Pip install from git repo fails through conda env create

[danmou]

I'm using the following environment.yml:

name: habitat
dependencies:
  - python=3.6
  - pip
  - pip:
    - git+git://github.com/facebookresearch/habitat-sim.git

I can install the package using pip (if you run this, note that the build takes a while and uses all cpu cores):

conda create -n test python=3.6
conda activate test
pip install git+git://github.com/facebookresearch/habitat-sim.git

And other github packages install successfully when specified in the same way in environment.yml, but with habitat-sim it fails due to:

  Traceback (most recent call last):
    File "/home/daniel/.conda/envs/habitat/bin/pip", line 7, in <module>
      from pip._internal import main
  ModuleNotFoundError: No module named 'pip'

Steps to Reproduce

With the environment.yml described above.

$ conda env create
Collecting package metadata (repodata.json): done
Solving environment: done
Preparing transaction: done
Verifying transaction: done
Executing transaction: done
Ran pip subprocess with arguments:
['/home/daniel/.conda/envs/habitat/bin/python', '-m', 'pip', 'install', '-U', '-r', '/home/daniel/habitat_test/condaenv.b1etf1uw.requirements.txt']
Pip subprocess output:
Collecting git+git://github.com/facebookresearch/habitat-sim.git (from -r /home/daniel/habitat_test/condaenv.b1etf1uw.requirements.txt (line 1))
  Cloning git://github.com/facebookresearch/habitat-sim.git to /tmp/pip-req-build-3z3266mp
  Installing build dependencies: started
  Installing build dependencies: finished with status 'done'
  Getting requirements to build wheel: started
  Getting requirements to build wheel: finished with status 'error'

Pip subprocess error:
  Running command git clone -q git://github.com/facebookresearch/habitat-sim.git /tmp/pip-req-build-3z3266mp
  Running command git submodule update --init --recursive -q
  ERROR: Command errored out with exit status 1:
   command: /home/daniel/.conda/envs/habitat/bin/python /home/daniel/.conda/envs/habitat/lib/python3.6/site-packages/pip/_vendor/pep517/_in_process.py get_requires_for_build_wheel /tmp/tmp0aq027ve
       cwd: /tmp/pip-req-build-3z3266mp
  Complete output (33 lines):
  running egg_info
  creating habitat_sim.egg-info
  writing habitat_sim.egg-info/PKG-INFO
  writing dependency_links to habitat_sim.egg-info/dependency_links.txt
  writing requirements to habitat_sim.egg-info/requires.txt
  writing top-level names to habitat_sim.egg-info/top_level.txt
  writing manifest file 'habitat_sim.egg-info/SOURCES.txt'
  reading manifest file 'habitat_sim.egg-info/SOURCES.txt'
  writing manifest file 'habitat_sim.egg-info/SOURCES.txt'
  Traceback (most recent call last):
    File "/home/daniel/.conda/envs/habitat/bin/pip", line 7, in <module>
      from pip._internal import main
  ModuleNotFoundError: No module named 'pip'
  Traceback (most recent call last):
    File "/home/daniel/.conda/envs/habitat/lib/python3.6/site-packages/pip/_vendor/pep517/_in_process.py", line 207, in <module>
      main()
    File "/home/daniel/.conda/envs/habitat/lib/python3.6/site-packages/pip/_vendor/pep517/_in_process.py", line 197, in main
      json_out['return_val'] = hook(**hook_input['kwargs'])
    File "/home/daniel/.conda/envs/habitat/lib/python3.6/site-packages/pip/_vendor/pep517/_in_process.py", line 54, in get_requires_for_build_wheel
      return hook(config_settings)
    File "/tmp/pip-build-env-zeo19gah/overlay/lib/python3.6/site-packages/setuptools/build_meta.py", line 146, in get_requires_for_build_wheel
      return self._get_build_requires(config_settings, requirements=['wheel'])
    File "/tmp/pip-build-env-zeo19gah/overlay/lib/python3.6/site-packages/setuptools/build_meta.py", line 127, in _get_build_requires
      self.run_setup()
    File "/tmp/pip-build-env-zeo19gah/overlay/lib/python3.6/site-packages/setuptools/build_meta.py", line 237, in run_setup
      self).run_setup(setup_script=setup_script)
    File "/tmp/pip-build-env-zeo19gah/overlay/lib/python3.6/site-packages/setuptools/build_meta.py", line 142, in run_setup
      exec(compile(code, __file__, 'exec'), locals())
    File "setup.py", line 371, in <module>
      subprocess.check_call(shlex.split(f"pip install {pymagnum_build_dir}"))
    File "/home/daniel/.conda/envs/habitat/lib/python3.6/subprocess.py", line 311, in check_call
      raise CalledProcessError(retcode, cmd)
  subprocess.CalledProcessError: Command '['pip', 'install', 'build/deps/magnum-bindings/src/python']' returned non-zero exit status 1.
  ----------------------------------------
ERROR: Command errored out with exit status 1: /home/daniel/.conda/envs/habitat/bin/python /home/daniel/.conda/envs/habitat/lib/python3.6/site-packages/pip/_vendor/pep517/_in_process.py get_requires_for_build_wheel /tmp/tmp0aq027ve Check the logs for full command output.


