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test: napari==0.5.3 related fixes, Constraints upgrades: imageio, ipython, numpy, qtconsole, scipy, simpleitk, tifffile #1183

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merged 8 commits into from
Sep 3, 2024
Merged

test: napari==0.5.3 related fixes, Constraints upgrades: imageio, ipython, numpy, qtconsole, scipy, simpleitk, tifffile #1183

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1e7781e
Update bundle dependencies.
Czaki Sep 2, 2024
6b9e71f
disable ststus checker thread
Czaki Sep 3, 2024
5a348c1
fix monkey patching
Czaki Sep 3, 2024
98377e9
try use ImportError
Czaki Sep 3, 2024
38d94bf
fix 2
Czaki Sep 3, 2024
67f3fd6
improve testing bundle procedure
Czaki Sep 3, 2024
d0ec818
disable PTC-W0043 warning in test bundle
Czaki Sep 3, 2024
9531aa7
Merge branch 'develop' into auto-dependency-upgrades
Czaki Sep 3, 2024
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1 change: 1 addition & 0 deletions package/tests/test_PartSeg/conftest.py
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Original file line number Diff line number Diff line change
Expand Up @@ -51,6 +51,7 @@ def _prepare_layers(self, image, parameters, replace):
self._add_image(napari_image_view._prepare_layers(image, parameters, replace))

monkeypatch.setattr(napari_image_view.ImageView, "_prepare_layers", _prepare_layers)
monkeypatch.setattr("napari._qt.threads.status_checker.StatusChecker.start", lambda x: None, raising=False)


