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envelope-from=MadalinIonel.Patrascu@mdc-berlin.de; helo=a2062.mx.srv.dfn.de X-Spam_score_int: -43 X-Spam_score: -4.4 X-Spam_bar: ---- X-Spam_report: (-4.4 / 5.0 requ) BAYES_00=-1.9, DKIM_SIGNED=0.1, DKIM_VALID=-0.1, DKIM_VALID_AU=-0.1, DKIM_VALID_EF=-0.1, RCVD_IN_DNSWL_MED=-2.3, SPF_HELO_PASS=-0.001, SPF_PASS=-0.001 autolearn=ham autolearn_force=no X-Spam_action: no action X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list X-BeenThere: guix-patches@gnu.org List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: guix-patches-bounces+patchwork=mira.cbaines.net@gnu.org Sender: guix-patches-bounces+patchwork=mira.cbaines.net@gnu.org X-getmail-retrieved-from-mailbox: Patches * 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(+) base-commit: 1d30ec935126f316187dfc26446347bc7de9868b 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.