Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

ccfwidgets fails to render #31

Open
rcpeene opened this issue Jun 15, 2023 · 5 comments
Open

ccfwidgets fails to render #31

rcpeene opened this issue Jun 15, 2023 · 5 comments

Comments

@rcpeene
Copy link

rcpeene commented Jun 15, 2023 •
edited
Loading

Running ccfwidgets with something very close to the default usage. Passing in an array of points to the CCFWidget constructor yields an error that I don't fully understand. I'm not familiar enough with the itk widgets to parse through it. This is with ccfwidget==0.5.3 and itkwidgets==0.32.6. A similar error with different error text is thrown with itkwidgets==0.32.4

The line:
ccf = CCFWidget(markers=[points])
where points is a numpy array with shape (1920, 3)

ccf = CCFWidget(markers=[points])
---------------------------------------------------------------------------
RuntimeError                              Traceback (most recent call last)
Cell In[7], line 1
----> 1 ccf = CCFWidget(markers=[points])

File /opt/hostedtoolcache/Python/3.9.17/x64/lib/python3.9/site-packages/ccfwidget/widget_ccf.py:122, in CCFWidget.__init__(self, tree, swc_morphologies, markers, marker_sizes, marker_opacities, marker_colors, selected_allen_ids, selected_acronyms, rotate, **kwargs)
    118 camera = np.array([[ 1.3441567e+03, -2.1723846e+04,  1.7496496e+04],
    119                    [ 6.5500000e+03,  3.9750000e+03,  5.6750000e+03],
    120                    [ 3.6606243e-01, -4.4908229e-01, -8.1506038e-01]], dtype=np.float32)
    121 size_limit_3d = [256,256,256]
--> 122 self.itk_viewer = view(image=self._image,
    123 label_image=self._label_image,
    124 opacity_gaussians=opacity_gaussians,
    125 label_image_blend=0.65,
    126 point_sets=markers.copy(),
    127 camera=camera,
    128 ui_collapsed=True,
    129 shadow=False,
    130 size_limit_3d=size_limit_3d,
    131 background=(0.85,)*3,
    132 units="μm",
    133 gradient_opacity=0.1)
    134 # Todo: initialization should work
    135 self.itk_viewer.opacity_gaussians = opacity_gaussians

File /opt/hostedtoolcache/Python/3.9.17/x64/lib/python3.9/site-packages/itkwidgets/widget_viewer.py:1090, in view(image, label_image, label_image_names, label_image_weights, label_image_blend, cmap, lut, select_roi, interpolation, gradient_opacity, opacity_gaussians, channels, slicing_planes, shadow, blend_mode, point_sets, point_set_colors, point_set_opacities, point_set_representations, point_set_sizes, geometries, geometry_colors, geometry_opacities, ui_collapsed, rotate, annotations, axes, mode, **kwargs)
   1087     if image is None and len(images):  # only one image is rendered
   1088         image = images[0]
-> 1090 viewer = Viewer(image=image,
   1091 label_image=label_image,
   1092 label_image_names=label_image_names,
   1093 label_image_blend=label_image_blend,
   1094 label_image_weights=label_image_weights,
   1095 cmap=cmap,
   1096 lut=lut,
   1097 select_roi=select_roi,
   1098 interpolation=interpolation,
   1099 gradient_opacity=gradient_opacity,
   1100 opacity_gaussians=opacity_gaussians,
   1101 slicing_planes=slicing_planes,
   1102 shadow=shadow,blend_mode=blend_mode,
   1103 point_sets=point_sets,
   1104 point_set_colors=point_set_colors,
   1105 point_set_opacities=point_set_opacities,
   1106 point_set_representations=point_set_representations,
   1107 point_set_sizes=point_set_sizes,
   1108 geometries=geometries,geometry_colors=geometry_colors,
   1109 geometry_opacities=geometry_opacities,
   1110 rotate=rotate,ui_collapsed=ui_collapsed,
   1111 annotations=annotations,axes=axes,mode=mode,
   1112 **kwargs)
   1113 return viewer

