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Merge branch 'dev' into release/5.0.0
2 parents 9b9153e + a5c4497 commit 219e403

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‎.github/ISSUE_TEMPLATE/bug_report.yml‎

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@@ -51,12 +51,13 @@ body:
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attributes:
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label: Python Version
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options:
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- "3.14"
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- "3.13"
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- "3.12"
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- "3.11"
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- "3.10"
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- "3.9"
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- "newer"
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- "other version (specify below)"
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validations:
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required: true
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- type: textarea

‎.github/workflows/check_sphinx_links.yml‎

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cancel-in-progress: true
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steps:
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- name: Checkout repo with submodules
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uses: actions/checkout@v5
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uses: actions/checkout@v6
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with:
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submodules: 'recursive'
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fetch-depth: 0 # tags are required to determine the version
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- name: Set up Python
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uses: actions/setup-python@v6
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with:
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python-version: '3.12' # TODO: Update to 3.13 when linkml and its deps support 3.13
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python-version: '3.13' # TODO: Update to 3.14 when linkml and its deps support 3.14
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- name: Install Sphinx dependencies and package
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run: |

‎.github/workflows/codespell.yml‎

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runs-on: ubuntu-latest
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steps:
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- name: Checkout repo
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uses: actions/checkout@v5
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uses: actions/checkout@v6
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- name: Codespell
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uses: codespell-project/actions-codespell@v2

‎.github/workflows/deploy_release.yml‎

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runs-on: ubuntu-latest
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steps:
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- name: Checkout repo with submodules
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uses: actions/checkout@v5
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uses: actions/checkout@v6
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with:
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submodules: 'recursive'
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fetch-depth: 0 # tags are required for versioneer to determine the version
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- name: Set up Python
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uses: actions/setup-python@v6
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with:
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python-version: '3.13'
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python-version: '3.14'
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- name: Install build dependencies
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run: |
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- name: Run tox tests
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run: |
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tox -e py313-upgraded
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tox -e pytest-py314-upgraded
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- name: Build wheel and source distribution
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run: |

‎.github/workflows/ruff.yml‎

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runs-on: ubuntu-latest
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steps:
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- name: Checkout repo
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uses: actions/checkout@v5
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uses: actions/checkout@v6
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- name: Run ruff
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uses: astral-sh/ruff-action@v3

