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Fix gh actions failures (#2016)
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* 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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@stephprince
stephprince authored Jan 9, 2025
1 parent 80fc386 commit b84b04a
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56 changes: 28 additions & 28 deletions .github/workflows/run_all_tests.yml
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Expand Up @@ -22,30 +22,30 @@ jobs:
fail-fast: false
matrix:
include:
- { name: linux-python3.9-minimum , test-tox-env: test-py39-minimum , build-tox-env: build-py39-minimum , python-ver: "3.9" , os: ubuntu-latest }
- { name: linux-python3.10 , test-tox-env: test-py310 , build-tox-env: build-py310 , python-ver: "3.10", os: ubuntu-latest }
- { name: linux-python3.11 , test-tox-env: test-py311 , build-tox-env: build-py311 , python-ver: "3.11", os: ubuntu-latest }
- { name: linux-python3.11-opt , test-tox-env: test-py311-optional , build-tox-env: build-py311 , python-ver: "3.11", os: ubuntu-latest }
- { name: linux-python3.12 , test-tox-env: test-py312 , build-tox-env: build-py312 , python-ver: "3.12", os: ubuntu-latest }
- { name: linux-python3.13 , test-tox-env: test-py313 , build-tox-env: build-py313 , python-ver: "3.13", os: ubuntu-latest }
- { name: linux-python3.13-upgraded , test-tox-env: test-py313-upgraded , build-tox-env: build-py313-upgraded , python-ver: "3.13", os: ubuntu-latest }
- { name: linux-python3.13-prerelease , test-tox-env: test-py313-prerelease, build-tox-env: build-py313-prerelease, python-ver: "3.13", os: ubuntu-latest }
- { name: windows-python3.9-minimum , test-tox-env: test-py39-minimum , build-tox-env: build-py39-minimum , python-ver: "3.9" , os: windows-latest }
- { name: windows-python3.10 , test-tox-env: test-py310 , build-tox-env: build-py310 , python-ver: "3.10", os: windows-latest }
- { name: windows-python3.11 , test-tox-env: test-py311 , build-tox-env: build-py311 , python-ver: "3.11", os: windows-latest }
- { name: windows-python3.11-opt , test-tox-env: test-py311-optional , build-tox-env: build-py311 , python-ver: "3.11", os: windows-latest }
- { name: windows-python3.12 , test-tox-env: test-py312 , build-tox-env: build-py312 , python-ver: "3.12", os: windows-latest }
- { name: windows-python3.13 , test-tox-env: test-py313 , build-tox-env: build-py313 , python-ver: "3.13", os: windows-latest }
- { name: windows-python3.13-upgraded , test-tox-env: test-py313-upgraded , build-tox-env: build-py313-upgraded , python-ver: "3.13", os: windows-latest }
- { name: windows-python3.13-prerelease, test-tox-env: test-py313-prerelease, build-tox-env: build-py313-prerelease, python-ver: "3.13", os: windows-latest }
- { name: macos-python3.9-minimum , test-tox-env: test-py39-minimum , build-tox-env: build-py39-minimum , python-ver: "3.9" , os: macos-13 }
- { name: macos-python3.10 , test-tox-env: test-py310 , build-tox-env: build-py310 , python-ver: "3.10", os: macos-latest }
- { name: macos-python3.11 , test-tox-env: test-py311 , build-tox-env: build-py311 , python-ver: "3.11", os: macos-latest }
- { name: macos-python3.11-opt , test-tox-env: test-py311-optional , build-tox-env: build-py311 , python-ver: "3.11", os: macos-latest }
- { name: macos-python3.12 , test-tox-env: test-py312 , build-tox-env: build-py312 , python-ver: "3.12", os: macos-latest }
- { name: macos-python3.13 , test-tox-env: test-py313 , build-tox-env: build-py313 , python-ver: "3.13", os: macos-latest }
- { name: macos-python3.13-upgraded , test-tox-env: test-py313-upgraded , build-tox-env: build-py313-upgraded , python-ver: "3.13", os: macos-latest }
- { name: macos-python3.13-prerelease , test-tox-env: test-py313-prerelease, build-tox-env: build-py313-prerelease, python-ver: "3.13", os: macos-latest }
- { name: linux-python3.9-minimum , test-tox-env: test-py39-minimum , build-tox-env: build-py39-minimum , python-ver: "3.9" , os: ubuntu-latest }
- { name: linux-python3.10 , test-tox-env: test-py310-pinned , build-tox-env: build-py310-pinned , python-ver: "3.10", os: ubuntu-latest }
- { name: linux-python3.11 , test-tox-env: test-py311-pinned , build-tox-env: build-py311-pinned , python-ver: "3.11", os: ubuntu-latest }
- { 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 }
