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stephprincestephprince
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Fix gh actions failures (#2016)
* link to stable hdmf-zarr docs * remove scipy misc import from tutorial * fix tox env setup * update CHANGELOG.md * update zarr intersphinx mapping
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‎.github/workflows/run_all_tests.yml‎

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fail-fast: false
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matrix:
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include:
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- { name: linux-python3.9-minimum , test-tox-env: test-py39-minimum , build-tox-env: build-py39-minimum , python-ver: "3.9" , os: ubuntu-latest }
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- { name: linux-python3.10 , test-tox-env: test-py310 , build-tox-env: build-py310 , python-ver: "3.10", os: ubuntu-latest }
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- { name: linux-python3.11 , test-tox-env: test-py311 , build-tox-env: build-py311 , python-ver: "3.11", os: ubuntu-latest }
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- { name: linux-python3.11-opt , test-tox-env: test-py311-optional , build-tox-env: build-py311 , python-ver: "3.11", os: ubuntu-latest }
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- { name: linux-python3.12 , test-tox-env: test-py312 , build-tox-env: build-py312 , python-ver: "3.12", os: ubuntu-latest }
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- { name: linux-python3.13 , test-tox-env: test-py313 , build-tox-env: build-py313 , python-ver: "3.13", os: ubuntu-latest }
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- { name: linux-python3.13-upgraded , test-tox-env: test-py313-upgraded , build-tox-env: build-py313-upgraded , python-ver: "3.13", os: ubuntu-latest }
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- { name: linux-python3.13-prerelease , test-tox-env: test-py313-prerelease, build-tox-env: build-py313-prerelease, python-ver: "3.13", os: ubuntu-latest }
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- { name: windows-python3.9-minimum , test-tox-env: test-py39-minimum , build-tox-env: build-py39-minimum , python-ver: "3.9" , os: windows-latest }
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- { name: windows-python3.10 , test-tox-env: test-py310 , build-tox-env: build-py310 , python-ver: "3.10", os: windows-latest }
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- { name: windows-python3.11 , test-tox-env: test-py311 , build-tox-env: build-py311 , python-ver: "3.11", os: windows-latest }
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- { name: windows-python3.11-opt , test-tox-env: test-py311-optional , build-tox-env: build-py311 , python-ver: "3.11", os: windows-latest }
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- { name: windows-python3.12 , test-tox-env: test-py312 , build-tox-env: build-py312 , python-ver: "3.12", os: windows-latest }
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- { name: windows-python3.13 , test-tox-env: test-py313 , build-tox-env: build-py313 , python-ver: "3.13", os: windows-latest }
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- { name: windows-python3.13-upgraded , test-tox-env: test-py313-upgraded , build-tox-env: build-py313-upgraded , python-ver: "3.13", os: windows-latest }
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- { name: windows-python3.13-prerelease, test-tox-env: test-py313-prerelease, build-tox-env: build-py313-prerelease, python-ver: "3.13", os: windows-latest }
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- { name: macos-python3.9-minimum , test-tox-env: test-py39-minimum , build-tox-env: build-py39-minimum , python-ver: "3.9" , os: macos-13 }
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- { name: macos-python3.10 , test-tox-env: test-py310 , build-tox-env: build-py310 , python-ver: "3.10", os: macos-latest }
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- { name: macos-python3.11 , test-tox-env: test-py311 , build-tox-env: build-py311 , python-ver: "3.11", os: macos-latest }
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- { name: macos-python3.11-opt , test-tox-env: test-py311-optional , build-tox-env: build-py311 , python-ver: "3.11", os: macos-latest }
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- { name: macos-python3.12 , test-tox-env: test-py312 , build-tox-env: build-py312 , python-ver: "3.12", os: macos-latest }
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- { name: macos-python3.13 , test-tox-env: test-py313 , build-tox-env: build-py313 , python-ver: "3.13", os: macos-latest }
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- { name: macos-python3.13-upgraded , test-tox-env: test-py313-upgraded , build-tox-env: build-py313-upgraded , python-ver: "3.13", os: macos-latest }
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- { name: macos-python3.13-prerelease , test-tox-env: test-py313-prerelease, build-tox-env: build-py313-prerelease, python-ver: "3.13", os: macos-latest }
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- { name: linux-python3.9-minimum , test-tox-env: test-py39-minimum , build-tox-env: build-py39-minimum , python-ver: "3.9" , os: ubuntu-latest }
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- { name: linux-python3.10 , test-tox-env: test-py310-pinned , build-tox-env: build-py310-pinned , python-ver: "3.10", os: ubuntu-latest }
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- { name: linux-python3.11 , test-tox-env: test-py311-pinned , build-tox-env: build-py311-pinned , python-ver: "3.11", os: ubuntu-latest }
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- { name: linux-python3.11-opt , test-tox-env: test-py311-optional-pinned, build-tox-env: build-py311-pinned , python-ver: "3.11", os: ubuntu-latest }
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- { name: linux-python3.12 , test-tox-env: test-py312-pinned , build-tox-env: build-py312-pinned , python-ver: "3.12", os: ubuntu-latest }
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- { name: linux-python3.13 , test-tox-env: test-py313-pinned , build-tox-env: build-py313-pinned , python-ver: "3.13", os: ubuntu-latest }
