Merge branch 'dev' into add_missing_api_docs

.github/ISSUE_TEMPLATE/bug_report.yml

@@ -36,7 +36,6 @@ body:
       label: Python Version
       options:
         - earlier
-        - 3.8
         - 3.9
         - "3.10"
         - "3.11"

.github/workflows/assess-file-changes.yml

@@ -7,21 +7,17 @@ on:
       SOURCE_CHANGED:
         description: "Whether or not the files under /src/ were changed."
         value: ${{ jobs.build.outputs.SOURCE_CHANGED }}
-      TESTING_CHANGED:
-        description: "Whether or not to regenerate the testing files and reupload them to DANI staging."
-        value: ${{ jobs.build.outputs.TESTING_CHANGED }}
 
 jobs:
   build:
     runs-on: ubuntu-latest
     # Map the job outputs to step outputs
     outputs:
       SOURCE_CHANGED: ${{ steps.flagged-changes.outputs.SOURCE_CHANGED }}
-      TESTING_CHANGED: ${{ steps.flagged-changes.outputs.TESTING_CHANGED }}
 
     name: Test changed-files
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
         with:
           fetch-depth: 0
 
@@ -33,7 +29,6 @@ jobs:
         id: flagged-changes
         run: |
           echo "::set-output name=SOURCE_CHANGED::false"
-          echo "::set-output name=TESTING_CHANGED::false"
           for file in ${{ steps.changed-files.outputs.all_changed_files }}; do
             echo $file
             if [[ $file == "src/nwbinspector/"* || $file == "requirements.txt" || $file == "setup.py" || $file == "tests/"* ]]
@@ -43,11 +38,4 @@ jobs:
             else
               echo "Source not changed"
             fi
-            if [[ $file == "src/nwbinspector/testing.py" ]]
-            then
-              echo "Testing changed"
-              echo "::set-output name=TESTING_CHANGED::true"
-            else
-              echo "Testing not changed"
-            fi
           done

.github/workflows/auto-publish.yml

@@ -11,17 +11,17 @@ jobs:
   deploy:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v4
       - name: Set up Python
-        uses: actions/setup-python@v2
+        uses: actions/setup-python@v5
         with:
-          python-version: "3.8"
+          python-version: "3.9"
       - name: Install dependencies
         run: |
           python -m pip install --upgrade pip
-          pip install wheel
+          python -m pip install --upgrade build
       - name: Build package
-        run: python setup.py sdist bdist_wheel
+        run: python -m build
       - name: pypi-publish
         uses: pypa/gh-action-pypi-publish@v1.4.2
         with:

.github/workflows/dailies.yml

@@ -16,13 +16,13 @@ jobs:
     uses: neurodatawithoutborders/nwbinspector/.github/workflows/doc-link-checks.yml@dev
 
   test-dandi-latest:
-    uses: neurodatawithoutborders/nwbinspector/.github/workflows/dandi_release.yml@dev
+    uses: neurodatawithoutborders/nwbinspector/.github/workflows/dandi-release.yml@dev
 
   test-dandi-dev:
-    uses: neurodatawithoutborders/nwbinspector/.github/workflows/dandi_dev.yml@dev
+    uses: neurodatawithoutborders/nwbinspector/.github/workflows/dandi-dev.yml@dev
 
   test-dandi-dev-live:
-    uses: neurodatawithoutborders/nwbinspector/.github/workflows/dandi_dev_live_service.yml@dev
+    uses: neurodatawithoutborders/nwbinspector/.github/workflows/dandi-dev-live-services.yml@dev
 
   notify:
     runs-on: ubuntu-latest
@@ -36,6 +36,6 @@ jobs:
         username: ${{ secrets.MAIL_USERNAME }}
         password: ${{ secrets.MAIL_PASSWORD }}
         subject: NWB Inspector Daily Failure
-        to: cody.c.baker.phd@gmail.com,smprince@lbl.gov
+        to: smprince@lbl.gov, rly@lbl.gov
         from: NWB Inspector
         body: "The daily workflow for the NWB Inspector failed: please check status at https://github.com/NeurodataWithoutBorders/nwbinspector/actions/workflows/dailies.yml"

.github/workflows/dandi-dev-live-services.yml

@@ -0,0 +1,32 @@
+name: Test against DANDI dev branch - all tests, including live services
+on: workflow_call
+
+jobs:
+  build-and-test:
+    name: Testing against current DANDI release and dev branch
+    runs-on: ubuntu-latest
+    strategy:
+      fail-fast: false
+
+    steps:
+      - name: Checkout local branch of source repository
+        uses: actions/checkout@v4
+      - run: git fetch --prune --unshallow --tags
+
+      - name: Setup Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: "3.12"
+
+      - name: Test against DANDI dev
+        run: |
+          pip install virtualenv
+          virtualenv --system-site-packages --python=python3 venvs/dandi_dev_tests
+          source venvs/dandi_dev_tests/bin/activate
+          pip install -e .[dandi]
+          cd ..
+          git clone https://github.com/dandi/dandi-cli
+          cd dandi-cli
+          pip install -e .[test]
+          pip install hdmf==3.14.3  # temporary: https://github.com/dandi/dandi-cli/issues/1494
+          pytest -vv

