chore: Switch to tox for testing and CI (#900)

* chore(deps): Update lower bounds so uv lowest-direct passes tests

* chore(tox): Adapt tox from fmriprep, use uv_resolution

* chore(ci): Switch to tox-gh-actions for testing

* Replace test workflow with tox

* chore: Pin pyyaml 5.4

* chore: Update pytest/coverage config

* ci: Add FORCE_COLOR to CI environment

* ci: Skip pre-release tests for 3.9/3.10

.github/workflows/pythonpackage.yml

@@ -1,7 +1,4 @@
-# This workflow will install Python dependencies, run tests and lint with a variety of Python versions
-# For more information see: https://help.github.com/actions/language-and-framework-guides/using-python-with-github-actions
-
-name: Python package
+name: Tox
 
 on:
   push:
@@ -13,42 +10,17 @@ on:
     - cron: '0 0 * * *'
 
 concurrency:
-  group: python-${{ github.ref }}
+  group: ${{ github.workflow }}-${{ github.ref }}
   cancel-in-progress: true
 
-jobs:
-  job_metadata:
-    if: github.repository == 'nipreps/niworkflows'
-    runs-on: ubuntu-latest
-    outputs:
-      commit_message: ${{ steps.get_commit_message.outputs.commit_message }}
-      version: ${{ steps.show_version.outputs.version }}
-    steps:
-      - name: Checkout
-        uses: actions/checkout@v4
-        with:
-          fetch-depth: 0
-      - name: Print head git commit message
-        id: get_commit_message
-        run: |
-          if [[ -z "$COMMIT_MSG" ]]; then
-            COMMIT_MSG=$(git show -s --format=%s $REF)
-          fi
-          echo commit_message=$COMMIT_MSG | tee -a $GITHUB_OUTPUT
-        env:
-          COMMIT_MSG: ${{ github.event.head_commit.message }}
-          REF: ${{ github.event.pull_request.head.sha }}
-      - name: Detect version
-        id: show_version
-        run: |
-          if [[ "$GITHUB_REF" == refs/tags/* ]]; then
-            VERSION=${GITHUB_REF##*/}
-          else
-            pipx run hatch version  # Once to avoid output of initial setup
-            VERSION=$( pipx run hatch version )
-          fi
-          echo version=$VERSION | tee -a $GITHUB_OUTPUT
+permissions:
+  contents: read
+
+env:
+  # Force tox and pytest to use color
+  FORCE_COLOR: true
 
+jobs:
   build:
     if: github.repository == 'nipreps/niworkflows'
     runs-on: ubuntu-latest
@@ -118,140 +90,73 @@ jobs:
         datalad get -J 2 -r ds000003 ds000030/sub-10228/func
 
