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Temporarily revert breaking changes for bugfix release (#1224)
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‎.github/ISSUE_TEMPLATE/bug_report.yml

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attributes:
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label: Python Version
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options:
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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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- "3.8"
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validations:
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required: true
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- type: textarea

‎.github/workflows/run_all_tests.yml

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- { name: linux-python3.9-minimum , test-tox-env: pytest-py39-minimum , python-ver: "3.9" , os: ubuntu-latest }
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- { name: linux-python3.8-minimum , test-tox-env: pytest-py38-minimum , python-ver: "3.8" , os: ubuntu-latest }
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- { name: linux-python3.9 , test-tox-env: pytest-py39-pinned , python-ver: "3.9" , os: ubuntu-latest }
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- { name: linux-python3.10 , test-tox-env: pytest-py310-pinned , python-ver: "3.10", os: ubuntu-latest }
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- { name: linux-python3.11 , test-tox-env: pytest-py311-pinned , python-ver: "3.11", os: ubuntu-latest }
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- { name: linux-python3.11-optional , test-tox-env: pytest-py311-optional-pinned , python-ver: "3.11", os: ubuntu-latest }
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- { name: linux-python3.12 , test-tox-env: pytest-py312-pinned , python-ver: "3.12", os: ubuntu-latest }
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- { name: linux-python3.13 , test-tox-env: pytest-py313-pinned , python-ver: "3.13", 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-prerelease , test-tox-env: pytest-py313-prerelease , python-ver: "3.13", 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: linux-python3.12-upgraded , test-tox-env: pytest-py312-upgraded , python-ver: "3.12", os: ubuntu-latest }
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- { name: linux-python3.12-prerelease , test-tox-env: pytest-py312-prerelease , python-ver: "3.12", os: ubuntu-latest }
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- { name: windows-python3.8-minimum , test-tox-env: pytest-py38-minimum , python-ver: "3.8" , os: windows-latest }
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- { name: windows-python3.9 , test-tox-env: pytest-py39-pinned , python-ver: "3.9" , os: windows-latest }
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- { name: windows-python3.10 , test-tox-env: pytest-py310-pinned , python-ver: "3.10", os: windows-latest }
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- { name: windows-python3.11 , test-tox-env: pytest-py311-pinned , python-ver: "3.11", os: windows-latest }
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- { name: windows-python3.11-optional , test-tox-env: pytest-py311-optional-pinned , python-ver: "3.11", os: windows-latest }
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- { name: windows-python3.12 , test-tox-env: pytest-py312-pinned , python-ver: "3.12", os: windows-latest }
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- { name: windows-python3.13 , test-tox-env: pytest-py313-pinned , python-ver: "3.13", 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-prerelease , test-tox-env: pytest-py313-prerelease , 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-python3.12-upgraded , test-tox-env: pytest-py312-upgraded , python-ver: "3.12", os: windows-latest }
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- { name: windows-python3.12-prerelease , test-tox-env: pytest-py312-prerelease , python-ver: "3.12", os: windows-latest }
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- { name: macos-python3.8-minimum , test-tox-env: pytest-py38-minimum , python-ver: "3.8" , os: macos-13 }
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- { name: macos-python3.9 , test-tox-env: pytest-py39-pinned , python-ver: "3.9" , os: macos-13 }
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- { name: macos-python3.10 , test-tox-env: pytest-py310-pinned , python-ver: "3.10", os: macos-latest }
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- { name: macos-python3.11 , test-tox-env: pytest-py311-pinned , python-ver: "3.11", os: macos-latest }
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- { name: macos-python3.11-optional , test-tox-env: pytest-py311-optional-pinned , python-ver: "3.11", os: macos-latest }
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- { name: macos-python3.12 , test-tox-env: pytest-py312-pinned , python-ver: "3.12", os: macos-latest }
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- { name: macos-python3.13 , test-tox-env: pytest-py313-pinned , python-ver: "3.13", 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-python3.13-prerelease , test-tox-env: pytest-py313-prerelease , python-ver: "3.13", 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-python3.12-prerelease , test-tox-env: pytest-py312-prerelease , python-ver: "3.12", os: macos-latest }
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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-python3.8-minimum , test-tox-env: gallery-py38-minimum , python-ver: "3.8" , os: ubuntu-latest }
