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

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From: help-debbugs <at> gnu.org (GNU bug Tracking System)
To: Mădălin Ionel Patrașcu
 <madalinionel.patrascu <at> mdc-berlin.de>
Subject: bug#66064: closed (Re: [bug#66064] [PATCH] gnu: python-plastid:
 Patch it for python 3.10.)
Date: Mon, 18 Sep 2023 08:35:01 +0000

[Message part 1 (text/plain, inline)]

Your bug report

#66064: [PATCH] gnu: python-plastid: Patch it for python 3.10.

which was filed against the guix-patches package, has been closed.

The explanation is attached below, along with your original report.
If you require more details, please reply to 66064 <at> debbugs.gnu.org.

-- 
66064: https://debbugs.gnu.org/cgi/bugreport.cgi?bug=66064
GNU Bug Tracking System
Contact help-debbugs <at> gnu.org with problems

[Message part 2 (message/rfc822, inline)]

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

[Message part 3 (message/rfc822, inline)]

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

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