@pytest.fixture(autouse=True)
Expand Down
41 changes: 20 additions & 21 deletions requirements/constraints_py3.10.txt
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Original file line number Diff line number Diff line change
Expand Up @@ -26,7 +26,7 @@ build==1.2.1
# via npe2
cachey==0.2.1
# via napari
certifi==2024.7.4
certifi==2024.8.30
# via
# napari
# requests
Expand All @@ -45,7 +45,7 @@ coverage==7.6.1
# via partseg (pyproject.toml)
czifile==2019.7.2
# via partseg (pyproject.toml)
dask==2024.8.0
dask==2024.8.2
# via napari
debugpy==1.8.5
# via ipykernel
Expand All @@ -63,15 +63,15 @@ exceptiongroup==1.2.2
# via
# ipython
# pytest
executing==2.0.1
executing==2.1.0
# via stack-data
flexcache==0.3
# via pint
flexparser==0.3.1
# via pint
fonticon-fontawesome6==6.4.0
# via partseg (pyproject.toml)
freetype-py==2.4.0
freetype-py==2.5.1
# via vispy
fsspec==2024.6.1
# via dask
Expand All @@ -81,11 +81,11 @@ heapdict==1.0.1
# via cachey
hsluv==5.0.4
# via vispy
idna==3.7
idna==3.8
# via requests
imagecodecs==2024.6.1
# via partseg (pyproject.toml)
imageio==2.35.0
imageio==2.35.1
# via
# -r requirements/version_denylist.txt
# partseg (pyproject.toml)
Expand All @@ -94,7 +94,7 @@ imageio==2.35.0
# scikit-image
imagesize==1.4.1
# via sphinx
importlib-metadata==8.2.0
importlib-metadata==8.4.0
# via
# build
# dask
Expand All @@ -107,7 +107,7 @@ ipykernel==6.29.5
# partseg (pyproject.toml)
# napari-console
# qtconsole
ipython==8.26.0
ipython==8.27.0
# via
# partseg (pyproject.toml)
# ipykernel
Expand Down Expand Up @@ -145,7 +145,7 @@ lxml==5.3.0
# via
# partseg (pyproject.toml)
# lxml-html-clean
lxml-html-clean==0.2.0
lxml-html-clean==0.2.2
# via lxml
magicgui==0.9.1
# via
Expand All @@ -165,7 +165,7 @@ mdurl==0.1.2
# via markdown-it-py
mpmath==1.3.0
# via sympy
napari==0.5.2
napari==0.5.3
# via partseg (pyproject.toml)
napari-console==0.0.9
# via napari
Expand All @@ -183,7 +183,7 @@ npe2==0.7.7
# via
# -r requirements/version_denylist.txt
# napari
numpy==1.26.4
numpy==2.1.0
# via
# partseg (pyproject.toml)
# czifile
Expand Down Expand Up @@ -346,14 +346,13 @@ pyyaml==6.0.2
# dask
# napari
# npe2
pyzmq==26.1.0
pyzmq==26.2.0
# via
# ipykernel
# jupyter-client
# qtconsole
qtawesome==1.3.1
# via partseg (pyproject.toml)
qtconsole==5.5.2
qtconsole==5.6.0
# via
# partseg (pyproject.toml)
# napari-console
Expand All @@ -376,7 +375,7 @@ requests==2.32.3
# pooch
# pyconify
# sphinx
rich==13.7.1
rich==13.8.0
# via
# npe2
# typer
Expand All @@ -388,7 +387,7 @@ scikit-image==0.24.0
# via
# partseg (pyproject.toml)
# napari
scipy==1.14.0
scipy==1.14.1
# via
# partseg (pyproject.toml)
# napari
Expand All @@ -397,7 +396,7 @@ sentry-sdk==2.13.0
# via
# -r requirements/version_denylist.txt
# partseg (pyproject.toml)
setuptools==72.2.0
setuptools==74.0.0
# via
# pyinstaller
# pyinstaller-hooks-contrib
Expand All @@ -410,7 +409,7 @@ shiboken6==6.4.2
# pyside6
# pyside6-addons
# pyside6-essentials
simpleitk==2.3.1
simpleitk==2.4.0
# via partseg (pyproject.toml)
six==1.16.0
# via
Expand Down Expand Up @@ -444,7 +443,7 @@ sympy==1.13.2
# via partseg (pyproject.toml)
tabulate==0.9.0
# via numpydoc
tifffile==2024.8.10
tifffile==2024.8.30
# via
# partseg (pyproject.toml)
# czifile
Expand Down Expand Up @@ -482,7 +481,7 @@ traitlets==5.14.3
# jupyter-core
# matplotlib-inline
# qtconsole
typer==0.12.3
typer==0.12.5
# via npe2
typing-extensions==4.12.2
# via
Expand Down Expand Up @@ -516,5 +515,5 @@ xlrd==2.0.1
# via partseg (pyproject.toml)
xlsxwriter==3.2.0
# via partseg (pyproject.toml)
zipp==3.20.0
zipp==3.20.1
# via importlib-metadata
43 changes: 21 additions & 22 deletions requirements/constraints_py3.10_pydantic_1.txt
