Python 2.7 will reach end-of-life in January 2020, over 9 years after it was released. This falls within the Fedora 31 lifetime. Packages that depend on Python 2 are being switched to Python 3 or removed from Fedora: https://fedoraproject.org/wiki/Changes/F31_Mass_Python_2_Package_Removal#Information_on_Remaining_Packages Python 2 will be retired in Fedora 32: https://fedoraproject.org/wiki/Changes/RetirePython2 To help planning, we'd like to know the plans for samtools's future. Specifically: - What is the reason for the Python2 dependency? (Is it software written in Python, or does it just provide Python bindings, or use Python in the build system or test runner?) - What are the upstream/community plans/timelines regarding Python 3? - What is the guidance for porting to Python 3? (Assuming that there is someone who generally knows how to port to Python 3, but doesn't know anything about the particular package, what are the next steps to take?) This bug is filed semi-automatically, and might not have all the context specific to samtools. If you need anything from us, or something is unclear, please mention it here. Thank you.
This bug appears to have been reported against 'rawhide' during the Fedora 31 development cycle. Changing version to 31.
Please answer the above questions. If you don't, the package can be orphaned: https://fedoraproject.org/wiki/Changes/F31_Mass_Python_2_Package_Removal#Information_on_Remaining_Packages If you need any information or help, or if you need some more time, please let us know.
Could indeed do with a bit more time on this, if possible.
It's another week after your last reply and almost a month since this bug was created. How much time do you need?
There is a script varfilter.py provided with samtools that was written for Python 2. This is a very old version of samtools - upstream is 1.9 - so it's very unlikely that they will work on porting this script to Python 3.
And why we cannot update this package?
Any news here? Could you please answer the previous question?
It's changed a great deal since then. There is already a review request for htslib, which is a prerequisite for the newer version: https://bugzilla.redhat.com/show_bug.cgi?id=1326504
It seems that the htslib is available in rawhide so we can update samtools.
I sent a pull-request to update samtools to the latest version 1.9 replacing the python2 with python3. https://src.fedoraproject.org/rpms/samtools/pull-request/1 Could you review it? Thanks.
We need to keep in mind that samtools python2 dependency has to be replaced until mid-November. List of Python 2 packages to be removed mid-November https://lists.fedoraproject.org/archives/list/devel@lists.fedoraproject.org/thread/2GYSDBIY7V66JAJZ6A7UHK657F4DIWPQ/
I sent a PR to fix only this ticket. https://src.fedoraproject.org/rpms/samtools/pull-request/2 Could you review it? Thank you.
FEDORA-2019-3a2e81e1ab has been submitted as an update to Fedora 29. https://bodhi.fedoraproject.org/updates/FEDORA-2019-3a2e81e1ab
FEDORA-2019-5790aff49a has been submitted as an update to Fedora 30. https://bodhi.fedoraproject.org/updates/FEDORA-2019-5790aff49a
As I was added as a co-maintainer of rpms/samtools by current maintainer Adam, I can build samtools. * f30, f29: now on Budhi. * f31: I faced the issue related to binutils RPM package's strip command when doing scratch build. I am asking it here. https://bugzilla.redhat.com/show_bug.cgi?id=1770464#c10
samtools-0.1.19-20.fc30 has been pushed to the Fedora 30 testing repository. If problems still persist, please make note of it in this bug report. See https://fedoraproject.org/wiki/QA:Updates_Testing for instructions on how to install test updates. You can provide feedback for this update here: https://bodhi.fedoraproject.org/updates/FEDORA-2019-5790aff49a
samtools-0.1.19-20.fc29 has been pushed to the Fedora 29 testing repository. If problems still persist, please make note of it in this bug report. See https://fedoraproject.org/wiki/QA:Updates_Testing for instructions on how to install test updates. You can provide feedback for this update here: https://bodhi.fedoraproject.org/updates/FEDORA-2019-3a2e81e1ab
FEDORA-2019-5c653711f3 has been submitted as an update to Fedora 31. https://bodhi.fedoraproject.org/updates/FEDORA-2019-5c653711f3
samtools-0.1.19-20.fc31 has been pushed to the Fedora 31 testing repository. If problems still persist, please make note of it in this bug report. See https://fedoraproject.org/wiki/QA:Updates_Testing for instructions on how to install test updates. You can provide feedback for this update here: https://bodhi.fedoraproject.org/updates/FEDORA-2019-5c653711f3
samtools-0.1.19-20.fc30 has been pushed to the Fedora 30 stable repository. If problems still persist, please make note of it in this bug report.
samtools-0.1.19-20.fc31 has been pushed to the Fedora 31 stable repository. If problems still persist, please make note of it in this bug report.