app import app - app(["event", "list"]) + with pytest.raises(SystemExit) as excinfo: + app(["event", "list"]) + + assert excinfo.value.code == 0 assert "AIMBAT Events" in capsys.readouterr().out @@ -294,7 +339,11 @@ def test_cli_dump_data( ) -> None: from aimbat.app import app - app(["event", "dump"]) + with pytest.raises(SystemExit) as excinfo: + app(["event", "dump"]) + + assert excinfo.value.code == 0 + captured = capsys.readouterr() loaded_json = json.loads(captured.out) assert isinstance(loaded_json, list) diff --git a/tests/test_project.py b/tests/test_project.py index 0ca5d832..8724aca9 100644 --- a/tests/test_project.py +++ b/tests/test_project.py @@ -36,7 +36,9 @@ def test_lib_create_project_when_one_exists( def test_cli_create_project(self, fixture_session_empty: Session) -> None: assert project._project_exists() is False - app(["project", "create"]) + with pytest.raises(SystemExit) as excinfo: + app(["project", "create"]) + assert excinfo.value.code == 0 assert project._project_exists() is True @@ -58,7 +60,9 @@ def test_lib_delete_project(self, fixture_session_with_project: Session) -> None def test_cli_delete_project(self, fixture_session_with_project: Session) -> None: assert project._project_exists() is True - app(["project", "delete"]) + with pytest.raises(SystemExit) as excinfo: + app(["project", "delete"]) + assert excinfo.value.code == 0 assert project._project_exists() is False @@ -92,7 +96,10 @@ def test_cli_print_project_info_with_active_event( ) -> None: assert project._project_exists() is True - app(["project", "info"]) + with pytest.raises(SystemExit) as excinfo: + app(["project", "info"]) + assert excinfo.value.code == 0 + captured = capsys.readouterr() assert "Project Info" in captured.out assert "(3/0)" in captured.out diff --git a/tests/test_seismogram.py b/tests/test_seismogram.py index a5078cae..c234a30f 100644 --- a/tests/test_seismogram.py +++ b/tests/test_seismogram.py @@ -2,7 +2,6 @@ from aimbat.lib.typing import SeismogramParameter from aimbat.lib.models import AimbatSeismogram from sqlmodel import Session, select -from sqlalchemy.exc import NoResultFound from importlib import reload from typing import Any from matplotlib.figure import Figure @@ -38,7 +37,11 @@ def test_cli_delete_seismogram_by_id(self, session: Session) -> None: aimbat_seismogram = random.choice(list(session.exec(select(AimbatSeismogram)))) id = aimbat_seismogram.id - app(["seismogram", "delete", str(id)]) + with pytest.raises(SystemExit) as excinfo: + app(["seismogram", "delete", str(id)]) + + assert excinfo.value.code == 0 + session.flush() assert ( session.exec( @@ -50,16 +53,26 @@ def test_cli_delete_seismogram_by_id(self, session: Session) -> None: def test_cli_delete_seismogram_by_id_with_wrong_id(self) -> None: import uuid + from aimbat.config import settings + + settings.debug = False + id = uuid.uuid4() - with pytest.raises(NoResultFound): + with pytest.raises(SystemExit) as excinfo: app(["seismogram", "delete", str(id)]) + assert excinfo.value.code == 1 + def test_cli_delete_seismogram_by_string(self, session: Session) -> None: aimbat_seismogram = random.choice(list(session.exec(select(AimbatSeismogram)))) id = aimbat_seismogram.id - app(["seismogram", "delete", str(id)[:5]]) + with pytest.raises(SystemExit) as excinfo: + app(["seismogram", "delete", str(id)[:5]]) + + assert excinfo.value.code == 0 + session.flush() assert ( session.exec( @@ -118,23 +131,36 @@ def