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| author | Sharlatan Hellseher <sharlatanus@gmail.com> | 2025-03-26 21:40:49 +0000 |
|---|---|---|
| committer | Andreas Enge <andreas@enge.fr> | 2025-04-16 11:46:22 +0200 |
| commit | 18a2ef9c6276e82a6a82bec1b41519feda6ee76f (patch) | |
| tree | 0ee5ce94feac1d861aa6f6c8009289eb95fdbd99 | |
| parent | a7885e4b3dd25d31b347a8a74071fc1540f993aa (diff) | |
gnu: python-gffutils: Update to 0.13 and fix build.
* 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
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 31 |
1 files changed, 16 insertions, 15 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 30d8c0d5b0..d25e2aec4f 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -23251,7 +23251,7 @@ alignments, trees and genomic annotations.") (define-public python-gffutils (package (name "python-gffutils") - (version "0.10.1") + (version "0.13") (source (origin (method git-fetch) @@ -23261,27 +23261,28 @@ alignments, trees and genomic annotations.") (file-name (git-file-name name version)) (sha256 (base32 - "1gkzk7ps6w3ai2r81js9s9bzpba0jmxychnd2da6n9ggdnf2xzqz")))) - (build-system python-build-system) + "148i7bk5bawrz19jp3nl0z859wdlldgrw8f0aw9wsprj8s3d713a")))) + (build-system pyproject-build-system) (arguments - '(#:phases - (modify-phases %standard-phases - (replace 'check - (lambda* (#:key tests? #:allow-other-keys) - (when tests? - ;; Tests need to access the HOME directory - (setenv "HOME" "/tmp") - (invoke "nosetests" "-a" "!slow"))))))) + (list + #:phases + #~(modify-phases %standard-phases + (add-before 'build 'set-HOME + (lambda _ + ;; FileNotFoundError: [Errno 2] No such file or directory: + ;; '/homeless-shelter/.gffutils.test' + (setenv "HOME" "/tmp")))))) + (native-inputs + (list python-pytest + python-setuptools + python-wheel)) (propagated-inputs (list python-argcomplete python-argh python-biopython python-pybedtools python-pyfaidx - python-simplejson - python-six)) - (native-inputs - (list python-nose)) + python-simplejson)) (home-page "https://github.com/daler/gffutils") (synopsis "Tool for manipulation of GFF and GTF files") (description |