   test:
-    needs: [build, get_data, job_metadata]
+    needs: [get_data]
     runs-on: ubuntu-latest
     strategy:
       matrix:
         python-version: ["3.9", "3.10", "3.11", "3.12"]
-        install: [repo]
+        dependencies: [latest, pre]
         include:
-          - python-version: "3.12"
-            install: sdist
-          - python-version: "3.12"
-            install: wheel
-          - python-version: "3.12"
-            install: editable
-
-    env:
-      INSTALL_TYPE: ${{ matrix.install }}
-
-    steps:
-    - uses: actions/checkout@v4
-      if: matrix.install == 'repo' || matrix.install == 'editable'
-      with:
-        fetch-depth: 0
-    - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v5
-      with:
-        python-version: ${{ matrix.python-version }}
-    - name: Load test data cache
-      uses: actions/cache@v4
-      id: stanford-crn
-      with:
-        path: ~/.cache/stanford-crn/
-        key: data-v0-${{ github.ref_name }}-${{ github.sha }}
-    - name: Load TemplateFlow cache
-      uses: actions/cache@v4
-      id: templateflow
-      with:
-        path: ~/.cache/templateflow
-        key: templateflow-v0-${{ github.ref_name }}-${{ strategy.job-index }}-${{ github.sha }}
-        restore-keys: |
-          templateflow-v0-${{ github.ref_name }}-
-          templateflow-v0-
-    - name: Fetch packages
-      if: matrix.install == 'sdist' || matrix.install == 'wheel'
-      uses: actions/download-artifact@v3
-      with:
-        name: dist
-        path: dist/
-    - name: Select archive
-      run: |
-        if [ "$INSTALL_TYPE" = "sdist" ]; then
-          ARCHIVE=$( ls dist/*.tar.gz )
-        elif [ "$INSTALL_TYPE" = "wheel" ]; then
-          ARCHIVE=$( ls dist/*.whl )
-        elif [ "$INSTALL_TYPE" = "repo" ]; then
-          ARCHIVE="."
-        elif [ "$INSTALL_TYPE" = "editable" ]; then
-          ARCHIVE="-e ."
-        fi
-        echo "ARCHIVE=$ARCHIVE" | tee -a $GITHUB_ENV
-    - name: Install package
-      run: python -m pip install $ARCHIVE
-    - name: Check version
-      run: |
-        INSTALLED_VERSION=$(python -c 'import niworkflows; print(niworkflows.__version__, end="")')
-        echo "INSTALLED: \"${INSTALLED_VERSION}\""
-        test "${INSTALLED_VERSION}" = "${VERSION}"
-      env:
-        VERSION: ${{ needs.job_metadata.outputs.version }}
-    - name: Install test dependencies
-      run: python -m pip install "niworkflows[tests]"
-    - name: Run tests
-      run: pytest -sv --doctest-modules --cov niworkflows --pyargs niworkflows
-    - uses: codecov/codecov-action@v4
-      name: Submit to CodeCov
-      with:
-        token: ${{ secrets.CODECOV_TOKEN }}
-
-  test-pre:
-    needs: [get_data, job_metadata]
-    if: ${{ !contains(needs.job_metadata.outputs.commit_message, '[skip pre]') }}
-    runs-on: ubuntu-latest
-    strategy:
-      matrix:
-        # Only run --pre tests on Python versions within SPEC0 support
-        python-version: ["3.11", "3.12"]
-        install: [repo]
-        pip-flags: ['--pre']
+          - python-version: "3.9"
+            dependencies: min
+        exclude:
+          # Do not test pre-releases for versions out of SPEC0
+          - python-version: "3.9"
+            dependencies: pre
+          - python-version: "3.10"
+            dependencies: pre
 
     env:
-      INSTALL_TYPE: ${{ matrix.install }}
-      PIP_FLAGS: ${{ matrix.pip-flags }}
+      DEPENDS: ${{ matrix.dependencies }}
 
     steps:
-    - name: Debug commit message
-      run: echo "${{ needs.job_metadata.outputs.commit_message }}"
-    - uses: actions/checkout@v4
-      with:
-        fetch-depth: 0
-    - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v5
-      with:
-        python-version: ${{ matrix.python-version }}
-    - name: Load test data cache
-      uses: actions/cache@v4
-      id: stanford-crn
-      with:
-        path: ~/.cache/stanford-crn/
-        key: data-v0-${{ github.ref_name }}-${{ github.sha }}
-    - name: Load TemplateFlow cache
-      uses: actions/cache@v4
-      id: templateflow
-      with:
-        path: ~/.cache/templateflow
-        key: templateflow-v0-${{ github.ref_name }}-${{ strategy.job-index }}-${{ github.sha }}
-        restore-keys: |
-          templateflow-v0-${{ github.ref_name }}-
-          templateflow-v0-
-    - name: Install package
-      run: python -m pip install $PIP_FLAGS .
-    - name: Check version
-      run: |
-        INSTALLED_VERSION=$(python -c 'import niworkflows; print(niworkflows.__version__, end="")')
-        echo "INSTALLED: \"${INSTALLED_VERSION}\""
-        test "${INSTALLED_VERSION}" = "${VERSION}"
-      env:
-        VERSION: ${{ needs.job_metadata.outputs.version }}
-    - name: Install test dependencies
-      run: python -m pip install $PIP_FLAGS "niworkflows[tests]"
-    - name: Run tests
-      run: pytest -sv --doctest-modules --cov niworkflows --pyargs niworkflows
-    - uses: codecov/codecov-action@v4
-      with:
-        token: ${{ secrets.CODECOV_TOKEN }}
-      name: Submit to CodeCov
+      - uses: actions/checkout@v4
+        with:
+          submodules: recursive
+          fetch-depth: 0
+      - name: Install the latest version of uv
+        uses: astral-sh/setup-uv@v3
+      - name: Load test data cache
+        uses: actions/cache@v4
+        id: stanford-crn
+        with:
+          path: ~/.cache/stanford-crn/
+          key: data-v0-${{ github.ref_name }}-${{ github.sha }}
+      - name: Load TemplateFlow cache
+        uses: actions/cache@v4
+        id: templateflow
+        with:
+          path: ~/.cache/templateflow
+          key: templateflow-v0-${{ github.ref_name }}-${{ strategy.job-index }}-${{ github.sha }}
+          restore-keys: |
+            templateflow-v0-${{ github.ref_name }}-
+            templateflow-v0-
+      - uses: actions/cache@v4
+        with:
+          path: ~/.cache/templateflow
+          key: templateflow-v1
+      - name: Install dependencies
+        run: |
+          sudo apt update
+          sudo apt install -y --no-install-recommends graphviz
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v5
+        with:
+          python-version: ${{ matrix.python-version }}
+      - name: Display Python version
+        run: python -c "import sys; print(sys.version)"
+      - name: Install tox
+        run: |
+          uv tool install tox --with=tox-uv --with=tox-gh-actions
+      - name: Show tox config
+        run: tox c
+      - name: Run tox
+        run: tox -v --exit-and-dump-after 1200
+      - uses: codecov/codecov-action@v4
+        with:
+          file: coverage.xml
+          token: ${{ secrets.CODECOV_TOKEN }}
+        if: ${{ always() }}
 
