gnodar01
commented
1 month ago Are you able to use python 3.9? If so, try it with that. 3.10 does work, but is somewhat problematic for CellProfiler 4
Open ATAICwillbebest opened 1 month ago
gnodar01
commented
1 month ago Are you able to use python 3.9? If so, try it with that. 3.10 does work, but is somewhat problematic for CellProfiler 4
OS: [Windows 11 Enterprise] CellProfiler Version [4.2.7] conda environment cellpose plugin with python3.10 git clone https://github.com/CellProfiler/CellProfiler-plugins.git Set the plugins path in CellProfiler C:\Users\86185\CellProfiler-plugins\active_plugins
Error messages Preparing metadata (setup.py) ... error error: subprocess-exited-with-error
× python setup.py egg_info did not run successfully. │ exit code: 1 ╰─> [9 lines of output] Traceback (most recent call last): File "", line 2, in
File "", line 34, in
File "C:\Users\86185\AppData\Local\Temp\pip-install-9r7yhel3\python-javabridge_026155e9a5eb4710ba15720efd54d85d\setup.py", line 412, in
ext_modules=ext_modules(),
^^^^^^^^^^^^^
File "C:\Users\86185\AppData\Local\Temp\pip-install-9r7yhel3\python-javabridge_026155e9a5eb4710ba15720efd54d85d\setup.py", line 100, in ext_modules
from numpy import get_include
ModuleNotFoundError: No module named 'numpy'
[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.
Describe the issue Installing plugins with dependencies, using CellProfiler from source，cellpose plugin installation failed
conda create -n pluginsCellpose python=3.10 conda activate pluginsCellpose git clone https://github.com/CellProfiler/CellProfiler-plugins.git cd CellProfiler-plugins pip install -e .[cellpose]
Obtaining file:///C:/Users/86185/CellProfiler-plugins Preparing metadata (setup.py) ... done Collecting cellprofiler (from cellprofiler_plugins==0.0.0) Using cached CellProfiler-4.2.7-py3-none-any.whl.metadata (2.0 kB) Collecting cellprofiler-core (from cellprofiler_plugins==0.0.0) Using cached cellprofiler_core-4.2.7-py3-none-any.whl.metadata (1.3 kB) Collecting cellpose<3.0,>=1.0.2 (from cellprofiler_plugins==0.0.0) Using cached cellpose-2.3.2-py3-none-any.whl.metadata (21 kB) Collecting numpy>=1.20.0 (from cellpose<3.0,>=1.0.2->cellprofiler_plugins==0.0.0) Using cached numpy-2.0.1-cp311-cp311-win_amd64.whl.metadata (60 kB) Collecting scipy (from cellpose<3.0,>=1.0.2->cellprofiler_plugins==0.0.0) Using cached scipy-1.14.0-cp311-cp311-win_amd64.whl.metadata (60 kB) Collecting natsort (from cellpose<3.0,>=1.0.2->cellprofiler_plugins==0.0.0) Using cached natsort-8.4.0-py3-none-any.whl.metadata (21 kB) Collecting tifffile (from cellpose<3.0,>=1.0.2->cellprofiler_plugins==0.0.0) Using cached tifffile-2024.7.24-py3-none-any.whl.metadata (31 kB) Collecting tqdm (from cellpose<3.0,>=1.0.2->cellprofiler_plugins==0.0.0) Using cached tqdm-4.66.5-py3-none-any.whl.metadata (57 kB) Collecting numba>=0.53.0 (from cellpose<3.0,>=1.0.2->cellprofiler_plugins==0.0.0) Using cached numba-0.60.0-cp311-cp311-win_amd64.whl.metadata (2.8 kB) Collecting llvmlite (from cellpose<3.0,>=1.0.2->cellprofiler_plugins==0.0.0) Using cached llvmlite-0.43.0-cp311-cp311-win_amd64.whl.metadata (4.9 kB) Collecting torch>=1.6 (from cellpose<3.0,>=1.0.2->cellprofiler_plugins==0.0.0) Using cached torch-2.4.0-cp311-cp311-win_amd64.whl.metadata (27 kB) Collecting opencv-python-headless (from cellpose<3.0,>=1.0.2->cellprofiler_plugins==0.0.0) Using cached opencv_python_headless-4.10.0.84-cp37-abi3-win_amd64.whl.metadata (20 kB) Collecting fastremap (from cellpose<3.0,>=1.0.2->cellprofiler_plugins==0.0.0) Using