Enable install descripastorus w/o pre-install rdkit.

[rgasper]

remove import for rdkit, add rdkit to requirements, add rdkit to install_requires.

This reflects changes in rdkit allowing it to be installed via pip (and all downstream tooling like pipenv, poetry, etc.): https://github.com/rdkit/rdkit/pull/5373

Closes #17

Testing

• rdkit is not installed

  (eis)  ✘  ~/P/p/descriptastorus   master ±  python
  Python 3.10.0 (default, Mar  3 2022, 03:57:21) [Clang 12.0.0 ] on darwin
  Type "help", "copyright", "credits" or "license" for more information.
  >>> import rdkit
  Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  ModuleNotFoundError: No module named 'rdkit'
  >>>

• install descriptastorus

  (eis)  ~/P/p/descriptastorus   master ±  pip install .
  Processing /Users/raymondgasper/Projects/personal/descriptastorus
  DEPRECATION: A future pip version will change local packages to be built in-place without first copying to a temporary directory. We recommend you use --use-feature=in-tree-build to test your packages with this new behavior before it becomes the default.
  pip 21.3 will remove support for this functionality. You can find discussion regarding this at https://github.com/pypa/pip/issues/7555.
  Collecting pandas_flavor
  Downloading pandas_flavor-0.3.0-py3-none-any.whl (6.3 kB)
  Collecting rdkit
  Downloading rdkit-2022.3.3-cp310-cp310-macosx_10_9_x86_64.whl (17.9 MB)
   |████████████████████████████████| 17.9 MB 26.8 MB/s
  Requirement already satisfied: pandas>=0.23 in /usr/local/anaconda3/envs/eis/lib/python3.10/site-packages (from pandas_flavor->descriptastorus==2.3.0.6) (1.4.1)
  Collecting lazy-loader==0.1rc2
  Downloading lazy_loader-0.1rc2-py3-none-any.whl (5.1 kB)
  Collecting xarray
  Downloading xarray-2022.3.0-py3-none-any.whl (870 kB)
   |████████████████████████████████| 870 kB 13.4 MB/s
  Requirement already satisfied: python-dateutil>=2.8.1 in /usr/local/anaconda3/envs/eis/lib/python3.10/site-packages (from pandas>=0.23->pandas_flavor->descriptastorus==2.3.0.6) (2.8.2)
  Requirement already satisfied: numpy>=1.21.0 in /usr/local/anaconda3/envs/eis/lib/python3.10/site-packages (from pandas>=0.23->pandas_flavor->descriptastorus==2.3.0.6) (1.22.3)
  Requirement already satisfied: pytz>=2020.1 in /usr/local/anaconda3/envs/eis/lib/python3.10/site-packages (from pandas>=0.23->pandas_flavor->descriptastorus==2.3.0.6) (2021.3)
  Requirement already satisfied: six>=1.5 in /usr/local/anaconda3/envs/eis/lib/python3.10/site-packages (from python-dateutil>=2.8.1->pandas>=0.23->pandas_flavor->descriptastorus==2.3.0.6) (1.16.0)
  Requirement already satisfied: Pillow in /usr/local/anaconda3/envs/eis/lib/python3.10/site-packages (from rdkit->descriptastorus==2.3.0.6) (9.0.1)
  Requirement already satisfied: packaging>=20.0 in /usr/local/anaconda3/envs/eis/lib/python3.10/site-packages (from xarray->pandas_flavor->descriptastorus==2.3.0.6) (21.3)
  Requirement already satisfied: pyparsing!=3.0.5,>=2.0.2 in /usr/local/anaconda3/envs/eis/lib/python3.10/site-packages (from packaging>=20.0->xarray->pandas_flavor->descriptastorus==2.3.0.6) (3.0.7)
  Building wheels for collected packages: descriptastorus
  Building wheel for descriptastorus (setup.py) ... done
  Created wheel for descriptastorus: filename=descriptastorus-2.3.0.6-py3-none-any.whl size=60706 sha256=c2f20d71a0f412c2022723c21b613d687a3ed7bfae43df9e7c14b22fdde90c3d
  Stored in directory: /private/var/folders/1m/281yfqmj42n90_znys0027y00000gp/T/pip-ephem-wheel-cache-7lzqoiy9/wheels/12/b1/15/40ac169c11f221b9c1f4bbfcd683fe6f7732156eda33346650
  Successfully built descriptastorus
  Installing collected packages: xarray, lazy-loader, rdkit, pandas-flavor, descriptastorus
  Successfully installed descriptastorus-2.3.0.6 lazy-loader-0.1rc2 pandas-flavor-0.3.0 rdkit-2022.3.3 xarray-2022.3.0