test_lib_get_seismogram_parameter_by_id( def test_cli_get_seismogram_parameter_with_uuid( self, random_seismogram: AimbatSeismogram, capsys: pytest.CaptureFixture ) -> None: - app( - ["seismogram", "get", str(random_seismogram.id), SeismogramParameter.SELECT] - ) + with pytest.raises(SystemExit) as excinfo: + app( + [ + "seismogram", + "get", + str(random_seismogram.id), + SeismogramParameter.SELECT, + ] + ) + + assert excinfo.value.code == 0 + captured = capsys.readouterr() assert "True" in captured.out def test_cli_get_seismogram_parameter_with_string( self, random_seismogram: AimbatSeismogram, capsys: pytest.CaptureFixture ) -> None: - app( - [ - "seismogram", - "get", - str(random_seismogram.id)[:6], - SeismogramParameter.SELECT, - ] - ) + with pytest.raises(SystemExit) as excinfo: + app( + [ + "seismogram", + "get", + str(random_seismogram.id)[:6], + SeismogramParameter.SELECT, + ] + ) + + assert excinfo.value.code == 0 + captured = capsys.readouterr() assert "True" in captured.out @@ -188,15 +214,19 @@ def test_lib_set_seismogram_parameter_by_id( def test_cli_set_seismogram_parameter_with_uuid( self, random_seismogram: AimbatSeismogram, session: Session ) -> None: - app( - [ - "seismogram", - "set", - str(random_seismogram.id), - SeismogramParameter.SELECT, - "False", - ] - ) + with pytest.raises(SystemExit) as excinfo: + app( + [ + "seismogram", + "set", + str(random_seismogram.id), + SeismogramParameter.SELECT, + "False", + ] + ) + + assert excinfo.value.code == 0 + session.refresh(random_seismogram) assert ( seismogram.get_seismogram_parameter( @@ -208,15 +238,19 @@ def test_cli_set_seismogram_parameter_with_uuid( def test_cli_set_seismogram_parameter_with_string( self, random_seismogram: AimbatSeismogram, session: Session ) -> None: - app( - [ - "seismogram", - "set", - str(random_seismogram.id)[:6], - SeismogramParameter.SELECT, - "False", - ] - ) + with pytest.raises(SystemExit) as excinfo: + app( + [ + "seismogram", + "set", + str(random_seismogram.id)[:6], + SeismogramParameter.SELECT, + "False", + ] + ) + + assert excinfo.value.code == 0 + session.refresh(random_seismogram) assert ( seismogram.get_seismogram_parameter( @@ -272,7 +306,10 @@ def test_lib_print_seismogram_table_short_all_events( assert "ID (shortened)" in captured.out def test_cli_print_seismogram_table(self, capsys: pytest.CaptureFixture) -> None: - app(["seismogram", "list"]) + with pytest.raises(SystemExit) as excinfo: + app(["seismogram", "list"]) + + assert excinfo.value.code == 0 captured = capsys.readouterr() assert "AIMBAT seismograms for event" in captured.out @@ -290,7 +327,11 @@ def test_lib_dump_data(self, capsys: pytest.CaptureFixture) -> None: _ = AimbatSeismogram(**i) def test_cli_dump_data(self, capsys: pytest.CaptureFixture) -> None: - app(["seismogram", "dump"]) + with pytest.raises(SystemExit) as excinfo: + app(["seismogram", "dump"]) + + assert excinfo.value.code == 0 + captured = capsys.readouterr() loaded_json = json.loads(captured.out) assert isinstance(loaded_json, list) @@ -311,4 +352,7 @@ def test_lib_plotseis_qt( _ = seismogram.plot_seismograms(use_qt=True) def test_cli_plotseis_mpl(self) -> None: - app(["seismogram", "plot"]) + with pytest.raises(SystemExit) as excinfo: + app(["seismogram", "plot"]) + + assert excinfo.value.code == 0 diff --git a/tests/test_settings.py b/tests/test_settings.py index a6abb30b..b0d6d74c 100644 --- a/tests/test_settings.py +++ b/tests/test_settings.py @@ -27,7 +27,10 @@ def test_cli_print_defaults( ) -> None: from aimbat.app import app - app(["settings", pretty]) + with pytest.raises(SystemExit) as excinfo: + app(["settings", pretty]) + + assert excinfo.value.code == 0 output = capsys.readouterr().out assert expected in output diff --git a/tests/test_snapshot.py b/tests/test_snapshot.py index 1ab8fd3c..a074e1f4 100644 --- a/tests/test_snapshot.py +++ b/tests/test_snapshot.py @@ -6,7 +6,6 @@ import aimbat.lib.snapshot as snapshot import pytest - RANDOM_COMMENT = "Random comment" @@ -140,15 +139,22 @@ def test_snapshot_table_short_all_events( class TestCliSnapshotUsage(TestSnapshotBase): - def test_usage(self, capsys: pytest.CaptureFixture) -> None: - app("snapshot") + def test_cli_usage(self, capsys: pytest.CaptureFixture) -> None: + with pytest.raises(SystemExit) as excinfo: + app(["snapshot", "--help"]) + + assert excinfo.value.code == 0 + captured = capsys.readouterr() assert "Usage" in captured.out class TestCliSnapshotCreate(TestSnapshotBase): def test_create_snapshot(self, session: Session) -> None: - app(["snapshot", "create", RANDOM_COMMENT]) + with pytest.raises(SystemExit) as excinfo: + app(["snapshot", "create", RANDOM_COMMENT]) + + assert excinfo.value.code == 0 all_snapshots = snapshot.get_snapshots(session) assert len(all_snapshots) == 1 @@ -168,7 +174,11 @@ def test_delete_snapshot_with_uuid(self, session: Session) -> None: assert len(all_snapshots) == 1 snapshot_id = all_snapshots[0].id - app(["snapshot", "delete", str(snapshot_id)]) + with pytest.raises(SystemExit) as excinfo: + app(["snapshot", "delete", str(snapshot_id)]) + + assert excinfo.value.code == 0 + session.flush() all_snapshots = snapshot.get_snapshots(session) assert len(all_snapshots) == 0 @@ -178,7 +188,11 @@ def test_delete_snapshot_with_string(self, session: Session) -> None: assert len(all_snapshots) == 1 snapshot_id = str(all_snapshots[0].id)[:8] - app(["snapshot", "delete", str(snapshot_id)]) + with pytest.raises(SystemExit) as excinfo: + app(["snapshot", "delete", str(snapshot_id)]) + + assert excinfo.value.code == 0 + session.flush() all_snapshots = snapshot.get_snapshots(session) assert len(all_snapshots) == 0 @@ -188,7 +202,11 @@ def test_rollback_to_snapshot_with_uuid(self, session: Session) -> None: assert len(all_snapshots) == 1 snapshot_id = all_snapshots[0].id - app(["snapshot", "rollback", str(snapshot_id)]) + with pytest.raises(SystemExit) as excinfo: + app(["snapshot", "rollback", str(snapshot_id)]) + + assert excinfo.value.code == 0 + session.flush() def test_rollback_to_snapshot_with_string(self, session: Session) -> None: @@ -196,7 +214,11 @@ def test_rollback_to_snapshot_with_string(self, session: Session) -> None: assert len(all_snapshots) == 1 snapshot_id = str(all_snapshots[0].id)[:8] - app(["snapshot", "rollback", str(snapshot_id)]) + with pytest.raises(SystemExit) as excinfo: + app(["snapshot", "rollback", str(snapshot_id)]) + + assert excinfo.value.code == 0 + session.flush() @@ -209,7 +231,10 @@ def create_snapshots(self, session: Session) -> Generator[None, Any, Any]: yield def test_snapshot_table_no_format(self, capsys: pytest.CaptureFixture) -> None: - app(["snapshot", "list"]) + with pytest.raises(SystemExit) as excinfo: + app(["snapshot", "list"]) + + assert excinfo.value.code == 0 captured = capsys.readouterr() assert RANDOM_COMMENT in captured.out diff --git a/tests/test_station.py b/tests/test_station.py