From 6ae00e8e3fac5796ca818b3054b1e62de820d84a Mon Sep 17 00:00:00 2001 From: James Kerns Date: Thu, 19 Sep 2024 12:41:11 -0700 Subject: [PATCH 01/16] =?UTF-8?q?move=20to=20uv=20=F0=9F=98=83?= MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit --- bitbucket-pipelines.yml | 74 +++++++++++++++-------------------------- 1 file changed, 26 insertions(+), 48 deletions(-) diff --git a/bitbucket-pipelines.yml b/bitbucket-pipelines.yml index 98e3652e..3ce361c9 100644 --- a/bitbucket-pipelines.yml +++ b/bitbucket-pipelines.yml @@ -1,32 +1,28 @@ -image: python:3.11-slim +image: uv:python3.11-bookworm-slim definitions: caches: testfiles: tests_basic/test_files + precommit: ~/.cache/pre-commit + uv: ~/.cache/uv steps: - step: &pre-commit-checks name: Pre-commit checks - image: python:3.11-slim script: - apt-get update - apt-get -y install git - - pip install pre-commit - pre-commit run --all-files + caches: + - precommit - step: &set-up-env name: Set up Env caches: - - pip + - uv script: - - apt-get update - - python -m venv venv - - source venv/bin/activate - - pip install .[dev] - - pip install .[docs] - - pip uninstall pylinac -y - - pip freeze + - uv sync --frozen artifacts: - - venv/** + - .venv/** - step: &push-to-github name: Push to Github clone: @@ -38,8 +34,7 @@ definitions: - step: &build-docs name: Build Docs script: - - source venv/bin/activate - - nox -s build_docs + - uv run nox -s build_docs condition: changesets: includePaths: @@ -49,8 +44,7 @@ definitions: name: Run CBCT Tests size: 2x script: - - source venv/bin/activate - - pytest tests_basic/test_cbct.py -n 2 --cov=pylinac.cbct --cov-report term --junitxml=./test-reports/pytest_results.xml + - uv run pytest tests_basic/test_cbct.py -n 2 --cov=pylinac.cbct --cov-report term --junitxml=./test-reports/pytest_results.xml caches: - testfiles condition: @@ -62,8 +56,7 @@ definitions: - step: &quart-tests name: Run Quart Tests script: - - source venv/bin/activate - - pytest tests_basic/test_quart.py --cov=pylinac.quart --cov-report term --junitxml=./test-reports/pytest_results.xml + - uv run pytest tests_basic/test_quart.py --cov=pylinac.quart --cov-report term --junitxml=./test-reports/pytest_results.xml caches: - testfiles condition: @@ -76,8 +69,7 @@ definitions: - step: &acr-tests name: Run ACR CT/MRI Tests script: - - source venv/bin/activate - - pytest tests_basic/test_acr.py --cov=pylinac.acr --cov-report term --junitxml=./test-reports/pytest_results.xml + - uv run pytest tests_basic/test_acr.py --cov=pylinac.acr --cov-report term --junitxml=./test-reports/pytest_results.xml caches: - testfiles condition: @@ -90,8 +82,7 @@ definitions: - step: &cheese-tests name: Run Cheese Phantom Tests script: - - source venv/bin/activate - - pytest tests_basic/test_cheese.py --cov=pylinac.cheese --cov-report term --junitxml=./test-reports/pytest_results.xml + - uv run pytest tests_basic/test_cheese.py --cov=pylinac.cheese --cov-report term --junitxml=./test-reports/pytest_results.xml caches: - testfiles condition: @@ -104,8 +95,7 @@ definitions: - step: &planar-tests name: Run Planar Imaging Tests script: - - source venv/bin/activate - - pytest tests_basic/test_planar_imaging.py --cov-report term --junitxml=./test-reports/pytest_results.xml + - uv run pytest tests_basic/test_planar_imaging.py --cov-report term --junitxml=./test-reports/pytest_results.xml caches: - testfiles condition: @@ -117,8 +107,7 @@ definitions: - step: &dlg-tests name: Run DLG Tests script: - - source venv/bin/activate - - pytest tests_basic/test_dlg.py --cov-report term --junitxml=./test-reports/pytest_results.xml + - uv run pytest tests_basic/test_dlg.py --cov-report term --junitxml=./test-reports/pytest_results.xml caches: - testfiles condition: @@ -130,8 +119,7 @@ definitions: - step: &field-analysis-tests name: Run Field Analysis Tests script: - - source venv/bin/activate - - pytest tests_basic/test_field_analysis.py --cov-report term --junitxml=./test-reports/pytest_results.xml + - uv run pytest tests_basic/test_field_analysis.py --cov-report term --junitxml=./test-reports/pytest_results.xml caches: - testfiles condition: @@ -143,8 +131,7 @@ definitions: - step: &machine-log-tests name: Run Machine Logs Tests script: - - source venv/bin/activate - - pytest tests_basic/test_logs.py --cov-report term --junitxml=./test-reports/pytest_results.xml + - uv run pytest tests_basic/test_logs.py --cov-report term --junitxml=./test-reports/pytest_results.xml caches: - testfiles condition: @@ -156,8 +143,7 @@ definitions: - step: &picket-fence-tests name: Run Picket Fence Tests script: - - source venv/bin/activate - - pytest tests_basic/test_picketfence.py --cov-report term --junitxml=./test-reports/pytest_results.xml + - uv run pytest tests_basic/test_picketfence.py --cov-report term --junitxml=./test-reports/pytest_results.xml caches: - testfiles condition: @@ -169,8 +155,7 @@ definitions: - step: &starshot-tests name: Run Starshot Tests script: - - source venv/bin/activate - - pytest tests_basic/test_starshot.py --cov-report term --junitxml=./test-reports/pytest_results.xml + - uv run pytest tests_basic/test_starshot.py --cov-report term --junitxml=./test-reports/pytest_results.xml caches: - testfiles condition: @@ -182,8 +167,7 @@ definitions: - step: &calibration-tests name: Run TG-51/TRS-398 Tests script: - - source venv/bin/activate - - pytest tests_basic/test_tg51.py tests_basic/test_trs398.py --cov-report term --junitxml=./test-reports/pytest_results.xml + - uv run pytest tests_basic/test_tg51.py tests_basic/test_trs398.py --cov-report term --junitxml=./test-reports/pytest_results.xml caches: - testfiles condition: @@ -196,8 +180,7 @@ definitions: - step: &vmat-tests name: Run VMAT Tests script: - - source venv/bin/activate - - pytest tests_basic/test_vmat.py --cov-report term --junitxml=./test-reports/pytest_results.xml + - uv run pytest tests_basic/test_vmat.py --cov-report term --junitxml=./test-reports/pytest_results.xml caches: - testfiles condition: @@ -210,8 +193,7 @@ definitions: name: Run Winston-Lutz Tests size: 2x script: - - source venv/bin/activate - - pytest tests_basic/test_winstonlutz.py --cov-report term --junitxml=./test-reports/pytest_results.xml + - uv run pytest tests_basic/test_winstonlutz.py --cov-report term --junitxml=./test-reports/pytest_results.xml condition: changesets: includePaths: @@ -222,8 +204,7 @@ definitions: name: Run Winston-Lutz Multi-Target Multi-Field Tests size: 2x script: - - source venv/bin/activate - - pytest tests_basic/test_winstonlutz_mtmf.py --cov-report term --junitxml=./test-reports/pytest_results.xml + - uv run pytest tests_basic/test_winstonlutz_mtmf.py --cov-report term --junitxml=./test-reports/pytest_results.xml condition: changesets: includePaths: @@ -233,8 +214,7 @@ definitions: - step: &plan-generator-tests name: Plan generator tests script: - - source venv/bin/activate - - pytest tests_basic/test_plan_generator.py tests_basic/test_generated_plans.py --cov-report term --junitxml=./test-reports/pytest_results.xml + - uv run pytest tests_basic/test_plan_generator.py tests_basic/test_generated_plans.py --cov-report term --junitxml=./test-reports/pytest_results.xml condition: changesets: