Merged in refactor/uv (pull request #447)

move to uv 😃 Approved-by: Randy Taylor Approved-by: Hasan Ammar
jrkerns · Sep 20, 2024 · 4706b46 · 4706b46
2 parents b3e9a2b + 320a51a
commit 4706b46
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diff --git a/bitbucket-pipelines.yml b/bitbucket-pipelines.yml
@@ -1,32 +1,24 @@
-image: python:3.11-slim
+image: ghcr.io/astral-sh/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
+    - step: &pre-commit-checks-and-setup
+        name: Pre-commit checks & env setup
         script:
           - apt-get update
           - apt-get -y install git
-          - pip install pre-commit
-          - pre-commit run --all-files
-    - step: &set-up-env
-        name: Set up Env
+          - uv sync --frozen
+          - uv tool run pre-commit run --all-files
         caches:
-          - pip
-        script:
-          - apt-get update
-          - python -m venv venv
-          - source venv/bin/activate
-          - pip install .[dev]
-          - pip install .[docs]
-          - pip uninstall pylinac -y
-          - pip freeze
+          - precommit
+          - uv
         artifacts:
-          - venv/**
+          - .venv/**
     - step: &push-to-github
         name: Push to Github
         clone:
@@ -38,8 +30,7 @@ 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 +40,7 @@ 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 --locked 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 +52,7 @@ 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 --locked pytest tests_basic/test_quart.py --cov=pylinac.quart --cov-report term --junitxml=./test-reports/pytest_results.xml
         caches:
           - testfiles
         condition:
@@ -76,8 +65,7 @@ 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 --locked pytest tests_basic/test_acr.py --cov=pylinac.acr --cov-report term --junitxml=./test-reports/pytest_results.xml
         caches:
           - testfiles
         condition:
@@ -90,8 +78,7 @@ 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 --locked pytest tests_basic/test_cheese.py --cov=pylinac.cheese --cov-report term --junitxml=./test-reports/pytest_results.xml
         caches:
           - testfiles
         condition:
@@ -104,8 +91,7 @@ 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 --locked pytest tests_basic/test_planar_imaging.py --cov-report term --junitxml=./test-reports/pytest_results.xml
         caches:
           - testfiles
         condition:
@@ -117,8 +103,7 @@ 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 --locked pytest tests_basic/test_dlg.py --cov-report term --junitxml=./test-reports/pytest_results.xml
         caches:
           - testfiles
         condition:
@@ -130,8 +115,7 @@ 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 --locked pytest tests_basic/test_field_analysis.py --cov-report term --junitxml=./test-reports/pytest_results.xml
         caches:
           - testfiles
         condition:
@@ -143,8 +127,7 @@ 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 --locked pytest tests_basic/test_logs.py --cov-report term --junitxml=./test-reports/pytest_results.xml
         caches:
           - testfiles
         condition:
@@ -156,8 +139,7 @@ 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 --locked pytest tests_basic/test_picketfence.py --cov-report term --junitxml=./test-reports/pytest_results.xml
         caches:
           - testfiles
         condition:
@@ -169,8 +151,7 @@ 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 --locked pytest tests_basic/test_starshot.py --cov-report term --junitxml=./test-reports/pytest_results.xml
         caches:
           - testfiles
         condition:
@@ -182,8 +163,7 @@ 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 --locked 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 +176,7 @@ 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 --locked pytest tests_basic/test_vmat.py --cov-report term --junitxml=./test-reports/pytest_results.xml
         caches:
           - testfiles
         condition:
@@ -210,8 +189,7 @@ 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 --locked pytest tests_basic/test_winstonlutz.py --cov-report term --junitxml=./test-reports/pytest_results.xml
         condition:
           changesets:
             includePaths:
@@ -222,8 +200,7 @@ 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 --locked pytest tests_basic/test_winstonlutz_mtmf.py --cov-report term --junitxml=./test-reports/pytest_results.xml
         condition:
           changesets:
             includePaths:
@@ -233,8 +210,7 @@ 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 --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:
@@ -245,8 +221,7 @@ 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 --locked pytest tests_basic/core --cov-report term --junitxml=./test-reports/pytest_results.xml
         caches:
           - testfiles
         condition:
@@ -259,19 +234,18 @@ 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 --locked nox -s update_dev_kraken
 
 pipelines:
 
   custom:
     update-kraken:
-      - step: *set-up-env
+      - step: *pre-commit-checks-and-setup
       - step: *update-dev-kraken
     pypi:
       - step:
@@ -297,9 +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/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.
+
 Starshot
 ^^^^^^^^
 

diff --git a/docs/source/contributing.rst b/docs/source/contributing.rst
@@ -53,13 +53,29 @@ Be sure to ask for help if you need it!
 * `Fork <https://github.com/jrkerns/pylinac/fork>`__ the pylinac repository.
 * Clone your `forked repository to your local machine <https://git-scm.com/book/en/v2/Git-Basics-Getting-a-Git-Repository>`__: ``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 <https://packaging.python.org/en/latest/guides/installing-using-pip-and-virtual-environments/>`__ to set up a new venv.
-* Install the requirements and developer requirements: ``pip install .[dev]``
+* Install the Python tool `uv <https://docs.astral.sh/uv/getting-started/installation/>`__.
+* 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.
+
+Building the package
+--------------------
+
+.. note::
+
+    This is for maintainers only.
+
+To build a distributable package of pylinac:
+
+.. code-block:: bash
+
+    uvx hatch version <new version>
+    uv build
+    uvx twine upload dist/pylinac-v<new version>*
diff --git a/pylinac/core/array_utils.py b/pylinac/core/array_utils.py
@@ -21,7 +21,7 @@
 
 
 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")
 

diff --git 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 = "[email protected]"}
@@ -28,45 +28,34 @@ 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.
+# this extra dependency entry point shouldn't be used outside of RTD.
+# Use `uv sync` for local development.
 [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"
+    "sphinx-autobuild>=2021.3.14",
+    "sphinx-copybutton>=0.5.2",
+    "sphinx-design>=0.6.0",
+    "sphinx>=7.1.2",
+    "furo>=2024.8.6",
 ]
 
 [build-system]
@@ -121,3 +110,19 @@ 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",
+    "nox>=2024.4.15",
+    "parameterized>=0.9.0",
+    "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>=0.6.0",
+    "sphinx>=7.1.2",
+]
diff --git 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)