installation issue

[HSvitina]

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?

[AlessiaLeclercq]

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/activate

I 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==3.20.2

When 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 :)

[ishwarvh]

I am facing this issue too.

'numpy' installation completes without any issues, however 'pip install velocyto' fails citing 'ModuleNotFoundError: No module named 'numpy''

I installed 'numpy' with Conda and pip, velocity installation fails with the same error message.