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error in scanpy setup command #24

Open mvonpapen opened 4 years ago

mvonpapen commented 4 years ago

Hi, I tried to install the required packages on a freshly set up conda environment with Python 3.6.9 and pip 19.2.3. After the command pip install -r requirements.txt I ran into a problem with scanpy:

Complete output (1 lines):
    error in scanpy setup command: "values of 'package_data' dict" must be a list of strings (got '*.txt')
    ----------------------------------------
ERROR: Command errored out with exit status 1: python setup.py egg_info Check the logs for full command output.

I am now trying to use the latest version of scanpy (1.4.4) and hope that the notebook will run. Any ideas?

chmreid commented 4 years ago

I encountered the same error trying to install scanpy 1.3.4 on Mac OS X 10.14.5:

$ python --version
Python 3.6.9

$ pip --version
pip 19.3.1 from /Users/charles/codes/single_cell_clustering_notebook/vp/lib/python3.6/site-packages/pip (python 3.6)

$ pip install scanpy==1.3.4
Collecting scanpy==1.3.4
  Using cached https://files.pythonhosted.org/packages/47/a2/3edd61806453cccad8828fc74b0d9377cf419abc14b737ed57187e446460/scanpy-1.3.4.tar.gz
    ERROR: Command errored out with exit status 1:
     command: /Users/charles/codes/single_cell_clustering_notebook/vp/bin/python3.6 -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/private/var/folders/qn/bgn0p0v96w1g6fxsdmvd3qrm0000gq/T/pip-install-qk28r2py/scanpy/setup.py'"'"'; __file__='"'"'/private/var/folders/qn/bgn0p0v96w1g6fxsdmvd3qrm0000gq/T/pip-install-qk28r2py/scanpy/setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(__file__);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' egg_info --egg-base /private/var/folders/qn/bgn0p0v96w1g6fxsdmvd3qrm0000gq/T/pip-install-qk28r2py/scanpy/pip-egg-info
         cwd: /private/var/folders/qn/bgn0p0v96w1g6fxsdmvd3qrm0000gq/T/pip-install-qk28r2py/scanpy/
    Complete output (1 lines):
    error in scanpy setup command: "values of 'package_data' dict" must be a list of strings (got '*.txt')
    ----------------------------------------
ERROR: Command errored out with exit status 1: python setup.py egg_info Check the logs for full command output.

Installing the latest version of scanpy (1.4.5.post2) goes okay, not sure if notebook will run though.