index f89832c5..26c738c7 100644 --- a/tests/test_station.py +++ b/tests/test_station.py @@ -1,7 +1,6 @@ from aimbat.lib.models import AimbatStation from aimbat.app import app from sqlmodel import Session, select -from sqlalchemy.exc import NoResultFound from importlib import reload from typing import Any from collections.abc import Generator @@ -36,7 +35,11 @@ def test_cli_delete_station_by_id(self, session: Session) -> None: seismogram = random.choice(list(session.exec(select(AimbatStation)))) id = seismogram.id - app(["station", "delete", str(id)]) + with pytest.raises(SystemExit) as excinfo: + app(["station", "delete", str(id)]) + + assert excinfo.value.code == 0 + session.flush() assert ( session.exec( @@ -46,18 +49,28 @@ def test_cli_delete_station_by_id(self, session: Session) -> None: ) def test_cli_delete_station_by_id_with_wrong_id(self) -> None: + from aimbat.config import settings + + settings.debug = False + import uuid id = uuid.uuid4() - with pytest.raises(NoResultFound): + with pytest.raises(SystemExit) as excinfo: app(["station", "delete", str(id)]) + assert excinfo.value.code == 1 + def test_cli_delete_station_by_string(self, session: Session) -> None: station = random.choice(list(session.exec(select(AimbatStation)))) id = station.id - app(["station", "delete", str(id)[:5]]) + with pytest.raises(SystemExit) as excinfo: + app(["station", "delete", str(id)[:5]]) + + assert excinfo.value.code == 0 + session.flush() assert ( session.exec( @@ -83,15 +96,26 @@ def test_sac_data(self, capsys: pytest.CaptureFixture) -> None: class TestCliStation(TestStationBase): - def test_usage(self, capsys: pytest.CaptureFixture) -> None: - app(["station"]) - assert "Usage" in capsys.readouterr().out + def test_cli_usage(self, capsys: pytest.CaptureFixture) -> None: + with pytest.raises(SystemExit) as excinfo: + app(["station", "--help"]) + + assert excinfo.value.code == 0 - def test_station_list( + captured = capsys.readouterr() + assert "Usage" in captured.out + + def test_cli_station_list( self, session: Session, capsys: pytest.CaptureFixture ) -> None: - app(["station", "list", "--all"]) - assert "# Seismograms" in capsys.readouterr().out + with pytest.raises(SystemExit) as excinfo: + app(["station", "list", "--all"]) + + assert excinfo.value.code == 0 + + captured = capsys.readouterr() + + assert "# Seismograms" in captured.out class TestDumpStation(TestStationBase): @@ -105,7 +129,11 @@ def test_lib_dump_data(self, capsys: pytest.CaptureFixture) -> None: _ = AimbatStation(**i) def test_cli_dump_data(self, capsys: pytest.CaptureFixture) -> None: - app(["station", "dump"]) + with pytest.raises(SystemExit) as excinfo: + app(["station", "dump"]) + + assert excinfo.value.code == 0 + captured = capsys.readouterr() loaded_json = json.loads(captured.out) assert isinstance(loaded_json, list) diff --git a/tests/test_utils.py b/tests/test_utils.py index 02758e67..e0b2146c 100644 --- a/tests/test_utils.py +++ b/tests/test_utils.py @@ -1,4 +1,4 @@ -from aimbat.config import Settings +from aimbat.config import Settings, settings from aimbat.app import app from pysmo.classes import SAC from datetime import datetime, timezone @@ -86,8 +86,13 @@ def test_check_seismogram_no_begin_time(self, sac_instance_good: SAC) -> None: assert "No seismogram data" in issues[0] def test_cli_usage(self, capsys: pytest.CaptureFixture) -> None: - app(["utils", "checkdata", "--help"]) - assert "Usage" in