chore(dev): Move to tox to simplify test/CI setup (#3326)

.github/workflows/stable.yml → .github/workflows/test.yml

@@ -16,6 +16,10 @@ defaults:
   run:
     shell: bash
 
+# Force tox and pytest to use color
+env:
+  FORCE_COLOR: true
+
 concurrency:
   group: ${{ github.workflow }}-${{ github.ref }}
   cancel-in-progress: true
@@ -24,47 +28,49 @@ permissions:
   contents: read
 
 jobs:
-  stable:
+  test:
     # Check each OS, all supported Python, minimum versions and latest releases
     runs-on: ${{ matrix.os }}
     strategy:
       matrix:
         os: ['ubuntu-latest']
         python-version: ['3.10', '3.11', '3.12']
-        install: ['pip']
-        check: ['tests']
-        pip-flags: ['']
+        dependencies: ['latest', 'pre']
+        include:
+          - os: ubuntu-latest
+            python-version: '3.10'
+            dependencies: 'min'
+
     env:
-      INSTALL_TYPE: ${{ matrix.install }}
-      CHECK_TYPE: ${{ matrix.check }}
-      EXTRA_PIP_FLAGS: ${{ matrix.pip-flags }}
-      OS_TYPE: ${{ matrix.os }}
+      DEPENDS: ${{ matrix.dependencies }}
 
     steps:
       - uses: actions/checkout@v4
         with:
           submodules: recursive
           fetch-depth: 0
+      - uses: actions/cache@v4
+        with:
+          path: ~/.cache/templateflow
+          key: templateflow-v1
       - name: Install dependencies
-        run: .maint/ci/install_dependencies.sh
+        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: ${{ matrix.python-version }}
       - name: Display Python version
         run: python -c "import sys; print(sys.version)"
-      - name: Create virtual environment
-        run: .maint/ci/create_venv.sh
-      - name: Build archive
+      - name: Install tox
         run: |
-          source .maint/ci/build_archive.sh
-          echo "ARCHIVE=$ARCHIVE" >> $GITHUB_ENV
-      - name: Install fMRIPrep
-        run: .maint/ci/install.sh
-      - name: Install extras
-        run: .maint/ci/install_extras.sh
-      - name: Run tests
-        run: .maint/ci/check.sh
+          python -m pip install --upgrade pip
+          python -m pip install tox 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

pyproject.toml

@@ -75,10 +75,11 @@ telemetry = [
     "sentry-sdk >= 1.3",
 ]
 test = [
-    "coverage",
+    "coverage[toml]",
     "pytest",
     "pytest-cov",
     "pytest-env",
+    "pytest-xdist",
 ]
 maint = [
     "fuzzywuzzy",
@@ -127,11 +128,21 @@ exclude = ".*"
 
 [tool.pytest.ini_options]
 minversion = "6"
-testpaths = ["fmriprep/tests"]
+testpaths = ["fmriprep"]
 log_cli_level = "INFO"
 xfail_strict = true
 norecursedirs = [".git"]
-addopts = ["-svx", "-ra", "--strict-config", "--strict-markers", "--doctest-modules"]
+addopts = [
+  "-svx",
+  "-ra",
+  "--strict-config",
+  "--strict-markers",
+  "--doctest-modules",
+  # Config pytest-cov
+  "--cov=fmriprep",
+  "--cov-report=xml",
+  "--cov-config=pyproject.toml",
+]
 doctest_optionflags = "ALLOW_UNICODE NORMALIZE_WHITESPACE ELLIPSIS"
 env = "PYTHONHASHSEED=0"
 filterwarnings = ["ignore::DeprecationWarning"]
@@ -181,3 +192,15 @@ inline-quotes = "single"
 
 [tool.ruff.format]
 quote-style = "single"
+
+[tool.coverage.run]
+branch = true
+omit = [
+    "*/_version.py"
+]
+
+[tool.coverage.paths]
+source = [
+  "fmriprep",
+  "**/site-packages/fmriprep"
+]