- { name: linux-python3.12 , test-tox-env: test-py312-pinned , build-tox-env: build-py312-pinned , python-ver: "3.12", os: ubuntu-latest }
- { name: linux-python3.13 , test-tox-env: test-py313-pinned , build-tox-env: build-py313-pinned , python-ver: "3.13", os: ubuntu-latest }
- { name: linux-python3.13-upgraded , test-tox-env: test-py313-upgraded , build-tox-env: build-py313-upgraded , python-ver: "3.13", os: ubuntu-latest }
- { name: linux-python3.13-prerelease , test-tox-env: test-py313-prerelease , build-tox-env: build-py313-prerelease, python-ver: "3.13", os: ubuntu-latest }
- { name: windows-python3.9-minimum , test-tox-env: test-py39-minimum , build-tox-env: build-py39-minimum , python-ver: "3.9" , os: windows-latest }
- { name: windows-python3.10 , test-tox-env: test-py310-pinned , build-tox-env: build-py310-pinned , python-ver: "3.10", os: windows-latest }
- { name: windows-python3.11 , test-tox-env: test-py311-pinned , build-tox-env: build-py311-pinned , python-ver: "3.11", os: windows-latest }
- { 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 }
- { name: windows-python3.12 , test-tox-env: test-py312-pinned , build-tox-env: build-py312-pinned , python-ver: "3.12", os: windows-latest }
- { name: windows-python3.13 , test-tox-env: test-py313-pinned , build-tox-env: build-py313-pinned , python-ver: "3.13", os: windows-latest }
- { name: windows-python3.13-upgraded , test-tox-env: test-py313-upgraded , build-tox-env: build-py313-upgraded , python-ver: "3.13", os: windows-latest }
- { name: windows-python3.13-prerelease, test-tox-env: test-py313-prerelease , build-tox-env: build-py313-prerelease, python-ver: "3.13", os: windows-latest }
- { name: macos-python3.9-minimum , test-tox-env: test-py39-minimum , build-tox-env: build-py39-minimum , python-ver: "3.9" , os: macos-13 }
- { name: macos-python3.10 , test-tox-env: test-py310-pinned , build-tox-env: build-py310-pinned , python-ver: "3.10", os: macos-latest }
- { name: macos-python3.11 , test-tox-env: test-py311-pinned , build-tox-env: build-py311-pinned , python-ver: "3.11", os: macos-latest }
- { 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 }
- { name: macos-python3.12 , test-tox-env: test-py312-pinned , build-tox-env: build-py312-pinned , python-ver: "3.12", os: macos-latest }
- { name: macos-python3.13 , test-tox-env: test-py313-pinned , build-tox-env: build-py313-pinned , python-ver: "3.13", os: macos-latest }
- { name: macos-python3.13-upgraded , test-tox-env: test-py313-upgraded , build-tox-env: build-py313-upgraded , python-ver: "3.13", os: macos-latest }
- { name: macos-python3.13-prerelease , test-tox-env: test-py313-prerelease , build-tox-env: build-py313-prerelease, python-ver: "3.13", os: macos-latest }
steps:
- name: Cancel non-latest runs
uses: styfle/[email protected]
Expand Down Expand Up @@ -139,10 +139,10 @@ jobs:
matrix:
include:
- { 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 }
- { name: conda-linux-python3.10 , test-tox-env: test-py310 , build-tox-env: build-py310 , python-ver: "3.10", os: ubuntu-latest }
- { name: conda-linux-python3.11 , test-tox-env: test-py311 , build-tox-env: build-py311 , python-ver: "3.11", os: ubuntu-latest }
- { name: conda-linux-python3.12 , test-tox-env: test-py312 , build-tox-env: build-py312 , python-ver: "3.12", os: ubuntu-latest }
- { name: conda-linux-python3.13 , test-tox-env: test-py313 , build-tox-env: build-py313 , python-ver: "3.13", os: ubuntu-latest }
- { name: conda-linux-python3.10 , test-tox-env: test-py310-pinned , build-tox-env: build-py310-pinned , python-ver: "3.10", os: ubuntu-latest }
- { name: conda-linux-python3.11 , test-tox-env: test-py311-pinned , build-tox-env: build-py311-pinned , python-ver: "3.11", os: ubuntu-latest }
- { name: conda-linux-python3.12 , test-tox-env: test-py312-pinned , build-tox-env: build-py312-pinned , python-ver: "3.12", os: ubuntu-latest }
- { name: conda-linux-python3.13 , test-tox-env: test-py313-pinned , build-tox-env: build-py313-pinned , python-ver: "3.13", os: ubuntu-latest }
- { 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 }
- { 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 }
steps:
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1 change: 1 addition & 0 deletions CHANGELOG.md
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Expand Up @@ -13,6 +13,7 @@