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- { name: linux-python3.13-upgraded , test-tox-env: test-py313-upgraded , build-tox-env: build-py313-upgraded , python-ver: "3.13", os: ubuntu-latest }
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- { name: linux-python3.13-prerelease , test-tox-env: test-py313-prerelease , build-tox-env: build-py313-prerelease, python-ver: "3.13", os: ubuntu-latest }
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- { name: windows-python3.9-minimum , test-tox-env: test-py39-minimum , build-tox-env: build-py39-minimum , python-ver: "3.9" , os: windows-latest }
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- { name: windows-python3.10 , test-tox-env: test-py310-pinned , build-tox-env: build-py310-pinned , python-ver: "3.10", os: windows-latest }
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- { name: windows-python3.11 , test-tox-env: test-py311-pinned , build-tox-env: build-py311-pinned , python-ver: "3.11", os: windows-latest }
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- { name: windows-python3.11-opt , test-tox-env: test-py311-optional-pinned, build-tox-env: build-py311-pinned , python-ver: "3.11", os: windows-latest }
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- { name: windows-python3.12 , test-tox-env: test-py312-pinned , build-tox-env: build-py312-pinned , python-ver: "3.12", os: windows-latest }
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- { name: windows-python3.13 , test-tox-env: test-py313-pinned , build-tox-env: build-py313-pinned , python-ver: "3.13", os: windows-latest }
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- { name: windows-python3.13-upgraded , test-tox-env: test-py313-upgraded , build-tox-env: build-py313-upgraded , python-ver: "3.13", os: windows-latest }
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- { name: windows-python3.13-prerelease, test-tox-env: test-py313-prerelease , build-tox-env: build-py313-prerelease, python-ver: "3.13", os: windows-latest }
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- { name: macos-python3.9-minimum , test-tox-env: test-py39-minimum , build-tox-env: build-py39-minimum , python-ver: "3.9" , os: macos-13 }
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- { name: macos-python3.10 , test-tox-env: test-py310-pinned , build-tox-env: build-py310-pinned , python-ver: "3.10", os: macos-latest }
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- { name: macos-python3.11 , test-tox-env: test-py311-pinned , build-tox-env: build-py311-pinned , python-ver: "3.11", os: macos-latest }
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- { name: macos-python3.11-opt , test-tox-env: test-py311-optional-pinned, build-tox-env: build-py311-pinned , python-ver: "3.11", os: macos-latest }
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- { name: macos-python3.12 , test-tox-env: test-py312-pinned , build-tox-env: build-py312-pinned , python-ver: "3.12", os: macos-latest }
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- { name: macos-python3.13 , test-tox-env: test-py313-pinned , build-tox-env: build-py313-pinned , python-ver: "3.13", os: macos-latest }
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- { name: macos-python3.13-upgraded , test-tox-env: test-py313-upgraded , build-tox-env: build-py313-upgraded , python-ver: "3.13", os: macos-latest }
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- { name: macos-python3.13-prerelease , test-tox-env: test-py313-prerelease , build-tox-env: build-py313-prerelease, python-ver: "3.13", os: macos-latest }
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steps:
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- name: Cancel non-latest runs
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uses: styfle/[email protected]
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matrix:
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include:
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- { name: conda-linux-python3.9-minimum , test-tox-env: test-py39-minimum , build-tox-env: build-py39-minimum , python-ver: "3.9" , os: ubuntu-latest }
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- { name: conda-linux-python3.10 , test-tox-env: test-py310 , build-tox-env: build-py310 , python-ver: "3.10", os: ubuntu-latest }
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- { name: conda-linux-python3.11 , test-tox-env: test-py311 , build-tox-env: build-py311 , python-ver: "3.11", os: ubuntu-latest }
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- { name: conda-linux-python3.12 , test-tox-env: test-py312 , build-tox-env: build-py312 , python-ver: "3.12", os: ubuntu-latest }
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- { name: conda-linux-python3.13 , test-tox-env: test-py313 , build-tox-env: build-py313 , python-ver: "3.13", os: ubuntu-latest }
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- { name: conda-linux-python3.10 , test-tox-env: test-py310-pinned , build-tox-env: build-py310-pinned , python-ver: "3.10", os: ubuntu-latest }
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- { name: conda-linux-python3.11 , test-tox-env: test-py311-pinned , build-tox-env: build-py311-pinned , python-ver: "3.11", os: ubuntu-latest }
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- { name: conda-linux-python3.12 , test-tox-env: test-py312-pinned , build-tox-env: build-py312-pinned , python-ver: "3.12", os: ubuntu-latest }
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- { name: conda-linux-python3.13 , test-tox-env: test-py313-pinned , build-tox-env: build-py313-pinned , python-ver: "3.13", os: ubuntu-latest }
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- { name: conda-linux-python3.13-upgraded , test-tox-env: test-py313-upgraded , build-tox-env: build-py313-upgraded , python-ver: "3.13", os: ubuntu-latest }
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- { name: conda-linux-python3.13-prerelease, test-tox-env: test-py313-prerelease, build-tox-env: build-py313-prerelease, python-ver: "3.13", os: ubuntu-latest }
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steps:

