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Change how optional deps are set up, tested
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@rly
rly authored Jan 13, 2025
1 parent 0f4194e commit 501d545
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Showing 20 changed files with 158 additions and 261 deletions.
11 changes: 4 additions & 7 deletions .github/PULL_REQUEST_TEMPLATE/release.md
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Expand Up @@ -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
Expand Down Expand Up @@ -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.
5 changes: 2 additions & 3 deletions .github/workflows/check_sphinx_links.yml
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Expand Up @@ -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: '3.13'

- 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 ".[test,docs,full]"
- name: Check Sphinx internal and external links
run: sphinx-build -W -b linkcheck ./docs/source ./test_build
4 changes: 2 additions & 2 deletions .github/workflows/deploy_release.yml
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Expand Up @@ -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: |
Expand All @@ -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: |
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80 changes: 37 additions & 43 deletions .github/workflows/run_all_tests.yml
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Expand Up @@ -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
Expand Down Expand Up @@ -97,18 +94,15 @@ 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 }
- { name: linux-gallery-python3.9-minimum , test-tox-env: gallery-py39-minimum , python-ver: "3.9" , os: ubuntu-latest }
- { name: linux-gallery-python3.13-upgraded-optional , test-tox-env: gallery-py313-upgraded-optional , python-ver: "3.13", os: ubuntu-latest }
- { name: linux-gallery-python3.13-prerelease-optional , test-tox-env: gallery-py313-prerelease-optional , 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-python3.13-upgraded-optional , test-tox-env: gallery-py313-upgraded-optional , python-ver: "3.13", os: windows-latest }
- { name: windows-gallery-python3.13-prerelease-optional , test-tox-env: gallery-py313-prerelease-optional , 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-python3.13-upgraded-optional , test-tox-env: gallery-py313-upgraded-optional , python-ver: "3.13", os: macos-latest }
- { name: macos-gallery-python3.13-prerelease-optional , test-tox-env: gallery-py313-prerelease-optional , python-ver: "3.13", os: macos-latest }
steps:
- name: Checkout repo with submodules
uses: actions/checkout@v4
Expand Down Expand Up @@ -144,13 +138,13 @@ jobs:
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 }
- { name: conda-linux-python3.9-minimum , test-tox-env: pytest-py39-minimum , python-ver: "3.9" , os: ubuntu-latest }
- { name: conda-linux-python3.10-upgraded , test-tox-env: pytest-py310-upgraded , python-ver: "3.10", os: ubuntu-latest }
- { name: conda-linux-python3.11-upgraded , test-tox-env: pytest-py311-upgraded , python-ver: "3.11", os: ubuntu-latest }
- { name: conda-linux-python3.12-upgraded , test-tox-env: pytest-py312-upgraded , python-ver: "3.12", 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-upgraded-optional , test-tox-env: pytest-py313-upgraded-optional , python-ver: "3.13", os: ubuntu-latest }
- { name: conda-linux-python3.13-prerelease-optional , test-tox-env: pytest-py313-prerelease-optional , python-ver: "3.13", os: ubuntu-latest }
steps:
- name: Checkout repo with submodules
uses: actions/checkout@v4
Expand Down
22 changes: 11 additions & 11 deletions .github/workflows/run_coverage.yml
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Expand Up @@ -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: '3.13'
steps:
- name: Checkout repo with submodules
uses: actions/checkout@v4
Expand All @@ -44,24 +44,24 @@ 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
run: |
python -m pip install .
python -m pip list
if: ! ${{ matrix.opt_req }}
run: python -m pip install ".[test]"

- name: Install package with optional dependencies
if: ${{ matrix.opt_req }}
run: python -m pip install ".[test,full]"

- 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
Expand Down
2 changes: 1 addition & 1 deletion .github/workflows/run_hdmf_zarr_tests.yml
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Expand Up @@ -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
Expand Down
2 changes: 1 addition & 1 deletion .github/workflows/run_pynwb_tests.yml
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Expand Up @@ -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
Expand Down
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