switch to gh-actions

Author: mr-c

.github/workflows/ci-tests.yml

@@ -0,0 +1,111 @@
+name: CI Tests
+
+on:
+  push:
+    branches: [ main ]
+  pull_request:
+    branches: [ main ]
+  workflow_dispatch:
+
+concurrency:
+  group: build-${{ github.event.pull_request.number || github.ref }}
+  cancel-in-progress: true
+
+env:
+  TOX_SKIP_MISSING_INTERPRETERS: False
+  # Rich (pip)
+  FORCE_COLOR: 1
+  # Tox
+  PY_COLORS: 1
+  # Mypy (see https://github.com/python/mypy/issues/7771)
+  TERM: xterm-color
+  MYPY_FORCE_COLOR: 1
+  MYPY_FORCE_TERMINAL_WIDTH: 200
+  # Pytest
+  PYTEST_ADDOPTS: --color=yes
+
+jobs:
+
+  tox:
+    name: Tox
+    runs-on: ubuntu-22.04
+    strategy:
+      matrix:
+        py-ver-major: [3]
+        py-ver-minor: [8, 9, 10, 11, 12]
+        step: [lint, unit, bandit, mypy]
+
+    env:
+      py-semver: ${{ format('{0}.{1}', matrix.py-ver-major, matrix.py-ver-minor) }}
+      TOXENV: ${{ format('py{0}{1}-{2}', matrix.py-ver-major, matrix.py-ver-minor, matrix.step) }}
+
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
+
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: ${{ env.py-semver }}
+          allow-prereleases: true
+          cache: pip
+
+      - name: Upgrade setuptools and install tox
+        run: |
+          pip install -U pip setuptools wheel
+          pip install "tox<4" "tox-gh-actions<3"
+
+      - name: MyPy cache
+        if: ${{ matrix.step == 'mypy' }}
+        uses: actions/cache@v4
+        with:
+          path: .mypy_cache/${{ env.py-semver }}
+          key: mypy-${{ env.py-semver }}
+
+      - name: Test with tox
+        run: tox
+
+      - name: Upload coverage to Codecov
+        if: ${{ matrix.step == 'unit' }}
+        uses: codecov/codecov-action@v4
+        with:
+          fail_ci_if_error: true
+        env:
+          CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
+
+  tox-style:
+    name: CI linters via Tox
+
+    runs-on: ubuntu-22.04
+
+    strategy:
+      matrix:
+        step: [lint-readme, pydocstyle]
+
+    env:
+      py-semver: "3.12"
+      TOXENV: ${{ format('py312-{0}', matrix.step) }}
+
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
+
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: ${{ env.py-semver }}
+          cache: pip
+
+      - name: Upgrade setuptools and install tox
+        run: |
+          pip install -U pip setuptools wheel
+          pip install "tox<4" "tox-gh-actions<3"
+
+      - if: ${{ matrix.step == 'pydocstyle' && github.event_name == 'pull_request'}}
+        name: Create local branch for diff-quality for PRs
+        run: git branch ${{github.base_ref}} origin/${{github.base_ref}}
+
+      - name: Test with tox
+        run: tox

.travis.yml

@@ -23,7 +23,7 @@
 MODULE1=wes_client
 MODULE2=wes_service
 PACKAGE=wes-service
-EXTRAS=
+EXTRAS=[toil,arvados]
 
 # `SHELL=bash` doesn't work for some, so don't use BASH-isms like
 # `[[` conditional expressions.
@@ -147,7 +147,7 @@ diff-cover.html: coverage.xml
 	diff-cover --compare-branch=main $^ --html-report $@
 
 ## test                   : run the wes-service test suite
-test: $(PYSOURCES)
+test: $(PYSOURCES) FORCE
 	python -m pytest -rsx ${PYTEST_EXTRA}
 
 ## testcov                : run the wes-service test suite and collect coverage

Makefile

@@ -0,0 +1,79 @@
+[tox]
+envlist =
+  py3{8,9,10,11,12}-lint,
+  py3{8,9,10,11,12}-unit,
+  py3{8,9,10,11,12}-bandit,
+  py3{8,9,10,11,12}-mypy,
+  py312-lintreadme,
+  py312-pydocstyle
+isolated_build = True
+skip_missing_interpreters = True
+
+[gh-actions]
+python =
+  3.8: py38
+  3.9: py39
+  3.10: py310
+  3.11: py311
+  3.12: py312
+
+[testenv]
+description =
+  py3{8,9,10,11,12}-unit: Run the unit tests
+  py3{8,9,10,11,12}-lint: Lint the Python code
+  py3{8,9,10,11,12}-bandit: Search for common security issues
+  py3{8,9,10,11,12}-mypy: Check for type safety
+  py312-pydocstyle: docstring style checker
+  py312-lintreadme: Lint the README.rst->.md conversion
+
+passenv =
+  CI
+  GITHUB_*
+deps =
+  py3{8,9,10,11,12}-{unit,mypy}: -rrequirements.txt
+  py3{8,9,10,11,12}-{unit,mypy}: -rtest-requirements.txt
+  py3{8,9,10,11,12}-lint: -rlint-requirements.txt
+  py3{8,9,10,11,12}-bandit: bandit
+  py3{8,9,10,11,12}-mypy: -rmypy-requirements.txt
+
+setenv =
+  py3{8,9,10,11,12}-unit: LC_ALL = C.UTF-8
+
+commands =
+  py3{8,9,10,11,12}-unit: python -m pip install -U pip setuptools wheel
+  py3{8,9,10,11,12}-unit: make coverage-report coverage.xml PYTEST_EXTRA={posargs}
+  py3{8,9,10,11,12}-bandit: bandit --recursive wes_client wes_service
+  py3{8,9,10,11,12}-lint: make flake8
+  py3{8,9,10,11,12}-lint: make format-check
+  py3{8,9,10,11,12}-mypy: make mypy mypyc
+
+allowlist_externals =
+  py3{8,9,10,11,12}-lint: flake8
+  py3{8,9,10,11,12}-lint: black
+  py3{8,9,10,11,12}-{mypy,memleak,shellcheck,lint,lintreadme,unit}: make
+
+skip_install =
+  py3{8,9,10,11,12}-lint: true
+  py3{8,9,10,11,12}-bandit: true
+
+extras =
+  py3{8,9,10,11,12}-unit: toil
+
+[testenv:py312-pydocstyle]
+allowlist_externals = make
+commands = make diff_pydocstyle_report
+deps =
+    pydocstyle
+    diff-cover
+skip_install = true
+
+[testenv:py312-lintreadme]
+description = Lint the README.md syntax
+commands =
+  make clean dist
+  twine check dist/schema[-_]salad*
+deps =
+    twine
+    build
+    readme_renderer[me]
+skip_install = true