Skip to content

Please port to Python3 #569

Closed
Closed
@tillea

Description

Hello,
the Debian Med team is maintaining freebayes for official Debian. The recently released Debian 10 was the last Debian release featuring Python2 since this programming language is EOL. If you are interested that we continue to maintain freebayes in official Debian (and that users of other modern distributions will have no problems to install freebayes on their systems) I'd recommend you port your code to Python3. The 2to3 tool might be of great help here. I have seen some commits about Python3 compatibility. It would be great if you could tag a new release if the conversion might be finished.
Kind regards, Andreas.

Activity

ekg

ekg commented on Sep 10, 2019

@ekg
Collaborator
tseemann

tseemann commented on Sep 11, 2019

@tseemann
Contributor

WE fixed it in vcflib but I don't have access to freebayes.

CURRENT

==> /home/linuxbrew/.linuxbrew/Cellar/freebayes/1.3.1/bin/fasta_generate_regions.py <==
==> /home/linuxbrew/.linuxbrew/Cellar/freebayes/1.3.1/bin/coverage_to_regions.py <==
#!/usr/bin/env python

needs to be changed to:

#!/usr/bin/env python3

AND the code moved to py3

tseemann

tseemann commented on Sep 11, 2019

@tseemann
Contributor

UPDATE: v1.3.1...master
It has already been done.
You need to make a new release @ekg !

ekg

ekg commented on Sep 11, 2019

@ekg
Collaborator
tseemann

tseemann commented on Sep 15, 2019

@tseemann
Contributor

Ping @ekg

tillea

tillea commented on Oct 9, 2019

@tillea
Author
tillea

tillea commented on Dec 17, 2019

@tillea
Author

Is there any problem to simply tag a release if the code is fixed in principle? 1.1.2020 is really comming soon and we are keen on cleaning up Python2 bugs right now.

ekg

ekg commented on Dec 17, 2019

@ekg
Collaborator

I have tagged a new release, v1.3.2.

Thank you for your support and patience!

tillea

tillea commented on Dec 17, 2019

@tillea
Author

@ekg Thanks for tagging.
I've downloaded the new version and spottet some remaining things 2to3 liked to fix. Here is the patch for your comfort and critical inspection.
Unfortunately I had build issues which I will report in a separate issue since its not related to the Python3 migration.
Kind regards, Andreas.

github-actions

github-actions commented on Dec 11, 2020

@github-actions

This issue is marked stale because it has been open 120 days with no activity. Remove stale label or comment or this will be closed in 5 days

tillea

tillea commented on Dec 11, 2020

@tillea
Author

@ekg Thanks for tagging.
I've downloaded the new version and spottet some remaining things 2to3 liked to fix. Here is the patch for your comfort and critical inspection.
Unfortunately I had build issues which I will report in a separate issue since its not related to the Python3 migration.
Kind regards, Andreas.

Is there anything more I can do than linking to the patch that is used in Debian?

pjotrp

pjotrp commented on Dec 11, 2020

@pjotrp
Collaborator

Thanks @tillea, it will go in.

self-assigned this
on Dec 11, 2020

6 remaining items

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment

Metadata

Assignees

Type

No type

Projects

No projects

Relationships

None yet

Development

No branches or pull requests

Issue actions

    Please port to Python3 · Issue #569 · freebayes/freebayes