Use GitHub Actions for CI (#1560)

NeurodataWithoutBorders · Oct 4, 2022 · 6e1f131 · 6e1f131
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diff --git a/.circleci/config.yml b/.circleci/config.yml
diff --git a/.github/workflows/check_external_links.yml b/.github/workflows/check_external_links.yml
@@ -0,0 +1,34 @@
+name: Check Sphinx external links
+on:
+  pull_request:
+  schedule:
+    - cron: '0 5 * * *'  # once per day at midnight ET
+  workflow_dispatch:
+
+jobs:
+  check-external-links:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Cancel any previous incomplete runs
+        uses: styfle/[email protected]
+        with:
+          all_but_latest: true
+          access_token: ${{ github.token }}
+
+      - uses: actions/checkout@v3
+        with:
+          submodules: 'recursive'
+
+      - name: Set up Python
+        uses: actions/setup-python@v3
+        with:
+          python-version: '3.8'  # allensdk requires 3.8
+
+      - name: Install Sphinx dependencies and package
+        run: |
+          python -m pip install --upgrade pip
+          python -m pip install -r requirements-doc.txt -r requirements.txt
+          python -m pip install .
+
+      - name: Check Sphinx external links
+        run: sphinx-build -b linkcheck ./docs/source ./test_build
diff --git a/.github/workflows/deploy_release.yml b/.github/workflows/deploy_release.yml
@@ -0,0 +1,54 @@
+name: Deploy release
+on:
+  push:
+    tags:  # run only on new tags that follow semver MAJOR.MINOR.PATCH
+      - '[0-9]+.[0-9]+.[0-9]+'
+
+jobs:
+  deploy-release:
+    name: Deploy release from tag
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout repo with submodules
+        uses: actions/checkout@v3
+        with:
+          submodules: 'recursive'
+          fetch-depth: 0  # tags are required for versioneer to determine the version
+
+      - name: Set up Python
+        uses: actions/setup-python@v3
+        with:
+          python-version: '3.10'
+
+      - name: Install build dependencies
+        run: |
+          python -m pip install --upgrade pip
+          python -m pip install tox
+          python -m pip list
+
+      - name: Run tox tests
+        run: |
+          tox -e py310-upgraded
+
+      - name: Build wheel and source distribution
+        run: |
+          tox -e build-py310-upgraded
+          ls -1 dist
+
+      - name: Test installation from a wheel
+        run: |
+          tox -e wheelinstall --recreate --installpkg dist/*-none-any.whl
+
+      - name: Upload wheel and source distributions to PyPI
+        run: |
+          python -m pip install twine
+          ls -1 dist
+          # twine upload --repository testpypi -u ${{ secrets.BOT_PYPI_USER }} -p ${{ secrets.BOT_PYPI_PASSWORD }} --skip-existing dist/*
+          twine upload -u ${{ secrets.BOT_PYPI_USER }} -p ${{ secrets.BOT_PYPI_PASSWORD }} --skip-existing dist/*
+
+      - name: Publish wheel and source distributions as a GitHub release
+        run: |
+          python -m pip install "githubrelease>=1.5.9"
+          githubrelease --github-token ${{ secrets.BOT_GITHUB_TOKEN }} release NeurodataWithoutBorders/pynwb \
+            create ${{ github.ref_name }} --name ${{ github.ref_name }} \
+            --publish dist/*
diff --git a/.github/workflows/run_all_tests.yml b/.github/workflows/run_all_tests.yml
@@ -0,0 +1,274 @@
+name: Run all tests
+on:
+  schedule:
+    - cron: '0 5 * * *'  # once per day at midnight ET
+  push:
+    tags:  # run only on new tags that follow semver
+      - '/^[0-9]+(\.[0-9]+)?(\.[0-9]+)?$/'
+  workflow_dispatch:
+
+jobs:
+  run-all-tests:
+    # the only differences between this job and "run_tests.yml" is the "strategy.matrix.include" and the upload
+    # distributions step.
