branch master updated: gnu: python-plastid: Patch it for python 3.10.

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rekado pushed a commit to branch master
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The following commit(s) were added to refs/heads/master by this push:
     new 1c8e159335 gnu: python-plastid: Patch it for python 3.10.
1c8e159335 is described below

commit 1c8e159335c3723194cd0e5357c89abb8d4edf13
Author: Mădălin Ionel Patrașcu <madalinionel.patrascu@mdc-berlin.de>
AuthorDate: Mon Sep 18 05:39:20 2023 +0200

    gnu: python-plastid: Patch it for python 3.10.
    
    * gnu/packages/bioinformatics.scm (python-plastid)[arguments]: Add new phase
    'patch-for-python-3.10.
    
    Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
---
 gnu/packages/bioinformatics.scm | 7 +++++++
 1 file changed, 7 insertions(+)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index c78f017a24..b909cd5ee0 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -3787,6 +3787,13 @@ UCSC genome browser.")
                       "-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.