Update dates and how optional deps are specified and tested

.github/ISSUE_TEMPLATE/bug_report.yml

@@ -46,15 +46,6 @@ body:
         - Linux
     validations:
       required: true
-  - type: dropdown
-    id: executable
-    attributes:
-      label: Python Executable
-      options:
-        - Conda
-        - Python
-    validations:
-      required: true
   - type: dropdown
     id: python_version
     attributes:
@@ -65,6 +56,7 @@ body:
         - "3.11"
         - "3.10"
         - "3.9"
+        - "newer"
     validations:
       required: true
   - type: textarea

.github/PULL_REQUEST_TEMPLATE/release.md

@@ -2,11 +2,8 @@ Prepare for release of HDMF [version]
 
 ### Before merging:
 - [ ] Make sure all PRs to be included in this release have been merged to `dev`.
-- [ ] 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.
-  Run `pip install pur && pur -r requirements-dev.txt -r requirements.txt -r requirements-opt.txt`
-  and manually update `environment-ros3.yml`.
+- [ ] Major and minor releases: Update dependency ranges in `pyproject.toml` and minimums in
+  `requirements-min.txt` as needed.
 - [ ] 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
@@ -34,5 +31,5 @@ Prepare for release of HDMF [version]
 4. Either monitor [conda-forge/hdmf-feedstock](https://github.com/conda-forge/hdmf-feedstock) for the
    regro-cf-autotick-bot bot to create a PR updating the version of HDMF to the latest PyPI release, usually within
    24 hours of release, or manually create a PR updating `recipe/meta.yaml` with the latest version number
-   and SHA256 retrieved from PyPI > HDMF > Download Files > View hashes for the `.tar.gz` file. Re-render and update
-   dependencies as needed.
+   and SHA256 retrieved from PyPI > HDMF > Download Files > View hashes for the `.tar.gz` file. Re-render and
+   update the dependencies as needed.

.github/workflows/check_sphinx_links.yml

@@ -21,13 +21,12 @@ jobs:
       - name: Set up Python
         uses: actions/setup-python@v5
         with:
-          python-version: '3.11'  # TODO update to 3.12 when optional reqs (e.g., oaklib) support 3.12
+          python-version: '3.12'  # TODO: Update to 3.13 when linkml and its deps support 3.13
 
       - name: Install Sphinx dependencies and package
         run: |
           python -m pip install --upgrade pip
-          python -m pip install -r requirements-doc.txt -r requirements-opt.txt
-          python -m pip install .
+          python -m pip install ".[all]"
 
       - name: Check Sphinx internal and external links
         run: sphinx-build -W -b linkcheck ./docs/source ./test_build

.github/workflows/deploy_release.yml

@@ -18,7 +18,7 @@ jobs:
       - name: Set up Python
         uses: actions/setup-python@v5
         with:
-          python-version: '3.12'
+          python-version: '3.13'
 
       - name: Install build dependencies
         run: |
@@ -28,7 +28,7 @@ jobs:
 
       - name: Run tox tests
         run: |
-          tox -e py312-upgraded
+          tox -e py313-upgraded
 
