169/207: gnu: python-gffutils: Update to 0.13 and fix build.

[guix-commits]

sharlatan pushed a commit to branch python-team
in repository guix.

commit 6f8f9746ee56c693c25e12600de76ec22953f2ce
Author: Sharlatan Hellseher <sharlata...@gmail.com>
AuthorDate: Wed Mar 26 21:40:49 2025 +0000

    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
---
 gnu/packages/bioinformatics.scm | 31 ++++++++++++++++---------------
 1 file changed, 16 insertions(+), 15 deletions(-)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 87b16c7e7c..84b59ba01f 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -23164,7 +23164,7 @@ 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)
@@ -23174,27 +23174,28 @@ 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