File /opt/hostedtoolcache/Python/3.9.17/x64/lib/python3.9/site-packages/itkwidgets/widget_viewer.py:403, in Viewer.__init__(self, **kwargs)
    401         if size[dim] > self.size_limit_3d[dim]:
    402             self._downsampling = True
--> 403 self._update_rendered_image()
    404 if self._downsampling:
    405     self.observe(self._on_roi_changed, ['roi'])

File /opt/hostedtoolcache/Python/3.9.17/x64/lib/python3.9/site-packages/itkwidgets/widget_viewer.py:520, in Viewer._update_rendered_image(self)
    517         return
    519 if self.image:
--> 520     self.shrinker.UpdateLargestPossibleRegion()
    521 if self.label_image:
    522     self.label_image_shrinker.UpdateLargestPossibleRegion()

RuntimeError: /work/ITK-source/ITK/Modules/Core/Common/src/itkDataObject.cxx:[367](https://github.com/AllenInstitute/openscope_databook/actions/runs/5283149469/jobs/9559011685#step:9:368):
Requested region is (at least partially) outside the largest possible region.
----------------------------- Captured stderr call -----------------------------
/work/ITK-source/ITK/Modules/ThirdParty/VNL/src/vxl/core/vnl/algo/vnl_svd.hxx: suspicious return value (3) from SVDC
/work/ITK-source/ITK/Modules/ThirdParty/VNL/src/vxl/core/vnl/algo/vnl_svd.hxx: M is 3x3
M = [ ...
             nan              nan              nan 
             nan              nan              nan 
             nan              nan              nan  ]
/work/ITK-source/ITK/Modules/ThirdParty/VNL/src/vxl/core/vnl/algo/vnl_svd.hxx: suspicious return value (3) from SVDC
/work/ITK-source/ITK/Modules/ThirdParty/VNL/src/vxl/core/vnl/algo/vnl_svd.hxx: M is 3x3
M = [ ...
             nan              nan              nan 
             nan              nan              nan 
             nan              nan              nan  ]
/work/ITK-source/ITK/Modules/ThirdParty/VNL/src/vxl/core/vnl/algo/vnl_svd.hxx: suspicious return value (3) from SVDC
/work/ITK-source/ITK/Modules/ThirdParty/VNL/src/vxl/core/vnl/algo/vnl_svd.hxx: M is 3x3
M = [ ...
             nan              nan              nan 
             nan              nan              nan 
             nan              nan              nan  ]
/work/ITK-source/ITK/Modules/ThirdParty/VNL/src/vxl/core/vnl/algo/vnl_svd.hxx: suspicious return value (3) from SVDC
/work/ITK-source/ITK/Modules/ThirdParty/VNL/src/vxl/core/vnl/algo/vnl_svd.hxx: M is 3x3
M = [ ...
             nan              nan              nan 
             nan              nan              nan 
             nan              nan              nan  ]
/work/ITK-source/ITK/Modules/ThirdParty/VNL/src/vxl/core/vnl/algo/vnl_svd.hxx: suspicious return value (3) from SVDC
/work/ITK-source/ITK/Modules/ThirdParty/VNL/src/vxl/core/vnl/algo/vnl_svd.hxx: M is 3x3
M = [ ...
             nan              nan              nan 
             nan              nan              nan 
             nan              nan              nan  ]
/work/ITK-source/ITK/Modules/ThirdParty/VNL/src/vxl/core/vnl/algo/vnl_svd.hxx: suspicious return value (3) from SVDC
/work/ITK-source/ITK/Modules/ThirdParty/VNL/src/vxl/core/vnl/algo/vnl_svd.hxx: M is 3x3
M = [ ...
             nan              nan              nan 
             nan              nan              nan 
             nan              nan              nan  ]
/work/ITK-source/ITK/Modules/ThirdParty/VNL/src/vxl/core/vnl/algo/vnl_svd.hxx: suspicious return value (3) from SVDC
/work/ITK-source/ITK/Modules/ThirdParty/VNL/src/vxl/core/vnl/algo/vnl_svd.hxx: M is 3x3
M = [ ...
             nan              nan              nan 
             nan              nan              nan 
             nan              nan              nan  ]
/work/ITK-source/ITK/Modules/ThirdParty/VNL/src/vxl/core/vnl/algo/vnl_svd.hxx: suspicious return value (3) from SVDC
/work/ITK-source/ITK/Modules/ThirdParty/VNL/src/vxl/core/vnl/algo/vnl_svd.hxx: M is 3x3
M = [ ...
             nan              nan              nan 
             nan              nan              nan 
             nan              nan              nan  ]
/work/ITK-source/ITK/Modules/ThirdParty/VNL/src/vxl/core/vnl/algo/vnl_svd.hxx: suspicious return value (3) from SVDC
/work/ITK-source/ITK/Modules/ThirdParty/VNL/src/vxl/core/vnl/algo/vnl_svd.hxx: M is 3x3
M = [ ...
             nan              nan              nan 
             nan              nan              nan 
             nan              nan              nan  ]
@rcpeene
Copy link
Author

