TestRequiresRDKit.test_converter_requires_rdkit fails on Azure Windows and with Azure Linux 3.10 #4687
Description
In the CI for PR #4682 I observed a test failure for a RDKit-related test TestRequiresRDKit.test_converter_requires_rdkit in the Windows Azure runners
- Azure_Tests Win-Python310-64bit-ful
- Azure_Tests Win-Python312-64bit-full
- Azure_Tests Win-Python310-64bit-full-wheel
- Azure_Tests Linux-Python310-64bit-full-wheel
Not failing with the RDKit issue:
- Azure_Tests Win-Python312-64bit-full-wheel
- Azure_Tests Linux-Python312-64bit-full-wheel
The GitHub Linux and macOS runners do not fail this test.
Windows Python 3.12
2024-08-23T15:10:56.7901745Z _______________ TestRequiresRDKit.test_converter_requires_rdkit _______________
2024-08-23T15:10:56.7902163Z [gw0] win32 -- Python 3.12.5 C:\hostedtoolcache\windows\Python\3.12.5\x64\python.exe
2024-08-23T15:10:56.7902438Z
2024-08-23T15:10:56.7902727Z self = <MDAnalysisTests.converters.test_rdkit.TestRequiresRDKit object at 0x00000167D7E47590>
2024-08-23T15:10:56.7903027Z
2024-08-23T15:10:56.7903319Z def test_converter_requires_rdkit(self):
2024-08-23T15:10:56.7904060Z u = mda.Universe(PDB_full)
2024-08-23T15:10:56.7904413Z with pytest.raises(ImportError,
2024-08-23T15:10:56.7904801Z match="RDKit is required for the RDKitConverter"):
2024-08-23T15:10:56.7905187Z > u.atoms.convert_to("RDKIT")
2024-08-23T15:10:56.7905353Z
2024-08-23T15:10:56.7905686Z D:\a\1\s\testsuite\MDAnalysisTests\converters\test_rdkit.py:61:
2024-08-23T15:10:56.7906060Z _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
2024-08-23T15:10:56.7906557Z C:\hostedtoolcache\windows\Python\3.12.5\x64\Lib\site-packages\MDAnalysis\core\accessors.py:204: in __call__
2024-08-23T15:10:56.7907339Z return convert(*args, **kwargs)
2024-08-23T15:10:56.7908145Z C:\hostedtoolcache\windows\Python\3.12.5\x64\Lib\site-packages\MDAnalysis\converters\RDKit.py:367: in convert
2024-08-23T15:10:56.7908564Z mol = atomgroup_to_mol(ag, **kwargs)
2024-08-23T15:10:56.7908968Z _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
2024-08-23T15:10:56.7909227Z
2024-08-23T15:10:56.7909497Z ag = <AtomGroup with 1877 atoms>, NoImplicit = True, max_iter = 200
2024-08-23T15:10:56.7909872Z force = False
2024-08-23T15:10:56.7910020Z
2024-08-23T15:10:56.7910337Z @lru_cache(maxsize=2)
2024-08-23T15:10:56.7911014Z def atomgroup_to_mol(ag, NoImplicit=True, max_iter=200, force=False):
2024-08-23T15:10:56.7911462Z """Converts an AtomGroup to an RDKit molecule without coordinates.
2024-08-23T15:10:56.7911769Z
2024-08-23T15:10:56.7912072Z Parameters
2024-08-23T15:10:56.7912399Z -----------
2024-08-23T15:10:56.7912689Z ag : MDAnalysis.core.groups.AtomGroup
2024-08-23T15:10:56.7913049Z The AtomGroup to convert
2024-08-23T15:10:56.7913379Z NoImplicit : bool
2024-08-23T15:10:56.7913756Z Prevent adding hydrogens to the molecule and allow bond orders and
2024-08-23T15:10:56.7914122Z formal charges to be guessed from the valence of each atom.
2024-08-23T15:10:56.7914489Z max_iter : int
2024-08-23T15:10:56.7914863Z Maximum number of iterations to standardize conjugated systems.
2024-08-23T15:10:56.7915271Z See :func:`_rebuild_conjugated_bonds`
2024-08-23T15:10:56.7915564Z force : bool
2024-08-23T15:10:56.7915939Z Force the conversion when no hydrogens were detected but
2024-08-23T15:10:56.7916344Z ``NoImplicit=True``. Mostly useful for inorganic molecules.
