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merged 5 commits into from
Jan 9, 2025
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Merged

Fix gh actions failures #2016

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590ea16
link to stable hdmf-zarr docs
stephprince Jan 9, 2025
425033b
remove scipy misc import from tutorial
stephprince Jan 9, 2025
32ed15e
fix tox env setup
stephprince Jan 9, 2025
dfc862c
update CHANGELOG.md
stephprince Jan 9, 2025
2ee7798
update zarr intersphinx mapping
stephprince Jan 9, 2025
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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:
Expand Down
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)

Expand Down
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(
Expand Down
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
Expand Down
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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