includePaths: @@ -245,8 +225,7 @@ definitions: - step: &core-module-tests name: Run core module tests script: - - source venv/bin/activate - - pytest tests_basic/core --cov-report term --junitxml=./test-reports/pytest_results.xml + - uv run pytest tests_basic/core --cov-report term --junitxml=./test-reports/pytest_results.xml caches: - testfiles condition: @@ -259,13 +238,12 @@ definitions: script: - apt-get update - apt-get install wget -y - - pip install nox # Get gcloud CLI - wget https://dl.google.com/dl/cloudsdk/channels/rapid/downloads/google-cloud-cli-416.0.0-linux-x86_64.tar.gz -O gcloud_cli.tar.gz - tar -xf gcloud_cli.tar.gz - ./google-cloud-sdk/install.sh --quiet - export PATH="./google-cloud-sdk/bin:$PATH" - - nox -s update_dev_kraken + - uv run nox -s update_dev_kraken pipelines: From d089d63c4ca8169c9623ba114be368f9005a108c Mon Sep 17 00:00:00 2001 From: James Kerns Date: Thu, 19 Sep 2024 12:49:21 -0700 Subject: [PATCH 02/16] more uv --- bitbucket-pipelines.yml | 4 ++-- pyproject.toml | 42 ++++++++++++++++++----------------------- 2 files changed, 20 insertions(+), 26 deletions(-) diff --git a/bitbucket-pipelines.yml b/bitbucket-pipelines.yml index 3ce361c9..4e4d6b2c 100644 --- a/bitbucket-pipelines.yml +++ b/bitbucket-pipelines.yml @@ -1,4 +1,4 @@ -image: uv:python3.11-bookworm-slim +image: ghcr.io/astral-sh/uv:python3.11-bookworm-slim definitions: @@ -277,7 +277,7 @@ pipelines: '**': - parallel: - step: *set-up-env - - step: *pre-commit-checks + - step: *pre-commit-checks - parallel: - step: *build-docs - step: *cbct-tests diff --git a/pyproject.toml b/pyproject.toml index 0aa06b8f..63cdf6a2 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -45,30 +45,6 @@ dependencies = [ "plotly>=5.0", ] -[project.optional-dependencies] -dev = [ - "pytest", - "pytest-xdist", - "pytest-cov", - "nox", - "furo", - "google-cloud-storage", - "sphinx", - "sphinx-design", - "sphinx-autobuild", - "sphinx-copybutton", - "pre-commit", - "hatch", - "parameterized", -] -docs = [ - "sphinx", - "sphinx-design", - "sphinx-copybutton", - "furo", - "autodoc_pydantic" -] - [build-system] requires = ["hatchling"] build-backend = "hatchling.build" @@ -121,3 +97,21 @@ ignore = ['E501'] "*/__init__.py" = ["F401"] "pylinac/calibration/trs398.py" = ["F401", "I001"] "pylinac/core/profile.py" = ['F821'] + +[tool.uv] +dev-dependencies = [ + "autodoc-pydantic>=2.1.0", + "furo>=2024.8.6", + "google-cloud-storage>=2.18.2", + "hatch>=1.12.0", + "nox>=2024.4.15", + "parameterized>=0.9.0", + "pre-commit>=3.5.0", + "pytest-cov>=5.0.0", + "pytest-xdist>=3.6.1", + "pytest>=8.3.2", + "sphinx-autobuild>=2021.3.14", + "sphinx-copybutton>=0.5.2", + "sphinx-design>=0.5.0", + 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12:56:49 -0700 Subject: [PATCH 04/16] uv run --- bitbucket-pipelines.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/bitbucket-pipelines.yml b/bitbucket-pipelines.yml index 4e4d6b2c..54549388 100644 --- a/bitbucket-pipelines.yml +++ b/bitbucket-pipelines.yml @@ -12,7 +12,7 @@ definitions: script: - apt-get update - apt-get -y install git - - pre-commit run --all-files + - uv run pre-commit run --all-files caches: - precommit - step: &set-up-env From a799b01dc1066ec064d3c2e1c9a819c75d6cb0a4 Mon Sep 17 00:00:00 2001 From: James Kerns Date: Thu, 19 Sep 2024 13:47:42 -0700 Subject: [PATCH 05/16] trigger tests --- pylinac/core/array_utils.