       - name: Build wheel and source distribution
         run: |

.github/workflows/run_all_tests.yml

@@ -25,30 +25,27 @@ jobs:
       fail-fast: false
       matrix:
         include:
-          - { name: linux-python3.9-minimum       , test-tox-env: pytest-py39-minimum          , python-ver: "3.9" , os: ubuntu-latest }
-          - { name: linux-python3.10              , test-tox-env: pytest-py310-pinned          , python-ver: "3.10", os: ubuntu-latest }
-          - { name: linux-python3.11              , test-tox-env: pytest-py311-pinned          , python-ver: "3.11", os: ubuntu-latest }
-          - { name: linux-python3.11-optional     , test-tox-env: pytest-py311-optional-pinned , python-ver: "3.11", os: ubuntu-latest }
-          - { name: linux-python3.12              , test-tox-env: pytest-py312-pinned          , python-ver: "3.12", os: ubuntu-latest }
-          - { name: linux-python3.13              , test-tox-env: pytest-py313-pinned          , python-ver: "3.13", os: ubuntu-latest }
-          - { name: linux-python3.13-upgraded     , test-tox-env: pytest-py313-upgraded        , python-ver: "3.13", os: ubuntu-latest }
-          - { name: linux-python3.13-prerelease   , test-tox-env: pytest-py313-prerelease      , python-ver: "3.13", os: ubuntu-latest }
-          - { name: windows-python3.9-minimum     , test-tox-env: pytest-py39-minimum          , python-ver: "3.9" , os: windows-latest }
-          - { name: windows-python3.10            , test-tox-env: pytest-py310-pinned          , python-ver: "3.10", os: windows-latest }
-          - { name: windows-python3.11            , test-tox-env: pytest-py311-pinned          , python-ver: "3.11", os: windows-latest }
-          - { name: windows-python3.11-optional   , test-tox-env: pytest-py311-optional-pinned , python-ver: "3.11", os: windows-latest }
-          - { name: windows-python3.12            , test-tox-env: pytest-py312-pinned          , python-ver: "3.12", os: windows-latest }
-          - { name: windows-python3.13            , test-tox-env: pytest-py313-pinned          , python-ver: "3.13", os: windows-latest }
-          - { name: windows-python3.13-upgraded   , test-tox-env: pytest-py313-upgraded        , python-ver: "3.13", os: windows-latest }
-          - { name: windows-python3.13-prerelease , test-tox-env: pytest-py313-prerelease      , python-ver: "3.13", os: windows-latest }
-          - { name: macos-python3.9-minimum       , test-tox-env: pytest-py39-minimum          , python-ver: "3.9" , os: macos-13 }
-          - { name: macos-python3.10              , test-tox-env: pytest-py310-pinned          , python-ver: "3.10", os: macos-latest }
-          - { name: macos-python3.11              , test-tox-env: pytest-py311-pinned          , python-ver: "3.11", os: macos-latest }
-          - { name: macos-python3.11-optional     , test-tox-env: pytest-py311-optional-pinned , python-ver: "3.11", os: macos-latest }
-          - { name: macos-python3.12              , test-tox-env: pytest-py312-pinned          , python-ver: "3.12", os: macos-latest }
-          - { name: macos-python3.13              , test-tox-env: pytest-py313-pinned          , python-ver: "3.13", os: macos-latest }
-          - { name: macos-python3.13-upgraded     , test-tox-env: pytest-py313-upgraded        , python-ver: "3.13", os: macos-latest }
-          - { name: macos-python3.13-prerelease   , test-tox-env: pytest-py313-prerelease      , python-ver: "3.13", os: macos-latest }
+          - { name: linux-python3.9-minimum                , test-tox-env: pytest-py39-minimum              , python-ver: "3.9" , os: ubuntu-latest }
+          - { name: linux-python3.10-upgraded              , test-tox-env: pytest-py310-upgraded            , python-ver: "3.10", os: ubuntu-latest }
+          - { name: linux-python3.11-upgraded              , test-tox-env: pytest-py311-upgraded            , python-ver: "3.11", os: ubuntu-latest }
+          - { name: linux-python3.12-upgraded              , test-tox-env: pytest-py312-upgraded            , python-ver: "3.12", os: ubuntu-latest }
+          - { name: linux-python3.13-upgraded              , test-tox-env: pytest-py313-upgraded            , python-ver: "3.13", os: ubuntu-latest }
+          - { name: linux-python3.13-upgraded-optional     , test-tox-env: pytest-py313-upgraded-optional   , python-ver: "3.13", os: ubuntu-latest }
+          - { name: linux-python3.13-prerelease-optional   , test-tox-env: pytest-py313-prerelease-optional , python-ver: "3.13", os: ubuntu-latest }
+          - { name: windows-python3.9-minimum              , test-tox-env: pytest-py39-minimum              , python-ver: "3.9" , os: windows-latest }
+          - { name: windows-python3.10-upgraded            , test-tox-env: pytest-py310-upgraded            , python-ver: "3.10", os: windows-latest }
+          - { name: windows-python3.11-upgraded            , test-tox-env: pytest-py311-upgraded            , python-ver: "3.11", os: windows-latest }
+          - { name: windows-python3.12-upgraded            , test-tox-env: pytest-py312-upgraded            , python-ver: "3.12", os: windows-latest }
+          - { name: windows-python3.13-upgraded            , test-tox-env: pytest-py313-upgraded            , python-ver: "3.13", os: windows-latest }
+          - { name: windows-python3.13-upgraded-optional   , test-tox-env: pytest-py313-upgraded-optional   , python-ver: "3.13", os: windows-latest }
+          - { name: windows-python3.13-prerelease-optional , test-tox-env: pytest-py313-prerelease-optional , python-ver: "3.13", os: windows-latest }
+          - { name: macos-python3.9-minimum                , test-tox-env: pytest-py39-minimum              , python-ver: "3.9" , os: macos-13 }
+          - { name: macos-python3.10-upgraded              , test-tox-env: pytest-py310-upgraded            , python-ver: "3.10", os: macos-latest }
+          - { name: macos-python3.11-upgraded              , test-tox-env: pytest-py311-upgraded            , python-ver: "3.11", os: macos-latest }
+          - { name: macos-python3.12-upgraded              , test-tox-env: pytest-py312-upgraded            , python-ver: "3.12", os: macos-latest }
+          - { name: macos-python3.13-upgraded              , test-tox-env: pytest-py313-upgraded            , python-ver: "3.13", os: macos-latest }
+          - { name: macos-python3.13-upgraded-optional     , test-tox-env: pytest-py313-upgraded-optional   , python-ver: "3.13", os: macos-latest }
+          - { name: macos-python3.13-prerelease-optional   , test-tox-env: pytest-py313-prerelease-optional , python-ver: "3.13", os: macos-latest }
     steps:
       - name: Checkout repo with submodules
         uses: actions/checkout@v4
@@ -97,18 +94,16 @@ jobs:
       fail-fast: false
       matrix:
         include:
-          - { name: linux-gallery-python3.9-minimum      , test-tox-env: gallery-py39-minimum          , python-ver: "3.9" , os: ubuntu-latest }
-          - { name: linux-gallery-python3.11-optional    , test-tox-env: gallery-py311-optional-pinned , python-ver: "3.11", os: ubuntu-latest }
-          - { name: linux-gallery-python3.13-upgraded    , test-tox-env: gallery-py313-upgraded        , python-ver: "3.13", os: ubuntu-latest }
-          - { name: linux-gallery-python3.13-prerelease  , test-tox-env: gallery-py313-prerelease      , python-ver: "3.13", os: ubuntu-latest }
-          - { name: windows-gallery-python3.9-minimum    , test-tox-env: gallery-py39-minimum          , python-ver: "3.9" , os: windows-latest }
-          - { name: windows-gallery-python3.11-optional  , test-tox-env: gallery-py311-optional-pinned , python-ver: "3.11", os: windows-latest }
-          - { name: windows-gallery-python3.13-upgraded  , test-tox-env: gallery-py313-upgraded        , python-ver: "3.13", os: windows-latest }
-          - { name: windows-gallery-python3.13-prerelease, test-tox-env: gallery-py313-prerelease      , python-ver: "3.13", os: windows-latest }
-          - { name: macos-gallery-python3.9-minimum      , test-tox-env: gallery-py39-minimum          , python-ver: "3.9" , os: macos-13 }
-          - { name: macos-gallery-python3.11-optional    , test-tox-env: gallery-py311-optional-pinned , python-ver: "3.11", os: macos-latest }
-          - { name: macos-gallery-python3.13-upgraded    , test-tox-env: gallery-py313-upgraded        , python-ver: "3.13", os: macos-latest }
-          - { name: macos-gallery-python3.13-prerelease  , test-tox-env: gallery-py313-prerelease      , python-ver: "3.13", os: macos-latest }
+          # TODO: Update to 3.13 when linkml and its deps support 3.13
+          - { name: linux-gallery-python3.9-minimum                , test-tox-env: gallery-py39-minimum              , python-ver: "3.9" , os: ubuntu-latest }
+          - { name: linux-gallery-python3.12-upgraded-optional     , test-tox-env: gallery-py312-upgraded-optional   , python-ver: "3.12", os: ubuntu-latest }
+          - { name: linux-gallery-python3.12-prerelease-optional   , test-tox-env: gallery-py312-prerelease-optional , python-ver: "3.12", os: ubuntu-latest }
+          - { name: windows-gallery-python3.9-minimum              , test-tox-env: gallery-py39-minimum              , python-ver: "3.9" , os: windows-latest }
+          - { name: windows-gallery-python3.12-upgraded-optional   , test-tox-env: gallery-py312-upgraded-optional   , python-ver: "3.12", os: windows-latest }
+          - { name: windows-gallery-python3.12-prerelease-optional , test-tox-env: gallery-py312-prerelease-optional , python-ver: "3.12", os: windows-latest }
+          - { name: macos-gallery-python3.9-minimum                , test-tox-env: gallery-py39-minimum              , python-ver: "3.9" , os: macos-13 }
+          - { name: macos-gallery-python3.12-upgraded-optional     , test-tox-env: gallery-py312-upgraded-optional   , python-ver: "3.12", os: macos-latest }
+          - { name: macos-gallery-python3.12-prerelease-optional   , test-tox-env: gallery-py312-prerelease-optional , python-ver: "3.12", os: macos-latest }
     steps:
       - name: Checkout repo with submodules
         uses: actions/checkout@v4
@@ -131,70 +126,6 @@ jobs:
         run: |
           tox -e ${{ matrix.test-tox-env }}
 