2024-08-23T15:10:56.7916690Z """
2024-08-23T15:10:56.7916936Z try:
2024-08-23T15:10:56.7917250Z elements = ag.elements
2024-08-23T15:10:56.7917580Z except NoDataError:
2024-08-23T15:10:56.7917930Z raise AttributeError(
2024-08-23T15:10:56.7918257Z "The `elements` attribute is required for the RDKitConverter "
2024-08-23T15:10:56.7918677Z "but is not present in this AtomGroup. Please refer to the "
2024-08-23T15:10:56.7919113Z "documentation to guess elements from other attributes or "
2024-08-23T15:10:56.7919521Z "type `help(MDAnalysis.topology.guessers)`") from None
2024-08-23T15:10:56.7919810Z
2024-08-23T15:10:56.7920478Z if "H" not in ag.elements:
2024-08-23T15:10:56.7921270Z if force:
2024-08-23T15:10:56.7921710Z warnings.warn(
2024-08-23T15:10:56.7922002Z "No hydrogen atom found in the topology. "
2024-08-23T15:10:56.7922341Z "Forcing to continue the conversion."
2024-08-23T15:10:56.7922634Z )
2024-08-23T15:10:56.7923283Z elif NoImplicit:
2024-08-23T15:10:56.7923530Z > raise AttributeError(
2024-08-23T15:10:56.7923869Z "No hydrogen atom could be found in the topology, but the "
2024-08-23T15:10:56.7924514Z "converter requires all hydrogens to be explicit. You can use "
2024-08-23T15:10:56.7925398Z "the parameter ``NoImplicit=False`` when using the converter "
2024-08-23T15:10:56.7925837Z "to allow implicit hydrogens and disable inferring bond "
2024-08-23T15:10:56.7926150Z "orders and charges. You can also use ``force=True`` to "
2024-08-23T15:10:56.7926482Z "ignore this error.")
2024-08-23T15:10:56.7927064Z E AttributeError: No hydrogen atom could be found in the topology, but the converter requires all hydrogens to be explicit. You can use the parameter ``NoImplicit=False`` when using the converter to allow implicit hydrogens and disable inferring bond orders and charges. You can also use ``force=True`` to ignore this error.
2024-08-23T15:10:56.7927487Z
2024-08-23T15:10:56.7927888Z C:\hostedtoolcache\windows\Python\3.12.5\x64\Lib\site-packages\MDAnalysis\converters\RDKit.py:426: AttributeError
2024-08-23T15:10:56.7928188Z
2024-08-23T15:10:56.7928426Z ---------- coverage: platform win32, python 3.12.5-final-0 -----------
Windows Python 3.10
2024-08-23T14:47:45.9462056Z _______________ TestRequiresRDKit.test_converter_requires_rdkit _______________
2024-08-23T14:47:45.9462567Z [gw0] win32 -- Python 3.10.11 C:\hostedtoolcache\windows\Python\3.10.11\x64\python.exe
2024-08-23T14:47:45.9462830Z
2024-08-23T14:47:45.9463276Z self = <MDAnalysisTests.converters.test_rdkit.TestRequiresRDKit object at 0x000001F061637AF0>
2024-08-23T14:47:45.9463599Z
2024-08-23T14:47:45.9463945Z def test_converter_requires_rdkit(self):
2024-08-23T14:47:45.9464354Z u = mda.Universe(PDB_full)
2024-08-23T14:47:45.9464755Z with pytest.raises(ImportError,
2024-08-23T14:47:45.9465135Z match="RDKit is required for the RDKitConverter"):
2024-08-23T14:47:45.9465559Z > u.atoms.convert_to("RDKIT")
2024-08-23T14:47:45.9465820Z
2024-08-23T14:47:45.9466200Z D:\a\1\s\testsuite\MDAnalysisTests\converters\test_rdkit.py:61:
2024-08-23T14:47:45.9466718Z _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
2024-08-23T14:47:45.9467407Z C:\hostedtoolcache\windows\Python\3.10.11\x64\lib\site-packages\MDAnalysis\core\accessors.py:204: in __call__
2024-08-23T14:47:45.9467916Z return convert(*args, **kwargs)
2024-08-23T14:47:45.9468388Z C:\hostedtoolcache\windows\Python\3.10.11\x64\lib\site-packages\MDAnalysis\converters\RDKit.py:367: in convert
2024-08-23T14:47:45.9468892Z mol = atomgroup_to_mol(ag, **kwargs)
2024-08-23T14:47:45.9469320Z _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
2024-08-23T14:47:45.9469551Z
2024-08-23T14:47:45.9469965Z ag = <AtomGroup with 1877 atoms>, NoImplicit = True, max_iter = 200
2024-08-23T14:47:45.9470378Z force = False
2024-08-23T14:47:45.9470579Z
2024-08-23T14:47:45.9470946Z @lru_cache(maxsize=2)
2024-08-23T14:47:45.9471334Z def atomgroup_to_mol(ag, NoImplicit=True, max_iter=200, force=False):
2024-08-23T14:47:45.9471808Z """Converts an AtomGroup to an RDKit molecule without coordinates.