• now we can import

  (eis)  ~/P/p/descriptastorus   master ±  python
  Python 3.10.0 (default, Mar  3 2022, 03:57:21) [Clang 12.0.0 ] on darwin
  Type "help", "copyright", "credits" or "license" for more information.
  >>> import rdkit
  >>> import descriptastorus
  WARNING:root:No normalization for BCUT2D_MWHI
  WARNING:root:No normalization for BCUT2D_MWLOW
  WARNING:root:No normalization for BCUT2D_CHGHI
  WARNING:root:No normalization for BCUT2D_CHGLO
  WARNING:root:No normalization for BCUT2D_LOGPHI
  WARNING:root:No normalization for BCUT2D_LOGPLOW
  WARNING:root:No normalization for BCUT2D_MRHI
  WARNING:root:No normalization for BCUT2D_MRLOW

• run tests

  
  (eis)  ~/P/p/descriptastorus   master  pytest tests
  ===================================================================================================================== test session starts =====================================================================================================================
  platform darwin -- Python 3.10.0, pytest-7.1.0, pluggy-1.0.0
  rootdir: /Users/raymondgasper/Projects/personal/descriptastorus
  plugins: anyio-3.5.0
  collected 7 items

tests/test_keyvalue.py .. [ 28%] tests/test_pandas.py . [ 42%] tests/test_rawStore.py . [ 57%] tests/test_smiles_reindex.py .. [ 85%] tests/test_test1.py . [100%]

====================================================================================================================== warnings summary ======================================================================================================================= tests/test_pandas.py::TestPandasDataFrame::test_pd_descriptors tests/test_pandas.py::TestPandasDataFrame::test_pd_descriptors tests/test_pandas.py::TestPandasDataFrame::test_pd_descriptors tests/test_pandas.py::TestPandasDataFrame::test_pddescriptors /usr/local/anaconda3/envs/eis/lib/python3.10/site-packages/descriptastorus/descriptors/DescriptorGenerator.py:100: DeprecationWarning: np.bool is a deprecated alias for the builtin bool. To silence this warning, use bool by itself. Doing this will not modify any behavior and is safe. If you specifically wanted the numpy scalar type, use `np.bool` here. Deprecated in NumPy 1.20; for more details and guidance: https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations return [ (self.NAME + "_calculated", numpy.bool) ] + self.columns

tests/test_pandas.py::TestPandasDataFrame::test_pd_descriptors tests/test_pandas.py::TestPandasDataFrame::test_pd_descriptors tests/test_pandas.py::TestPandasDataFrame::test_pd_descriptors tests/test_pandas.py::TestPandasDataFrame::test_pd_descriptors tests/test_pandas.py::TestPandasDataFrame::test_pd_descriptors tests/test_pandas.py::TestPandasDataFrame::test_pd_descriptors tests/test_pandas.py::TestPandasDataFrame::test_pd_descriptors tests/test_pandas.py::TestPandasDataFrame::test_pd_descriptors tests/test_pandas.py::TestPandasDataFrame::test_pd_descriptors /usr/local/anaconda3/envs/eis/lib/python3.10/site-packages/rdkit/Chem/Graphs.py:43: DeprecationWarning: np.float is a deprecated alias for the builtin float. To silence this warning, use float by itself. Doing this will not modify any behavior and is safe. If you specifically wanted the numpy scalar type, use np.float64 here. Deprecated in NumPy 1.20; for more details and guidance: https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations res = numpy.zeros(nAtoms + 1, numpy.float)

-- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html =============================================================================================================== 7 passed, 13 warnings in 7.33s ================================================================================================================

[SagiPolaczek]

@bp-kelley

Hey :) Is this one ready to merge?

[bp-kelley]

I'm doing some testing before the rdkit UGM and will make sure it is released prior to next wednesday.

Thanks for the contribution.

On Fri, Oct 7, 2022 at 10:48 AM Sagi Polaczek @.***> wrote:

@bp-kelley https://github.com/bp-kelley

Hey :) Is this one ready to merge?

— Reply to this email directly, view it on GitHub https://github.com/bp-kelley/descriptastorus/pull/18#issuecomment-1271695668, or unsubscribe https://github.com/notifications/unsubscribe-auth/ACLOFIHNYELRVLLR2ZZJ34DWCAZ27ANCNFSM52NQCB6A . You are receiving this because you were mentioned.Message ID: @.***>

[SagiPolaczek]

Thanks!