khmer: python update to support python 3.8-3.11 #53327
Open
+28,407
−12
Conversation
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
- @mr-c for the python version updates dib-lab/khmer#1917 - added SETUPTOOLS_USE_DISTUTILS=stdlib to use older directory convention for temp .o files during setup.py - remove linux-aarch64 as unsupported until cqf library is ported
…) to the actual directory used by recent setuptools. Set setuptools minimum version to > 62.1 (https://stackoverflow.com/questions/14320220/testing-python-c-libraries-get-build-path)
we encounter a bug in python versioneer.
|
@BiocondaBot please add label |
martin-g
approved these changes
Jan 20, 2025
| @@ -55,8 +58,9 @@ about: | |||
|
|
|||
| extra: | |||
| additional-platforms: | |||
| - linux-aarch64 | |||
| - osx-arm64 | |||
| # needs cqf porting | |||
There was a problem hiding this comment.
https://github.com/splatlab/cqf
actually - looks like this only needs a tiny part to be done - gqf.c which has just 5 asm instructions to swap out: a popcnt (x2), bsr, pdep, tzcnt
There was a problem hiding this comment.
Should we merge this PR ?
Or you want to work on cqf first ?
|
Let’s merge this - it might take longer to get some time or someone onto this. Thanks!
From: Martin Grigorov ***@***.***>
Date: Monday, 20 January 2025 at 14:06
To: bioconda/bioconda-recipes ***@***.***>
Cc: David Lecomber ***@***.***>, Author ***@***.***>
Subject: Re: [bioconda/bioconda-recipes] khmer: python update to support python 3.8-3.11 (PR #53327)
@martin-g commented on this pull request.
________________________________
In recipes/khmer/meta.yaml<#53327 (comment)>:
@@ -55,8 +58,9 @@ about:
extra:
additional-platforms:
- - linux-aarch64
- - osx-arm64
+# needs cqf porting
Should we merge this PR ?
Or you want to work on cqf first ?
—
Reply to this email directly, view it on GitHub<#53327 (comment)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/AJFYTFT3FNTO4VSE5TNLLVL2LT7HBAVCNFSM6AAAAABVP76LSGVHI2DSMVQWIX3LMV43YUDVNRWFEZLROVSXG5CSMV3GSZLXHMZDKNRSGQ4DENRWGY>.
You are receiving this because you authored the thread.Message ID: ***@***.***>
IMPORTANT NOTICE: The contents of this email and any attachments are confidential and may also be privileged. If you are not the intended recipient, please notify the sender immediately and do not disclose the contents to any other person, use it for any purpose, or store or copy the information in any medium. Thank you.
|
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
Net result should be a re-enabled for python 3.8-3.11 (prior versions fail, to enable 3.12, it may require cython files to be regenerated, but that should be a separate PR.
Describe your pull request here
Please read the guidelines for Bioconda recipes before opening a pull request (PR).
General instructions
@BiocondaBot please add labelcommand.@bioconda/corein a comment.Instructions for avoiding API, ABI, and CLI breakage issues
Conda is able to record and lock (a.k.a. pin) dependency versions used at build time of other recipes.
This way, one can avoid that expectations of a downstream recipe with regards to API, ABI, or CLI are violated by later changes in the recipe.
If not already present in the meta.yaml, make sure to specify
run_exports(see here for the rationale and comprehensive explanation).Add a
run_exportssection like this:with
...being one of:{{ pin_subpackage("myrecipe", max_pin="x") }}{{ pin_subpackage("myrecipe", max_pin="x.x") }}{{ pin_subpackage("myrecipe", max_pin="x.x") }}(in such a case, please add a note that shortly mentions your evidence for that){{ pin_subpackage("myrecipe", max_pin="x.x.x") }}(in such a case, please add a note that shortly mentions your evidence for that){{ pin_subpackage("myrecipe", max_pin=None) }}while replacing
"myrecipe"with eithernameif aname|lowervariable is defined in your recipe or with the lowercase name of the package in quotes.Bot commands for PR management
Please use the following BiocondaBot commands:
Everyone has access to the following BiocondaBot commands, which can be given in a comment:
@BiocondaBot please update@BiocondaBot please add labelplease review & mergelabel.@BiocondaBot please fetch artifactsYou can use this to test packages locally.
Note that the
@BiocondaBot please mergecommand is now depreciated. Please just squash and merge instead.Also, the bot watches for comments from non-members that include
@bioconda/<team>and will automatically re-post them to notify the addressed<team>.