Update from latest template

hed-standard · Oct 22, 2023 · fd6fc5a · fd6fc5a
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diff --git a/.github/workflows/check_external_links.yml b/.github/workflows/check_external_links.yml
@@ -0,0 +1,39 @@
+name: Check Sphinx external links
+on:
+  push:
+  pull_request:
+  schedule:
+    - cron: '0 5 * * *'  # once per day at midnight ET
+  workflow_dispatch:
+
+jobs:
+  check-external-links:
+    name: Check for broken Sphinx 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'
+          fetch-depth: 0  # tags are required for versioneer to determine the version
+
+      - name: Set up Python
+        uses: actions/setup-python@v4
+        with:
+          python-version: '3.11'
+
+      - name: Install Sphinx dependencies and package
+        run: |
+          python -m pip install --upgrade pip
+          python -m pip install -r requirements-dev.txt
+          python -m pip install .
+
+      - name: Check Sphinx external links
+        run: |
+          cd docs  # run_doc_autogen assumes spec is found in ../spec/
+          sphinx-build -b linkcheck ./source ./test_build
diff --git a/.github/workflows/codespell.yml b/.github/workflows/codespell.yml
@@ -0,0 +1,15 @@
+name: Codespell
+on:
+  push:
+  pull_request:
+  workflow_dispatch:
+
+jobs:
+  codespell:
+    name: Check for spelling errors
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v3
+      - name: Codespell
+        uses: codespell-project/actions-codespell@v2
diff --git a/.github/workflows/ruff.yml b/.github/workflows/ruff.yml
@@ -0,0 +1,15 @@
+name: Ruff
+on:
+  push:
+  pull_request:
+  workflow_dispatch:
+
+jobs:
+  ruff:
+    name: Check for style errors and common problems
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v3
+      - name: Ruff
+        uses: chartboost/ruff-action@v1
diff --git a/.github/workflows/run_all_tests.yml b/.github/workflows/run_all_tests.yml
@@ -0,0 +1,184 @@
+name: Run all tests
+on:
+  push:
+  pull_request:
+  schedule:
+    - cron: '0 5 * * *'  # once per day at midnight ET
+  workflow_dispatch:
+
+jobs:
+  run-all-tests:
+    name: ${{ matrix.name }}
+    runs-on: ${{ matrix.os }}
+    defaults:
+      run:
+        shell: bash
+    strategy:
+      fail-fast: false
+      matrix:
+        include:
+          - { name: linux-python3.8-minimum      , requirements: minimum    , python-ver: "3.8" , os: ubuntu-latest }
+          - { name: linux-python3.8              , requirements: pinned     , python-ver: "3.8" , os: ubuntu-latest }
+          - { name: linux-python3.9              , requirements: pinned     , python-ver: "3.9" , os: ubuntu-latest }
+          - { name: linux-python3.10             , requirements: pinned     , python-ver: "3.10", os: ubuntu-latest }
+          - { name: linux-python3.11             , requirements: pinned     , python-ver: "3.11", os: ubuntu-latest }
+          - { name: linux-python3.12             , requirements: pinned     , python-ver: "3.12", os: ubuntu-latest }
+          - { name: linux-python3.12-upgraded    , requirements: upgraded   , python-ver: "3.12", os: ubuntu-latest }
+          - { name: windows-python3.8-minimum    , requirements: minimum    , python-ver: "3.8" , os: windows-latest }
+          - { name: windows-python3.8            , requirements: pinned     , python-ver: "3.8" , os: windows-latest }
+          - { name: windows-python3.9            , requirements: pinned     , python-ver: "3.9" , os: windows-latest }
+          - { name: windows-python3.10           , requirements: pinned     , python-ver: "3.10", os: windows-latest }
+          - { name: windows-python3.11           , requirements: pinned     , python-ver: "3.11", os: windows-latest }
+          - { name: windows-python3.12           , requirements: pinned     , python-ver: "3.12", os: windows-latest }
+          - { name: windows-python3.12-upgraded  , requirements: upgraded   , python-ver: "3.12", os: windows-latest }
+          - { name: macos-python3.8-minimum      , requirements: minimum    , python-ver: "3.8" , os: macos-latest }
+          - { name: macos-python3.8              , requirements: pinned     , python-ver: "3.8" , os: macos-latest }
+          - { name: macos-python3.9              , requirements: pinned     , python-ver: "3.9" , os: macos-latest }
+          - { name: macos-python3.10             , requirements: pinned     , python-ver: "3.10", os: macos-latest }
+          - { name: macos-python3.11             , requirements: pinned     , python-ver: "3.11", os: macos-latest }
+          - { name: macos-python3.12             , requirements: pinned     , python-ver: "3.12", os: macos-latest }
+          - { name: macos-python3.12-upgraded    , requirements: upgraded   , python-ver: "3.12", os: macos-latest }
+    steps:
+      - name: Cancel non-latest runs
+        uses: styfle/[email protected]
+        with:
+          all_but_latest: true
+          access_token: ${{ github.token }}
+
+      - uses: actions/checkout@v3
+        with:
+          submodules: 'recursive'
+          fetch-depth: 0  # fetch tags
+
+      - name: Set up Python
+        uses: actions/setup-python@v4
+        with:
+          python-version: ${{ matrix.python-ver }}
