From 1c8e159335c3723194cd0e5357c89abb8d4edf13 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?M=C4=83d=C4=83lin=20Ionel=20Patra=C8=99cu?= Date: Mon, 18 Sep 2023 05:39:20 +0200 Subject: [PATCH] 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 --- 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.