rcpeene commented Jun 16, 2023

This only appears to be an issue when running tests on my github ubuntu runner. On my windows machine this problem does not occur.

@bendichter
Copy link
Contributor

@rcpeene this sounds like it could be an issue due to different dependencies. Could you provide pip freeze on the two different systems?

@rcpeene
Copy link
Author

rcpeene commented Jun 20, 2023

I have what I believe to be the same relevant dependencies on both.
Here's my local machine

accessible-pygments==0.0.4
aiohttp==3.8.3
aiosignal==1.3.1
alabaster==0.7.12
anyio==3.6.2
appdirs==1.4.4
argon2-cffi==21.3.0
argon2-cffi-bindings==21.2.0
argschema==2.0.2
arrow==1.2.3
asciitree==0.3.3
asttokens==2.2.0
async-timeout==4.0.2        
attrs==21.4.0
Babel==2.10.3
backcall==0.2.0
beautifulsoup4==4.11.1      
bg-atlasapi==1.0.2
bg-space==0.6.0
bidsschematools==0.6.0      
bleach==5.0.1
boto3==1.17.21
botocore==1.20.112
bqplot==0.12.36
brainrender==2.0.5.5
bs4==0.0.1
cachetools==4.2.4
ccfwidget==0.5.3
certifi==2022.9.24
cffi==1.15.1
chardet==3.0.4
charset-normalizer==2.1.1
ci-info==0.3.0
click==8.1.3
click-didyoumean==0.3.0
cloudpickle==2.2.0
colorama==0.4.6
colorcet==3.0.1
commonmark==0.9.1
contourpy==1.0.6
coverage==7.2.1
cycler==0.11.0
dandi==0.46.6
dandischema==0.7.1
dask==2022.11.1
databook-utils @ file:///C:/Users/carter.peene/Desktop/Projects/openscope_databook
debugpy==1.6.4
decorator==5.1.1
defusedxml==0.7.1
Deprecated==1.2.13
distro==1.8.0
dnspython==2.2.1
docutils==0.17.1
elephant==0.12.0
email-validator==1.3.0
entrypoints==0.4
etelemetry==0.3.0
exceptiongroup==1.1.0
execnet==1.9.0
executing==1.2.0
fasteners==0.18
fastjsonschema==2.16.2
fonttools==4.38.0
fqdn==1.5.1
frozenlist==1.3.3
fscacher==0.2.0
fsspec==2022.11.0
future==0.18.2
gast==0.4.0
gitdb==4.0.9
GitPython==3.1.27
Glymur==0.8.19
google==3.0.0
greenlet==1.1.3
h5py==3.7.0
hdmf==3.6.1
humanize==4.4.0
idna==3.4
imagecodecs==2022.9.26
imageio==2.22.4
imagesize==1.4.1
importlib-metadata==4.13.0
importlib-resources==5.10.0
iniconfig==2.0.0
interleave==0.2.1
ipycanvas==0.13.1
ipydatagrid==1.1.14
ipydatawidgets==4.3.2
