GNU bug report logs - #66064
[PATCH] gnu: python-plastid: Patch it for python 3.10.

Previous Next

Package: guix-patches;

Reported by: Mădălin Ionel Patrașcu <madalinionel.patrascu <at> mdc-berlin.de>

Date: Mon, 18 Sep 2023 03:41:01 UTC

Severity: normal

Tags: patch

Done: Ricardo Wurmus <rekado <at> elephly.net>

Bug is archived. No further changes may be made.

To add a comment to this bug, you must first unarchive it, by sending
a message to control AT debbugs.gnu.org, with unarchive 66064 in the body.
You can then email your comments to 66064 AT debbugs.gnu.org in the normal way.

Toggle the display of automated, internal messages from the tracker.

View this report as an mbox folder, status mbox, maintainer mbox


Report forwarded to rekado <at> elephly.net, guix-patches <at> gnu.org:
bug#66064; Package guix-patches. (Mon, 18 Sep 2023 03:41:01 GMT) Full text and rfc822 format available.

Acknowledgement sent to Mădălin Ionel Patrașcu <madalinionel.patrascu <at> mdc-berlin.de>:
New bug report received and forwarded. Copy sent to rekado <at> elephly.net, guix-patches <at> gnu.org. (Mon, 18 Sep 2023 03:41:02 GMT) Full text and rfc822 format available.

Message #5 received at submit <at> debbugs.gnu.org (full text, mbox):

From: Mădălin Ionel Patrașcu
 <madalinionel.patrascu <at> mdc-berlin.de>
To: <guix-patches <at> gnu.org>
Subject: [PATCH] gnu: python-plastid: Patch it for python 3.10.
Date: Mon, 18 Sep 2023 05:39:20 +0200
* gnu/packages/bioinformatics.scm (python-plastid)[arguments]: Add
new phase patch-for-python-3.10.
---
 gnu/packages/bioinformatics.scm | 7 +++++++
 1 file changed, 7 insertions(+)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index c78f017a24..d7a9697c6e 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -3787,6 +3787,13 @@ (define-public python-plastid
                       "-xf" (assoc-ref inputs "test-data"))
               ;; This one requires bowtie-build
               (delete-file "plastid/test/functional/test_crossmap.py")))
+          (add-after 'unpack 'patch-for-python-3.10
+              (lambda _
+                ;; Some classes were moved from collections to collections.abc
+                ;; in Python 3.10.
+                (substitute* "plastid/readers/bigbed.pyx"
+                  ((", Iterable")
+                   "\nfrom collections.abc import Iterable"))))
           (add-before 'check 'build-extensions
             (lambda _
               ;; Cython extensions have to be built before running the tests.

base-commit: 1d30ec935126f316187dfc26446347bc7de9868b
-- 
2.41.0





Reply sent to Ricardo Wurmus <rekado <at> elephly.net>:
You have taken responsibility. (Mon, 18 Sep 2023 08:35:01 GMT) Full text and rfc822 format available.

Notification sent to Mădălin Ionel Patrașcu <madalinionel.patrascu <at> mdc-berlin.de>:
bug acknowledged by developer. (Mon, 18 Sep 2023 08:35:01 GMT) Full text and rfc822 format available.

Message #10 received at 66064-done <at> debbugs.gnu.org (full text, mbox):

From: Ricardo Wurmus <rekado <at> elephly.net>
To: Mădălin Ionel Patrașcu
 <madalinionel.patrascu <at> mdc-berlin.de>
Cc: 66064-done <at> debbugs.gnu.org
Subject: Re: [bug#66064] [PATCH] gnu: python-plastid: Patch it for python 3.10.
Date: Mon, 18 Sep 2023 10:33:37 +0200
Mădălin Ionel Patrașcu <madalinionel.patrascu <at> mdc-berlin.de> writes:

> * gnu/packages/bioinformatics.scm (python-plastid)[arguments]: Add
> new phase patch-for-python-3.10.

Applied, thanks!

-- 
Ricardo




bug archived. Request was from Debbugs Internal Request <help-debbugs <at> gnu.org> to internal_control <at> debbugs.gnu.org. (Mon, 16 Oct 2023 11:24:09 GMT) Full text and rfc822 format available.

This bug report was last modified 1 year and 243 days ago.

Previous Next


GNU bug tracking system
Copyright (C) 1999 Darren O. Benham, 1997,2003 nCipher Corporation Ltd, 1994-97 Ian Jackson.