CondaEnvException: Pip failed

Environment Information

`conda info`

     active environment : None
            shell level : 0
       user config file : /home/daniel/.condarc
 populated config files : /home/daniel/.condarc
          conda version : 4.7.11
    conda-build version : not installed
         python version : 3.7.4.final.0
       virtual packages : 
       base environment : /home/daniel/miniconda  (writable)
           channel URLs : https://repo.anaconda.com/pkgs/main/linux-64
                          https://repo.anaconda.com/pkgs/main/noarch
                          https://repo.anaconda.com/pkgs/r/linux-64
                          https://repo.anaconda.com/pkgs/r/noarch
          package cache : /home/daniel/.conda/pkgs
       envs directories : /home/daniel/.conda/envs
                          /home/daniel/miniconda/envs
               platform : linux-64
             user-agent : conda/4.7.11 requests/2.22.0 CPython/3.7.4 Linux/4.19.66-1-MANJARO manjaro/18.0.4 glibc/2.29
                UID:GID : 1000:1000
             netrc file : None
           offline mode : False

`conda config --show-sources`

==> /home/daniel/.condarc <==
envs_dirs:
  - ~/.conda/envs
pkgs_dirs:
  - ~/.conda/pkgs

`conda list --show-channel-urls`

# packages in environment at /home/daniel/miniconda:
#
# Name                    Version                   Build  Channel
_libgcc_mutex             0.1                        main    defaults
asn1crypto                0.24.0                   py37_0    defaults
bzip2                     1.0.8                h7b6447c_0    defaults
ca-certificates           2019.5.15                     1    defaults
certifi                   2019.6.16                py37_1    defaults
cffi                      1.12.3           py37h2e261b9_0    defaults
chardet                   3.0.4                    py37_1    defaults
conda                     4.7.11                   py37_0    defaults
conda-package-handling    1.3.11                   py37_0    defaults
cryptography              2.7              py37h1ba5d50_0    defaults
idna                      2.8                      py37_0    defaults
libarchive                3.3.3                h5d8350f_5    defaults
libedit                   3.1.20181209         hc058e9b_0    defaults
libffi                    3.2.1                hd88cf55_4    defaults
libgcc-ng                 9.1.0                hdf63c60_0    defaults
libstdcxx-ng              9.1.0                hdf63c60_0    defaults
libxml2                   2.9.9                hea5a465_1    defaults
lz4-c                     1.8.1.2              h14c3975_0    defaults
lzo                       2.10                 h49e0be7_2    defaults
ncurses                   6.1                  he6710b0_1    defaults
openssl                   1.1.1c               h7b6447c_1    defaults
pip                       19.1.1                   py37_0    defaults
pycosat                   0.6.3            py37h14c3975_0    defaults
pycparser                 2.19                     py37_0    defaults
pyopenssl                 19.0.0                   py37_0    defaults
pysocks                   1.7.0                    py37_0    defaults
python                    3.7.4                h265db76_1    defaults
python-libarchive-c       2.8                     py37_11    defaults
readline                  7.0                  h7b6447c_5    defaults
requests                  2.22.0                   py37_0    defaults
ruamel_yaml               0.15.46          py37h14c3975_0    defaults
setuptools                41.0.1                   py37_0    defaults
six                       1.12.0                   py37_0    defaults
sqlite                    3.29.0               h7b6447c_0    defaults
tk                        8.6.8                hbc83047_0    defaults
tqdm                      4.32.1                     py_0    defaults
urllib3                   1.24.2                   py37_0    defaults
wheel                     0.33.4                   py37_0    defaults
xz                        5.2.4                h14c3975_4    defaults
yaml                      0.1.7                had09818_2    defaults
zlib                      1.2.11               h7b6447c_3    defaults
zstd                      1.3.7                h0b5b093_0    defaults

[github-actions]

Hi there, thank you for your contribution!

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