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TestRequiresRDKit.test_converter_requires_rdkit fails on Azure Windows and with Azure Linux 3.10 #4687

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orbeckst opened this issue Aug 25, 2024 · 1 comment · Fixed by #4688
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TestRequiresRDKit.test_converter_requires_rdkit fails on Azure Windows and with Azure Linux 3.10 #4687

orbeckst opened this issue Aug 25, 2024 · 1 comment · Fixed by #4688
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Component-Converters OpSys-Linux OpSys-Windows

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@orbeckst
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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

https://dev.azure.com/mdanalysis/cefe1135-cd6a-4689-8710-15bd37ad81e6/_apis/build/builds/7149/logs/95

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

https://dev.azure.com/mdanalysis/cefe1135-cd6a-4689-8710-15bd37ad81e6/_apis/build/builds/7149/logs/84

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 ----------
@orbeckst orbeckst mentioned this issue Aug 25, 2024
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@IAlibay IAlibay mentioned this issue Aug 25, 2024
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@IAlibay
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IAlibay commented Aug 25, 2024

This seems like a legitimate failure, the azure pipelines are picking up a leftover from the numpy 2.0 migration. Now that rdkit supports numpy 2.0, the import checks are failing in the wrong way.

yuxuanzhuang pushed a commit to yuxuanzhuang/mdanalysis that referenced this issue Sep 9, 2024
@IAlibay @yuxuanzhuang
Fix MDAnalysis#4687 -- rdkit values in azure CI (MDAnalysis#4688)
acc60b8 
* Investigate rdkit issue

* Update azure-pipelines.yml

* fix numpy 2.0 import block

* fix imports
hmacdope pushed a commit that referenced this issue Sep 10, 2024
@yuxuanzhuang @MattTDavies
@IAlibay @orbeckst
Remove GSD from optional test dependencies (#4707)
319b667 
* Fixed high dimensional GroupBase indexing.

* fixed pep8 issues

* Removed sanitisation

* Fix #4687 -- rdkit values in azure CI (#4688)

* Investigate rdkit issue

* Update azure-pipelines.yml

* fix numpy 2.0 import block

* fix imports

* mark analysis.pca.PCA as not parallelizable (#4684)

- fix #4680
- PCA explicitly marked as not parallelizable (at least not with
  simple split-apply-combine)
- add tests
- update CHANGELOG

* disable gsd

* disable gsd in azure

* reduce timeout and set logical

* fix azure

* restore timeout to 200

---------

Co-authored-by: Matthew Davies <128810112+MattTDavies@users.noreply.github.com>
Co-authored-by: Irfan Alibay <IAlibay@users.noreply.github.com>
Co-authored-by: Oliver Beckstein <orbeckst@gmail.com>
RMeli pushed a commit to RMeli/mdanalysis that referenced this issue Oct 3, 2024
@IAlibay @RMeli
Fix MDAnalysis#4687 -- rdkit values in azure CI (MDAnalysis#4688)
b38ee33 
* Investigate rdkit issue

* Update azure-pipelines.yml

* fix numpy 2.0 import block

* fix imports
RMeli pushed a commit to RMeli/mdanalysis that referenced this issue Oct 3, 2024
@yuxuanzhuang @MattTDavies
@IAlibay @orbeckst @RMeli
Remove GSD from optional test dependencies (MDAnalysis#4707)
007b211 
* Fixed high dimensional GroupBase indexing.

* fixed pep8 issues

* Removed sanitisation

* Fix MDAnalysis#4687 -- rdkit values in azure CI (MDAnalysis#4688)

* Investigate rdkit issue

* Update azure-pipelines.yml

* fix numpy 2.0 import block

* fix imports

* mark analysis.pca.PCA as not parallelizable (MDAnalysis#4684)

- fix MDAnalysis#4680
- PCA explicitly marked as not parallelizable (at least not with
  simple split-apply-combine)
- add tests
- update CHANGELOG

* disable gsd

* disable gsd in azure

* reduce timeout and set logical

* fix azure

* restore timeout to 200

---------

Co-authored-by: Matthew Davies <128810112+MattTDavies@users.noreply.github.com>
Co-authored-by: Irfan Alibay <IAlibay@users.noreply.github.com>
Co-authored-by: Oliver Beckstein <orbeckst@gmail.com>
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Fix #4687 -- rdkit values in azure CI MDAnalysis/mdanalysis
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@orbeckst @IAlibay