   flake8:
     if: github.event_name != 'schedule'

pyproject.toml

@@ -24,26 +24,26 @@ classifiers = [
 ]
 dependencies = [
     "acres",
-    "attrs",
+    "attrs >=20.1",
     "importlib_resources >= 5.7; python_version < '3.11'",
-    "jinja2",
+    "jinja2 >=3",
     "looseversion",
-    "matplotlib >= 3.4.2",
+    "matplotlib >= 3.5",
     "nibabel >= 3.0",
-    "nilearn >= 0.5.2",
+    "nilearn >= 0.8",
     "nipype >= 1.8.5",
-    "nitransforms >= 21.0.0",
-    "numpy",
+    "nitransforms >= 22.0.0",
+    "numpy >= 1.20",
     "packaging",
-    "pandas",
+    "pandas >= 1.2",
     "pybids >= 0.15.1",
-    "PyYAML",
-    "scikit-image",
-    "scipy",
-    "seaborn",
+    "PyYAML >= 5.4",
+    "scikit-image >= 0.18",
+    "scipy >= 1.8",
+    "seaborn >= 0.11",
     "svgutils >= 0.3.4",
-    "templateflow >= 0.7.2",
-    "transforms3d",
+    "templateflow >= 23.1",
+    "transforms3d >= 0.4",
 ]
 
 [project.optional-dependencies]
@@ -62,12 +62,12 @@ style = [
     "flake8 >= 3.7.0",
 ]
 tests = [
-    "coverage >=5.2.1",
-    "pytest >= 4.4",
-    "pytest-cov",
+    "coverage[toml] >=5.2.1",
+    "pytest >= 6",
+    "pytest-cov >= 2.11",
     "pytest-env",
-    "pytest-xdist >= 1.28",
-    "pytest-xvfb",
+    "pytest-xdist >= 2.5",
+    "pytest-xvfb >= 2",
 ]
 # Aliases
 all = ["niworkflows[doc,pointclouds,style,tests]"]
@@ -116,23 +116,31 @@ skip-string-normalization = true
 extend-exclude = '_version.py'
 
 [tool.pytest.ini_options]
-norecursedirs = ".git"
-addopts = "-sv --doctest-modules"
+minversion = "6"
+testpaths = ["niworkflows"]
+log_cli_level = "INFO"
+xfail_strict = true
+norecursedirs = [".git"]
+addopts = [
+  "-svx",
+  "-ra",
+  "--strict-config",
+  "--strict-markers",
+  "--doctest-modules",
+  # Config pytest-cov
+  "--cov=niworkflows",
+  "--cov-report=xml",
+  "--cov-config=pyproject.toml",
+]
 doctest_optionflags = "ALLOW_UNICODE NORMALIZE_WHITESPACE ELLIPSIS"
-env = """
-    PYTHONHASHSEED=0
-"""
-filterwarnings = """
-    ignore::DeprecationWarning
-"""
+env = "PYTHONHASHSEED=0"
+filterwarnings = ["ignore::DeprecationWarning"]
 junit_family = "xunit2"
 
 [tool.coverage.run]
 branch = true
 omit = [
-    "*/tests/*",
-    "niworkflows/_version.py",
-    "niworkflows/conftest.py",
+    "*/_version.py",
 ]
 
 [tool.coverage.report]
@@ -141,3 +149,9 @@ exclude_lines = [
     "raise NotImplementedError",
     "warnings\\.warn",
 ]
+
+[tool.coverage.paths]
+source = [
+  "niworkflows",
+  "**/site-packages/niworkflows"
+]