bp-kelley / descriptastorus

Descriptor computation(chemistry) and (optional) storage for machine learning
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Remove "RDKit Not Installable by Pip" error #17

Closed rgasper closed 1 year ago

rgasper commented 2 years ago

When trying to install descriptastorus via pip (through poetry), I see the following error:

poetry add git+https://github.com/bp-kelley/descriptastorus
  PackageInfoError

  Unable to determine package info for path: /var/folders/1m/281yfqmj42n90_znys0027y00000gp/T/pypoetry-git-descriptastorusw440te64

  Fallback egg_info generation failed.

  Command ['/var/folders/1m/281yfqmj42n90_znys0027y00000gp/T/tmp72kvq807/.venv/bin/python', 'setup.py', 'egg_info'] errored with the following return code 1, and output:
  Descriptastorus requires rkdit to function, this is not installable by pip
   see https://rdkit.org for more information

  at ~/.poetry/lib/poetry/inspection/info.py:501 in _pep517_metadata
      497│                     venv.run_python("setup.py", "egg_info")
      498│                     return cls.from_metadata(path)
      499│                 except EnvCommandError as fbe:
      500│                     raise PackageInfoError(
    → 501│                         path, "Fallback egg_info generation failed.", fbe
      502│                     )
      503│                 finally:
      504│                     os.chdir(cwd.as_posix())
      505│

This error is now incorrect with the stable packaging of rdkit as rdkit-pypi

rgasper commented 2 years ago

Demonstration of successful rdkit installation:

poetry run python
Python 3.7.6 (default, Jan  8 2020, 13:42:34)
[Clang 4.0.1 (tags/RELEASE_401/final)] :: Anaconda, Inc. on darwin
Type "help", "copyright", "credits" or "license" for more information.
>>> from rdkit import Chem; print(Chem.MolToMolBlock(Chem.MolFromSmiles('C1CCC1')))

     RDKit          2D

  4  4  0  0  0  0  0  0  0  0999 V2000
    1.0607    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0000   -1.0607    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0607    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    1.0607    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  1  0
  4  1  1  0
M  END