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gnu: python-gffutils: Update to 0.13 and fix build.

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* gnu/packages/bioinformatics.scm (python-gffutils): Update to 0.13.
[build-system]: Swap to pypproject-build-system.
[arguments] <phases>: Use default 'check, add 'set-HOME.
[propagated-inputs]: Remove python-six.
[native-inputs]: Remove python-nose; add python-pytest,
python-setuptools, and python-wheel.

Change-Id: I77b1ed5be8750bdd2f2cdff3135430207b80f6fc
This commit is contained in:
Sharlatan Hellseher 2025-03-26 21:40:49 +00:00 • committed by Andreas Enge
parent a7885e4b3d
commit 18a2ef9c62
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GPG key ID: F7D5C9BF765C61E3
1 changed files with 16 additions and 15 deletions
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@ -23251,7 +23251,7 @@ alignments, trees and genomic annotations.")
(define-public python-gffutils (define-public python-gffutils
(package (package
(name "python-gffutils") (name "python-gffutils")
(version "0.10.1") (version "0.13")
(source (source
(origin (origin
(method git-fetch) (method git-fetch)
@ -23261,27 +23261,28 @@ alignments, trees and genomic annotations.")
(file-name (git-file-name name version)) (file-name (git-file-name name version))
(sha256 (sha256
(base32 (base32
"1gkzk7ps6w3ai2r81js9s9bzpba0jmxychnd2da6n9ggdnf2xzqz")))) "148i7bk5bawrz19jp3nl0z859wdlldgrw8f0aw9wsprj8s3d713a"))))
(build-system python-build-system) (build-system pyproject-build-system)
(arguments (arguments
'(#:phases (list
(modify-phases %standard-phases #:phases
(replace 'check #~(modify-phases %standard-phases
(lambda* (#:key tests? #:allow-other-keys) (add-before 'build 'set-HOME
(when tests? (lambda _
;; Tests need to access the HOME directory ;; FileNotFoundError: [Errno 2] No such file or directory:
(setenv "HOME" "/tmp") ;; '/homeless-shelter/.gffutils.test'
(invoke "nosetests" "-a" "!slow"))))))) (setenv "HOME" "/tmp"))))))
(native-inputs
(list python-pytest
python-setuptools
python-wheel))
(propagated-inputs (propagated-inputs
(list python-argcomplete (list python-argcomplete
python-argh python-argh
python-biopython python-biopython
python-pybedtools python-pybedtools
python-pyfaidx python-pyfaidx
python-simplejson python-simplejson))
python-six))
(native-inputs
(list python-nose))
(home-page "https://github.com/daler/gffutils") (home-page "https://github.com/daler/gffutils")
(synopsis "Tool for manipulation of GFF and GTF files") (synopsis "Tool for manipulation of GFF and GTF files")
(description (description