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- { name: linux-gallery-python3.11-optional , test-tox-env: gallery-py311-optional-pinned , python-ver: "3.11", os: ubuntu-latest }
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- { name: linux-gallery-python3.13-upgraded , test-tox-env: gallery-py313-upgraded , python-ver: "3.13", os: ubuntu-latest }
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- { name: linux-gallery-python3.13-prerelease , test-tox-env: gallery-py313-prerelease , 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: linux-gallery-python3.12-upgraded , test-tox-env: gallery-py312-upgraded , python-ver: "3.12", os: ubuntu-latest }
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- { name: linux-gallery-python3.12-prerelease , test-tox-env: gallery-py312-prerelease , python-ver: "3.12", os: ubuntu-latest }
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- { name: windows-gallery-python3.8-minimum , test-tox-env: gallery-py38-minimum , python-ver: "3.8" , os: windows-latest }
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- { name: windows-gallery-python3.11-optional , test-tox-env: gallery-py311-optional-pinned , python-ver: "3.11", os: windows-latest }
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- { name: windows-gallery-python3.13-upgraded , test-tox-env: gallery-py313-upgraded , python-ver: "3.13", os: windows-latest }
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- { name: windows-gallery-python3.13-prerelease, test-tox-env: gallery-py313-prerelease , 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-13 }
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- { name: windows-gallery-python3.12-upgraded , test-tox-env: gallery-py312-upgraded , python-ver: "3.12", os: windows-latest }
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- { name: windows-gallery-python3.12-prerelease, test-tox-env: gallery-py312-prerelease , python-ver: "3.12", os: windows-latest }
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- { name: macos-gallery-python3.8-minimum , test-tox-env: gallery-py38-minimum , python-ver: "3.8" , os: macos-13 }
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- { name: macos-gallery-python3.11-optional , test-tox-env: gallery-py311-optional-pinned , python-ver: "3.11", os: macos-latest }
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- { name: macos-gallery-python3.13-upgraded , test-tox-env: gallery-py313-upgraded , python-ver: "3.13", os: macos-latest }
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- { name: macos-gallery-python3.13-prerelease , test-tox-env: gallery-py313-prerelease , python-ver: "3.13", os: macos-latest }
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- { name: macos-gallery-python3.12-upgraded , test-tox-env: gallery-py312-upgraded , python-ver: "3.12", os: macos-latest }
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- { name: macos-gallery-python3.12-prerelease , test-tox-env: gallery-py312-prerelease , python-ver: "3.12", os: macos-latest }
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include:
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- { name: conda-linux-python3.9-minimum , test-tox-env: pytest-py39-minimum , python-ver: "3.9" , os: ubuntu-latest }
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- { name: conda-linux-python3.8-minimum , test-tox-env: pytest-py38-minimum , python-ver: "3.8" , os: ubuntu-latest }
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- { name: conda-linux-python3.9 , test-tox-env: pytest-py39-pinned , python-ver: "3.9" , os: ubuntu-latest }
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- { name: conda-linux-python3.10 , test-tox-env: pytest-py310-pinned , python-ver: "3.10", os: ubuntu-latest }
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- { name: conda-linux-python3.11 , test-tox-env: pytest-py311-pinned , python-ver: "3.11", os: ubuntu-latest }
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- { name: conda-linux-python3.11-optional , test-tox-env: pytest-py311-optional-pinned , python-ver: "3.11", os: ubuntu-latest }
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- { name: conda-linux-python3.13 , test-tox-env: pytest-py313-pinned , python-ver: "3.13", os: ubuntu-latest }
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- { name: conda-linux-python3.13-upgraded , test-tox-env: pytest-py313-upgraded , python-ver: "3.13", os: ubuntu-latest }
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- { name: conda-linux-python3.13-prerelease , test-tox-env: pytest-py313-prerelease , python-ver: "3.13", os: ubuntu-latest }
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- { name: conda-linux-python3.12 , test-tox-env: pytest-py312-pinned , python-ver: "3.12", os: ubuntu-latest }
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- { name: conda-linux-python3.12-upgraded , test-tox-env: pytest-py312-upgraded , python-ver: "3.12", os: ubuntu-latest }
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- { name: conda-linux-python3.12-prerelease , test-tox-env: pytest-py312-prerelease , python-ver: "3.12", os: ubuntu-latest }
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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-python3.12-ros3 , python-ver: "3.12", os: ubuntu-latest }
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- { name: windows-python3.12-ros3 , python-ver: "3.12", os: windows-latest }
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- { name: macos-python3.12-ros3 , python-ver: "3.12", os: macos-latest }
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‎.github/workflows/run_coverage.yml