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pylinac/core/array_utils.py b/pylinac/core/array_utils.py index 62b36353..c3d85c73 100644 --- a/pylinac/core/array_utils.py +++ b/pylinac/core/array_utils.py @@ -14,7 +14,7 @@ def array_not_empty(array: np.ndarray) -> None: - """Check an array isn't empty""" + """Check an array isn't empty.""" if not array.size: raise ValueError("Array must not be empty") From c1d447a2707d589015f83b9077d0ebb3c9b2e944 Mon Sep 17 00:00:00 2001 From: James Kerns Date: Thu, 19 Sep 2024 14:16:42 -0700 Subject: [PATCH 06/16] tweak contrib doc --- bitbucket-pipelines.yml | 16 +++++----------- docs/source/contributing.rst | 9 +++++---- 2 files changed, 10 insertions(+), 15 deletions(-) diff --git a/bitbucket-pipelines.yml b/bitbucket-pipelines.yml index 54549388..b42b46a1 100644 --- a/bitbucket-pipelines.yml +++ b/bitbucket-pipelines.yml @@ -7,20 +7,16 @@ definitions: precommit: ~/.cache/pre-commit uv: ~/.cache/uv steps: - - step: &pre-commit-checks - name: Pre-commit checks + - step: &pre-commit-checks-and-setup + name: Pre-commit checks & env setup script: - apt-get update - apt-get -y install git + - uv sync --frozen - uv run pre-commit run --all-files caches: - precommit - - step: &set-up-env - name: Set up Env - caches: - uv - script: - - uv sync --frozen artifacts: - .venv/** - step: &push-to-github @@ -249,7 +245,7 @@ pipelines: custom: update-kraken: - - step: *set-up-env + - step: *pre-commit-checks-and-setup - step: *update-dev-kraken pypi: - step: @@ -275,9 +271,7 @@ pipelines: pull-requests: '**': - - parallel: - - step: *set-up-env - - step: *pre-commit-checks + - step: *pre-commit-checks-and-setup - parallel: - step: *build-docs - step: *cbct-tests diff --git a/docs/source/contributing.rst b/docs/source/contributing.rst index 8a529b37..07b6fdc4 100644 --- a/docs/source/contributing.rst +++ b/docs/source/contributing.rst @@ -53,13 +53,14 @@ Be sure to ask for help if you need it! * `Fork `__ the pylinac repository. * Clone your `forked repository to your local machine `__: ``git clone`` followed by the URL of your forked repository. Some IDEs also have a GUI for this. See also :ref:`distro_stack`. -* Create a virtual environment. This is optional but highly recommended. See the `Python guide `__ to set up a new venv. -* Install the requirements and developer requirements: ``pip install .[dev]`` +* Install the Python tool `uv `__. +* Install Python if necessary: ``uv python install``. +* Install the requirements: ``uv sync --frozen``. This will create a new virtual environment at ``.venv`` and install all required dependencies. * Create a new branch for your work: ``git checkout -b my_new_branch`` -* Make your changes +* Make your changes. * Write tests for your changes. Most test modules in pylinac have a 1:1 correlation with the library modules and thus the expected location should be straightforward. -* Run the tests locally: ``pytest`` +* Run the tests locally: ``uv run pytest`` * If the tests pass, commit your changes: ``git commit -m "my new feature!"`` * Push your changes to your forked repository: ``git push origin my_new_branch`` * Make a new pull request to the main pylinac repository. From 1ccb5a2a70aa65884250a6c635c5ac9088673e73 Mon Sep 17 00:00:00 2001 From: James Kerns Date: Thu, 19 Sep 2024 14:50:43 -0700 Subject: [PATCH 07/16] use uv tool where appropriate --- bitbucket-pipelines.yml | 2 +- docs/source/contributing.rst | 15 + pyproject.toml | 2 - uv.lock | 640 +---------------------------------- 4 files changed, 17 insertions(+), 642 deletions(-) diff --git a/bitbucket-pipelines.yml b/bitbucket-pipelines.yml index b42b46a1..5d259304 100644 --- a/bitbucket-pipelines.yml +++ b/bitbucket-pipelines.yml @@ -13,7 +13,7 @@ definitions: - apt-get update - apt-get -y install git - uv sync --frozen - - uv run pre-commit run --all-files + - uvx pre-commit run --all-files caches: - precommit - uv diff --git a/docs/source/contributing.rst b/docs/source/contributing.rst index 07b6fdc4..5a43db49 100644 --- a/docs/source/contributing.rst +++ b/docs/source/contributing.rst @@ -64,3 +64,18 @@ Be sure to ask for help if you need it! * If the tests pass, commit your changes: ``git 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b/docs/source/contributing.rst @@ -78,4 +78,4 @@ To build a distributable package of pylinac: uvx hatch version uv build - twine upload dist/pylinac-v* + uvx twine upload dist/pylinac-v* diff --git a/pyproject.toml b/pyproject.toml index d61d75d7..21dd66a0 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -43,7 +43,6 @@ dependencies = [ "eval-type-backport; python_version<='3.8'", "quaac", "plotly>=5.0", - "nox>=2024.4.15", ] [build-system] @@ -104,6 +103,7 @@ dev-dependencies = [ "autodoc-pydantic>=2.1.0", "furo>=2024.8.6", "google-cloud-storage>=2.18.2", + "nox>=2024.4.15", "parameterized>=0.9.0", "pytest-cov>=5.0.0", "pytest-xdist>=3.6.1", diff --git a/uv.lock b/uv.lock index 432f5687..7a12da24 100644 --- a/uv.lock +++ b/uv.lock @@ -1478,7 +1478,6 @@ dependencies = [ { name = "argue" }, { name = "eval-type-backport", marker = "python_full_version < '3.9'" }, { name = "matplotlib" }, - { name = "nox" }, { name = "numpy" }, { name = "pillow" }, { name = "plotly" }, @@ -1498,6 +1497,7 @@ dev = [ { name = "autodoc-pydantic" }, { name = "furo" }, { name = "google-cloud-storage" }, + { name = "nox" }, { name = "parameterized" }, { name = "pytest" }, { name = "pytest-cov" }, @@ -1513,7 +1513,6 @@ requires-dist = [ { name = "argue", specifier = "~=0.3.1" }, { name = "eval-type-backport", marker = "python_full_version < '3.9'" }, { name = "matplotlib", specifier = ">=2.0" }, - { name = "nox", specifier = ">=2024.4.15" }, { name = "numpy", specifier = ">=0.16,<2" }, { name = "pillow", specifier = ">=4.0" }, { name = "plotly", specifier = ">=5.0" }, @@ -1533,6 +1532,7 @@ dev = [ { name = "autodoc-pydantic", specifier = ">=2.1.0" }, { name = "furo", specifier = ">=2024.8.6" }, { name = "google-cloud-storage", specifier = ">=2.18.2" }, + { name = "nox", specifier = ">=2024.4.15" }, { name = "parameterized", specifier = ">=0.9.0" }, { name = "pytest", specifier = ">=8.3.2" }, { name = "pytest-cov", specifier = ">=5.0.0" }, From 73594f751959d6008337cfbb29d1e0d287341113 Mon Sep 17 00:00:00 2001 From: James Kerns Date: Thu, 19 Sep 2024 16:39:26 -0700 Subject: [PATCH 11/16] restore rtd behavior --- pyproject.toml | 12 ++++++++++++ 1 file changed, 12 insertions(+) diff --git a/pyproject.toml b/pyproject.toml index 21dd66a0..d09ebe86 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -45,6 +45,18 @@ dependencies = [ "plotly>=5.0", ] +# unfortunately, RTD doesn't support custom installes like `uv sync`. Only "extra" dependencies are supported. +# this extra dependency entry point shouldn't be used outside of RTD. +# Use `uv sync` for local development. +[project.optional-dependencies] +docs = [ + "sphinx-autobuild>=2021.3.14", + "sphinx-copybutton>=0.5.2", + "sphinx-design>=0.5.0", + "sphinx>=7.1.2", + "furo>=2024.8.6", +] + [build-system] requires = ["hatchling"] build-backend = "hatchling.build" From 794fcef75da7d9edc1bc0e3b46507bc8540414c8 Mon Sep 17 00:00:00 2001 From: James Kerns Date: Thu, 19 Sep 2024 17:04:54 -0700 Subject: [PATCH 12/16] bump min versions --- pyproject.toml | 15 +- uv.lock | 1061 ++++++++++++++++++++++++------------------------ 2 files changed, 534 insertions(+), 542 deletions(-) diff --git