‎CHANGELOG.md‎

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### Documentation and tutorial enhancements
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- Updated `SpikeEventSeries`, `DecompositionSeries`, and `FilteredEphys` examples. @stephprince [#2012](https://github.com/NeurodataWithoutBorders/pynwb/pull/2012)
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- Replaced deprecated `scipy.misc.face` dataset in the images tutorial with another example. @stephprince [#2016](https://github.com/NeurodataWithoutBorders/pynwb/pull/2016)
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## PyNWB 2.8.3 (November 19, 2024)
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‎docs/gallery/domain/images.py‎

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# :py:class:`~pynwb.image.IndexSeries` that indexes into the
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# :py:class:`~pynwb.base.Images`.
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from scipy import misc
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from pynwb.base import ImageReferences
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from pynwb.image import GrayscaleImage, Images, IndexSeries, RGBImage
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gs_face = GrayscaleImage(
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name="gs_face",
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data=misc.face(gray=True),
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description="Grayscale version of a raccoon.",
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resolution=35.433071,
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)
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rgb_face = RGBImage(
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name="rgb_face",
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data=misc.face(),
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resolution=70.0,
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description="RGB version of a raccoon.",
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)
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images = Images(
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name="raccoons",
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images=[rgb_face, gs_face],
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images=[rgb_logo, gs_logo],
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description="A collection of raccoons.",
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order_of_images=ImageReferences("order_of_images", [rgb_face, gs_face]),
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order_of_images=ImageReferences("order_of_images", [rgb_logo, gs_logo]),
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)
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idx_series = IndexSeries(

‎docs/source/conf.py‎

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'fsspec': ("https://filesystem-spec.readthedocs.io/en/latest/", None),
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'nwbwidgets': ("https://nwb-widgets.readthedocs.io/en/latest/", None),
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'nwb-overview': ("https://nwb-overview.readthedocs.io/en/latest/", None),
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'zarr': ("https://zarr.readthedocs.io/en/stable/", None),
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'hdmf-zarr': ("https://hdmf-zarr.readthedocs.io/en/latest/", None),
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'zarr': ("https://zarr.readthedocs.io/en/v2.18.4/", None), # TODO - update when hdmf-zarr supports Zarr 3.0
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'hdmf-zarr': ("https://hdmf-zarr.readthedocs.io/en/stable/", None),
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'numcodecs': ("https://numcodecs.readthedocs.io/en/latest/", None),
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}
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'hdmf-docs': ('https://hdmf.readthedocs.io/en/stable/%s', '%s'),
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'dandi': ('https://www.dandiarchive.org/%s', '%s'),
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"nwbinspector": ("https://nwbinspector.readthedocs.io/en/dev/%s", "%s"),
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'hdmf-zarr': ('https://hdmf-zarr.readthedocs.io/en/latest/%s', '%s'),
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'hdmf-zarr': ('https://hdmf-zarr.readthedocs.io/en/stable/%s', '%s'),
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}
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nitpicky = True

‎tox.ini‎

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# and then run "tox" from this directory.
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[tox]
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envlist = test-py{39,310,311,312,313}-pinned
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requires = pip >= 22.0
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[testenv]
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build: python -m build
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wheelinstall: python -c "import pynwb"
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# list of pre-defined environments. (Technically environments not listed here
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# like build-py312 can also be used.)
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# list of pre-defined environments.
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[testenv:test-py313-upgraded]
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[testenv:test-py313-prerelease]
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[testenv:test-py311-optional-pinned] # some optional reqs not compatible with py312 yet

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