update base template

catalystneuro · Dec 18, 2024 · 064c034 · 064c034
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commit 064c034
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Showing 43 changed files with 1,211 additions and 2,031 deletions.
diff --git a/.gitattributes b/.gitattributes
diff --git a/.github/workflows/add-to-dashboard.yml b/.github/workflows/add-to-dashboard.yml
diff --git a/.github/workflows/check_external_links.yml b/.github/workflows/check_external_links.yml
@@ -0,0 +1,32 @@
+name: Check Sphinx external links
+on:
+  push:
+  schedule:
+    - cron: '0 5 * * 0'  # once every Sunday at midnight ET
+  workflow_dispatch:
+
+jobs:
+  check-external-links:
+    name: Check for broken Sphinx external links
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout repo
+        uses: actions/checkout@v4
+        with:
+          fetch-depth: 0  # tags are required to determine the version
+
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: "3.12"
+
+      - 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
@@ -1,6 +1,6 @@
 name: Codespell
 on:
-  pull_request:
+  push:
   workflow_dispatch:
 
 jobs:
@@ -9,6 +9,6 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Checkout
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
       - name: Codespell
         uses: codespell-project/actions-codespell@v2
diff --git a/.github/workflows/ruff.yml b/.github/workflows/ruff.yml
@@ -0,0 +1,14 @@
+name: Ruff
+on:
+  push:
+  workflow_dispatch:
+
+jobs:
+  ruff:
+    name: Check for style errors and common problems
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v4
+      - name: Ruff
+        uses: chartboost/ruff-action@v1
diff --git a/.github/workflows/run_all_tests.yml b/.github/workflows/run_all_tests.yml
@@ -1,6 +1,6 @@
 name: Run all tests
 on:
-  pull_request:
+  push:
   schedule:
     - cron: '0 5 * * 0'  # once every Sunday at midnight ET
   workflow_dispatch:
@@ -12,6 +12,9 @@ jobs:
     defaults:
       run:
         shell: bash
+    concurrency:
+      group: ${{ github.workflow }}-${{ github.ref }}-${{ matrix.name }}
+      cancel-in-progress: true
     strategy:
       fail-fast: false
       matrix:
@@ -38,19 +41,13 @@ jobs:
           - { 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/cancel-workflow-action@0.11.0
+      - name: Checkout repo
+        uses: actions/checkout@v4
         with:
-          all_but_latest: true
-          access_token: ${{ github.token }}
-
-      - uses: actions/checkout@v3
-        with:
-          submodules: 'recursive'
-          fetch-depth: 0  # fetch tags
+          fetch-depth: 0  # tags are required to determine the version
 
       - name: Set up Python
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v5
         with:
           python-version: ${{ matrix.python-ver }}
 
@@ -64,19 +61,20 @@ jobs:
         if: ${{ matrix.requirements == 'minimum' }}
         run: |
           python -m pip install -r requirements-min.txt -r requirements-dev.txt
-          python -m pip install -e .
+          python -m pip install .
 
       - name: Install run requirements (pinned)
         if: ${{ matrix.requirements == 'pinned' }}
         run: |
           python -m pip install -r requirements-dev.txt
-          python -m pip install -e .
+          python -m pip install .
 
       - name: Install run requirements (upgraded)
         if: ${{ matrix.requirements == 'upgraded' }}
         run: |
           python -m pip install -r requirements-dev.txt
-          python -m pip install -U -e .
+          # force upgrade of all dependencies to latest versions within allowed range
+          python -m pip install -U --upgrade-strategy eager .
 
