pip3 install fails due to glmnet_py git version vs pip version

[tseemann]

It seems you want a git version of glmnet_py that isn't in pip?

% python3 -m pip install pyseer

Collecting glmnet_py
  Downloading https://files.pythonhosted.org/packages/f5/1a/55b708789a66f2405783bce0f53e02b86128ea3f21d329c87dc6dbef8e51/glmnet_py-0.1.0b2.tar.gz (1.2MB)
     |████████████████████████████████| 1.2MB 24.3MB/s
    ERROR: Command errored out with exit status 1:
     command: /home/linuxbrew/.linuxbrew/opt/python/bin/python3.7 -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-y3jr_1iw/glmnet-py/setup.py'"'"'; __file__='"'"'/tmp/pip-install-y3jr_1iw/glmnet-py/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 /tmp/pip-install-y3jr_1iw/glmnet-py/pip-egg-info
         cwd: /tmp/pip-install-y3jr_1iw/glmnet-py/
    Complete output (6 lines):
    sh: gfortran: command not found
    Traceback (most recent call last):
      File "<string>", line 1, in <module>
      File "/tmp/pip-install-y3jr_1iw/glmnet-py/setup.py", line 11, in <module>
        long_description=open('README.md').read(),
    FileNotFoundError: [Errno 2] No such file or directory: 'README.md'
    ----------------------------------------
ERROR: Command errored out with exit status 1: python setup.py egg_info Check the logs for full command output.

[mgalardini]

Hi Torsten,

the best way to get around this is to use conda, as glmnet_py requires some compilation; I will look into this, but maybe you can try install gfortran first?

M

[tseemann]

@mgalardini i just realised that was the real error - missing gfortran - trying to fix now. !

[tseemann]

It has gotten further - but i think i'll need to install the git version? This one is not your fauly, glmnet_py is broken

    Complete output (6 lines):
    gfortran: error: ./glmnet_py/GLMnet.f: No such file or directory
    Traceback (most recent call last):
      File "<string>", line 1, in <module>
      File "/tmp/pip-install-dvf_22x5/glmnet-py/setup.py", line 11, in <module>
        long_description=open('README.md').read(),
    FileNotFoundError: [Errno 2] No such file or directory: 'README.md'

[tseemann]

This works:

pip3 install git+https://github.com/hanfang/glmnet_py.git

    Running setup.py install for glmnet-py ... done
Successfully installed glmnet-py-0.1.0b1

Do i need the exact commit you specify?

[mgalardini]

Thanks for inspecting this; yeah, I think we need to change the setup.py entry, as indicated here

[mgalardini]

And no, I don't believe we require an exact commit