ipyevents==2.0.1
ipykernel==6.17.1
ipympl==0.9.2
ipysheet==0.5.0
ipython==8.7.0
ipython-genutils==0.2.0
ipytree==0.2.2
ipyvolume==0.6.0a10
ipyvtklink==0.2.3
ipyvue==1.8.0
ipyvuetify==1.8.4
ipywebrtc==0.6.0
ipywidgets==7.7.2
isoduration==20.11.0
itk-core==5.3.0
itk-filtering==5.3.0
itk-meshtopolydata==0.10.0
itk-numerics==5.3.0
itkwidgets==0.32.4
jaraco.classes==3.2.3
jedi==0.18.2
Jinja2==3.1.2
JIT==0.0.1
jmespath==0.10.0
joblib==1.2.0
jsonpointer==2.3
jsonschema==3.2.0
jupyter==1.0.0
jupyter-book==0.13.0
jupyter-cache==0.4.3
jupyter-console==6.4.4
jupyter-server==1.23.3
jupyter-server-mathjax==0.2.6
jupyter-sphinx==0.3.2
jupyter_client==7.4.7
jupyter_core==5.1.0
jupyterlab-pygments==0.2.2
jupyterlab-widgets==1.1.1
K3D==2.7.4
keyring==23.11.0
keyrings.alt==4.2.0
kiwisolver==1.4.4
latexcodec==2.0.1
linkify-it-py==1.0.3
llvmlite==0.39.1
locket==1.0.0
loguru==0.6.0
lxml==4.9.1
markdown-it-py==1.1.0
MarkupSafe==2.1.1
marshmallow==3.0.0rc6
matplotlib==3.6.2
matplotlib-inline==0.1.6
matplotlib-venn==0.11.9
mdit-py-plugins==0.2.8
meshio==5.3.4
mistune==0.8.4
more-itertools==9.0.0
morphapi==0.1.7
MorphIO==3.3.3
mpl-interactions==0.22.0
msgpack==1.0.4
multidict==6.0.2
myst-nb==0.13.2
myst-parser==0.15.2
myterial==1.2.1
natsort==8.2.0
nbclassic==0.4.8
nbclient==0.5.13
nbconvert==6.5.4
nbdime==3.1.1
nbformat==5.7.0
nbmake==1.3.5
ndx-events==0.2.0
ndx-grayscalevolume==0.0.2
ndx-icephys-meta==0.1.0
ndx-spectrum==0.2.2
neo==0.12.0
nest-asyncio==1.5.6
networkx==2.8.8
neurom==3.2.2
notebook==6.5.2
notebook_shim==0.2.2
numba==0.56.4
numcodecs==0.10.2
numexpr==2.8.3
numpy==1.22.4
nwbinspector==0.4.20
nwbwidgets==0.10.0
opencv-python==4.6.0.66
ophys-nway-matching @ git+https://github.com/AllenInstitute/ophys_nway_matching@545504ab55922717ab623f8ede2c521a60aa1458
packaging==21.3
pandas==1.5.2
pandocfilters==1.5.0
param==1.12.2
parso==0.8.3
partd==1.3.0
patsy==0.5.3
pickleshare==0.7.5
Pillow==9.3.0
pkgutil_resolve_name==1.3.10
platformdirs==2.5.4
plotly==5.11.0
pluggy==1.0.0
prometheus-client==0.15.0
prompt-toolkit==3.0.33
psutil==5.9.4
psycopg2-binary==2.9.5
pure-eval==0.2.2