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

## PyNWB 2.8.3 (November 19, 2024)

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20 changes: 2 additions & 18 deletions docs/gallery/domain/images.py
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Expand Up @@ -296,30 +296,14 @@
# :py:class:`~pynwb.image.IndexSeries` that indexes into the
# :py:class:`~pynwb.base.Images`.

from scipy import misc

from pynwb.base import ImageReferences
from pynwb.image import GrayscaleImage, Images, IndexSeries, RGBImage

gs_face = GrayscaleImage(
name="gs_face",
data=misc.face(gray=True),
description="Grayscale version of a raccoon.",
resolution=35.433071,
)

rgb_face = RGBImage(
name="rgb_face",
data=misc.face(),
resolution=70.0,
description="RGB version of a raccoon.",
)

images = Images(
name="raccoons",
images=[rgb_face, gs_face],
images=[rgb_logo, gs_logo],
description="A collection of raccoons.",
order_of_images=ImageReferences("order_of_images", [rgb_face, gs_face]),
order_of_images=ImageReferences("order_of_images", [rgb_logo, gs_logo]),
)

idx_series = IndexSeries(
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6 changes: 3 additions & 3 deletions docs/source/conf.py
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Expand Up @@ -147,8 +147,8 @@ def __call__(self, filename):
'fsspec': ("https://filesystem-spec.readthedocs.io/en/latest/", None),
'nwbwidgets': ("https://nwb-widgets.readthedocs.io/en/latest/", None),
'nwb-overview': ("https://nwb-overview.readthedocs.io/en/latest/", None),
'zarr': ("https://zarr.readthedocs.io/en/stable/", None),
'hdmf-zarr': ("https://hdmf-zarr.readthedocs.io/en/latest/", None),
'zarr': ("https://zarr.readthedocs.io/en/v2.18.4/", None), # TODO - update when hdmf-zarr supports Zarr 3.0
'hdmf-zarr': ("https://hdmf-zarr.readthedocs.io/en/stable/", None),
'numcodecs': ("https://numcodecs.readthedocs.io/en/latest/", None),
}

Expand All @@ -161,7 +161,7 @@ def __call__(self, filename):
'hdmf-docs': ('https://hdmf.readthedocs.io/en/stable/%s', '%s'),
'dandi': ('https://www.dandiarchive.org/%s', '%s'),
"nwbinspector": ("https://nwbinspector.readthedocs.io/en/dev/%s", "%s"),
'hdmf-zarr': ('https://hdmf-zarr.readthedocs.io/en/latest/%s', '%s'),
'hdmf-zarr': ('https://hdmf-zarr.readthedocs.io/en/stable/%s', '%s'),
}

nitpicky = True
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4 changes: 2 additions & 2 deletions tox.ini
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Expand Up @@ -4,6 +4,7 @@
# and then run "tox" from this directory.

[tox]
envlist = test-py{39,310,311,312,313}-pinned
requires = pip >= 22.0

[testenv]
Expand Down Expand Up @@ -32,8 +33,7 @@ commands =
build: python -m build
wheelinstall: python -c "import pynwb"

# list of pre-defined environments. (Technically environments not listed here
# like build-py312 can also be used.)
# list of pre-defined environments.
[testenv:test-py313-upgraded]
[testenv:test-py313-prerelease]
[testenv:test-py311-optional-pinned] # some optional reqs not compatible with py312 yet
Expand Down

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