Bug 1793926 - pymol fails to build with Python 3.9: invalid open() mode U
Summary: pymol fails to build with Python 3.9: invalid open() mode U
Keywords:
Status: CLOSED RAWHIDE
Alias: None
Product: Fedora
Classification: Fedora
Component: pymol
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: PYTHON39
TreeView+ depends on / blocked
 
Reported: 2020-01-22 09:45 UTC by Miro Hrončok
Modified: 2020-01-22 23:12 UTC (History)
5 users (show)

Fixed In Version:
Doc Type: If docs needed, set a value
Doc Text:
Clone Of:
Environment:
Last Closed: 2020-01-22 23:12:27 UTC
Type: Bug
Embargoed:


Attachments (Terms of Use)

Description Miro Hrončok 2020-01-22 09:45:50 UTC
pymol fails to build with Python 3.9.0a2.

+ /usr/bin/python3 setup.py build '--executable=/usr/bin/python3 -s' --use-msgpackc=c++11 --glut
Traceback (most recent call last):
  File "/builddir/build/BUILD/pymol-open-source-2.3.0/setup.py", line 225, in <module>
    create_shadertext.create_all(generated_dir)
  File "/builddir/build/BUILD/pymol-open-source-2.3.0/create_shadertext.py", line 21, in create_all
    create_shadertext(
  File "/builddir/build/BUILD/pymol-open-source-2.3.0/create_shadertext.py", line 84, in create_shadertext
    with open(shaderfile, 'rU') as handle:
ValueError: invalid mode: 'rU'


See https://docs.python.org/3.9/whatsnew/3.9.html#changes-in-the-python-api

"open(), io.open(), codecs.open() and fileinput.FileInput no longer accept 'U' (“universal newline”) in the file mode. This flag was deprecated since Python 3.3. In Python 3, the “universal newline” is used by default when a file is open in text mode. The newline parameter of open() controls how universal newlines works."


For the build logs, see:
https://copr-be.cloud.fedoraproject.org/results/@python/python3.9/fedora-rawhide-x86_64/01171841-pymol/

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

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 Karthikeyan Singaravelan 2020-01-22 16:56:56 UTC
Upstream issue : https://github.com/schrodinger/pymol-open-source/issues/78

Comment 2 Antonio T. (sagitter) 2020-01-22 21:32:18 UTC
(In reply to Karthikeyan Singaravelan from comment #1)
> Upstream issue : https://github.com/schrodinger/pymol-open-source/issues/78

Patch included on Rawhide; please, test the release `pymol-2.3.0-6.fc32` with Python 3.9
https://koji.fedoraproject.org/koji/buildinfo?buildID=1431679

Does exist a koji build for testing Python 3.9?

Comment 3 Miro Hrončok 2020-01-22 23:12:27 UTC
No, but the copr should pick all commits: https://copr.fedorainfracloud.org/coprs/g/python/python3.9/package/pymol/  -- this has built, thanks.


Note You need to log in before you can comment on or make changes to this bug.