Merge branch 'dev' into docs/ext_autosummary

hdmf-dev · Apr 22, 2022 · c6f2cda · c6f2cda
2 parents 6f5b77d + 5a4beb1
commit c6f2cda
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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 +1,33 @@
+name: Check Sphinx external links
+on:
+  pull_request:
+  schedule:
+    - cron: '0 5 * * *'  # once per day at midnight ET
+
+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: ${{ github.token }}
+
+      - uses: actions/checkout@v3
+        with:
+          submodules: 'recursive'
+
+      - name: Set up Python
+        uses: actions/setup-python@v3
+        with:
+          python-version: '3.10'
+
+      - name: Install Sphinx dependencies and package
+        run: |
+          python -m pip install --upgrade pip
+          python -m pip install -r requirements-doc.txt -r requirements.txt
+          python -m pip install .
+
+      - name: Check Sphinx external links
+        run: sphinx-build -b linkcheck ./docs/source ./test_build
diff --git a/.github/workflows/deploy_release.yml b/.github/workflows/deploy_release.yml
@@ -0,0 +1,55 @@
+name: Deploy release
+on:
+  push:
+    tags:  # run only on new tags that follow semver
+      - '/^[0-9]+(\.[0-9]+)?(\.[0-9]+)?$/'
+
+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  # TODO remove the --repository flag after testing
+        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/*
+
+      - name: Publish wheel and source distributions as a GitHub release
+        run: |
+          # use click<8 until https://github.com/j0057/github-release/issues/62 is resolved
+          python -m pip install "click<8" githubrelease
+          githubrelease release hdmf-dev/hdmf \
+            create ${{ github.ref_name }} --name ${{ github.ref_name }} \
+            --github-token ${{ secrets.BOT_GITHUB_TOKEN }} \
+            --publish dist/*
diff --git a/.github/workflows/run_all_tests.yml b/.github/workflows/run_all_tests.yml
@@ -0,0 +1,176 @@
+name: Run all tests
+on:
+  schedule:
+    - cron: '0 5 * * *'  # once per day at midnight ET
+  push:
+    tags:  # run only on new tags that follow semver
+      - '/^[0-9]+(\.[0-9]+)?(\.[0-9]+)?$/'
+
+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-python3.10-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-python3.10-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-python3.10-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: 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 }
+    steps:
+      - name: Cancel any previous incomplete runs
+        uses: styfle/[email protected]
+        with:
+          access_token: ${{ github.token }}
+
+      - uses: actions/checkout@v3
+        with:
+          submodules: 'recursive'
+
+      - name: Set up Conda
+        uses: conda-incubator/setup-miniconda@v2
+        with:
+          auto-update-conda: true
+          auto-activate-base: true
+          activate-environment: ""
+
+      - name: Install build dependencies
+        run: |
+          conda update -n base -c defaults conda
+          conda config --set always_yes yes --set changeps1 no
+          conda config --add channels conda-forge
+          conda install python=${{ matrix.python-ver }}
+          conda install 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
diff --git a/.github/workflows/run_coverage.yml b/.github/workflows/run_coverage.yml
@@ -0,0 +1,70 @@
+name: Run code coverage
+on:
+  push:
+    branches:
+      - dev
+    tags-ignore:  # exclude tags created by "ci_addons publish_github_release"
+      - 'latest'
+      - 'latest-tmp'
+  pull_request:
+
+jobs:
+  run-coverage:
+    name: ${{ matrix.os }}, opt reqs ${{ matrix.opt_req }}
+    runs-on: ${{ matrix.os }}
+    # TODO
+    # run pipeline on either a push event or a PR event on a fork
+    # if: github.event_name != 'pull_request' || github.event.pull_request.head.repo.full_name != github.event.pull_request.base.repo.full_name
+    defaults:
+      run:
+        shell: bash
+    strategy:
+      matrix:
+        include:
+          - { os: ubuntu-latest , opt_req: true }
+          - { os: ubuntu-latest , opt_req: false }
+          - { os: windows-latest, opt_req: false }
+          - { os: macos-latest  , opt_req: false }
+    env:
+      OS: ${{ matrix.os }}
+      PYTHON: '3.10'
+    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: '3.10'
+
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          python -m pip install -r requirements-dev.txt -r requirements.txt
+
+      - name: Install optional dependencies
+        if: ${{ matrix.opt_req }}
+        run: python -m pip install -r requirements-opt.txt
+
+      - name: Install package
+        run: |
+          python -m pip install -e .  # must install in editable mode for coverage to find sources
+          python -m pip list
+
+      - name: Run tests and generate coverage report
+        run: |
+          python -m coverage run test.py -u
+          python -m coverage xml  # codecov uploader requires xml format
+          python -m coverage report -m
+
+      - name: Upload coverage to Codecov
+        uses: codecov/codecov-action@v3
+        with:
+          fail_ci_if_error: true
diff --git a/.github/workflows/run_flake8.yml b/.github/workflows/run_flake8.yml
@@ -0,0 +1,30 @@
+name: Run style check
+on: pull_request
+
+jobs:
+  run-flake8:
+    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: '3.10'
+
+    - name: Install flake8
+      run: |
+        python -m pip install --upgrade pip
+        python -m pip install flake8
+        python -m pip list
+
+    - name: Run flake8
+      run: flake8