Tests don't find py3Dmol

[yurivict]

2 tests always fail and the message about py3Dmol is printed:

==================================================================================== test session starts =====================================================================================
platform freebsd13 -- Python 3.8.13, pytest-7.1.2, pluggy-1.0.0
rootdir: /disk-samsung/freebsd-ports/science/py-qcelemental/work-py38/qcelemental-0.25.0
plugins: forked-1.4.0, hypothesis-6.47.0, xdist-2.5.0, cov-2.9.0, rerunfailures-10.1
collected 1066 items                                                                                                                                                                         

qcelemental/molutil/test_molutil.py .....................................                                                                                                              [  3%]
qcelemental/tests/test_constants.py .........................................x....                                                                                                     [  7%]
qcelemental/tests/test_covalentradii.py .........................                                                                                                                      [ 10%]
qcelemental/tests/test_datum.py ..............                                                                                                                                         [ 11%]
qcelemental/tests/test_importing.py ..........................                                                                                                                         [ 13%]
qcelemental/tests/test_info.py ........................................                                                                                                                [ 17%]
qcelemental/tests/test_model_general.py ........                                                                                                                                       [ 18%]
qcelemental/tests/test_model_results.py ............................................                                                                                                   [ 22%]
qcelemental/tests/test_molecule.py .............................................s...........                                                                                           [ 27%]
qcelemental/tests/test_molparse_align_chiral.py ..........                                                                                                                             [ 28%]
qcelemental/tests/test_molparse_from_schema.py ............                                                                                                                            [ 29%]
qcelemental/tests/test_molparse_from_string.py .....................................................................................................                                   [ 39%]
qcelemental/tests/test_molparse_parse_nucleus_label.py .............                                                                                                                   [ 40%]
qcelemental/tests/test_molparse_pubchem.py .........                                                                                                                                   [ 41%]
qcelemental/tests/test_molparse_reconcile_nucleus.py ...................................................                                                                               [ 46%]
qcelemental/tests/test_molparse_to_schema.py ..............                                                                                                                            [ 47%]
qcelemental/tests/test_molparse_to_string.py ................................                                                                                                          [ 50%]
qcelemental/tests/test_molparse_validate_and_fill_chgmult.py ...................................................................                                                       [ 56%]
qcelemental/tests/test_periodictable.py ....................................................................................................................x                          [ 67%]
qcelemental/tests/test_testing.py ............................................................                                                                                         [ 73%]
qcelemental/tests/test_units.py ...........................................................................................................................                            [ 84%]
qcelemental/tests/test_utils.py ........................................................................................                                                               [ 93%]
qcelemental/tests/test_vanderwaalsradii.py ........................                                                                                                                    [ 95%]
qcelemental/tests/test_zqcschema.py ssssssssssssssssssssssssssssssssssssssssss                                                                                                         [ 99%]
qcelemental/util/test_gph_uno_bipartite.py ....                                                                                                                                        [ 99%]
qcelemental/util/test_scipy_hungarian.py ..                                                                                                                                            [100%]

====================================================================================== warnings summary ======================================================================================
qcelemental/molutil/test_molutil.py::test_scramble_descrambles_chiral
qcelemental/molutil/test_molutil.py::test_model_b787
qcelemental/molutil/test_molutil.py::test_tropolone_b787
qcelemental/tests/test_molparse_align_chiral.py::test_simpleS
  /disk-samsung/freebsd-ports/science/py-qcelemental/work-py38/qcelemental-0.25.0/qcelemental/molutil/align.py:411: RuntimeWarning: invalid value encountered in reciprocal
    ccnremat = np.reciprocal(ccdistmat)

qcelemental/molutil/test_molutil.py::test_scramble_descrambles_chiral
qcelemental/molutil/test_molutil.py::test_model_b787
qcelemental/molutil/test_molutil.py::test_tropolone_b787
qcelemental/tests/test_molparse_align_chiral.py::test_simpleS
  /disk-samsung/freebsd-ports/science/py-qcelemental/work-py38/qcelemental-0.25.0/qcelemental/molutil/align.py:412: RuntimeWarning: invalid value encountered in reciprocal
    rrnremat = np.reciprocal(rrdistmat)

qcelemental/util/test_gph_uno_bipartite.py::test_example2[2]
  /usr/local/lib/python3.8/site-packages/scipy/sparse/_index.py:137: SparseEfficiencyWarning: Changing the sparsity structure of a csr_matrix is expensive. lil_matrix is more efficient.
    self._set_arrayXarray_sparse(i, j, x)

qcelemental/util/test_gph_uno_bipartite.py: 17 warnings
  /usr/local/lib/python3.8/site-packages/networkx/convert_matrix.py:680: DeprecationWarning: from_numpy_matrix is deprecated and will be removed in NetworkX 3.0.
  Use from_numpy_array instead, e.g. from_numpy_array(A, **kwargs)
    warnings.warn(

-- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html
================================================================================== short test summary info ===================================================================================
SKIPPED [1] qcelemental/tests/test_molecule.py:646: Not detecting module py3Dmol. Install package if necessary and add to envvar PYTHONPATH
SKIPPED [42] qcelemental/conftest.py:27: can't run with --validate option
================================================================= 1021 passed, 43 skipped, 2 xfailed, 26 warnings in 22.43s ==================================================================

Version: 0.25.0
py38-py3Dmol-1.8.0
FreeBSD 13.1

[loriab]

Two tests "xfail" or expected fail, which is good.

On the py3Dmol, the environment must be failing import nglview, https://github.com/MolSSI/QCElemental/blob/master/qcelemental/tests/addons.py#L38, which would trigger that single test to skip. NGL is used for a single function, so it's not a required dependency.

[yurivict]

On the py3Dmol, the environment must be failing import nglview [...]

So it should be listed in setup.py as a test dependency?

[loriab]

So it should be listed in setup.py as a test dependency?

I'd think required test dependencies like pytest should be in tests in setup.py, which they are. The nglview is the "viz" variant in setup.py, https://github.com/MolSSI/QCElemental/blob/master/setup.py#L51-L53 . You can package qcel w/ or w/o the viz, but I expect nglview brings in a lot of extras (qcel alone is plain numpy, pint, and pydantic).

[coltonbh]

Fixed in #308 and further addressed in #310. Dependencies are now fully specified in (formerly setup.py in #308), now pyproject.tom in #310. All tests are passing.