2024-08-23T14:47:45.9472213Z
2024-08-23T14:47:45.9472567Z Parameters
2024-08-23T14:47:45.9472884Z -----------
2024-08-23T14:47:45.9473282Z ag : MDAnalysis.core.groups.AtomGroup
2024-08-23T14:47:45.9473774Z The AtomGroup to convert
2024-08-23T14:47:45.9474157Z NoImplicit : bool
2024-08-23T14:47:45.9474535Z Prevent adding hydrogens to the molecule and allow bond orders and
2024-08-23T14:47:45.9474997Z formal charges to be guessed from the valence of each atom.
2024-08-23T14:47:45.9475409Z max_iter : int
2024-08-23T14:47:45.9475838Z Maximum number of iterations to standardize conjugated systems.
2024-08-23T14:47:45.9476242Z See :func:`_rebuild_conjugated_bonds`
2024-08-23T14:47:45.9476645Z force : bool
2024-08-23T14:47:45.9477059Z Force the conversion when no hydrogens were detected but
2024-08-23T14:47:45.9477566Z ``NoImplicit=True``. Mostly useful for inorganic molecules.
2024-08-23T14:47:45.9477935Z """
2024-08-23T14:47:45.9478287Z try:
2024-08-23T14:47:45.9478658Z elements = ag.elements
2024-08-23T14:47:45.9478995Z except NoDataError:
2024-08-23T14:47:45.9479387Z raise AttributeError(
2024-08-23T14:47:45.9479817Z "The `elements` attribute is required for the RDKitConverter "
2024-08-23T14:47:45.9480281Z "but is not present in this AtomGroup. Please refer to the "
2024-08-23T14:47:45.9480685Z "documentation to guess elements from other attributes or "
2024-08-23T14:47:45.9481142Z "type `help(MDAnalysis.topology.guessers)`") from None
2024-08-23T14:47:45.9481543Z
2024-08-23T14:47:45.9481910Z if "H" not in ag.elements:
2024-08-23T14:47:45.9482237Z if force:
2024-08-23T14:47:45.9482610Z warnings.warn(
2024-08-23T14:47:45.9483021Z "No hydrogen atom found in the topology. "
2024-08-23T14:47:45.9483443Z "Forcing to continue the conversion."
2024-08-23T14:47:45.9483775Z )
2024-08-23T14:47:45.9484144Z elif NoImplicit:
2024-08-23T14:47:45.9484528Z > raise AttributeError(
2024-08-23T14:47:45.9485373Z "No hydrogen atom could be found in the topology, but the "
2024-08-23T14:47:45.9485791Z "converter requires all hydrogens to be explicit. You can use "
2024-08-23T14:47:45.9486257Z "the parameter ``NoImplicit=False`` when using the converter "
2024-08-23T14:47:45.9486713Z "to allow implicit hydrogens and disable inferring bond "
2024-08-23T14:47:45.9487205Z "orders and charges. You can also use ``force=True`` to "
2024-08-23T14:47:45.9487576Z "ignore this error.")
2024-08-23T14:47:45.9488356Z E AttributeError: No hydrogen atom could be found in the topology, but the converter requires all hydrogens to be explicit. You can use the parameter ``NoImplicit=False`` when using the converter to allow implicit hydrogens and disable inferring bond orders and charges. You can also use ``force=True`` to ignore this error.
2024-08-23T14:47:45.9488892Z
2024-08-23T14:47:45.9489401Z C:\hostedtoolcache\windows\Python\3.10.11\x64\lib\site-packages\MDAnalysis\converters\RDKit.py:426: AttributeError
2024-08-23T14:47:45.9489724Z
2024-08-23T14:47:45.9490143Z ---------- coverage: platform win32, python 3.10.11-final-0 ----------