Merge branch 'dev' into prop/herd_get_key

.github/ISSUE_TEMPLATE/bug_report.yml

@@ -64,6 +64,7 @@ body:
         - "3.9"
         - "3.10"
         - "3.11"
+        - "3.12"
     validations:
       required: true
   - type: textarea

.github/PULL_REQUEST_TEMPLATE/release.md

@@ -3,7 +3,9 @@ Prepare for release of HDMF [version]
 ### Before merging:
 - [ ] Major and minor releases: Update package versions in `requirements.txt`, `requirements-dev.txt`,
   `requirements-doc.txt`, `requirements-opt.txt`, and `environment-ros3.yml` to the latest versions,
-  and update dependency ranges in `pyproject.toml` and minimums in `requirements-min.txt` as needed
+  and update dependency ranges in `pyproject.toml` and minimums in `requirements-min.txt` as needed.
+  Run `pip install pur && pur -r requirements-dev.txt -r requirements.txt -r requirements-opt.txt`
+  and manually update `environment-ros3.yml`.
 - [ ] Check legal file dates and information in `Legal.txt`, `license.txt`, `README.rst`, `docs/source/conf.py`,
   and any other locations as needed
 - [ ] Update `pyproject.toml` as needed
@@ -14,6 +16,8 @@ Prepare for release of HDMF [version]
   (`pytest && python test_gallery.py`)
 - [ ] Run PyNWB tests locally including gallery and validation tests, and inspect all warnings and outputs
   (`cd pynwb; python test.py -v > out.txt 2>&1`)
+- [ ] Run HDMF-Zarr tests locally including gallery and validation tests, and inspect all warnings and outputs
+  (`cd hdmf-zarr; pytest && python test_gallery.py`)
 - [ ] Test docs locally and inspect all warnings and outputs `cd docs; make clean && make html`
 - [ ] Push changes to this PR and make sure all PRs to be included in this release have been merged
 - [ ] Check that the readthedocs build for this PR succeeds (build latest to pull the new branch, then activate and

.github/dependabot.yml

@@ -0,0 +1,18 @@
+version: 2
+updates:
+  # disable checking python requirements files because there are too
+  # many updates and dependabot will not ignore requirements-min.txt
+  # until https://github.com/dependabot/dependabot-core/issues/2883 is resolved
+  # workaround is to continue updating these files manually
+
+  # - package-ecosystem: "pip"
+  #   directory: "/"
+  #   schedule:
+  #     # Check for updates to requirements files and pyproject.toml every week
+  #     interval: "weekly"
+
+  - package-ecosystem: "github-actions"
+    directory: "/"
+    schedule:
+      # Check for updates to GitHub Actions every week
+      interval: "weekly"

.github/workflows/check_external_links.yml

@@ -8,22 +8,20 @@ on:
 jobs:
   check-external-links:
     runs-on: ubuntu-latest
+    concurrency:
+      group: ${{ github.workflow }}-${{ github.ref }}
+      cancel-in-progress: true
     steps:
-      - name: Cancel non-latest runs
-        uses: styfle/[email protected]
-        with:
-          all_but_latest: true
-          access_token: ${{ github.token }}
-
-      - uses: actions/checkout@v3
+      - name: Checkout repo with submodules
+        uses: actions/checkout@v4
         with:
           submodules: 'recursive'
-          fetch-depth: 0  # tags are required for versioneer to determine the version
+          fetch-depth: 0  # tags are required to determine the version
 
       - name: Set up Python
         uses: actions/setup-python@v4
         with:
-          python-version: '3.11'
+          python-version: '3.11'  # TODO update to 3.12 when optional reqs (e.g., oaklib) support 3.12
 
       - name: Install Sphinx dependencies and package
         run: |

.github/workflows/codespell.yml

@@ -1,19 +1,14 @@
----
 name: Codespell
-
 on:
-  push:
-    branches: [dev]
   pull_request:
-    branches: [dev]
+  workflow_dispatch:
 
 jobs:
   codespell:
     name: Check for spelling errors
     runs-on: ubuntu-latest
-
     steps:
-      - name: Checkout
-        uses: actions/checkout@v3
+      - name: Checkout repo
+        uses: actions/checkout@v4
       - name: Codespell
         uses: codespell-project/actions-codespell@v2

.github/workflows/deploy_release.yml

@@ -10,15 +10,15 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Checkout repo with submodules
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
         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'
+          python-version: '3.12'
 
       - name: Install build dependencies
         run: |
@@ -28,20 +28,20 @@ jobs:
 
       - name: Run tox tests
         run: |
-          tox -e py311-upgraded
+          tox -e py312-upgraded
 
       - name: Build wheel and source distribution
         run: |
-          tox -e build-py311-upgraded
+          tox -e build
           ls -1 dist
 
       - name: Test installation from a wheel
         run: |
-          tox -e wheelinstall --recreate --installpkg dist/*-none-any.whl
+          tox -e wheelinstall --installpkg dist/*-none-any.whl
 
       - name: Test installation from a source distribution
         run: |
-          tox -e wheelinstall --recreate --installpkg dist/*.tar.gz
+          tox -e wheelinstall --installpkg dist/*.tar.gz
 
       - name: Upload wheel and source distributions to PyPI
         run: |

.github/workflows/project_action.yml

@@ -12,23 +12,23 @@ jobs:
     steps:
       - name: GitHub App token
         id: generate_token
-        uses: tibdex/github-app-token@v1.7.0
+        uses: tibdex/github-app-token@v2
         with:
           app_id: ${{ secrets.APP_ID }}
           private_key: ${{ secrets.APP_PEM }}
 
       - name: Add to Developer Board
         env:
           TOKEN: ${{ steps.generate_token.outputs.token }}
-        uses: actions/add-to-project@v0.4.0
+        uses: actions/add-to-project@v0.5.0
         with:
           project-url: https://github.com/orgs/hdmf-dev/projects/7
           github-token: ${{ env.TOKEN }}
 
       - name: Add to Community Board
         env:
           TOKEN: ${{ steps.generate_token.outputs.token }}
-        uses: actions/add-to-project@v0.4.0
+        uses: actions/add-to-project@v0.5.0
         with:
           project-url: https://github.com/orgs/hdmf-dev/projects/8
           github-token: ${{ env.TOKEN }}

.github/workflows/ruff.yml

@@ -5,5 +5,7 @@ jobs:
   ruff:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v3
-      - uses: chartboost/ruff-action@v1
+      - name: Checkout repo
+        uses: actions/checkout@v4
+      - name: Run ruff
+        uses: chartboost/ruff-action@v1