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Original file line number Diff line number Diff line change
Expand Up @@ -24,7 +24,7 @@ build==1.2.1
# via npe2
cachey==0.2.1
# via napari
certifi==2024.7.4
certifi==2024.8.30
# via
# napari
# requests
Expand All @@ -43,7 +43,7 @@ coverage==7.6.1
# via partseg (pyproject.toml)
czifile==2019.7.2
# via partseg (pyproject.toml)
dask==2024.8.0
dask==2024.8.2
# via napari
debugpy==1.8.5
# via ipykernel
Expand All @@ -61,15 +61,15 @@ exceptiongroup==1.2.2
# via
# ipython
# pytest
executing==2.0.1
executing==2.1.0
# via stack-data
flexcache==0.3
# via pint
flexparser==0.3.1
# via pint
fonticon-fontawesome6==6.4.0
# via partseg (pyproject.toml)
freetype-py==2.4.0
freetype-py==2.5.1
# via vispy
fsspec==2024.6.1
# via dask
Expand All @@ -79,11 +79,11 @@ heapdict==1.0.1
# via cachey
hsluv==5.0.4
# via vispy
idna==3.7
idna==3.8
# via requests
imagecodecs==2024.6.1
# via partseg (pyproject.toml)
imageio==2.35.0
imageio==2.35.1
# via
# -r requirements/version_denylist.txt
# partseg (pyproject.toml)
Expand All @@ -92,7 +92,7 @@ imageio==2.35.0
# scikit-image
imagesize==1.4.1
# via sphinx
importlib-metadata==8.2.0
importlib-metadata==8.4.0
# via
# build
# dask
Expand All @@ -105,7 +105,7 @@ ipykernel==6.29.5
# partseg (pyproject.toml)
# napari-console
# qtconsole
ipython==8.26.0
ipython==8.27.0
# via
# partseg (pyproject.toml)
# ipykernel
Expand Down Expand Up @@ -143,7 +143,7 @@ lxml==5.3.0
# via
# partseg (pyproject.toml)
# lxml-html-clean
lxml-html-clean==0.2.0
lxml-html-clean==0.2.2
# via lxml
magicgui==0.9.1
# via
Expand All @@ -163,7 +163,7 @@ mdurl==0.1.2
# via markdown-it-py
mpmath==1.3.0
# via sympy
napari==0.5.2
napari==0.5.3
# via partseg (pyproject.toml)
napari-console==0.0.9
# via napari
Expand All @@ -181,7 +181,7 @@ npe2==0.7.7
# via
# -r requirements/version_denylist.txt
# napari
numpy==1.26.4
numpy==2.1.0
# via
# partseg (pyproject.toml)
# czifile
Expand Down Expand Up @@ -272,7 +272,7 @@ pure-eval==0.2.3
# via stack-data
pyconify==0.1.6
# via superqt
pydantic==1.10.17
pydantic==1.10.18
# via
# -c requirements/pydantic_1.txt
# partseg (pyproject.toml)
Expand Down Expand Up @@ -343,14 +343,13 @@ pyyaml==6.0.2
# dask
# napari
# npe2
pyzmq==26.1.0
pyzmq==26.2.0
# via
# ipykernel
# jupyter-client
# qtconsole
qtawesome==1.3.1
# via partseg (pyproject.toml)
qtconsole==5.5.2
qtconsole==5.6.0
# via
# partseg (pyproject.toml)
# napari-console
Expand All @@ -373,7 +372,7 @@ requests==2.32.3
# pooch
# pyconify
# sphinx
rich==13.7.1
rich==13.8.0
# via
# npe2
# typer
Expand All @@ -385,7 +384,7 @@ scikit-image==0.24.0
# via
# partseg (pyproject.toml)
# napari
scipy==1.14.0
scipy==1.14.1
# via
# partseg (pyproject.toml)
# napari
Expand All @@ -394,7 +393,7 @@ sentry-sdk==2.13.0
# via
# -r requirements/version_denylist.txt
# partseg (pyproject.toml)
setuptools==72.2.0
setuptools==74.0.0
# via
# pyinstaller
# pyinstaller-hooks-contrib
Expand All @@ -407,7 +406,7 @@ shiboken6==6.4.2
# pyside6
# pyside6-addons
# pyside6-essentials
simpleitk==2.3.1
simpleitk==2.4.0
# via partseg (pyproject.toml)
six==1.16.0
# via
Expand Down Expand Up @@ -441,7 +440,7 @@ sympy==1.13.2
# via partseg (pyproject.toml)
tabulate==0.9.0
# via numpydoc
tifffile==2024.8.10
tifffile==2024.8.30
# via
# partseg (pyproject.toml)
# czifile
Expand Down Expand Up @@ -479,7 +478,7 @@ traitlets==5.14.3
# jupyter-core
# matplotlib-inline
# qtconsole
typer==0.12.3
typer==0.12.5
# via npe2
typing-extensions==4.12.2
# via
Expand Down Expand Up @@ -512,5 +511,5 @@ xlrd==2.0.1
# via partseg (pyproject.toml)
xlsxwriter==3.2.0
# via partseg (pyproject.toml)
zipp==3.20.0
zipp==3.20.1
# via importlib-metadata
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