+    # GitHub Actions does not yet support YAML anchors, easily reusable components, or easy dynamic matrix
+    # configurations based on the github event, so this job is duplicated for the most part
+    name: ${{ matrix.name }}
+    runs-on: ${{ matrix.os }}
+    defaults:
+      run:
+        shell: bash
+    strategy:
+      fail-fast: false
+      matrix:
+        include:
+          - { name: linux-python3.7-minimum      , test-tox-env: py37-minimum    , build-tox-env: build-py37-minimum    , python-ver: "3.7" , os: ubuntu-latest }
+          - { name: linux-python3.7              , test-tox-env: py37            , build-tox-env: build-py37            , python-ver: "3.7" , os: ubuntu-latest }
+          - { name: linux-python3.8              , test-tox-env: py38            , build-tox-env: build-py38            , python-ver: "3.8" , os: ubuntu-latest }
+          - { name: linux-python3.9              , test-tox-env: py39            , build-tox-env: build-py39            , python-ver: "3.9" , os: ubuntu-latest }
+          - { name: linux-python3.10             , test-tox-env: py310           , build-tox-env: build-py310           , python-ver: "3.10", os: ubuntu-latest }
+          - { name: linux-python3.10-optional    , test-tox-env: py310-optional  , build-tox-env: build-py310-optional  , python-ver: "3.10", os: ubuntu-latest }
+          - { name: linux-python3.10-upgraded    , test-tox-env: py310-upgraded  , build-tox-env: build-py310-upgraded  , python-ver: "3.10", os: ubuntu-latest }
+          - { name: linux-python3.10-prerelease  , test-tox-env: py310-prerelease, build-tox-env: build-py310-prerelease, python-ver: "3.10", os: ubuntu-latest }
+          - { name: windows-python3.7-minimum    , test-tox-env: py37-minimum    , build-tox-env: build-py37-minimum    , python-ver: "3.7" , os: windows-latest }
+          - { name: windows-python3.7            , test-tox-env: py37            , build-tox-env: build-py37            , python-ver: "3.7" , os: windows-latest }
+          - { name: windows-python3.8            , test-tox-env: py38            , build-tox-env: build-py38            , python-ver: "3.8" , os: windows-latest }
+          - { name: windows-python3.9            , test-tox-env: py39            , build-tox-env: build-py39            , python-ver: "3.9" , os: windows-latest }
+          - { name: windows-python3.10           , test-tox-env: py310           , build-tox-env: build-py310           , python-ver: "3.10", os: windows-latest }
+          - { name: windows-python3.10-optional  , test-tox-env: py310-optional  , build-tox-env: build-py310-optional  , python-ver: "3.10", os: windows-latest }
+          - { name: windows-python3.10-upgraded  , test-tox-env: py310-upgraded  , build-tox-env: build-py310-upgraded  , python-ver: "3.10", os: windows-latest }
+          - { name: windows-python3.10-prerelease, test-tox-env: py310-prerelease, build-tox-env: build-py310-prerelease, python-ver: "3.10", os: windows-latest }
+          - { name: macos-python3.7-minimum      , test-tox-env: py37-minimum    , build-tox-env: build-py37-minimum    , python-ver: "3.7" , os: macos-latest }
+          - { name: macos-python3.7              , test-tox-env: py37            , build-tox-env: build-py37            , python-ver: "3.7" , os: macos-latest }
+          - { name: macos-python3.8              , test-tox-env: py38            , build-tox-env: build-py38            , python-ver: "3.8" , os: macos-latest }
+          - { name: macos-python3.9              , test-tox-env: py39            , build-tox-env: build-py39            , python-ver: "3.9" , os: macos-latest }
+          - { name: macos-python3.10             , test-tox-env: py310           , build-tox-env: build-py310           , python-ver: "3.10", os: macos-latest }
+          - { name: macos-python3.10-optional    , test-tox-env: py310-optional  , build-tox-env: build-py310-optional  , python-ver: "3.10", os: macos-latest }
+          - { name: macos-python3.10-upgraded    , test-tox-env: py310-upgraded  , build-tox-env: build-py310-upgraded  , python-ver: "3.10", os: macos-latest }
+          - { name: macos-python3.10-prerelease  , test-tox-env: py310-prerelease, build-tox-env: build-py310-prerelease, python-ver: "3.10", os: macos-latest }
+    steps:
+      - uses: actions/checkout@v3
+        with:
+          submodules: 'recursive'
+
+      - name: Set up Python
+        uses: actions/setup-python@v3
+        with:
+          python-version: ${{ matrix.python-ver }}
+
