Bug 1793926
| Summary: | pymol fails to build with Python 3.9: invalid open() mode U | ||
|---|---|---|---|
| Product: | [Fedora] Fedora | Reporter: | Miro Hrončok <mhroncok> |
| Component: | pymol | Assignee: | Antonio T. (sagitter) <anto.trande> |
| Status: | CLOSED RAWHIDE | QA Contact: | Fedora Extras Quality Assurance <extras-qa> |
| Severity: | unspecified | Docs Contact: | |
| Priority: | unspecified | ||
| Version: | rawhide | CC: | anto.trande, cstratak, mhroncok, sergio, tir.karthi |
| Target Milestone: | --- | ||
| Target Release: | --- | ||
| Hardware: | Unspecified | ||
| OS: | Unspecified | ||
| Whiteboard: | |||
| Fixed In Version: | Doc Type: | If docs needed, set a value | |
| Doc Text: | Story Points: | --- | |
| Clone Of: | Environment: | ||
| Last Closed: | 2020-01-22 23:12:27 UTC | Type: | Bug |
| Regression: | --- | Mount Type: | --- |
| Documentation: | --- | CRM: | |
| Verified Versions: | Category: | --- | |
| oVirt Team: | --- | RHEL 7.3 requirements from Atomic Host: | |
| Cloudforms Team: | --- | Target Upstream Version: | |
| Embargoed: | |||
| Bug Depends On: | |||
| Bug Blocks: | 1785415 | ||
Upstream issue : https://github.com/schrodinger/pymol-open-source/issues/78 (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? No, but the copr should pick all commits: https://copr.fedorainfracloud.org/coprs/g/python/python3.9/package/pymol/ -- this has built, thanks. |
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.