pip install fails

I’ve created the conda env, and ran pip install scispacy see the result:

(scispacy) lucas-mbp:jats lfoppiano$ pip install scispacy
Collecting scispacy
  Using cached https://files.pythonhosted.org/packages/72/55/30b30a78abafaaf34d0d8368a090cf713964d6c97c5e912fb2016efadab0/scispacy-0.2.2-py3-none-any.whl
Collecting numpy (from scispacy)
  Downloading https://files.pythonhosted.org/packages/0f/c9/3526a357b6c35e5529158fbcfac1bb3adc8827e8809a6d254019d326d1cc/numpy-1.16.4-cp36-cp36m-macosx_10_6_intel.macosx_10_9_intel.macosx_10_9_x86_64.macosx_10_10_intel.macosx_10_10_x86_64.whl (13.9MB)
     |████████████████████████████████| 13.9MB 3.5MB/s 
Collecting joblib (from scispacy)
  Using cached https://files.pythonhosted.org/packages/cd/c1/50a758e8247561e58cb87305b1e90b171b8c767b15b12a1734001f41d356/joblib-0.13.2-py2.py3-none-any.whl
Collecting spacy>=2.1.3 (from scispacy)
  Downloading https://files.pythonhosted.org/packages/cb/ef/cccdeb1ababb2cb04ae464098183bcd300b8f7e4979ce309669de8a56b9d/spacy-2.1.6-cp36-cp36m-macosx_10_6_intel.macosx_10_9_intel.macosx_10_9_x86_64.macosx_10_10_intel.macosx_10_10_x86_64.whl (34.6MB)
     |████████████████████████████████| 34.6MB 33.6MB/s 
Collecting conllu (from scispacy)
  Downloading https://files.pythonhosted.org/packages/ae/54/b0ae1199f3d01666821b028cd967f7c0ac527ab162af433d3da69242cea2/conllu-1.3.1-py2.py3-none-any.whl
Collecting awscli (from scispacy)
  Using cached https://files.pythonhosted.org/packages/e6/48/8c5ac563a88239d128aa3fb67415211c19bd653fab01c7f11cecf015c343/awscli-1.16.203-py2.py3-none-any.whl
Collecting nmslib>=1.7.3.6 (from scispacy)
  Using cached https://files.pythonhosted.org/packages/b2/4d/4d110e53ff932d7a1ed9c2f23fe8794367087c29026bf9d4b4d1e27eda09/nmslib-1.8.1.tar.gz
    ERROR: Complete output from command python setup.py egg_info:
    ERROR: Download error on https://pypi.org/simple/numpy/: [Errno 8] nodename nor servname provided, or not known -- Some packages may not be found!
    Couldn't find index page for 'numpy' (maybe misspelled?)
    Download error on https://pypi.org/simple/: [Errno 8] nodename nor servname provided, or not known -- Some packages may not be found!
    No local packages or working download links found for numpy
    Traceback (most recent call last):
      File "<string>", line 1, in <module>
      File "/private/var/folders/mk/scd8428n18jfgh3jdthbvpz00000gn/T/pip-install-l00jm4xn/nmslib/setup.py", line 172, in <module>
        zip_safe=False,
      File "/anaconda3/envs/scispacy/lib/python3.6/site-packages/setuptools/__init__.py", line 144, in setup
        _install_setup_requires(attrs)
      File "/anaconda3/envs/scispacy/lib/python3.6/site-packages/setuptools/__init__.py", line 139, in _install_setup_requires
        dist.fetch_build_eggs(dist.setup_requires)
      File "/anaconda3/envs/scispacy/lib/python3.6/site-packages/setuptools/dist.py", line 717, in fetch_build_eggs
        replace_conflicting=True,
      File "/anaconda3/envs/scispacy/lib/python3.6/site-packages/pkg_resources/__init__.py", line 782, in resolve
        replace_conflicting=replace_conflicting
      File "/anaconda3/envs/scispacy/lib/python3.6/site-packages/pkg_resources/__init__.py", line 1065, in best_match
        return self.obtain(req, installer)
      File "/anaconda3/envs/scispacy/lib/python3.6/site-packages/pkg_resources/__init__.py", line 1077, in obtain
        return installer(requirement)
      File "/anaconda3/envs/scispacy/lib/python3.6/site-packages/setuptools/dist.py", line 784, in fetch_build_egg
        return cmd.easy_install(req)
      File "/anaconda3/envs/scispacy/lib/python3.6/site-packages/setuptools/command/easy_install.py", line 673, in easy_install
        raise DistutilsError(msg)
    distutils.errors.DistutilsError: Could not find suitable distribution for Requirement.parse('numpy')
    ----------------------------------------
ERROR: Command "python setup.py egg_info" failed with error code 1 in /private/var/folders/mk/scd8428n18jfgh3jdthbvpz00000gn/T/pip-install-l00jm4xn/nmslib/
(scispacy) lucas-mbp:jats lfoppiano$ 

To solve the issue I had to install numpy and nmslib:

conda install numpy
conda install -c akode nmslib

It seems to work, but maybe is not the proper way to solve it - the pip script should be updated perhaps?

[searchivarius]

@danielkingai2 very nice, many thanks!

[dakinggg]

You can create a conda environment with python 3.6 like so conda create -n myenv python=3.6. See more about working with conda environments here: https://docs.conda.io/projects/conda/en/latest/user-guide/tasks/manage-environments.html