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new 1c8e159335 gnu: python-plastid: Patch it for python 3.10.
1c8e159335 is described below
commit 1c8e159335c3723194cd0e5357c89abb8d4edf13
Author: Mădălin Ionel Patrașcu <[email protected]>
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 <[email protected]>
---
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.
