Bug 1738176
| Summary: | samtools depends on Python 2 | ||
|---|---|---|---|
| Product: | [Fedora] Fedora | Reporter: | Lumír Balhar <lbalhar> |
| Component: | samtools | Assignee: | Jun Aruga <jaruga> |
| Status: | CLOSED ERRATA | QA Contact: | Fedora Extras Quality Assurance <extras-qa> |
| Severity: | unspecified | Docs Contact: | |
| Priority: | unspecified | ||
| Version: | rawhide | CC: | bloch, jaruga, ron |
| Target Milestone: | --- | ||
| Target Release: | --- | ||
| Hardware: | Unspecified | ||
| OS: | Unspecified | ||
| Whiteboard: | |||
| Fixed In Version: | samtools-0.1.19-20.fc32 samtools-0.1.19-20.fc30 samtools-0.1.19-20.fc31 | Doc Type: | If docs needed, set a value |
| Doc Text: | Story Points: | --- | |
| Clone Of: | Environment: | ||
| Last Closed: | 2019-12-02 01:29:29 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: | 1326504, 1759940 | ||
| Bug Blocks: | 1698500 | ||
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Description
Lumír Balhar
2019-08-06 13:22:16 UTC
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. 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. |