cached fastremap-1.15.0-cp311-cp311-win_amd64.whl.metadata (9.8 kB) Collecting imagecodecs (from cellpose<3.0,>=1.0.2->cellprofiler_plugins==0.0.0) Using cached imagecodecs-2024.6.1-cp311-cp311-win_amd64.whl.metadata (19 kB) Collecting roifile (from cellpose<3.0,>=1.0.2->cellprofiler_plugins==0.0.0) Using cached roifile-2024.5.24-py3-none-any.whl.metadata (4.6 kB) Collecting boto3>=1.12.28 (from cellprofiler->cellprofiler_plugins==0.0.0) Using cached boto3-1.34.154-py3-none-any.whl.metadata (6.6 kB) Collecting centrosome<1.3,>=1.2.3 (from cellprofiler->cellprofiler_plugins==0.0.0) Using cached centrosome-1.2.3.tar.gz (657 kB) Installing build dependencies ... done Getting requirements to build wheel ... done Installing backend dependencies ... done Preparing metadata (pyproject.toml) ... done Collecting docutils==0.15.2 (from cellprofiler->cellprofiler_plugins==0.0.0) Using cached docutils-0.15.2-py3-none-any.whl.metadata (2.6 kB) Collecting h5py<4,~=3.6.0 (from cellprofiler->cellprofiler_plugins==0.0.0) Using cached h5py-3.6.0.tar.gz (384 kB) Installing build dependencies ... done Getting requirements to build wheel ... done Preparing metadata (pyproject.toml) ... done Collecting imageio>=2.5 (from cellprofiler->cellprofiler_plugins==0.0.0) Using cached imageio-2.34.2-py3-none-any.whl.metadata (4.9 kB) Collecting inflect<7,>=2.1 (from cellprofiler->cellprofiler_plugins==0.0.0) Using cached inflect-6.2.0-py3-none-any.whl.metadata (21 kB) Collecting Jinja2>=2.11.2 (from cellprofiler->cellprofiler_plugins==0.0.0) Using cached jinja2-3.1.4-py3-none-any.whl.metadata (2.6 kB) Collecting joblib>=0.13 (from cellprofiler->cellprofiler_plugins==0.0.0) Using cached joblib-1.4.2-py3-none-any.whl.metadata (5.4 kB) Collecting mahotas>=1.4 (from cellprofiler->cellprofiler_plugins==0.0.0) Using cached mahotas-1.4.18-cp311-cp311-win_amd64.whl.metadata (14 kB) Collecting matplotlib<4,>=3.1.3 (from cellprofiler->cellprofiler_plugins==0.0.0) Using cached matplotlib-3.9.0-cp311-cp311-win_amd64.whl.metadata (11 kB) Collecting mysqlclient==1.4.6 (from cellprofiler->cellprofiler_plugins==0.0.0) Using cached mysqlclient-1.4.6.tar.gz (85 kB) Preparing metadata (setup.py) ... done Collecting Pillow>=7.1.0 (from cellprofiler->cellprofiler_plugins==0.0.0) Using cached pillow-10.4.0-cp311-cp311-win_amd64.whl.metadata (9.3 kB) Collecting prokaryote==2.4.4 (from cellprofiler->cellprofiler_plugins==0.0.0) Using cached prokaryote-2.4.4.tar.gz (84.2 MB) Preparing metadata (setup.py) ... done Collecting python-bioformats==4.0.7 (from cellprofiler->cellprofiler_plugins==0.0.0) Using cached python_bioformats-4.0.7-py3-none-any.whl.metadata (1.7 kB) Collecting python-javabridge==4.0.3 (from cellprofiler->cellprofiler_plugins==0.0.0) Using cached python-javabridge-4.0.3.tar.gz (1.3 MB) Preparing metadata (setup.py) ... error error: subprocess-exited-with-error
× python setup.py egg_info did not run successfully. │ exit code: 1 ╰─> [9 lines of output] Traceback (most recent call last): File "", line 2, in
File "", line 34, in
File "C:\Users\86185\AppData\Local\Temp\pip-install-9r7yhel3\python-javabridge_026155e9a5eb4710ba15720efd54d85d\setup.py", line 412, in
ext_modules=ext_modules(),
^^^^^^^^^^^^^
File "C:\Users\86185\AppData\Local\Temp\pip-install-9r7yhel3\python-javabridge_026155e9a5eb4710ba15720efd54d85d\setup.py", line 100, in ext_modules
from numpy import get_include
ModuleNotFoundError: No module named 'numpy'
[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.