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When installing napari, an error originates from a subprocess error: metadata-generation-failed #78
0) (4.65.0)
Collecting vispy<0.12,>=0.11.0
Using cached vispy-0.11.0.tar.gz (2.4 MB)
Installing build dependencies ... done
Getting requirements to build wheel ... done
Preparing metadata (pyproject.toml) ... done
Requirement already satisfied: wrapt>=1.11.1 in /Users/macbook/miniconda3/envs/ome/lib/python3.11/site-packages (from napari[all]->napari-spatialdata==0.1.0) (1.15.0)
Collecting PyQt5!=5.15.0,>=5.12.3
Downloading PyQt5-5.15.9.tar.gz (3.2 MB)
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 3.2/3.2 MB 19.9 MB/s eta 0:00:00
Installing build dependencies ... done
Getting requirements to build wheel ... done
Preparing metadata (pyproject.toml) ... error
error: subprocess-exited-with-error
× Preparing metadata (pyproject.toml) did not run successfully.
│ exit code: 1
╰─> [20 lines of output]
Querying qmake about your Qt installation...
Traceback (most recent call last):
File "/Users/macbook/miniconda3/envs/ome/lib/python3.11/site-packages/pip/_vendor/pyproject_hooks/_in_process/_in_process.py", line 353, in <module>
main()
File "/Users/macbook/miniconda3/envs/ome/lib/python3.11/site-packages/pip/_vendor/pyproject_hooks/_in_process/_in_process.py", line 335, in main
json_out['return_val'] = hook(**hook_input['kwargs'])
^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/macbook/miniconda3/envs/ome/lib/python3.11/site-packages/pip/_vendor/pyproject_hooks/_in_process/_in_process.py", line 152, in prepare_metadata_for_build_wheel
whl_basename = backend.build_wheel(metadata_directory, config_settings)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/private/tmp/pip-build-env-wx_q2j85/overlay/lib/python3.11/site-packages/sipbuild/api.py", line 46, in build_wheel
project = AbstractProject.bootstrap('wheel',
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/private/tmp/pip-build-env-wx_q2j85/overlay/lib/python3.11/site-packages/sipbuild/abstract_project.py", line 87, in bootstrap
project.setup(pyproject, tool, tool_description)
File "/private/tmp/pip-build-env-wx_q2j85/overlay/lib/python3.11/site-packages/sipbuild/project.py", line 602, in setup
self.update(tool)
File "/private/tmp/pip-install-jcxal8c7/pyqt5_32d3bc3caad54e24a9c755b581b79574/project.py", line 165, in update
raise UserException(
sipbuild.exceptions.UserException
[end of output]
note: This error originates from a subprocess, and is likely not a problem with pip.
error: metadata-generation-failed
× Encountered error while generating package metadata.
╰─> See above for output.
note: This is an issue with the package mentioned above, not pip.
hint: See above for details.
In my case a workaround was to install from source and change a bit the dependencies. Here are the steps:
clone the repo
in setup.cfg, replace napari[all] with napari
pip install -e .
pip install PyQt6 (or even PyQt5 if you are not with an Apple Silicon chip (so not with the arm64 architecture, which is not supported by PyQt5)
This may work already. In my case the installation didn't give me errors, but I was getting runtime errors due to Apple Silicon packages incompatibility with numcodecs and vispy. A workaround was simply
Hi!
I am using Mac and pip install with python 3.9.
pip install spatialdata
import spatialdata as sd
from napari_spatialdata import Interactive
Now I met with another problem. When I launched napari, I cannot use console. ***@***.***
And my terminal of pycharm looks like this
***@***.***
From: LucaMarconato ***@***.***>
Date: Friday, May 19, 2023 at 2:32 PM
To: scverse/napari-spatialdata ***@***.***>
Cc: Naiqiao Ye ***@***.***>, Mention ***@***.***>
Subject: Re: [scverse/napari-spatialdata] When installing napari, an error originates from a subprocess error: metadata-generation-failed (Issue #78)
Hi @yedeer12<https://github.com/yedeer12>, I have never encountered this issue. To help me understand better I kindly ask you to share the following information:
* operating system
* environment used (pip/conda/etc)
* python version
* commands to reproduce the installation and the error
Thank you 😊
—
Reply to this email directly, view it on GitHub<#78 (comment)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/AY3QENB5MI3N3NJZF6U7WWDXG64DTANCNFSM6AAAAAAYH7W5AI>.
You are receiving this because you were mentioned.Message ID: ***@***.***>
In my case a workaround was to install from source and change a bit the dependencies. Here are the steps:
clone the repo
in setup.cfg, replace napari[all] with napari
pip install -e .
pip install PyQt6 (or even PyQt5 if you are not with an Apple Silicon chip (so not with the arm64 architecture, which is not supported by PyQt5)
This may work already. In my case the installation didn't give me errors, but I was getting runtime errors due to Apple Silicon packages incompatibility with numcodecs and vispy. A workaround was simply
In my case a workaround was to install from source and change a bit the dependencies. Here are the steps:
clone the repo
in setup.cfg, replace napari[all] with napari
pip install -e .
pip install PyQt6 (or even PyQt5 if you are not with an Apple Silicon chip (so not with the arm64 architecture, which is not supported by PyQt5)
This may work already. In my case the installation didn't give me errors, but I was getting runtime errors due to Apple Silicon packages incompatibility with numcodecs and vispy. A workaround was simply
Activity
LucaMarconato commentedon May 19, 2023
Hi @yedeer12, I have never encountered this issue. To help me understand better I kindly ask you to share the following information:
Thank you 😊
LucaMarconato commentedon May 20, 2023
I could reproduce with
mamba, Apple Silicon Mac, Python 3.11.I did the following:
the last command give the error:
LucaMarconato commentedon May 20, 2023
In my case a workaround was to install from source and change a bit the dependencies. Here are the steps:
setup.cfg, replacenapari[all]withnaparipip install -e .pip install PyQt6(or evenPyQt5if you are not with an Apple Silicon chip (so not with thearm64architecture, which is not supported byPyQt5)This may work already. In my case the installation didn't give me errors, but I was getting runtime errors due to Apple Silicon packages incompatibility with
numcodecsandvispy. A workaround was simplyThe incompatibility with
numcodecsmay be due to a dependency ofmultiscale_spatial_image(see here spatial-image/multiscale-spatial-image#77).@yedeer12 if you try please let me know if it works for you.
LucaMarconato commentedon May 22, 2023
@berombau also pointed out that is better to remove
[all]cc @giovpyedeer12 commentedon Jun 5, 2023
yedeer12 commentedon Jun 5, 2023
It works
yedeer12 commentedon Jun 5, 2023
This works! But I have another problem after launched napari.
yedeer12 commentedon Jun 5, 2023
When I try to save the shape by shift+E, there is no response and my console in napari looks empty.
I wonder how to save the shape.
giovp commentedon Jun 5, 2023
hi @yedeer12 , the save shape functionality is currently being reworked by @melonora , will keep you posted once it's ready but should be soon!
yedeer12 commentedon Jun 5, 2023
Thanks!
melonora commentedon Oct 16, 2023
Bit late but draft PR is open #168, it has some dependencies on work in SpatialData itself though, but will be available soon.
LucaMarconato commentedon Oct 16, 2023
(closed because the installation has been fixed by #111)