Use simpler tox.ini, add testing for Python 3.12, and other small updates

.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/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@v4
+      - 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
+      - name: Checkout repo
         uses: actions/checkout@v4
       - name: Codespell
         uses: codespell-project/actions-codespell@v2

.github/workflows/deploy_release.yml

@@ -18,7 +18,7 @@ jobs:
       - 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

@@ -12,7 +12,7 @@ jobs:
     steps:
       - name: GitHub App token
         id: generate_token
-        uses: tibdex/github-app-token@v2.1.0
+        uses: tibdex/github-app-token@v2
         with:
           app_id: ${{ secrets.APP_ID }}
           private_key: ${{ secrets.APP_PEM }}

.github/workflows/ruff.yml

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

.github/workflows/run_coverage.yml

@@ -19,6 +19,9 @@ jobs:
     defaults:
       run:
         shell: bash
+    concurrency:
+      group: ${{ github.workflow }}-${{ github.ref }}-${{ matrix.os }}-${{ matrix.opt_req }}
+      cancel-in-progress: true
     strategy:
       matrix:
         include:
@@ -28,18 +31,13 @@ jobs:
           - { os: macos-latest  , opt_req: false }
     env:  # used by codecov-action
       OS: ${{ matrix.os }}
-      PYTHON: '3.11'
+      PYTHON: '3.11'  # TODO update to 3.12 when optional reqs (e.g., oaklib) support 3.12
     steps:
-      - name: Cancel non-latest runs
-        uses: styfle/[email protected]
-        with:
-          all_but_latest: true
-          access_token: ${{ github.token }}
-
-      - uses: actions/checkout@v4
+      - 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

.github/workflows/run_hdmf_zarr_tests.yml

@@ -8,22 +8,20 @@ on:
 jobs:
   run-hdmf-zarr-tests:
     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@v4
+      - 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: '3.10'
+          python-version: '3.10'  # use 3.10 until hdmf-zarr updates versioneer.py which breaks on newer python
 
       - name: Update pip
         run: python -m pip install --upgrade pip
@@ -33,11 +31,11 @@ jobs:
           python -m pip list
           git clone https://github.com/hdmf-dev/hdmf-zarr.git --recurse-submodules
           cd hdmf-zarr
-          python -m pip install -r requirements-dev.txt -r requirements.txt
+          python -m pip install -r requirements-dev.txt  # do not install the pinned install requirements
           # must install in editable mode for coverage to find sources
-          python -m pip install -e .  # this will install a pinned version of hdmf instead of the current one
+          python -m pip install -e .  # this will install a different version of hdmf from the current one
           cd ..
-          python -m pip uninstall -y hdmf  # uninstall the pinned version of hdmf
+          python -m pip uninstall -y hdmf  # uninstall the other version of hdmf
           python -m pip install .  # reinstall current branch of hdmf
           python -m pip list
 

.github/workflows/run_pynwb_tests.yml

@@ -8,22 +8,20 @@ on:
 jobs:
   run-pynwb-tests:
     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@v4
+      - 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: '3.12'
 
       - name: Update pip
         run: python -m pip install --upgrade pip
@@ -33,11 +31,11 @@ jobs:
           python -m pip list
           git clone https://github.com/NeurodataWithoutBorders/pynwb.git --recurse-submodules
           cd pynwb
-          python -m pip install -r requirements-dev.txt -r requirements.txt
+          python -m pip install -r requirements-dev.txt  # do not install the pinned install requirements
           # must install in editable mode for coverage to find sources
-          python -m pip install -e .  # this will install a pinned version of hdmf instead of the current one
+          python -m pip install -e .  # this will install a different version of hdmf from the current one
           cd ..
-          python -m pip uninstall -y hdmf  # uninstall the pinned version of hdmf
+          python -m pip uninstall -y hdmf  # uninstall the other version of hdmf
           python -m pip install .  # reinstall current branch of hdmf
           python -m pip list