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- { name: linux-python3.12-ros3 , python-ver: "3.12", os: ubuntu-latest }
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‎.github/workflows/run_tests.yml

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# NOTE config below with "upload-wheels: true" specifies that wheels should be uploaded as an artifact
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- { name: linux-python3.9-minimum , test-tox-env: pytest-py39-minimum , python-ver: "3.9" , os: ubuntu-latest }
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- { name: linux-python3.13 , test-tox-env: pytest-py313-pinned , python-ver: "3.13", 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 , upload-wheels: true }
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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-python3.13-upgraded , test-tox-env: pytest-py313-upgraded , 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: macos-python3.13-upgraded , test-tox-env: pytest-py313-upgraded , python-ver: "3.13", os: macos-latest }
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- { name: linux-python3.8-minimum , test-tox-env: pytest-py38-minimum , python-ver: "3.8" , os: ubuntu-latest }
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- { name: linux-python3.12 , test-tox-env: pytest-py312-pinned , python-ver: "3.12", 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 , upload-wheels: true }
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- { name: windows-python3.8-minimum , test-tox-env: pytest-py38-minimum , python-ver: "3.8" , 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: macos-python3.8-minimum , test-tox-env: pytest-py38-minimum , python-ver: "3.8" , os: macos-13 }
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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: 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-python3.13-upgraded , test-tox-env: gallery-py313-upgraded , 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-python3.13-upgraded , test-tox-env: gallery-py313-upgraded , python-ver: "3.13", os: windows-latest }
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- { name: linux-gallery-python3.8-minimum , test-tox-env: gallery-py38-minimum , python-ver: "3.8" , os: ubuntu-latest }
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- { name: linux-gallery-python3.12-upgraded , test-tox-env: gallery-py312-upgraded , python-ver: "3.12", os: ubuntu-latest }
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- { name: windows-gallery-python3.8-minimum , test-tox-env: gallery-py38-minimum , python-ver: "3.8" , os: windows-latest }
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- { name: windows-gallery-python3.12-upgraded , test-tox-env: gallery-py312-upgraded , python-ver: "3.12", os: windows-latest }
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- { name: conda-linux-python3.13-upgraded , test-tox-env: pytest-py313-upgraded , python-ver: "3.13", os: ubuntu-latest }
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- { name: conda-linux-python3.8-minimum , test-tox-env: pytest-py38-minimum , python-ver: "3.8" , os: ubuntu-latest }
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- { name: conda-linux-python3.12-upgraded , test-tox-env: pytest-py312-upgraded , python-ver: "3.12", os: ubuntu-latest }
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‎.readthedocs.yaml

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‎CHANGELOG.md

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# HDMF Changelog
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## HDMF 4.0.0 (Upcoming)
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### Deprecations
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- The following classes have been deprecated and removed: Array, AbstractSortedArray, SortedArray, LinSpace, Query, RegionSlicer, ListSlicer, H5RegionSlicer, DataRegion, RegionBuilder. The following methods have been deprecated and removed: fmt_docval_args, call_docval_func, get_container_cls, add_child, set_dataio (now refactored as set_data_io). We have also removed all early development for region references. @mavaylon1, @rly [#1998](https://github.com/hdmf-dev/hdmf/pull/1198), [#1212](https://github.com/hdmf-dev/hdmf/pull/1212)
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- Importing from hdmf.build.map is no longer supported. Import from hdmf.build instead. @rly [#1221](https://github.com/hdmf-dev/hdmf/pull/1221)
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- Python 3.8 has been deprecated. Python 3.9 is the new minimum with support for Python 3.13. @mavaylon1 [#1209](https://github.com/hdmf-dev/hdmf/pull/1209)
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## HDMF 3.14.6 (Upcoming)
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### Enhancements
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- Added support for expandable datasets of references for untyped and compound data types. @stephprince [#1188](https://github.com/hdmf-dev/hdmf/pull/1188)

‎docs/source/conf.py

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‎docs/source/install_users.rst

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Installing HDMF
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---------------
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HDMF requires having Python 3.9-3.13 installed. If you don't have Python installed and want the simplest way to
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HDMF requires having Python 3.8, 3.9, 3.10, 3.11, or 3.12 installed. If you don't have Python installed and want the simplest way to
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get started, we recommend you install and use the `Anaconda Distribution`_. It includes Python, NumPy, and many other
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commonly used packages for scientific computing and data science.
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‎docs/source/overview_software_architecture.rst

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* :py:class:`~hdmf.build.builders.GroupBuilder` - represents a collection of objects
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* :py:class:`~hdmf.build.builders.RegionBuilder` - represents a slice into data (Subclass of :py:class:`~hdmf.build.builders.DatasetBuilder`)
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* **Main Module:** :py:class:`hdmf.build.builders`
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‎environment-ros3.yml

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- conda-forge
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- h5py==3.12.1
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- matplotlib==3.9.2
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- numpy==2.1.3
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- pandas==2.2.3
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- python==3.12
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- h5py==3.11.0
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- matplotlib==3.8.4
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- numpy==2.0.0
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- pandas==2.2.2
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- python-dateutil==2.8.2
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- pytest==8.1.2 # regression introduced in pytest 8.2.*, will be fixed in 8.3.0
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- pytest-cov==5.0.0

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