Bug 2256748 - smoldyn fails to build with Python 3.13: 67% tests passed, 1 tests failed out of 3
Summary: smoldyn fails to build with Python 3.13: 67% tests passed, 1 tests failed out...
Keywords:
Status: CLOSED WORKSFORME
Alias: None
Product: Fedora
Classification: Fedora
Component: smoldyn
Version: rawhide
Hardware: Unspecified
OS: Unspecified
unspecified
unspecified
Target Milestone: ---
Assignee: Antonio T. sagitter
QA Contact: Fedora Extras Quality Assurance
URL:
Whiteboard:
Depends On:
Blocks: PYTHON3.13
TreeView+ depends on / blocked
 
Reported: 2024-01-04 10:52 UTC by Karolina Surma
Modified: 2024-05-31 10:19 UTC (History)
5 users (show)

Fixed In Version:
Clone Of:
Environment:
Last Closed: 2024-05-31 10:19:18 UTC
Type: Bug
Embargoed:


Attachments (Terms of Use)

Description Karolina Surma 2024-01-04 10:52:08 UTC
smoldyn fails to build with Python 3.13.0a2.

+ xvfb-run ctest -j1 -VV -R 'test_api|test_sanity|test_biosimulator' --output-on-failure --debug

<snip> 

/builddir/build/BUILD/cmake-3.27.7/Source/CTest/cmCTestRunTest.cxx:526     Start  3: test_biosimulators

/builddir/build/BUILD/cmake-3.27.7/Source/CTest/cmCTestRunTest.cxx:687 
3: Test command: /usr/bin/python3.13 "/builddir/build/BUILD/Smoldyn-2.72/tests/test_biosimulators.py"

/builddir/build/BUILD/cmake-3.27.7/Source/CTest/cmCTestRunTest.cxx:695 3: Working Directory: /builddir/build/BUILD/Smoldyn-2.72/tests

/builddir/build/BUILD/cmake-3.27.7/Source/CTest/cmCTestRunTest.cxx:703 3: Environment variables: 

/builddir/build/BUILD/cmake-3.27.7/Source/CTest/cmCTestRunTest.cxx:708 3:  PYTHONPATH=/builddir/build/BUILD/Smoldyn-2.72/redhat-linux-build/py

/builddir/build/BUILD/cmake-3.27.7/Source/CTest/cmCTestRunTest.cxx:708 3:  SMOLDYN_NO_PROMPT=1

/builddir/build/BUILD/cmake-3.27.7/Source/cmCTest.cxx:309    Current_Time: Dec 22 16:43 UTC

/builddir/build/BUILD/cmake-3.27.7/Source/CTest/cmCTestRunTest.cxx:807 3: Test timeout computed to be: 10000000

/builddir/build/BUILD/cmake-3.27.7/Source/CTest/cmCTestRunTest.cxx:39 3: ssssssssssssssssssssssss

/builddir/build/BUILD/cmake-3.27.7/Source/CTest/cmCTestRunTest.cxx:39 3: ----------------------------------------------------------------------

/builddir/build/BUILD/cmake-3.27.7/Source/CTest/cmCTestRunTest.cxx:39 3: Ran 0 tests in 0.000s

/builddir/build/BUILD/cmake-3.27.7/Source/CTest/cmCTestRunTest.cxx:39 3: 

/builddir/build/BUILD/cmake-3.27.7/Source/CTest/cmCTestRunTest.cxx:39 3: NO TESTS RAN (skipped=24)

/builddir/build/BUILD/cmake-3.27.7/Source/CTest/cmCTestRunTest.cxx:986 2/3 Test  #3: test_biosimulators ...............
/builddir/build/BUILD/cmake-3.27.7/Source/CTest/cmCTestRunTest.cxx:989 Testing test_biosimulators ... 
/builddir/build/BUILD/cmake-3.27.7/Source/CTest/cmCTestRunTest.cxx:256 ***Failed    0.24 sec

/builddir/build/BUILD/cmake-3.27.7/Source/CTest/cmCTestRunTest.cxx:260 ssssssssssssssssssssssss
----------------------------------------------------------------------
Ran 0 tests in 0.000s

NO TESTS RAN (skipped=24)


/builddir/build/BUILD/cmake-3.27.7/Source/CTest/cmCTestTestHandler.cxx:613 
67% tests passed, 1 tests failed out of 3

/builddir/build/BUILD/cmake-3.27.7/Source/CTest/cmCTestTestHandler.cxx:629 
Total Test time (real) =   0.64 sec

/builddir/build/BUILD/cmake-3.27.7/Source/CTest/cmCTestTestHandler.cxx:668 
The following tests FAILED:
/builddir/build/BUILD/cmake-3.27.7/Source/CTest/cmCTestTestHandler.cxx:682 	  3 - test_biosimulators (Failed)
/builddir/build/BUILD/cmake-3.27.7/Source/cmCTest.cxx:1026 Errors while running CTest
/builddir/build/BUILD/cmake-3.27.7/Source/cmCTest.cxx:2942 Running a test(s) failed returning : 8


https://docs.python.org/3.13/whatsnew/3.13.html

For the build logs, see:
https://copr-be.cloud.fedoraproject.org/results/@python/python3.13/fedora-rawhide-x86_64/06784100-smoldyn/

For all our attempts to build smoldyn with Python 3.13, see:
https://copr.fedorainfracloud.org/coprs/g/python/python3.13/package/smoldyn/

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 3.13:
https://copr.fedorainfracloud.org/coprs/g/python/python3.13/

Let us know here if you have any questions.

Python 3.13 is planned to be included in Fedora 41.
To make that update smoother, we're building Fedora packages with all pre-releases of Python 3.13.
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 Aoife Moloney 2024-02-15 23:08:45 UTC
This bug appears to have been reported against 'rawhide' during the Fedora Linux 40 development cycle.
Changing version to 40.

Comment 2 Sandro 2024-05-31 10:19:18 UTC
Builds fine now with Python 3.13. Latest build in Python 3.13 Copr also succeeded.


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