py==1.11.0
py2vega==0.6.1
pybtex==0.24.0
pybtex-docutils==1.0.2
pycparser==2.21
pycryptodomex==3.16.0
pyct==0.4.8
pydantic==1.10.2
pydata-sphinx-theme==0.8.1
Pygments==2.13.0
pyinspect==0.1.0
pynrrd==0.4.3
pynwb==2.3.2
pyout==0.7.2
pyparsing==3.0.9
PyPDF2==3.0.1
pyrsistent==0.19.2
pytest==7.2.1
pytest-cov==4.0.0
pytest-xdist==3.2.1
python-dateutil==2.8.2
pythreejs==2.4.1
pytz==2022.6
PyWavelets==1.4.1
pywin32==306
pywin32-ctypes==0.2.0
pywinpty==2.0.10
PyYAML==6.0
pyzmq==24.0.1
qtconsole==5.4.0
QtPy==2.3.0
quantities==0.14.1
requests==2.28.1
requests-toolbelt==0.10.1
retry==0.9.2
rfc3339-validator==0.1.4
rfc3987==1.3.8
rich==12.6.0
ruamel.yaml==0.17.21
ruamel.yaml.clib==0.2.7
s3transfer==0.3.7
scikit-build==0.16.4
scikit-image==0.19.3
scikit-learn==1.1.2
scipy==1.9.3
seaborn==0.12.1
semantic-version==2.10.0
semver==2.13.0
Send2Trash==1.8.0
SimpleITK==2.2.1
simplejson==3.18.0
six==1.16.0
smmap==5.0.0
sniffio==1.3.0
snowballstemmer==2.2.0
soupsieve==2.3.2.post1
Sphinx==4.5.0
sphinx-book-theme==0.3.3
sphinx-comments==0.0.3
sphinx-copybutton==0.5.0
sphinx-external-toc==0.2.4
sphinx-jupyterbook-latex==0.4.7
sphinx-multitoc-numbering==0.1.3
sphinx-thebe==0.1.2
sphinx-togglebutton==0.3.2
sphinx_design==0.1.0
sphinxcontrib-applehelp==1.0.2
sphinxcontrib-bibtex==2.5.0
sphinxcontrib-devhelp==1.0.2
sphinxcontrib-htmlhelp==2.0.0
sphinxcontrib-jsmath==1.0.1
sphinxcontrib-qthelp==1.0.3
sphinxcontrib-serializinghtml==1.1.5
SQLAlchemy==1.4.41
stack-data==0.6.2
statsmodels==0.13.0
strict-rfc3339==0.7
tables==3.7.0
tabulate==0.9.0
tenacity==8.1.0
terminado==0.17.0
threadpoolctl==3.1.0
tifffile==2022.10.10
tinycss2==1.2.1
tomli==2.0.1
toolz==0.12.0
tornado==6.2
tqdm==4.64.1
traitlets==5.6.0
traittypes==0.2.1
treelib==1.6.1
trimesh==3.16.4
typing_extensions==4.4.0
uc-micro-py==1.0.1
uri-template==1.2.0
urllib3==1.26.13
util-colleenjg==0.0.1
vedo==2021.0.5
vtk==9.2.2
wcwidth==0.2.5
webcolors==1.12
webencodings==0.5.1
websocket-client==1.4.2
widgetsnbextension==3.6.1
win32-setctime==1.1.0
wrapt==1.14.1
wslink==1.8.4
xarray==2022.11.0
yarl==1.8.1
zarr==2.13.3
zipp==3.11.0
zstandard==0.19.0