+      - name: Install build dependencies
+        run: |
+          python -m pip install --upgrade pip
+          python -m pip install tox
+          python -m pip list
+
+      - name: Run tox tests
+        run: |
+          tox -e ${{ matrix.test-tox-env }}
+
+      - name: Build wheel and source distribution
+        run: |
+          tox -e ${{ matrix.build-tox-env }}
+          ls -1 dist
+
+      - name: Test installation from a wheel
+        run: |
+          tox -e wheelinstall --recreate --installpkg dist/*-none-any.whl
+
+  run-all-gallery-tests:
+    name: ${{ matrix.name }}
+    runs-on: ${{ matrix.os }}
+    defaults:
+      run:
+        shell: bash
+    strategy:
+      fail-fast: false
+      matrix:
+        include:
+          - { name: linux-gallery-python3.7-minimum      , test-tox-env: gallery-py37-minimum    , python-ver: "3.7" , os: ubuntu-latest }
+          - { name: linux-gallery-python3.8-upgraded     , test-tox-env: gallery-py38-upgraded   , python-ver: "3.8" , os: ubuntu-latest }
+          - { name: linux-gallery-python3.8-prerelease   , test-tox-env: gallery-py38-prerelease , python-ver: "3.8" , os: ubuntu-latest }
+          # allensdk is not compatible with python 3.9+, so run gallery tests only on python <=3.8
+          # - { name: linux-gallery-python3.10-upgraded    , test-tox-env: gallery-py310-upgraded  , python-ver: "3.10", os: ubuntu-latest }
+          # - { name: linux-gallery-python3.10-prerelease  , test-tox-env: gallery-py310-prerelease, python-ver: "3.10", os: ubuntu-latest }
+          - { name: windows-gallery-python3.7-minimum    , test-tox-env: gallery-py37-minimum    , python-ver: "3.7" , os: windows-latest }
+          - { name: windows-gallery-python3.8-upgraded   , test-tox-env: gallery-py38-upgraded   , python-ver: "3.8" , os: windows-latest }
+          - { name: windows-gallery-python3.8-prerelease , test-tox-env: gallery-py38-prerelease , python-ver: "3.8" , os: windows-latest }
+          # - { name: windows-gallery-python3.10-upgraded  , test-tox-env: gallery-py310-upgraded  , python-ver: "3.10", os: windows-latest }
+          # - { name: windows-gallery-python3.10-prerelease, test-tox-env: gallery-py310-prerelease, python-ver: "3.10", os: windows-latest }
+          - { name: macos-gallery-python3.7-minimum      , test-tox-env: gallery-py37-minimum    , python-ver: "3.7" , os: macos-latest }
+          - { name: macos-gallery-python3.8-upgraded     , test-tox-env: gallery-py38-upgraded   , python-ver: "3.8" , os: macos-latest }
+          - { name: macos-gallery-python3.8-prerelease   , test-tox-env: gallery-py38-prerelease , python-ver: "3.8" , os: macos-latest }
+          # - { name: macos-gallery-python3.10-upgraded    , test-tox-env: gallery-py310-upgraded  , python-ver: "3.10", os: macos-latest }
+          # - { name: macos-gallery-python3.10-prerelease  , test-tox-env: gallery-py310-prerelease, python-ver: "3.10", os: macos-latest }
+    steps:
+      - name: Cancel any previous incomplete runs
+        uses: styfle/[email protected]
+        with:
+          access_token: ${{ github.token }}
+
+      - uses: actions/checkout@v3
+        with:
+          submodules: 'recursive'
+
+      - name: Set up Python
+        uses: actions/setup-python@v3
+        with:
+          python-version: ${{ matrix.python-ver }}
+
+      - name: Install build dependencies
+        run: |
+          python -m pip install --upgrade pip
+          python -m pip install tox
+          python -m pip list
+
+      - name: Run tox tests
+        run: |
+          tox -e ${{ matrix.test-tox-env }}
+
+  run-all-tests-on-conda:
+    name: ${{ matrix.name }}
+    runs-on: ubuntu-latest
+    defaults:
+     run:
+       shell: bash -l {0}  # needed for conda environment to work
+    strategy:
+      fail-fast: false
+      matrix:
+        include:
+          - { name: conda-linux-python3.7-minimum    , test-tox-env: py37-minimum    , build-tox-env: build-py37-minimum    , python-ver: "3.7" , os: ubuntu-latest }
+          - { name: conda-linux-python3.7            , test-tox-env: py37            , build-tox-env: build-py37            , python-ver: "3.7" , os: ubuntu-latest }
+          - { name: conda-linux-python3.8            , test-tox-env: py38            , build-tox-env: build-py38            , python-ver: "3.8" , os: ubuntu-latest }
+          - { name: conda-linux-python3.9            , test-tox-env: py39            , build-tox-env: build-py39            , python-ver: "3.9" , os: ubuntu-latest }