‎.github/workflows/run_all_tests.yml‎

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- { name: linux-python3.11-upgraded , test-tox-env: pytest-py311-upgraded , python-ver: "3.11", os: ubuntu-latest }
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- { name: linux-python3.12-upgraded , test-tox-env: pytest-py312-upgraded , python-ver: "3.12", os: ubuntu-latest }
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- { name: linux-python3.13-upgraded , test-tox-env: pytest-py313-upgraded , python-ver: "3.13", os: ubuntu-latest }
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- { name: linux-python3.13-upgraded-optional , test-tox-env: pytest-py313-upgraded-optional , python-ver: "3.13", os: ubuntu-latest }
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- { name: linux-python3.13-prerelease-optional , test-tox-env: pytest-py313-prerelease-optional , python-ver: "3.13", os: ubuntu-latest }
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- { name: linux-python3.14-upgraded , test-tox-env: pytest-py314-upgraded , python-ver: "3.14", os: ubuntu-latest }
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- { name: linux-python3.14-upgraded-optional , test-tox-env: pytest-py314-upgraded-optional , python-ver: "3.14", os: ubuntu-latest }
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- { name: linux-python3.14-prerelease-optional , test-tox-env: pytest-py314-prerelease-optional , python-ver: "3.14", os: ubuntu-latest }
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- { name: windows-python3.9-minimum , test-tox-env: pytest-py39-minimum , python-ver: "3.9" , os: windows-latest }
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- { name: windows-python3.10-upgraded , test-tox-env: pytest-py310-upgraded , python-ver: "3.10", os: windows-latest }
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- { name: windows-python3.11-upgraded , test-tox-env: pytest-py311-upgraded , python-ver: "3.11", os: windows-latest }
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- { name: windows-python3.12-upgraded , test-tox-env: pytest-py312-upgraded , python-ver: "3.12", os: windows-latest }
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- { name: windows-python3.13-upgraded , test-tox-env: pytest-py313-upgraded , python-ver: "3.13", os: windows-latest }
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- { name: windows-python3.13-upgraded-optional , test-tox-env: pytest-py313-upgraded-optional , python-ver: "3.13", os: windows-latest }
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- { name: windows-python3.13-prerelease-optional , test-tox-env: pytest-py313-prerelease-optional , python-ver: "3.13", os: windows-latest }
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- { name: macos-python3.9-minimum , test-tox-env: pytest-py39-minimum , python-ver: "3.9" , os: macos-13 }
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- { name: windows-python3.14-upgraded , test-tox-env: pytest-py314-upgraded , python-ver: "3.14", os: windows-latest }
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- { name: windows-python3.14-upgraded-optional , test-tox-env: pytest-py314-upgraded-optional , python-ver: "3.14", os: windows-latest }
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- { name: windows-python3.14-prerelease-optional , test-tox-env: pytest-py314-prerelease-optional , python-ver: "3.14", os: windows-latest }
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- { name: macos-python3.9-minimum , test-tox-env: pytest-py39-minimum , python-ver: "3.9" , os: macos-15-intel }
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- { name: macos-python3.10-upgraded , test-tox-env: pytest-py310-upgraded , python-ver: "3.10", os: macos-latest }
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- { name: macos-python3.11-upgraded , test-tox-env: pytest-py311-upgraded , python-ver: "3.11", os: macos-latest }
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- { name: macos-python3.12-upgraded , test-tox-env: pytest-py312-upgraded , python-ver: "3.12", os: macos-latest }
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- { name: macos-python3.13-upgraded , test-tox-env: pytest-py313-upgraded , python-ver: "3.13", os: macos-latest }
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- { name: macos-python3.14-upgraded , test-tox-env: pytest-py314-upgraded , python-ver: "3.14", os: macos-latest }
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- { name: macos-python3.14-prerelease , test-tox-env: pytest-py314-prerelease , python-ver: "3.14", os: macos-latest }
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# No prebuilt wheels for numcodecs==0.15.1 for Python 3.14 on PyPI and cannot build numcodecs == 0.15.1 on macos-latest
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# So optional requirements testing on macos-latest (arm64) is disabled. See https://github.com/hdmf-dev/hdmf/pull/1367
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- { name: macos-python3.13-upgraded-optional , test-tox-env: pytest-py313-upgraded-optional , python-ver: "3.13", os: macos-latest }
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- { name: macos-python3.13-prerelease-optional , test-tox-env: pytest-py313-prerelease-optional , python-ver: "3.13", os: macos-latest }
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steps:
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- name: Checkout repo with submodules
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uses: actions/checkout@v5
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uses: actions/checkout@v6
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with:
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submodules: 'recursive'
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fetch-depth: 0 # tags are required to determine the version
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fail-fast: false
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matrix:
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include:
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# TODO: Update to 3.13 when linkml and its deps support 3.13
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# TODO: Update to 3.14 when linkml and its deps support 3.14
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- { name: linux-gallery-python3.9-minimum , test-tox-env: gallery-py39-minimum , python-ver: "3.9" , os: ubuntu-latest }
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- { name: linux-gallery-python3.12-upgraded-optional , test-tox-env: gallery-py312-upgraded-optional , python-ver: "3.12", os: ubuntu-latest }
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- { name: linux-gallery-python3.12-prerelease-optional , test-tox-env: gallery-py312-prerelease-optional , python-ver: "3.12", os: ubuntu-latest }
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- { name: linux-gallery-python3.13-upgraded-optional , test-tox-env: gallery-py313-upgraded-optional , python-ver: "3.13", os: ubuntu-latest }
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- { name: linux-gallery-python3.13-prerelease-optional , test-tox-env: gallery-py313-prerelease-optional , python-ver: "3.13", os: ubuntu-latest }
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- { name: windows-gallery-python3.9-minimum , test-tox-env: gallery-py39-minimum , python-ver: "3.9" , os: windows-latest }
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- { name: windows-gallery-python3.12-upgraded-optional , test-tox-env: gallery-py312-upgraded-optional , python-ver: "3.12", os: windows-latest }
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- { name: windows-gallery-python3.12-prerelease-optional , test-tox-env: gallery-py312-prerelease-optional , python-ver: "3.12", os: windows-latest }
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- { name: macos-gallery-python3.9-minimum , test-tox-env: gallery-py39-minimum , python-ver: "3.9" , os: macos-13 }
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- { name: macos-gallery-python3.12-upgraded-optional , test-tox-env: gallery-py312-upgraded-optional , python-ver: "3.12", os: macos-latest }
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- { name: macos-gallery-python3.12-prerelease-optional , test-tox-env: gallery-py312-prerelease-optional , python-ver: "3.12", os: macos-latest }
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- { name: windows-gallery-python3.13-upgraded-optional , test-tox-env: gallery-py313-upgraded-optional , python-ver: "3.13", os: windows-latest }
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- { name: windows-gallery-python3.13-prerelease-optional , test-tox-env: gallery-py313-prerelease-optional , python-ver: "3.13", os: windows-latest }
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- { name: macos-gallery-python3.9-minimum , test-tox-env: gallery-py39-minimum , python-ver: "3.9" , os: macos-15-intel }
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- { name: macos-gallery-python3.13-upgraded-optional , test-tox-env: gallery-py313-upgraded-optional , python-ver: "3.13", os: macos-latest }
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- { name: macos-gallery-python3.13-prerelease-optional , test-tox-env: gallery-py313-prerelease-optional , python-ver: "3.13", os: macos-latest }
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steps:
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- name: Checkout repo with submodules
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uses: actions/checkout@v5
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uses: actions/checkout@v6
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with:
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submodules: 'recursive'
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fetch-depth: 0 # tags are required to determine the version
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fail-fast: false
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matrix:
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include:
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- { name: linux-python3.13-ros3 , python-ver: "3.13", os: ubuntu-latest }
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- { name: windows-python3.13-ros3 , python-ver: "3.13", os: windows-latest }
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- { name: macos-python3.13-ros3 , python-ver: "3.13", os: macos-latest }
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- { name: linux-python3.14-ros3 , python-ver: "3.14", os: ubuntu-latest }
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- { name: windows-python3.14-ros3 , python-ver: "3.14", os: windows-latest }
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- { name: macos-python3.14-ros3 , python-ver: "3.14", os: macos-latest }
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steps:
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- name: Checkout repo with submodules
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uses: actions/checkout@v5
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uses: actions/checkout@v6
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with:
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submodules: 'recursive'
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fetch-depth: 0 # tags are required to determine the version

