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.): rdkit/rdkit#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_pd_descriptors
  /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 ================================================================================================================

[rgasper]

Only edited this line and removed the import rdkit try-except up top. The rest is black formatter.

[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 <#18 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ACLOFIHNYELRVLLR2ZZJ34DWCAZ27ANCNFSM52NQCB6A> . You are receiving this because you were mentioned.Message ID: ***@***.***>

[SagiPolaczek]

Thanks!