.github/workflows/dandi-dev.yml

@@ -0,0 +1,35 @@
+name: Test against DANDI dev branch - no network
+on: workflow_call
+
+env:
+  DANDI_TESTS_NONETWORK: "1"
+
+jobs:
+  build-and-test:
+    name: Testing against current DANDI release and dev branch
+    runs-on: ubuntu-latest
+    strategy:
+      fail-fast: false
+
+    steps:
+      - name: Checkout local branch of source repository
+        uses: actions/checkout@v4
+      - run: git fetch --prune --unshallow --tags
+
+      - name: Setup Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: "3.12"
+
+      - name: Test local branch of NWB Inspector against DANDI dev branch
+        run: |
+          pip install virtualenv
+          virtualenv --system-site-packages --python=python3 venvs/dandi_dev_tests
+          source venvs/dandi_dev_tests/bin/activate
+          pip install -e .[dandi]
+          cd ..
+          git clone https://github.com/dandi/dandi-cli
+          cd dandi-cli
+          pip install -e .[test]
+          pip install hdmf==3.14.3  # temporary: https://github.com/dandi/dandi-cli/issues/1494
+          pytest -rsx

.github/workflows/dandi_release.yml → .github/workflows/dandi-release.yml

@@ -1,4 +1,4 @@
-name: Test against latest DANDI release - no network
+name: Run NWB Inspector tests against latest DANDI release - no network
 on: workflow_call
 
 env:
@@ -25,7 +25,7 @@ jobs:
           - '3.11'
 
     steps:
-    - name: Set up environment
+    - name: Checkout local branch of source repository
       uses: actions/checkout@v4
       with:
         # Fetch all commits so that versioneer will return something compatible
@@ -43,7 +43,9 @@ jobs:
         pip install "dandi[extras,test]"
 
     - name: Install this branch of NWB Inspector
-      run: pip install -e .
+      run: |
+        pip install -e .
+        pip install hdmf==3.14.3  # temporary: https://github.com/dandi/dandi-cli/issues/1494
 
     - name: Run all NWB Inspector tests
-      run: python -m pytest -s -v
+      run: pytest -rsx

.github/workflows/deploy-tests.yml

@@ -3,13 +3,12 @@ name: Deploy tests
 on:
   pull_request:
 
-jobs:
-  cancel-previous-runs:
-    runs-on: ubuntu-latest
-    steps:
-      - name: Cancel Previous Runs
-        uses: styfle/cancel-workflow-action@0.11.0
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
 
+
+jobs:
   assess-file-changes:
     uses: catalystneuro/neuroconv/.github/workflows/assess-file-changes.yml@main
 
@@ -40,6 +39,15 @@ jobs:
     needs: assess-file-changes
     if: ${{ needs.assess-file-changes.outputs.SOURCE_CHANGED == 'true' }}
     uses: ./.github/workflows/streaming-tests.yml
+    secrets:
+      CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
+
+  run-read-nwbfile-tests:
+    needs: assess-file-changes
+    if: ${{ needs.assess-file-changes.outputs.SOURCE_CHANGED == 'true' }}
+    uses: ./.github/workflows/read-nwbfile-tests.yml
+    secrets:
+      CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
 
   run-dev-gallery:
     needs: assess-file-changes
@@ -49,17 +57,17 @@ jobs:
   test-dandi-latest:
     needs: assess-file-changes
     if: ${{ needs.assess-file-changes.outputs.SOURCE_CHANGED == 'true' }}
-    uses: ./.github/workflows/dandi_release.yml
+    uses: ./.github/workflows/dandi-release.yml
 
   test-dandi-dev:
     needs: assess-file-changes
     if: ${{ needs.assess-file-changes.outputs.SOURCE_CHANGED == 'true' }}
-    uses: ./.github/workflows/dandi_dev.yml
+    uses: ./.github/workflows/dandi-dev.yml
 
   test-dandi-dev-live:
     needs: assess-file-changes
     if: ${{ needs.assess-file-changes.outputs.SOURCE_CHANGED == 'true' }}
-    uses: ./.github/workflows/dandi_dev_live_service.yml
+    uses: ./.github/workflows/dandi-dev-live-services.yml
 
   check-final-status:
     name: All tests passing

.github/workflows/dev-gallery.yml

@@ -1,35 +1,36 @@
 name: Development Version Gallery
 on: workflow_call
 
+env:
+  TESTING_FILES_FOLDER_PATH: ./204919/testing_files/
+
 jobs:
   build-and-test:
     name: Testing against dev PyNWB version
     runs-on: ubuntu-latest
     strategy:
       fail-fast: false
     steps:
-      - uses: s-weigand/setup-conda@v1
+      - uses: actions/checkout@v4
+      - run: git fetch --prune --unshallow --tags
+
+      - name: Setup Python
+        uses: actions/setup-python@v5
         with:
-          update-conda: true
           python-version: 3.9
-          conda-channels: conda-forge
-      - uses: actions/checkout@v3
-      - run: git fetch --prune --unshallow --tags
 
-      - name: Install ROS3
-        run: conda install -c conda-forge h5py
       - name: Install pytest
         run: |
           pip install pytest
           pip install pytest-cov
+
       - name: Install package
         run: |
           pip install -e ".[dandi]"
           pip install git+https://github.com/neurodatawithoutborders/pynwb@dev
+
       - name: Download testing data and set config path
-        run: |
-          dandi download "https://gui-staging.dandiarchive.org/#/dandiset/204919"
-          python -c "from nwbinspector.testing import update_testing_config; update_testing_config(key='LOCAL_PATH', value='./204919/testing_files/')"
+        run: dandi download "https://gui-staging.dandiarchive.org/#/dandiset/204919"
 
-      - name: Run pytest with coverage
+      - name: Run pytest
         run: pytest -rsx