+
+      - name: Install build dependencies
+        run: |
+          python -m pip install --upgrade pip
+          python -m pip list
+          python -m pip check
+
+      - name: Install run requirements (minimum)
+        if: ${{ matrix.requirements == 'minimum' }}
+        run: |
+          python -m pip install -r requirements-min.txt -r requirements-dev.txt
+          python -m pip install -e .
+
+      - name: Install run requirements (pinned)
+        if: ${{ matrix.requirements == 'pinned' }}
+        run: |
+          python -m pip install -r requirements-dev.txt
+          python -m pip install -e .
+
+      - name: Install run requirements (upgraded)
+        if: ${{ matrix.requirements == 'upgraded' }}
+        run: |
+          python -m pip install -r requirements-dev.txt
+          python -m pip install -U -e .
+
+      - name: Run tests
+        run: |
+          pytest -v
+
+      - name: Build wheel and source distribution
+        run: |
+          python -m pip install --upgrade build
+          python -m build
+          ls -1 dist
+
+      - name: Test installation from a wheel (POSIX)
+        if: ${{ matrix.os != 'windows-latest' }}
+        run: |
+          python -m venv test-wheel-env
+          source test-wheel-env/bin/activate
+          python -m pip install dist/*-none-any.whl
+          python -c "import ndx_hed"
+
+      - name: Test installation from a wheel (windows)
+        if: ${{ matrix.os == 'windows-latest' }}
+        run: |
+          python -m venv test-wheel-env
+          test-wheel-env/Scripts/activate.bat
+          python -m pip install dist/*-none-any.whl
+          python -c "import ndx_hed"
+
+  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-python3.8-minimum    , requirements: minimum    , python-ver: "3.8" , os: ubuntu-latest }
+          - { name: conda-linux-python3.8            , requirements: pinned     , python-ver: "3.8" , os: ubuntu-latest }
+          - { name: conda-linux-python3.9            , requirements: pinned     , python-ver: "3.9" , os: ubuntu-latest }
+          - { name: conda-linux-python3.10           , requirements: pinned     , python-ver: "3.10", os: ubuntu-latest }
+          - { name: conda-linux-python3.11           , requirements: pinned     , python-ver: "3.11", os: ubuntu-latest }
+          - { name: conda-linux-python3.12           , requirements: pinned     , python-ver: "3.12", os: ubuntu-latest }
+          - { name: conda-linux-python3.12-upgraded  , requirements: upgraded   , python-ver: "3.12", 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'
+          fetch-depth: 0  # fetch tags
+
+      - 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 config --show-sources
+          conda list --show-channel-urls
+
+      - name: Install run requirements (minimum)
+        if: ${{ matrix.requirements == 'minimum' }}
+        run: |
+          python -m pip install -r requirements-min.txt -r requirements-dev.txt
+          python -m pip install -e .
+
+      - name: Install run requirements (pinned)
+        if: ${{ matrix.requirements == 'pinned' }}
+        run: |
+          python -m pip install -r requirements-dev.txt
+          python -m pip install -e .
+
+      - name: Install run requirements (upgraded)
+        if: ${{ matrix.requirements == 'upgraded' }}
+        run: |
+          python -m pip install -r requirements-dev.txt
+          python -m pip install -U -e .
+
+      - name: Run tests
+        run: |
+          pytest -v
+
+      - name: Build wheel and source distribution
+        run: |
+          python -m pip install --upgrade build
+          python -m build
+          ls -1 dist
+
+      - name: Test installation from a wheel (POSIX)
+        run: |
+          python -m venv test-wheel-env
+          source test-wheel-env/bin/activate
+          python -m pip install dist/*-none-any.whl
+          python -c "import ndx_hed"
diff --git a/.github/workflows/run_coverage.yml b/.github/workflows/run_coverage.yml
@@ -0,0 +1,60 @@
+name: Run code coverage
+on:
+  push:
+  pull_request:
+  workflow_dispatch:
+
+jobs:
+  run-coverage:
+    name: ${{ matrix.os }}
+    runs-on: ${{ matrix.os }}
+    # TODO handle forks
+    # 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:
+        os: [ubuntu-latest, windows-latest, macos-latest]
+    env:  # used by codecov-action
+      OS: ${{ matrix.os }}
+      PYTHON: '3.11'
+    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'
+          fetch-depth: 0  # fetch tags
+
+      - name: Set up Python
+        uses: actions/setup-python@v4
+        with:
+          python-version: ${{ env.PYTHON }}
+
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          python -m pip install -r requirements-dev.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: |
+          pytest --cov
+          python -m coverage xml  # codecov uploader requires xml format
+          python -m coverage report -m
+
+      # TODO uncomment after setting up repo on codecov.io
+      # - name: Upload coverage to Codecov
+      #   uses: codecov/codecov-action@v3
+      #   with:
+      #     fail_ci_if_error: true
diff --git a/NEXTSTEPS.md b/NEXTSTEPS.md
@@ -69,6 +69,13 @@ your extension.
 