capsys.readouterr().out + with pytest.raises(SystemExit) as excinfo: + app(["utils", "checkdata", "--help"]) + + assert excinfo.value.code == 0 + + captured = capsys.readouterr() + assert "Usage" in captured.out def test_cli_checkdata( self, tmp_path_factory: pytest.TempPathFactory, capsys: pytest.CaptureFixture @@ -99,7 +104,9 @@ def test_cli_checkdata( sac = SAC() sac.write(testfile) - app(["utils", "checkdata", testfile]) + with pytest.raises(SystemExit) as excinfo: + app(["utils", "checkdata", testfile]) + assert excinfo.value.code == 0 output = capsys.readouterr().out for item in ["name", "latitude", "longitude"]: assert f"No station {item} found in file" in output @@ -115,7 +122,9 @@ def test_cli_checkdata( sac.event.longitude = 19.1 sac.seismogram.data = np.random.rand(100) sac.write(testfile) - app(["utils", "checkdata", testfile]) + with pytest.raises(SystemExit) as excinfo: + app(["utils", "checkdata", testfile]) + assert excinfo.value.code == 0 output = capsys.readouterr().out for item in ["name", "latitude", "longitude"]: assert f"No station {item} found in file" not in output @@ -142,25 +151,37 @@ def test_lib_delete_sampledata(self, download_dir: Path) -> None: assert download_dir.exists() is False def test_cli_usage(self, capsys: pytest.CaptureFixture) -> None: - app(["utils", "sampledata"]) + with pytest.raises(SystemExit) as excinfo: + app(["utils", "sampledata", "--help"]) + assert excinfo.value.code == 0 assert "Usage" in capsys.readouterr().out def test_cli_download_sampledata(self, download_dir: Path) -> None: assert len(os.listdir((download_dir))) == 0 - app(["utils", "sampledata", "download"]) + with pytest.raises(SystemExit) as excinfo: + app(["utils", "sampledata", "download"]) + assert excinfo.value.code == 0 assert len(os.listdir((download_dir))) > 0 # can't download if it is already there - with pytest.raises(FileExistsError): + settings.debug = False + with pytest.raises(SystemExit) as excinfo: app(["utils", "sampledata", "download"]) + assert excinfo.value.code == 1 # unless we use force - app(["utils", "sampledata", "download", "--force"]) + with pytest.raises(SystemExit) as excinfo: + app(["utils", "sampledata", "download", "--force"]) + assert excinfo.value.code == 0 def test_cli__delete_sampledata(self, download_dir: Path) -> None: assert len(os.listdir((download_dir))) == 0 - app(["utils", "sampledata", "download"]) + with pytest.raises(SystemExit) as excinfo: + app(["utils", "sampledata", "download"]) + assert excinfo.value.code == 0 assert len(os.listdir((download_dir))) > 0 - app(["utils", "sampledata", "delete"]) + with pytest.raises(SystemExit) as excinfo: + app(["utils", "sampledata", "delete"]) + assert excinfo.value.code == 0 assert not download_dir.exists() diff --git a/tox.ini b/tox.ini index 76c3039f..d6a9f68e 100644 --- a/tox.ini +++ b/tox.ini @@ -1,18 +1,19 @@ [tox] -env_list = lint, py{312,313}, report +env_list = lint, py{312,313,314}, report isolated_build = true [gh-actions] python = 3.12: py312 - 3.13: py313, lint + 3.13: py313 + 3.14: py314, lint [testenv] description = run the tests with pytest setenv = - py{312,313}: COVERAGE_FILE = {env:COVERAGE_FILE:.coverage.{envname}} + py{312,313,314}: COVERAGE_FILE = {env:COVERAGE_FILE:.coverage.{envname}} depends = - report: py312, py313 + report: py312, py313, py314 allowlist_externals = uv commands_pre = uv sync --active --no-managed-python 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