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Bug 1705452 - rdkit fails to rebuild with Python 3.8
Summary: rdkit fails to rebuild with Python 3.8
Keywords:
Status: CLOSED RAWHIDE
Alias: None
Product: Fedora
Classification: Fedora
Component: rdkit
Version: rawhide
Hardware: Unspecified
OS: Unspecified
unspecified
unspecified
Target Milestone: ---
Assignee: Gianluca Sforna
QA Contact: Fedora Extras Quality Assurance
URL:
Whiteboard:
Depends On:
Blocks: PYTHON38
TreeView+ depends on / blocked
 
Reported: 2019-05-02 10:42 UTC by Miro Hrončok
Modified: 2019-07-13 09:45 UTC (History)
1 user (show)

Fixed In Version:
Doc Type: If docs needed, set a value
Doc Text:
Clone Of:
Environment:
Last Closed: 2019-07-13 08:04:54 UTC
Type: Bug
Embargoed:

Attachments (Terms of Use)
Full log from Copr (2.34 MB, text/plain)
2019-05-02 10:42 UTC, Miro Hrončok 		no flags Details
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Description Miro Hrončok 2019-05-02 10:42:58 UTC 
Created attachment 1561519 [details]
Full log from Copr

rdkit 2018.09.2-5.fc31 fails to rebuild with Python 3.8 due to test failures. Those might not be Python 3.8 related, but the package needs to rebuild, otherwise it won't be installable once we update Python.

140: ======================================================================
140: FAIL: testEnumerateStereoisomersRandomSamplingShouldBeDeterministicAndPortable (__main__.TestCase)
140: ----------------------------------------------------------------------
140: Traceback (most recent call last):
140:   File "UnitTestMol3D.py", line 218, in testEnumerateStereoisomersRandomSamplingShouldBeDeterministicAndPortable
140:     self.assertEqual(smiles, expected)
140: AssertionError: Items in the first set but not the second:
140: 'C/C(F)=C/[C@@H](Cl)/C=C(\\Br)[C@H](N)I'
140: 'C/C(F)=C\\[C@H](Cl)/C=C(\\Br)[C@H](N)I'
140: Items in the second set but not the first:
140: 'C/C(F)=C/[C@H](Cl)/C=C(\\Br)[C@H](N)I'
140: 'C/C(F)=C/[C@@H](Cl)/C=C(/Br)[C@@H](N)I'
140: 
140: ----------------------------------------------------------------------

140: ======================================================================
140: FAIL: EnumerateStereoisomers (rdkit.Chem.EnumerateStereoisomers)
140: Doctest: rdkit.Chem.EnumerateStereoisomers.EnumerateStereoisomers
140: ----------------------------------------------------------------------
140: Traceback (most recent call last):
140:   File "/usr/lib64/python3.8/doctest.py", line 2196, in runTest
140:     raise self.failureException(self.format_failure(new.getvalue()))
140: AssertionError: Failed doctest test for rdkit.Chem.EnumerateStereoisomers.EnumerateStereoisomers
140:   File "/builddir/build/BUILD/rdkit-Release_2018_09_2/python3/rdkit/Chem/EnumerateStereoisomers.py", line 98, in EnumerateStereoisomers
140: 
140: ----------------------------------------------------------------------
140: File "/builddir/build/BUILD/rdkit-Release_2018_09_2/python3/rdkit/Chem/EnumerateStereoisomers.py", line 210, in rdkit.Chem.EnumerateStereoisomers.EnumerateStereoisomers
140: Failed example:
140:     for smi in sorted(Chem.MolToSmiles(x, isomericSmiles=True) for x in isomers):
140:         print(smi)
140: Expected:
140:     F[C@@H](Cl)[C@@H](Cl)[C@@H](Cl)[C@H](Cl)[C@H](Cl)[C@@H](Cl)[C@@H](Cl)[C@@H](Cl)[C@@H](Cl)[C@H](Cl)[C@@H](Cl)[C@H](Cl)[C@@H](Cl)[C@@H](Cl)[C@H](Cl)[C@H](Cl)[C@H](Cl)[C@H](Cl)[C@H](Cl)[C@@H](Cl)Br
140:     F[C@@H](Cl)[C@H](Cl)[C@@H](Cl)[C@H](Cl)[C@@H](Cl)[C@H](Cl)[C@H](Cl)[C@H](Cl)[C@H](Cl)[C@H](Cl)[C@@H](Cl)[C@@H](Cl)[C@@H](Cl)[C@@H](Cl)[C@@H](Cl)[C@@H](Cl)[C@@H](Cl)[C@@H](Cl)[C@H](Cl)[C@@H](Cl)Br
140:     F[C@H](Cl)[C@H](Cl)[C@@H](Cl)[C@@H](Cl)[C@H](Cl)[C@@H](Cl)[C@@H](Cl)[C@@H](Cl)[C@H](Cl)[C@H](Cl)[C@H](Cl)[C@H](Cl)[C@H](Cl)[C@@H](Cl)[C@H](Cl)[C@@H](Cl)[C@@H](Cl)[C@@H](Cl)[C@H](Cl)[C@@H](Cl)Br
140: Got:
140:     F[C@@H](Cl)[C@@H](Cl)[C@@H](Cl)[C@@H](Cl)[C@H](Cl)[C@@H](Cl)[C@@H](Cl)[C@H](Cl)[C@H](Cl)[C@@H](Cl)[C@H](Cl)[C@@H](Cl)[C@@H](Cl)[C@@H](Cl)[C@H](Cl)[C@@H](Cl)[C@H](Cl)[C@H](Cl)[C@H](Cl)[C@@H](Cl)Br
140:     F[C@@H](Cl)[C@H](Cl)[C@H](Cl)[C@H](Cl)[C@H](Cl)[C@H](Cl)[C@@H](Cl)[C@@H](Cl)[C@H](Cl)[C@@H](Cl)[C@@H](Cl)[C@H](Cl)[C@@H](Cl)[C@@H](Cl)[C@@H](Cl)[C@@H](Cl)[C@@H](Cl)[C@H](Cl)[C@@H](Cl)[C@@H](Cl)Br
140:     F[C@H](Cl)[C@@H](Cl)[C@@H](Cl)[C@H](Cl)[C@@H](Cl)[C@@H](Cl)[C@@H](Cl)[C@H](Cl)[C@@H](Cl)[C@H](Cl)[C@@H](Cl)[C@@H](Cl)[C@@H](Cl)[C@H](Cl)[C@@H](Cl)[C@@H](Cl)[C@H](Cl)[C@@H](Cl)[C@H](Cl)[C@H](Cl)Br
140: 
140: 
140: ----------------------------------------------------------------------


Full log attached.
Comment 1 Miro Hrončok 2019-07-10 10:11:18 UTC 
Please respond.
Comment 2 Gianluca Sforna 2019-07-13 08:04:54 UTC 
As you suspected the test failures are not related to python 3.8. I'm getting different failures on other platforms, some of them reported upstream, but right now I had to disable the tests until all of them are fixed.

Without tests the build succeeded, and I updated to the latest upstream release in rawhide
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