 8. Update the `CHANGELOG.md` to document changes to your extension.
 
+8. Push your repository to GitHub. A default set of GitHub Actions workflows is set up to
+test your code on Linux, Windows, Mac OS, and Linux using conda; upload code coverage
+stats to codecov.io; check for spelling errors; check for style errors; and check for broken
+links in the documentation. For the code coverage workflow to work, you will need to
+set up the repo on codecov.io and uncomment the "Upload coverage to Codecov" step
+in `.github/workflows/run_coverage.yml`.
+
 8. Make a release for the extension on GitHub with the version number specified. e.g. if version is 0.1.0, then this page should exist: https://github.com/rly/ndx-hed/releases/tag/0.1.0 . For instructions on how to make a release on GitHub see [here](https://help.github.com/en/github/administering-a-repository/creating-releases).
 
 9. Publish your updated extension on [PyPI](https://pypi.org/).

diff --git a/pyproject.toml b/pyproject.toml
@@ -34,7 +34,8 @@ keywords = [
     'ndx-extension',
 ]
 dependencies = [
-    "pynwb>=2",
+    "pynwb>=2.5.0",
+    "hdmf>=3.10.0",
 ]
 
 # TODO: add URLs before release

diff --git a/requirements-dev.txt b/requirements-dev.txt
@@ -3,8 +3,10 @@
 black==23.9.1
 codespell==2.2.6
 coverage==7.3.2
+hdmf==3.10.0
 hdmf-docutils==0.4.5
 pre-commit==3.4.0
+pynwb==2.5.0
 pytest==7.4.2
 pytest-cov==4.1.0
 python-dateutil==2.8.2

diff --git a/requirements-min.txt b/requirements-min.txt
@@ -0,0 +1,5 @@
+# minimum versions of package dependencies for installation
+# these should match the minimum versions specified in pyproject.toml
+# NOTE: it may be possible to relax these minimum requirements
+pynwb==2.5.0
+hdmf==3.10.0