AlessiaLeclercq
commented
2 weeks ago hello, I have the same problem here while trying to install it. I first created a virtual environment and activated it
> python3 --version
Python 3.9.6
> python3 -m venv virtualEnv
> source virtualEnv/bin/activateI then proceeded by installing velocyto using pip
> pip install velocyto I got the following error messagge
ERROR: Command errored out with exit status 1:
command: /Users/lrcq/Documents/devtraj/virtualEnv/bin/python3 -c 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '"'"'/private/var/folders/kx/jq__74vx39z9tptjlhbh6m400000gn/T/pip-install-l7nk6mlv/velocyto_39181c4ec1d14fac87aec8f2aeb4d34f/setup.py'"'"'; __file__='"'"'/private/var/folders/kx/jq__74vx39z9tptjlhbh6m400000gn/T/pip-install-l7nk6mlv/velocyto_39181c4ec1d14fac87aec8f2aeb4d34f/setup.py'"'"';f = getattr(tokenize, '"'"'open'"'"', open)(__file__) if os.path.exists(__file__) else io.StringIO('"'"'from setuptools import setup; setup()'"'"');code = f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' egg_info --egg-base /private/var/folders/kx/jq__74vx39z9tptjlhbh6m400000gn/T/pip-pip-egg-info-gmv_k1sc
cwd: /private/var/folders/kx/jq__74vx39z9tptjlhbh6m400000gn/T/pip-install-l7nk6mlv/velocyto_39181c4ec1d14fac87aec8f2aeb4d34f/
Complete output (5 lines):
Traceback (most recent call last):
File "<string>", line 1, in <module>
File "/private/var/folders/kx/jq__74vx39z9tptjlhbh6m400000gn/T/pip-install-l7nk6mlv/velocyto_39181c4ec1d14fac87aec8f2aeb4d34f/setup.py", line 3, in <module>
import numpy as np
ModuleNotFoundError: No module named 'numpy'So I proceeded by manually installing the dependencies into the virtualEnv
> python3 -m pip install --upgrade pip
Requirement already satisfied: pip in ./virtualEnv/lib/python3.9/site-packages (21.2.4)
Collecting pip
Using cached pip-24.3.1-py3-none-any.whl (1.8 MB)
Installing collected packages: pip
Attempting uninstall: pip
Found existing installation: pip 21.2.4
Uninstalling pip-21.2.4:
Successfully uninstalled pip-21.2.4
Successfully installed pip-24.3.1
> pip install numpy pysam scipy cython numba scikit-learn h5py click matplotlib
> pip freeze
click==8.1.7
contourpy==1.3.0
cycler==0.12.1
Cython==3.0.11
fonttools==4.54.1
h5py==3.12.1
importlib_resources==6.4.5
joblib==1.4.2
kiwisolver==1.4.7
llvmlite==0.43.0
matplotlib==3.9.2
numba==0.60.0
numpy==2.0.2
packaging==24.1
pillow==11.0.0
pyparsing==3.2.0
pysam==0.22.1
python-dateutil==2.9.0.post0
scikit-learn==1.5.2
scipy==1.13.1
six==1.16.0
threadpoolctl==3.5.0
zipp==3.20.2When I try then to install again velocyto I get the following:
pip install velocyto
Collecting velocyto
Using cached velocyto-0.17.17.tar.gz (198 kB)
Installing build dependencies ... done
Getting requirements to build wheel ... error
error: subprocess-exited-with-error
× Getting requirements to build wheel did not run successfully.
│ exit code: 1
╰─> [17 lines of output]
Traceback (most recent call last):
File "/Users/lrcq/Documents/devtraj/virtualEnv/lib/python3.9/site-packages/pip/_vendor/pyproject_hooks/_in_process/_in_process.py", line 353, in <module>
main()
File "/Users/lrcq/Documents/devtraj/virtualEnv/lib/python3.9/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/lrcq/Documents/devtraj/virtualEnv/lib/python3.9/site-packages/pip/_vendor/pyproject_hooks/_in_process/_in_process.py", line 118, in get_requires_for_build_wheel
return hook(config_settings)
File "/private/var/folders/kx/jq__74vx39z9tptjlhbh6m400000gn/T/pip-build-env-7bt1ubw0/overlay/lib/python3.9/site-packages/setuptools/build_meta.py", line 333, in get_requires_for_build_wheel
return self._get_build_requires(config_settings, requirements=[])
File "/private/var/folders/kx/jq__74vx39z9tptjlhbh6m400000gn/T/pip-build-env-7bt1ubw0/overlay/lib/python3.9/site-packages/setuptools/build_meta.py", line 303, in _get_build_requires
self.run_setup()
File "/private/var/folders/kx/jq__74vx39z9tptjlhbh6m400000gn/T/pip-build-env-7bt1ubw0/overlay/lib/python3.9/site-packages/setuptools/build_meta.py", line 521, in run_setup
super().run_setup(setup_script=setup_script)
File "/private/var/folders/kx/jq__74vx39z9tptjlhbh6m400000gn/T/pip-build-env-7bt1ubw0/overlay/lib/python3.9/site-packages/setuptools/build_meta.py", line 319, in run_setup
exec(code, locals())
File "<string>", line 3, in <module>
ModuleNotFoundError: No module named 'numpy'
[end of output]
note: This error originates from a subprocess, and is likely not a problem with pip.
error: subprocess-exited-with-error
× Getting requirements to build wheel did not run successfully.
│ exit code: 1
╰─> See above for output.
What am I missing? currently running onto arm64 M3 with macOS Sonoma 14.5 :)
Dear developers
I have problems to install velocyto through anaconda mini-conda, through the Sryder console. pip install velocyto did not go on python 3.9 or 3.11.
Collecting velocyto Using cached velocyto-0.17.17.tar.gz (198 kB) Preparing metadata (setup.py): started Preparing metadata (setup.py): finished with status 'error' Note: you may need to restart the kernel to use updated packages. error: subprocess-exited-with-error
python setup.py egg_info did not run successfully. exit code: 1
[6 lines of output] Traceback (most recent call last): File "", line 2, in
File "", line 34, in
File "C:\Users\u0153852\AppData\Local\Temp\pip-install-55o8yc8v\velocyto_f8958368a200418ab96f142c9b467509\setup.py", line 3, in
import numpy as np
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.
Can you suggest my mistake, please?