And here's the github runner

accessible-pygments==0.0.4
aiohttp==3.8.4
aiosignal==1.3.1
alabaster==0.7.[13](https://github.com/AllenInstitute/openscope_databook/actions/runs/5294722262/jobs/9584356568#step:8:14)
appdirs==1.4.4
argon2-cffi==21.3.0
argon2-cffi-bindings==21.2.0
argschema==2.0.2
arrow==1.2.3
asciitree==0.3.3
asttokens==2.2.1
async-timeout==4.0.2
attrs==23.1.0
Babel==2.12.1
backcall==0.2.0
beautifulsoup4==4.12.2
bidsschematools==0.7.1
bleach==6.0.0
blessed==1.20.0
bqplot==0.12.39
ccfwidget==0.5.3
certifi==2023.5.7
cffi==1.15.1
charset-normalizer==3.1.0
ci-info==0.3.0
click==8.1.3
click-didyoumean==0.3.0
cloudpickle==2.2.1
colorcet==3.0.1
comm==0.1.3
contourpy==1.1.0
coverage==7.2.7
cryptography==41.0.1
cycler==0.11.0
dandi==0.46.6
dandischema==0.7.1
dask==2023.6.0
-e git+https://github.com/AllenInstitute/openscope_databook@b271327c48689c0c0548df8488222d17342d4dbe#egg=databook_utils
debugpy==1.6.7
decorator==5.1.1
defusedxml==0.7.1
dnspython==2.3.0
docutils==0.18.1
elephant==0.12.0
email-validator==2.0.0.post2
entrypoints==0.4
etelemetry==0.3.0
exceptiongroup==1.1.1
execnet==1.9.0
executing==1.2.0
fasteners==0.18
fastjsonschema==2.17.1
fonttools==4.40.0
fqdn==1.5.1
frozenlist==1.3.3
fscacher==0.3.0
fsspec==2022.11.0
gast==0.4.0
greenlet==2.0.2
h5py==3.7.0
hdmf==3.6.1
humanize==4.6.0
idna==3.4
imageio==2.31.1
imagesize==1.4.1
importlib-metadata==4.13.0
iniconfig==2.0.0
interleave==0.2.1
ipydatagrid==1.1.16
ipydatawidgets==4.3.2
ipykernel==6.23.2
ipympl==0.9.3
ipython==8.[14](https://github.com/AllenInstitute/openscope_databook/actions/runs/5294722262/jobs/9584356568#step:8:15).0
ipython-genutils==0.2.0
ipytree==0.2.2
ipyvolume==0.6.3
ipyvue==1.9.2
ipyvuetify==1.8.10
ipywebrtc==0.6.0
ipywidgets==7.7.5
isodate==0.6.1
isoduration==20.11.0
itk-core==5.3.0
itk-filtering==5.3.0
itk-meshtopolydata==0.10.0
itk-numerics==5.3.0
itkwidgets==0.32.6
jaraco.classes==3.2.3
jedi==0.18.2
jeepney==0.8.0
Jinja2==3.1.2
joblib==1.2.0
jsonpointer==2.4
jsonschema==4.17.3
jupyter==1.0.0
jupyter-book==0.[15](https://github.com/AllenInstitute/openscope_databook/actions/runs/5294722262/jobs/9584356568#step:8:16).1
jupyter-cache==0.6.1
jupyter-console==6.6.3
jupyter_client==8.2.0
jupyter_core==5.3.1
jupyterlab-pygments==0.2.2
jupyterlab-widgets==1.1.4
keyring==23.13.1
keyrings.alt==4.2.0
kiwisolver==1.4.4
latexcodec==2.0.1
lazy_loader==0.2
linkify-it-py==2.0.2
locket==1.0.0
markdown-it-py==2.2.0
MarkupSafe==2.0.1
marshmallow==3.0.0rc6
matplotlib==3.6.2
matplotlib-inline==0.1.6
mdit-py-plugins==0.3.5
mdurl==0.1.2
mistune==2.0.5
more-itertools==9.1.0
mpl-interactions==0.22.0
multidict==6.0.4
myst-nb==0.17.2
myst-parser==0.18.1
natsort==8.3.1
nbclient==0.6.8
nbconvert==7.5.0
nbformat==5.9.0
nbmake==1.4.1
ndx-grayscalevolume==0.0.2
ndx-icephys-meta==0.1.0
ndx-spectrum==0.2.2
neo==0.12.0
nest-asyncio==1.5.6
networkx==3.1
notebook==6.4.12
numcodecs==0.11.0
numpy==1.22.4
nwbinspector==0.4.28
nwbwidgets==0.10.0
opencv-python==4.7.0.72