       - name: Run tests
         run: |
@@ -110,6 +108,9 @@ jobs:
     defaults:
      run:
        shell: bash -l {0}  # needed for conda environment to work
+    concurrency:
+      group: ${{ github.workflow }}-${{ github.ref }}-${{ matrix.name }}
+      cancel-in-progress: true
     strategy:
       fail-fast: false
       matrix:
@@ -122,18 +123,13 @@ jobs:
           - { 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/cancel-workflow-action@0.11.0
-        with:
-          access_token: ${{ github.token }}
-
-      - uses: actions/checkout@v3
+      - name: Checkout repo
+        uses: actions/checkout@v4
         with:
-          submodules: 'recursive'
-          fetch-depth: 0  # fetch tags
+          fetch-depth: 0  # tags are required to determine the version
 
       - name: Set up Conda
-        uses: conda-incubator/setup-miniconda@v2
+        uses: conda-incubator/setup-miniconda@v3
         with:
           auto-update-conda: true
           auto-activate-base: true
@@ -151,19 +147,20 @@ jobs:
         if: ${{ matrix.requirements == 'minimum' }}
         run: |
           python -m pip install -r requirements-min.txt -r requirements-dev.txt
-          python -m pip install -e .
+          python -m pip install .
 
       - name: Install run requirements (pinned)
         if: ${{ matrix.requirements == 'pinned' }}
         run: |
           python -m pip install -r requirements-dev.txt
-          python -m pip install -e .
+          python -m pip install .
 
       - name: Install run requirements (upgraded)
         if: ${{ matrix.requirements == 'upgraded' }}
         run: |
           python -m pip install -r requirements-dev.txt
-          python -m pip install -U -e .
+          # force upgrade of all dependencies to latest versions within allowed range
+          python -m pip install -U --upgrade-strategy eager .
 
       - name: Run tests
         run: |

diff --git a/.github/workflows/run_coverage.yml b/.github/workflows/run_coverage.yml
@@ -1,6 +1,6 @@
 name: Run code coverage
 on:
-  pull_request:
+  push:
   workflow_dispatch:
 
 jobs:
@@ -13,26 +13,23 @@ jobs:
     defaults:
       run:
         shell: bash
+    concurrency:
+      group: ${{ github.workflow }}-${{ github.ref }}-${{ matrix.os }}
+      cancel-in-progress: true
     strategy:
       matrix:
         os: [ubuntu-latest, windows-latest, macos-latest]
     env:  # used by codecov-action
       OS: ${{ matrix.os }}
-      PYTHON: '3.11'
+      PYTHON: '3.12'
     steps:
-      - name: Cancel any previous incomplete runs
-        uses: styfle/cancel-workflow-action@0.11.0
+      - name: Checkout repo
+        uses: actions/checkout@v4
         with:
-          all_but_latest: true
-          access_token: ${{ github.token }}
-
-      - uses: actions/checkout@v3
-        with:
-          submodules: 'recursive'
-          fetch-depth: 0  # fetch tags
+          fetch-depth: 0  # tags are required to determine the version
 
       - name: Set up Python
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v5
         with:
           python-version: ${{ env.PYTHON }}
 
@@ -43,17 +40,18 @@ jobs:
 
       - name: Install package
         run: |
-          python -m pip install -e .  # must install in editable mode for coverage to find sources
+          python -m pip install .
           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
+          pytest --cov --cov-report=xml --cov-report=term  # codecov uploader requires xml format
 
-      # TODO uncomment after setting up repo on codecov.io
+      # TODO uncomment after setting up repo on codecov.io and adding token
       # - name: Upload coverage to Codecov
-      #   uses: codecov/codecov-action@v3
+      #   uses: codecov/codecov-action@v4
       #   with:
       #     fail_ci_if_error: true
+      #     file: ./coverage.xml
+      #   env:
+      #     CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
diff --git a/.github/workflows/validate_schema.yml b/.github/workflows/validate_schema.yml
@@ -0,0 +1,22 @@
+name: Validate schema
+
+on: [push, pull_request, workflow_dispatch]
+
+jobs:
+  validate:
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v4
+    - name: Set up Python 3.12
+      uses: actions/setup-python@v4
+      with:
+        python-version: "3.12"
+    - name: Install HDMF
+      run: |
+        pip install hdmf
+    - name: Download latest nwb schema language specification
+      run: |
+        curl -L https://raw.githubusercontent.com/NeurodataWithoutBorders/nwb-schema/dev/nwb.schema.json -o nwb.schema.json
+    - name: Validate schema specification
+      run: |
+        validate_hdmf_spec spec -m nwb.schema.json