a/pyproject.toml b/pyproject.toml index d09ebe86..12759ac8 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -1,6 +1,6 @@ [project] name = "pylinac" -requires-python = ">=3.8" +requires-python = ">=3.9" description = "A toolkit for performing TG-142 QA-related tasks on a linear accelerator" authors = [ {name = "James Kerns", email = "jkerns100@gmail.com"} @@ -28,21 +28,22 @@ classifiers=[ ] dependencies = [ - "scikit-image>=0.17.3", - "numpy>=0.16,<2", - "scipy>=1.1", + "scikit-image>=0.18", + "numpy>=1.20,<2", + "scipy>=1.11", "tqdm>=3.8", "Pillow>=4.0", "argue~=0.3.1", "py-linq~=1.4.0", "reportlab>=3.3", "pydicom>=2.0,<3", - "matplotlib>=2.0", + "matplotlib>=3.0", "tabulate~=0.9.0", "pydantic>=2.0", "eval-type-backport; python_version<='3.8'", "quaac", "plotly>=5.0", + "sphinx-design>=0.6.0", ] # unfortunately, RTD doesn't support custom installes like `uv sync`. Only "extra" dependencies are supported. @@ -52,7 +53,7 @@ dependencies = [ docs = [ "sphinx-autobuild>=2021.3.14", "sphinx-copybutton>=0.5.2", - "sphinx-design>=0.5.0", + "sphinx-design>=0.6.0", "sphinx>=7.1.2", "furo>=2024.8.6", ] @@ -122,6 +123,6 @@ dev-dependencies = [ "pytest>=8.3.2", "sphinx-autobuild>=2021.3.14", "sphinx-copybutton>=0.5.2", - "sphinx-design>=0.5.0", + "sphinx-design>=0.6.0", "sphinx>=7.1.2", ] diff --git a/uv.lock b/uv.lock index 7a12da24..fc08b1e4 100644 --- a/uv.lock +++ b/uv.lock @@ -1,32 +1,43 @@ version = 1 -requires-python = ">=3.8" +requires-python = ">=3.9" resolution-markers = [ - "python_full_version < '3.12'", - "python_full_version == '3.12.*'", + "python_full_version < '3.13'", "python_full_version >= '3.13'", ] [[package]] name = "alabaster" -version = "0.7.13" +version = "0.7.16" source = { registry = "https://pypi.org/simple" } -sdist = { url = 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update - apt-get -y install git - uv sync --frozen - - uvx pre-commit run --all-files + - uv tool run pre-commit run --all-files caches: - precommit - uv From 02103232f5c4ea01da4cf3d01726be1d3e2bb950 Mon Sep 17 00:00:00 2001 From: James Kerns Date: Fri, 20 Sep 2024 10:22:44 -0700 Subject: [PATCH 14/16] add locked and changelog --- bitbucket-pipelines.yml | 34 +++++++++++++++++----------------- docs/source/changelog.rst | 6 ++++++ 2 files changed, 23 insertions(+), 17 deletions(-) diff --git a/bitbucket-pipelines.yml b/bitbucket-pipelines.yml index 0c561234..3b8c63e4 100644 --- a/bitbucket-pipelines.yml +++ b/bitbucket-pipelines.yml @@ -40,7 +40,7 @@ definitions: name: Run CBCT Tests size: 2x script: - - uv run pytest tests_basic/test_cbct.py -n 2 --cov=pylinac.cbct --cov-report term --junitxml=./test-reports/pytest_results.xml + - uv run --locked pytest tests_basic/test_cbct.py -n 2 --cov=pylinac.cbct --cov-report term --junitxml=./test-reports/pytest_results.xml caches: - testfiles condition: @@ -52,7 +52,7 @@ definitions: - step: &quart-tests name: Run Quart Tests script: - - uv run pytest tests_basic/test_quart.py --cov=pylinac.quart --cov-report term --junitxml=./test-reports/pytest_results.xml + - uv run --locked pytest tests_basic/test_quart.py --cov=pylinac.quart --cov-report term --junitxml=./test-reports/pytest_results.xml caches: - testfiles condition: @@ -65,7 +65,7 @@ definitions: - step: &acr-tests name: Run ACR CT/MRI Tests script: - - uv run pytest tests_basic/test_acr.py --cov=pylinac.acr --cov-report term --junitxml=./test-reports/pytest_results.xml + - uv run --locked pytest tests_basic/test_acr.py --cov=pylinac.acr --cov-report term --junitxml=./test-reports/pytest_results.xml caches: - testfiles condition: @@ -78,7 +78,7 @@ definitions: - step: &cheese-tests name: Run Cheese Phantom Tests script: - - uv run pytest tests_basic/test_cheese.py --cov=pylinac.cheese --cov-report term --junitxml=./test-reports/pytest_results.xml + - uv run --locked pytest tests_basic/test_cheese.py --cov=pylinac.cheese --cov-report term --junitxml=./test-reports/pytest_results.xml caches: - testfiles condition: @@ -91,7 +91,7 @@ definitions: - step: &planar-tests name: Run Planar Imaging Tests script: - - uv run pytest tests_basic/test_planar_imaging.py --cov-report term --junitxml=./test-reports/pytest_results.xml + - uv run --locked pytest tests_basic/test_planar_imaging.py --cov-report term --junitxml=./test-reports/pytest_results.xml caches: - testfiles condition: @@ -103,7 +103,7 @@ definitions: - step: &dlg-tests name: Run DLG Tests script: - - uv run pytest tests_basic/test_dlg.py --cov-report term --junitxml=./test-reports/pytest_results.xml + - uv run --locked pytest tests_basic/test_dlg.py --cov-report term --junitxml=./test-reports/pytest_results.xml caches: - testfiles condition: @@ -115,7 +115,7 @@ definitions: - step: &field-analysis-tests name: Run Field Analysis Tests script: - - uv run pytest tests_basic/test_field_analysis.py --cov-report term --junitxml=./test-reports/pytest_results.xml + - uv run --locked pytest tests_basic/test_field_analysis.py --cov-report term --junitxml=./test-reports/pytest_results.xml caches: - testfiles condition: @@ -127,7 +127,7 @@ definitions: - step: &machine-log-tests name: Run Machine Logs Tests script: - - uv run pytest tests_basic/test_logs.py --cov-report term --junitxml=./test-reports/pytest_results.xml + - uv run --locked pytest tests_basic/test_logs.py --cov-report term --junitxml=./test-reports/pytest_results.xml caches: - testfiles condition: @@ -139,7 +139,7 @@ definitions: - step: &picket-fence-tests name: Run Picket Fence Tests script: - - uv run pytest tests_basic/test_picketfence.py --cov-report term --junitxml=./test-reports/pytest_results.xml + - uv run --locked pytest tests_basic/test_picketfence.py --cov-report term --junitxml=./test-reports/pytest_results.xml caches: - testfiles condition: @@ -151,7 +151,7 @@ definitions: - step: &starshot-tests name: Run Starshot Tests script: - - uv run pytest tests_basic/test_starshot.py --cov-report term --junitxml=./test-reports/pytest_results.xml + - uv run --locked pytest tests_basic/test_starshot.py --cov-report term --junitxml=./test-reports/pytest_results.xml caches: - testfiles condition: @@ -163,7 +163,7 @@ definitions: - step: &calibration-tests name: Run TG-51/TRS-398 Tests script: - - uv run pytest tests_basic/test_tg51.py tests_basic/test_trs398.py --cov-report term --junitxml=./test-reports/pytest_results.xml + - uv run --locked pytest tests_basic/test_tg51.py tests_basic/test_trs398.py --cov-report term --junitxml=./test-reports/pytest_results.xml caches: - testfiles condition: @@ -176,7 +176,7 @@ definitions: - step: &vmat-tests name: Run VMAT Tests script: - - uv run pytest tests_basic/test_vmat.py --cov-report term --junitxml=./test-reports/pytest_results.xml + - uv run --locked pytest tests_basic/test_vmat.py --cov-report term --junitxml=./test-reports/pytest_results.xml caches: - testfiles condition: @@ -189,7 +189,7 @@ definitions: name: Run Winston-Lutz Tests size: 2x script: - - uv run pytest tests_basic/test_winstonlutz.py --cov-report term --junitxml=./test-reports/pytest_results.xml + - uv run --locked pytest tests_basic/test_winstonlutz.py --cov-report term --junitxml=./test-reports/pytest_results.xml condition: changesets: includePaths: @@ -200,7 +200,7 @@ definitions: name: Run Winston-Lutz Multi-Target Multi-Field Tests size: 2x script: - - uv run pytest tests_basic/test_winstonlutz_mtmf.py --cov-report term --junitxml=./test-reports/pytest_results.xml + - uv run --locked pytest tests_basic/test_winstonlutz_mtmf.py --cov-report term --junitxml=./test-reports/pytest_results.xml condition: changesets: includePaths: @@ -210,7 +210,7 @@ definitions: - step: &plan-generator-tests name: Plan generator tests script: - - uv run pytest tests_basic/test_plan_generator.py tests_basic/test_generated_plans.py --cov-report term --junitxml=./test-reports/pytest_results.xml + - uv run --locked pytest tests_basic/test_plan_generator.py tests_basic/test_generated_plans.py --cov-report term --junitxml=./test-reports/pytest_results.xml condition: changesets: includePaths: @@ -221,7 +221,7 @@ definitions: - step: &core-module-tests name: Run core module tests script: - - uv run pytest tests_basic/core --cov-report term --junitxml=./test-reports/pytest_results.xml + - uv run --locked pytest tests_basic/core --cov-report term --junitxml=./test-reports/pytest_results.xml caches: - testfiles condition: @@ -239,7 +239,7 @@ definitions: - tar -xf gcloud_cli.tar.gz - ./google-cloud-sdk/install.sh --quiet - export PATH="./google-cloud-sdk/bin:$PATH" - - uv run nox -s update_dev_kraken + - uv run --locked nox -s update_dev_kraken pipelines: diff --git a/docs/source/changelog.rst b/docs/source/changelog.rst index c73671f0..9bad8e51 100644 --- a/docs/source/changelog.rst +++ b/docs/source/changelog.rst @@ -13,6 +13,12 @@ Legend v 3.28.0 -------- +General +^^^^^^^ + +* The minimum version of Python supported is now 3.9 as the end-of-life of Python 3.8 is October 2024. +* Along with this, minimum versions of numpy, scipy, and matplotlib have been bumped to versions that support Python 3.9. + Core ^^^^ From e1e0c3196342d73fb0722742c4c1afc1bdb6d62c Mon Sep 17 00:00:00 2001 From: James Kerns Date: Fri, 20 Sep 2024 10:50:28 -0700 Subject: [PATCH 15/16] better file existing handling --- tests_basic/utils.py | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/tests_basic/utils.py b/tests_basic/utils.py index 75d03ff7..7ef8ed8a 100644 --- a/tests_basic/utils.py +++ b/tests_basic/utils.py @@ -127,8 +127,7 @@ def get_file_from_cloud_test_repo(path: List[str], force: bool = False) -> str: if len(path) > 1: for idx in range(1, len(path)): local_dir = osp.join(osp.dirname(__file__), LOCAL_TEST_DIR, *path[:idx]) - if not osp.isdir(local_dir): - os.mkdir(local_dir) + os.makedirs(local_dir, exist_ok=True) blob.download_to_filename(local_filename) time.sleep(2) From 320a51a1bfcd1d7c2cc83b33ac42527b06333a1b Mon Sep 17 00:00:00 2001 From: James Kerns Date: Fri, 20 Sep 2024 10:56:32 -0700 Subject: [PATCH 16/16] changelog --- docs/source/changelog.rst | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/docs/source/changelog.rst b/docs/source/changelog.rst index 10426c06..8db3a708 100644 --- a/docs/source/changelog.rst +++ b/docs/source/changelog.rst @@ -13,17 +13,17 @@ Legend v 3.28.0 -------- -Starshot -^^^^^^^^ - -* :bdg-warning:`Fixed` Certain types of starshot sets where the pixel values were extremely low would fail to analyze. - General ^^^^^^^ * The minimum version of Python supported is now 3.9 as the end-of-life of Python 3.8 is October 2024. * Along with this, minimum versions of numpy, scipy, and matplotlib have been bumped to versions that support Python 3.9. +Starshot +^^^^^^^^ + +* :bdg-warning:`Fixed` Certain types of starshot sets where the pixel values were extremely low would fail to analyze. + Core ^^^^