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Bug 1838445 - python-MDAnalysis fails to build with Python 3.9: AttributeError: module 'MDAnalysis.analysis.encore' has no attribute 'AffinityPropagation'
Summary: python-MDAnalysis fails to build with Python 3.9: AttributeError: module 'MDA...
Keywords:
Status: CLOSED RAWHIDE
Alias: None
Product: Fedora
Classification: Fedora
Component: python-MDAnalysis
Version: rawhide
Hardware: Unspecified
OS: Unspecified
unspecified
unspecified
Target Milestone: ---
Assignee: Christoph Junghans
QA Contact: Fedora Extras Quality Assurance
URL:
Whiteboard:
Depends On: 1838489
Blocks: F33FTBFS PYTHON39
TreeView+ depends on / blocked
 
Reported: 2020-05-21 07:47 UTC by Miro Hrončok
Modified: 2020-06-11 11:47 UTC (History)
5 users (show)

Fixed In Version:
Doc Type: If docs needed, set a value
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Clone Of:
Environment:
Last Closed: 2020-06-11 11:47:59 UTC
Type: Bug
Embargoed:

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System ID Private Priority Status Summary Last Updated
Github MDAnalysis mdanalysis issues 2688 0 None open python3.9: AttributeError: module 'MDAnalysis.analysis.encore' has no attribute 'KMeans' 2020-12-11 14:56:35 UTC

Description Miro Hrončok 2020-05-21 07:47:29 UTC 
python-MDAnalysis fails to build with Python 3.9.0b1.

___________ TestEncore.test_ces_error_estimation_ensemble_bootstrap ____________
[gw0] linux -- Python 3.9.0 /usr/bin/python3

self = <MDAnalysisTests.analysis.test_encore.TestEncore object at 0x7f10a25a16a0>
ens1 = <Universe with 3341 atoms>

    def test_ces_error_estimation_ensemble_bootstrap(self, ens1):
        # Error estimation using a method that does not take a distance
        # matrix as input, and therefore relies on bootstrapping the ensembles
        # instead
    
        pytest.importorskip('sklearn')
    
        expected_average = 0.03
        expected_stdev = 0.02
        averages, stdevs = encore.ces([ens1, ens1],
                                      estimate_error = True,
                                      bootstrapping_samples=10,
>                                     clustering_method=encore.KMeans(n_clusters=2),
                                      selection="name CA and resnum 1-10")
E       AttributeError: module 'MDAnalysis.analysis.encore' has no attribute 'KMeans'

analysis/test_encore.py:377: AttributeError
______________ TestEncoreClustering.test_clustering_DBSCAN_direct ______________
[gw0] linux -- Python 3.9.0 /usr/bin/python3

self = <MDAnalysisTests.analysis.test_encore.TestEncoreClustering object at 0x7f109b9c13d0>
ens1 = <Universe with 3341 atoms>

    def test_clustering_DBSCAN_direct(self, ens1):
        pytest.importorskip('sklearn')
>       method = encore.DBSCAN(eps=0.5, min_samples=2)
E       AttributeError: module 'MDAnalysis.analysis.encore' has no attribute 'DBSCAN'

analysis/test_encore.py:489: AttributeError
____________ TestEncoreClustering.test_sklearn_affinity_propagation ____________
[gw0] linux -- Python 3.9.0 /usr/bin/python3

self = <MDAnalysisTests.analysis.test_encore.TestEncoreClustering object at 0x7f10a6bde610>
ens1 = <Universe with 3341 atoms>

    def test_sklearn_affinity_propagation(self, ens1):
        pytest.importorskip('sklearn')
        cc1 = encore.cluster([ens1])
        cc2 = encore.cluster([ens1],
>                            method=encore.AffinityPropagation())
E       AttributeError: module 'MDAnalysis.analysis.encore' has no attribute 'AffinityPropagation'

analysis/test_encore.py:526: AttributeError
_______ TestEncoreClustering.test_clustering_AffinityPropagation_direct ________
[gw1] linux -- Python 3.9.0 /usr/bin/python3