‎.github/workflows/run_coverage.yml‎

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- { os: macos-latest , opt_req: false }
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env: # used by codecov-action
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OS: ${{ matrix.os }}
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PYTHON: '3.12' # TODO: Update to 3.13 when linkml and its deps support 3.13
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PYTHON: '3.13' # TODO: Update to 3.14 when linkml and its deps support 3.14
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steps:
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- name: Checkout repo with submodules
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uses: actions/checkout@v5
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uses: actions/checkout@v6
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include:
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- { name: linux-python3.13-ros3 , python-ver: "3.13", os: ubuntu-latest }
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- { name: linux-python3.14-ros3 , python-ver: "3.14", os: ubuntu-latest }
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steps:
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- name: Checkout repo with submodules
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uses: actions/checkout@v5
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uses: actions/checkout@v6
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with:
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submodules: 'recursive'
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fetch-depth: 0 # tags are required to determine the version

‎.github/workflows/run_hdmf_zarr_tests.yml‎

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cancel-in-progress: true
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- name: Checkout repo with submodules
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uses: actions/checkout@v5
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uses: actions/checkout@v6
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with:
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submodules: 'recursive'
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fetch-depth: 0 # tags are required to determine the version
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- name: Set up Python
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uses: actions/setup-python@v6
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with:
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python-version: '3.13'
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python-version: '3.14'
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- name: Update pip
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run: python -m pip install --upgrade pip

‎.github/workflows/run_nwb_extension_tests.yml‎

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matrix: ${{ steps.generate-matrix.outputs.matrix }}
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steps:
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- name: Checkout repo
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uses: actions/checkout@v6
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- name: Set up Python
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fail-fast: false # Continue testing other extensions even if one fails
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- name: Checkout repo with submodules
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uses: actions/checkout@v6
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fetch-depth: 0 # tags are required to determine the version

‎.github/workflows/run_pynwb_tests.yml‎

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cancel-in-progress: true
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- name: Checkout repo with submodules
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uses: actions/checkout@v5
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uses: actions/checkout@v6
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with:
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submodules: 'recursive'
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fetch-depth: 0 # tags are required to determine the version
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- name: Set up Python
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uses: actions/setup-python@v6
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with:
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python-version: '3.13'
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python-version: '3.14'
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- name: Update pip
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run: python -m pip install --upgrade pip

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