Merge pull request #404 from nipreps/maint/tox

MAINT: Automate testing with tox

.github/workflows/pytest.yml

@@ -2,15 +2,18 @@ name: Pytest
 
 on:
   push:
-    branches: [ '*' ]
-    tags: [ '*' ]
+    branches: ['*']
+    tags: ['*']
   pull_request:
-    branches: [ master, 'maint/*' ]
+    branches: [master, 'maint/*']
 
 defaults:
   run:
     shell: bash
 
+env:
+  FORCE_COLOR: true
+
 concurrency:
   group: ${{ github.workflow }}-${{ github.ref }}
   cancel-in-progress: true
@@ -19,32 +22,50 @@ permissions:
   contents: read
 
 jobs:
-  build:
-    if: "!contains(github.event.head_commit.message, '[skip ci]')"
-    runs-on: ubuntu-latest
+  test:
+    runs-on: ${{ matrix.os }}
     strategy:
       matrix:
-        python-version: ['3.10', '3.11']
+        os: ['ubuntu-latest']
+        python-version: ['3.10', '3.11', '3.12']
+        dependencies: ['latest', 'pre']
+        include:
+        - os: ubuntu-latest
+          python-version: '3.10'
+          dependencies: 'min'
+
+    env:
+      DEPENDS: ${{ matrix.dependencies }}
 
     steps:
-    - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v5
-      with:
-        python-version: ${{ matrix.python-version }}
     - uses: actions/checkout@v4
       with:
+        submodules: recursive
         fetch-depth: 0
-    - name: Install nibabies
+    - uses: actions/cache@v4
+      with:
+        path: ~/.cache/templateflow
+        key: templateflow-v1
+    - name: Install dependencies
       run: |
-        python -m venv /tmp/venv
-        source /tmp/venv/bin/activate
-        python -m pip install -U pip
-        python -m pip install ".[test]"
-    - name: Run Pytest
+        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: |
-        source /tmp/venv/bin/activate
-        pytest -sv --doctest-modules --cov nibabies --cov-report xml nibabies
-    - name: Submit coverage
-      uses: codecov/codecov-action@v3
+        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:
-        files: coverage.xml
+        file: coverage.xml
+        token: ${{ secrets.CODECOV_TOKEN }}
+      if: ${{ always() }}

pyproject.toml

@@ -37,6 +37,7 @@ dependencies = [
     "tedana >= 23.0.2",
     "templateflow >= 24.2.0",
     "toml",
+    "typing_extensions; python_version<'3.11'",
 ]
 dynamic = ["version"]
 
@@ -71,10 +72,11 @@ maint = [
     "python-Levenshtein",
 ]
 test = [
-    "coverage",
+    "coverage[toml]",
     "pytest",
     "pytest-cov",
     "pytest-env",
+    "pytest-xdist",
 ]
 telemetry = ["migas >= 0.4.0"]
 # Aliases
@@ -120,8 +122,22 @@ per-file-ignores = [
 ]
 
 [tool.pytest.ini_options]
+minversion = "6"
+testpaths = ["nibabies"]
+log_cli_level = "INFO"
+xfail_strict = true
 norecursedirs = [".git"]
-addopts = "-svx --doctest-modules"
+addopts = [
+  "-svx",
+  "-ra",
+  "--strict-config",
+  "--strict-markers",
+  "--doctest-modules",
+  # Config pytest-cov
+  "--cov=nibabies",
+  "--cov-report=xml",
+  "--cov-config=pyproject.toml",
+]
 doctest_optionflags = "ALLOW_UNICODE NORMALIZE_WHITESPACE ELLIPSIS"
 env = "PYTHONHASHSEED=0"
 filterwarnings = ["ignore::DeprecationWarning"]
@@ -177,3 +193,15 @@ inline-quotes = "single"
 
 [tool.ruff.format]
 quote-style = "single"
+
+[tool.coverage.run]
+branch = true
+omit = [
+    "*/_version.py"
+]
+
+[tool.coverage.paths]
+source = [
+  "nibabies",
+  "**/site-packages/nibabies"
+]

tox.ini

@@ -0,0 +1,113 @@
+[tox]
+requires =
+  tox>=4
+envlist =
+  py3{10,11,12}-latest
+  py310-min
+  py3{10,11,12}-pre
+skip_missing_interpreters = true
+
+# Configuration that allows us to split tests across GitHub runners effectively
+[gh-actions]
+python =
+  3.10: py310
+  3.11: py311
+  3.12: py312
+
+[gh-actions:env]
+DEPENDS =
+  min: min
+  latest: latest
+  pre: pre
+
+[testenv]
+description = Pytest with coverage
+labels = test
+pip_pre =
+  pre: true
+pass_env =
+  # getpass.getuser() sources for Windows:
+  LOGNAME
+  USER
+  LNAME
+  USERNAME
+  # Pass user color preferences through
+  PY_COLORS
+  FORCE_COLOR
+  NO_COLOR
+  CLICOLOR
+  CLICOLOR_FORCE
+  PYTHON_GIL
+extras = test
+setenv =
+  pre: PIP_EXTRA_INDEX_URL=https://pypi.anaconda.org/scientific-python-nightly-wheels/simple
+deps =
+  min: nibabel == 4.0.1
+  min: nipype == 1.8.5
+  min: nitransforms == 21.0.0
+  min: numpy == 1.22
+  min: psutil == 5.4
+  min: pybids == 0.15.2
+  min: tedana == 23.0.2
+  min: templateflow == 24.1.0
+
+commands_pre =
+  python scripts/fetch_templates.py
+commands =
+  pytest --cov-report term-missing --durations=20 --durations-min=1.0 {posargs:-n auto}
+
+[testenv:style]
+description = Check our style guide
+labels = check
+deps =
+  ruff
+skip_install = true
+commands =
+  ruff check --diff
+  ruff format --diff
+
+[testenv:style-fix]
+description = Auto-apply style guide to the extent possible
+labels = pre-release
+deps =
+  ruff
+skip_install = true
+commands =
+  ruff check --fix
+  ruff format
+  ruff check --select ISC001
+
+[testenv:spellcheck]
+description = Check spelling
+labels = check
+deps =
+  codespell[toml]
+skip_install = true
+commands =
+  codespell . {posargs}
+
+[testenv:build{,-strict}]
+labels =
+  check
+  pre-release
+deps =
+  build
+  twine
+skip_install = true
+set_env =
+  # Ignore specific known warnings:
+  # https://github.com/pypa/pip/issues/11684
+  # https://github.com/pypa/pip/issues/12243
+  strict: PYTHONWARNINGS=error,once:pkg_resources is deprecated as an API.:DeprecationWarning:pip._internal.metadata.importlib._envs,once:Unimplemented abstract methods {'locate_file'}:DeprecationWarning:pip._internal.metadata.importlib._dists
+commands =
+  python -m build
+  python -m twine check dist/*
+
+[testenv:publish]
+depends = build
+labels = release
+deps =
+  twine
+skip_install = true
+commands =
+  python -m twine upload dist/*