self = <MDAnalysisTests.analysis.test_encore.TestEncoreClustering object at 0x7f4107ae8550>
ens1 = <Universe with 3341 atoms>

    def test_clustering_AffinityPropagation_direct(self, ens1):
        pytest.importorskip('sklearn')
>       method = encore.AffinityPropagation()
E       AttributeError: module 'MDAnalysis.analysis.encore' has no attribute 'AffinityPropagation'

analysis/test_encore.py:469: AttributeError
__________ TestEncoreClustering.test_clustering_two_different_methods __________
[gw1] linux -- Python 3.9.0 /usr/bin/python3

self = <MDAnalysisTests.analysis.test_encore.TestEncoreClustering object at 0x7f41073b0f10>
ens1 = <Universe with 3341 atoms>

    def test_clustering_two_different_methods(self, ens1):
        pytest.importorskip('sklearn')
        cluster_collection = encore.cluster(
            [ens1],
>           method=[encore.AffinityPropagation(preference=-7.5),
                    encore.DBSCAN(min_samples=2)])
E       AttributeError: module 'MDAnalysis.analysis.encore' has no attribute 'AffinityPropagation'

analysis/test_encore.py:500: AttributeError
= 5 failed, 15404 passed, 69 skipped, 2 xfailed, 1 xpassed, 186055 warnings in 813.76 seconds =

For the build logs, see:
https://copr-be.cloud.fedoraproject.org/results/@python/python3.9/fedora-rawhide-x86_64/01396414-python-MDAnalysis/

For all our attempts to build python-MDAnalysis with Python 3.9, see:
https://copr.fedorainfracloud.org/coprs/g/python/python3.9/package/python-MDAnalysis/

Testing and mass rebuild of packages is happening in copr. You can follow these instructions to test locally in mock if your package builds with Python 3.9:
https://copr.fedorainfracloud.org/coprs/g/python/python3.9/

Let us know here if you have any questions.

Python 3.9 will be included in Fedora 33. To make that update smoother, we're building Fedora packages with early pre-releases of Python 3.9.
A build failure prevents us from testing all dependent packages (transitive [Build]Requires), so if this package is required a lot, it's important for us to get it fixed soon.
We'd appreciate help from the people who know this package best, but if you don't want to work on this now, let us know so we can try to work around it on our side.
Comment 1 Miro Hrončok 2020-05-25 13:01:41 UTC 
This comment is mass posted to all bugs blocking the Python 3.9 tracker, sorry if it is not 100 % relevant. When in doubt, please ask.


The Python 3.9 rebuild is in progress in a Koji side tag.

If you fix this bug, please don't rebuild the package in regular rawhide, but do it in the side tag with:

    $ fedpkg build --target=f33-python

The rebuild is progressing slowly and it is possible this package won't have all the required build dependencies yet. If that's the case, please just leave the fix committed and pushed and we will eventually rebuild it for you.

You are not asked to go and try rebuild all the missing dependencies yourself. If you know there is a bootstrap loop in the dependencies, let me know and we can untangle it together.

If you want to test your fix or reproduce the failure, you can still use the Copr repo mentioned in the initial comment of this bug: https://copr.fedorainfracloud.org/coprs/g/python/python3.9/
Comment 2 Dominik 'Rathann' Mierzejewski 2020-05-25 13:06:03 UTC 
Upstream says it's a sklearn issue.
Comment 3 Miro Hrončok 2020-05-29 07:11:38 UTC 
Python 3.9 update: The f33-python side tag is currently being merged.

New builds in f33-python are no longer possible, but python3 is not yet updated to Python 3.9 in rawhide. You can check when Python is Python 3.9 with:

    $ koji wait-repo f33-build --build python3.9-3.9.0~b1-3.fc3

And build the packages normally after that.
Comment 4 Miro Hrončok 2020-06-11 11:47:59 UTC 
This is a bulk close of Python 3.9 bugzillas of packages that successfully built.
If this remained open for a reason, I am sorry and feel free to reopen.
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