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new cfb5331b36 gnu: python-parabam: Update to 3.0.1-0.be5bd35, fix build.
cfb5331b36 is described below
commit cfb5331b36fc92af507987aa7eff99f57ffe92fc
Author: Sharlatan Hellseher <[email protected]>
AuthorDate: Wed Oct 29 21:44:10 2025 +0000
gnu: python-parabam: Update to 3.0.1-0.be5bd35, fix build.
* gnu/packages/bioinformatics.scm (python-parabam): Update to
be5bd35012d37df8cfa88771325a0273519c8c98 commit.
[source]: Switch to git-fetch.
[arguments] <tests?>: No tests.
<phases>: Add 'cythonize.
[native-inputs]: Remove python-wheel; add python-cython.
Change-Id: I56e2dbeac106f2942289e2b751520b3bf1abb60f
---
gnu/packages/bioinformatics.scm | 37 ++++++++++++++++++++++++++-----------
1 file changed, 26 insertions(+), 11 deletions(-)
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 4e7950c32f..81b46be02f 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -3333,25 +3333,40 @@ phylogenetic trees also goes by the name
simulationmethods for phylogenetic
trees, synthetic data generation, or just phylogenetic tree simulation.")
(license license:expat)))
-;; XXX: Probably unmaintained, build fails with Python 3.11, see
-;; <https://github.com/cancerit/parabam/issues/10>.
(define-public python-parabam
(package
(name "python-parabam")
- (version "3.0.1")
+ ;; XXX: Upstream works on modernization of the project, use the latest
+ ;; commit providing fixes.
+ ;; See: <https://github.com/cancerit/parabam/issues/10>.
+ (properties '((commit . "be5bd35012d37df8cfa88771325a0273519c8c98")
+ (revision . "0")))
+ (version (git-version "3.0.1"
+ (assoc-ref properties 'revision)
+ (assoc-ref properties 'commit)))
(source
(origin
- (method url-fetch)
- (uri (pypi-uri "parabam" version))
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/cancerit/parabam";)
+ (commit (assoc-ref properties 'commit))))
+ (file-name (git-file-name name version))
(sha256
- (base32 "1cy9q3gzdawi1kilycpd7waymjmrwsg8czwycfp13g301ir9xyp3"))
- (modules '((guix build utils)))
- (snippet
- '(substitute* "setup.py"
- (("'argparse',") "")))))
+ (base32 "1x0c1zhlfplhm4n07vibvh4jprjsdlypnlig87a8r07d26d4qphh"))))
(build-system pyproject-build-system)
+ (arguments
+ (list
+ #:tests? #f ;no tests
+ #:phases
+ #~(modify-phases %standard-phases
+ (add-before 'build 'cythonize
+ (lambda _
+ (with-directory-excursion "parabam"
+ (for-each (lambda (file)
+ (invoke "cython" "-3" file "-I" "."))
+ (find-files "." ".*\\.pyx$"))))))))
(propagated-inputs (list python-numpy python-pysam))
- (native-inputs (list python-setuptools python-wheel))
+ (native-inputs (list python-cython python-setuptools))
(home-page "https://github.com/cancerit/parabam";)
(synopsis "Parallel BAM File Analysis")
(description "Parabam is a tool for processing sequencing files in