-  run-all-tests-on-conda:
-    name: ${{ matrix.name }}
-    runs-on: ubuntu-latest
-    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:
-        include:
-          - { name: conda-linux-python3.9-minimum     , test-tox-env: pytest-py39-minimum          , python-ver: "3.9" , os: ubuntu-latest }
-          - { name: conda-linux-python3.10            , test-tox-env: pytest-py310-pinned          , python-ver: "3.10", os: ubuntu-latest }
-          - { name: conda-linux-python3.11            , test-tox-env: pytest-py311-pinned          , python-ver: "3.11", os: ubuntu-latest }
-          - { name: conda-linux-python3.11-optional   , test-tox-env: pytest-py311-optional-pinned , python-ver: "3.11", os: ubuntu-latest }
-          - { name: conda-linux-python3.13            , test-tox-env: pytest-py313-pinned          , python-ver: "3.13", os: ubuntu-latest }
-          - { name: conda-linux-python3.13-upgraded   , test-tox-env: pytest-py313-upgraded        , python-ver: "3.13", os: ubuntu-latest }
-          - { name: conda-linux-python3.13-prerelease , test-tox-env: pytest-py313-prerelease      , python-ver: "3.13", os: ubuntu-latest }
-    steps:
-      - name: Checkout repo with submodules
-        uses: actions/checkout@v4
-        with:
-          submodules: 'recursive'
-          fetch-depth: 0  # tags are required to determine the version
-
-      - name: Set up Conda
-        uses: conda-incubator/setup-miniconda@v3
-        with:
-          auto-update-conda: true
-          python-version: ${{ matrix.python-ver }}
-          channels: conda-forge
-
-      - name: Install build dependencies
-        run: |
-          conda config --set always_yes yes --set changeps1 no
-          conda info
-          conda install -c conda-forge "tox>=4"
-
-      - name: Conda reporting
-        run: |
-          conda info
-          conda config --show-sources
-          conda list --show-channel-urls
-
-      # NOTE tox installs packages from PyPI not conda-forge...
-      - name: Run tox tests
-        run: |
-          tox -e ${{ matrix.test-tox-env }}
-
-      - name: Build wheel and source distribution
-        run: |
-          tox -e build
-          ls -1 dist
-
-      - name: Test installation from a wheel
-        run: |
-          tox -e wheelinstall --installpkg dist/*-none-any.whl
-
-      - name: Test installation from a source distribution
-        run: |
-          tox -e wheelinstall --installpkg dist/*.tar.gz
-
   run-ros3-tests:
     name: ${{ matrix.name }}
     runs-on: ${{ matrix.os }}

