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Bug 1738176 - samtools depends on Python 2
Summary: samtools depends on Python 2
Keywords:
Status: CLOSED ERRATA
Alias: None
Product: Fedora
Classification: Fedora
Component: samtools
Version: rawhide
Hardware: Unspecified
OS: Unspecified
unspecified
unspecified
Target Milestone: ---
Assignee: Jun Aruga
QA Contact: Fedora Extras Quality Assurance
URL:
Whiteboard:
Depends On: 1326504 1759940
Blocks: F31_PY2REMOVAL
TreeView+ depends on / blocked
 
Reported: 2019-08-06 13:22 UTC by Lumír Balhar
Modified: 2019-12-07 01:50 UTC (History)
3 users (show)

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:
Clone Of:
Environment:
Last Closed: 2019-12-02 01:29:29 UTC
Type: Bug
Embargoed:

Attachments (Terms of Use)

Description Lumír Balhar 2019-08-06 13:22:16 UTC 
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.
Comment 1 Ben Cotton 2019-08-13 17:39:44 UTC 
This bug appears to have been reported against 'rawhide' during the Fedora 31 development cycle.
Changing version to 31.
Comment 2 Lumír Balhar 2019-08-15 07:47:44 UTC 
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.
Comment 3 Lumír Balhar 2019-08-22 07:02:14 UTC 
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.
Comment 4 Adam Huffman 2019-08-27 15:49:17 UTC 
Could indeed do with a bit more time on this, if possible.
Comment 5 Lumír Balhar 2019-09-04 06:39:45 UTC 
It's another week after your last reply and almost a month since this bug was created. How much time do you need?
Comment 6 Adam Huffman 2019-09-05 21:41:40 UTC 
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.
Comment 7 Lumír Balhar 2019-09-06 05:15:37 UTC 
And why we cannot update this package?
Comment 8 Lumír Balhar 2019-09-13 10:21:20 UTC 
Any news here? Could you please answer the previous question?
Comment 9 Adam Huffman 2019-09-13 10:50:36 UTC 
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
Comment 10 Lumír Balhar 2019-10-25 10:04:53 UTC 
It seems that the htslib is available in rawhide so we can update samtools.
Comment 11 Jun Aruga 2019-10-28 23:08:56 UTC 
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.
Comment 12 Jun Aruga 2019-10-29 16:31:41 UTC 
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/
Comment 13 Jun Aruga 2019-11-01 21:32:33 UTC 
I sent a PR to fix only this ticket.
https://src.fedoraproject.org/rpms/samtools/pull-request/2

Could you review it?
Thank you.
Comment 14 Fedora Update System 2019-11-23 00:09:14 UTC 
FEDORA-2019-3a2e81e1ab has been submitted as an update to Fedora 29. https://bodhi.fedoraproject.org/updates/FEDORA-2019-3a2e81e1ab
Comment 15 Fedora Update System 2019-11-23 00:09:15 UTC 
FEDORA-2019-5790aff49a has been submitted as an update to Fedora 30. https://bodhi.fedoraproject.org/updates/FEDORA-2019-5790aff49a
Comment 16 Jun Aruga 2019-11-23 00:16:31 UTC 
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
Comment 17 Fedora Update System 2019-11-24 03:06:54 UTC 
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
Comment 18 Fedora Update System 2019-11-24 03:58:54 UTC 
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
Comment 19 Fedora Update System 2019-11-28 22:18:21 UTC 
FEDORA-2019-5c653711f3 has been submitted as an update to Fedora 31. https://bodhi.fedoraproject.org/updates/FEDORA-2019-5c653711f3
Comment 20 Fedora Update System 2019-11-29 01:31:06 UTC 
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
Comment 21 Fedora Update System 2019-12-02 01:29:29 UTC 
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.
Comment 22 Fedora Update System 2019-12-07 01:50:18 UTC 
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.
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