ophys-nway-matching @ git+https://github.com/AllenInstitute/ophys_nway_matching@545504ab55922717ab623f8ede2c521a60aa1458
packaging==23.1
pandas==1.5.2
pandocfilters==1.5.0
param==1.13.0
parso==0.8.3
partd==1.4.0
pexpect==4.8.0
pickleshare==0.7.5
Pillow==9.3.0
platformdirs==3.5.3
plotly==5.15.0
pluggy==1.0.0
prometheus-client==0.17.0
prompt-toolkit==3.0.38
psutil==5.9.5
ptyprocess==0.7.0
pure-eval==0.2.2
py2vega==0.6.1
pybtex==0.24.0
pybtex-docutils==1.0.2
pycparser==2.21
pycryptodomex==3.18.0
pyct==0.5.0
pydantic==1.10.9
pydata-sphinx-theme==0.13.3
Pygments==2.15.1
pynwb==2.2.0
pyout==0.7.3
pyparsing==3.0.9
PyPDF2==3.0.1
pyrsistent==0.19.3
pytest==7.3.2
pytest-cov==4.1.0
pytest-xdist==3.3.1
python-dateutil==2.8.2
pythreejs==2.4.2
pytz==2023.3
PyWavelets==1.4.1
PyYAML==6.0
pyzmq==25.1.0
qtconsole==5.4.3
QtPy==2.3.1
quantities==0.14.1
requests==2.31.0
rfc3339-validator==0.1.4
rfc3987==1.3.8
ruamel.yaml==0.17.31
ruamel.yaml.clib==0.2.7
scikit-image==0.19.3
scipy==1.9.3
SecretStorage==3.3.3
semantic-version==2.10.0
Send2Trash==1.8.2
six==1.[16](https://github.com/AllenInstitute/openscope_databook/actions/runs/5294722262/jobs/9584356568#step:8:17).0
snowballstemmer==2.2.0
soupsieve==2.4.1
Sphinx==5.0.2
sphinx-book-theme==1.0.1
sphinx-comments==0.0.3
sphinx-copybutton==0.5.2
sphinx-jupyterbook-latex==0.5.2
sphinx-multitoc-numbering==0.1.3
sphinx-thebe==0.2.1
sphinx-togglebutton==0.3.2
sphinx_design==0.3.0
sphinx_external_toc==0.3.1
sphinxcontrib-applehelp==1.0.4
sphinxcontrib-bibtex==2.5.0
sphinxcontrib-devhelp==1.0.2
sphinxcontrib-htmlhelp==2.0.1
sphinxcontrib-jsmath==1.0.1
sphinxcontrib-qthelp==1.0.3
sphinxcontrib-serializinghtml==1.1.5
SQLAlchemy==2.0.16
stack-data==0.6.2
tabulate==0.9.0
tenacity==8.2.2
terminado==0.[17](https://github.com/AllenInstitute/openscope_databook/actions/runs/5294722262/jobs/9584356568#step:8:18).1
tifffile==[20](https://github.com/AllenInstitute/openscope_databook/actions/runs/5294722262/jobs/9584356568#step:8:21)23.4.12
tinycss2==1.2.1
tomli==2.0.1
toolz==0.12.0
tornado==6.3.2
tqdm==4.65.0
traitlets==5.6.0
traittypes==0.2.1
trimesh==3.22.1
typing_extensions==4.6.3
uc-micro-py==1.0.2
uri-template==1.2.0
urllib3==2.0.3
wcwidth==0.2.6
webcolors==1.13
webencodings==0.5.1
widgetsnbextension==3.6.4
xarray==2023.5.0
yarl==1.9.2
zarr==2.15.0
zipp==3.15.0
zstandard==0.[21](https://github.com/AllenInstitute/openscope_databook/actions/runs/5294722262/jobs/9584356568#step:8:22).0

@rcpeene
Copy link
Author

rcpeene commented Jun 21, 2023

I specified itkwidgets==0.32.4 but same error.

@rcpeene
Copy link
Author

rcpeene commented Jun 26, 2023

Problem was missing the right version of zarr on github runner. pip install ccfwidget not requiring the right zarr version?

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Assignees
No one assigned
Labels
None yet
Projects
None yet
Milestone
No milestone
Development

No branches or pull requests
2 participants
@bendichter @rcpeene