.github/workflows/run_coverage.yml

@@ -31,7 +31,7 @@ jobs:
           - { os: macos-latest  , opt_req: false }
     env:  # used by codecov-action
       OS: ${{ matrix.os }}
-      PYTHON: '3.11'  # TODO update to 3.12 when optional reqs (e.g., oaklib) support 3.12
+      PYTHON: '3.12'  # TODO: Update to 3.13 when linkml and its deps support 3.13
     steps:
       - name: Checkout repo with submodules
         uses: actions/checkout@v4
@@ -44,24 +44,26 @@ jobs:
         with:
           python-version: ${{ env.PYTHON }}
 
-      - name: Install dependencies
+      - name: Upgrade pip
         run: |
           python -m pip install --upgrade pip
-          python -m pip install -r requirements-dev.txt -r requirements.txt
-
-      - name: Install optional dependencies
-        if: ${{ matrix.opt_req }}
-        run: python -m pip install -r requirements-opt.txt
 
       - name: Install package
+        if: ${{ ! matrix.opt_req }}
         run: |
-          python -m pip install .
-          python -m pip list
+          python -m pip install ".[test]"
+
+      - name: Install package with optional dependencies
+        if: ${{ matrix.opt_req }}
+        run: |
+          python -m pip install ".[test,tqdm,zarr,termset]"
 
       - name: Run tests and generate coverage report
         run: |
           # coverage is configured in pyproject.toml
-          pytest --cov --cov-report=xml --cov-report=term  # codecov uploader requires xml format
+          # codecov uploader requires xml format
+          python -m pip list
+          pytest --cov --cov-report=xml --cov-report=term
 
       - name: Upload coverage to Codecov
         uses: codecov/codecov-action@v5

.github/workflows/run_hdmf_zarr_tests.yml

@@ -31,7 +31,7 @@ jobs:
           python -m pip list
           git clone https://github.com/hdmf-dev/hdmf-zarr.git
           cd hdmf-zarr
-          python -m pip install .[test]  # this will install a different version of hdmf from the current one
+          python -m pip install ".[test]"  # this will install a different version of hdmf from the current one
           cd ..
           python -m pip uninstall -y hdmf  # uninstall the other version of hdmf
           python -m pip install .  # reinstall current branch of hdmf

.github/workflows/run_pynwb_tests.yml

@@ -21,7 +21,7 @@ jobs:
       - name: Set up Python
         uses: actions/setup-python@v5
         with:
-          python-version: '3.12'
+          python-version: '3.13'
 
       - name: Update pip
         run: python -m pip install --upgrade pip