+          - { name: conda-linux-python3.10           , test-tox-env: py310           , build-tox-env: build-py310           , python-ver: "3.10", os: ubuntu-latest }
+          - { name: conda-linux-python3.10-optional  , test-tox-env: py310-optional  , build-tox-env: build-py310-optional  , python-ver: "3.10", os: ubuntu-latest }
+          - { name: conda-linux-python3.10-upgraded  , test-tox-env: py310-upgraded  , build-tox-env: build-py310-upgraded  , python-ver: "3.10", os: ubuntu-latest }
+          - { name: conda-linux-python3.10-prerelease, test-tox-env: py310-prerelease, build-tox-env: build-py310-prerelease, python-ver: "3.10", os: ubuntu-latest }
+    steps:
+      - name: Cancel any previous incomplete runs
+        uses: styfle/[email protected]
+        with:
+          access_token: ${{ github.token }}
+
+      - uses: actions/checkout@v3
+        with:
+          submodules: 'recursive'
+
+      - name: Set up Conda
+        uses: conda-incubator/setup-miniconda@v2
+        with:
+          auto-update-conda: true
+          auto-activate-base: true
+          activate-environment: true
+          python-version: ${{ matrix.python-ver }}
+
+      - name: Install build dependencies
+        run: |
+          conda config --set always_yes yes --set changeps1 no
+          conda info
+          conda install -c conda-forge tox
+          conda list
+
+      - name: Run tox tests
+        run: |
+          tox -e ${{ matrix.test-tox-env }}
+
+      - name: Build wheel and source distribution
+        run: |
+          tox -e ${{ matrix.build-tox-env }}
+          ls -1 dist
+
+      - name: Test installation from a wheel
+        run: |
+          tox -e wheelinstall --recreate --installpkg dist/*-none-any.whl
+
+
+  run-ros3-tests:  # tox and conda do not play nicely so do not use tox here
+    name: ${{ matrix.name }}
+    runs-on: ${{ matrix.os }}
+    defaults:
+      run:
+        shell: bash -l {0}  # necessary for conda
+    strategy:
+      fail-fast: false
+      matrix:
+        include:
+          - { name: linux-python3.9-ros3  , python-ver: "3.9", os: ubuntu-latest }
+          - { name: windows-python3.9-ros3, python-ver: "3.9", os: windows-latest }
+          - { name: macos-python3.9-ros3  , python-ver: "3.9", os: macos-latest }
+    steps:
+      - name: Cancel any previous incomplete runs
+        uses: styfle/[email protected]
+        with:
+          access_token: ${{ github.token }}
+
+      - uses: actions/checkout@v3
+        with:
+          submodules: 'recursive'
+
+      - name: Set up Conda
+        uses: conda-incubator/setup-miniconda@v2
+        with:
+          auto-update-conda: true
+          activate-environment: ros3
+          environment-file: environment-ros3.yml
+          python-version: ${{ matrix.python-ver }}
+          channels: conda-forge
+          auto-activate-base: false
+
+      - name: Install run dependencies
+        run: |
+          pip install -r requirements-dev.txt
+          pip install -e .
+          conda info
+          conda list
+          pip list
+
+      - name: Run gallery ros3 tests
+        run: |
+          python test.py --ros3
+
+  run-gallery-ros3-tests:
+    name: ${{ matrix.name }}
+    runs-on: ${{ matrix.os }}
+    defaults:
+      run:
+        shell: bash -l {0}  # necessary for conda
+    strategy:
+      fail-fast: false
+      matrix:
+        include:
+          - { name: linux-gallery-python3.9-ros3  , python-ver: "3.9", os: ubuntu-latest }
+          - { name: windows-gallery-python3.9-ros3, python-ver: "3.9", os: windows-latest }
+          - { name: macos-gallery-python3.9-ros3  , python-ver: "3.9", os: macos-latest }
+    steps:
+      - name: Cancel any previous incomplete runs
+        uses: styfle/[email protected]
+        with:
+          access_token: ${{ github.token }}
+
+      - uses: actions/checkout@v3
+        with:
+          submodules: 'recursive'
+
+      - name: Set up Conda
+        uses: conda-incubator/setup-miniconda@v2
+        with:
+          auto-update-conda: true
+          activate-environment: ros3
+          environment-file: environment-ros3.yml
+          python-version: ${{ matrix.python-ver }}
+          channels: conda-forge
+          auto-activate-base: false
+
+      - name: Install run dependencies
+        run: |
+          pip install matplotlib
+          pip install -e .
+          conda info
+          conda list
+          pip list
+
+      - name: Run gallery ros3 tests
+        run: |
+          python test.py --example-ros3