sharlatan pushed a commit to branch python-team
in repository guix.
commit ad1417060ac8f40f5ffd2b537b62d2bc0a27a7b5
Author: Nicolas Graves <ngra...@ngraves.fr>
AuthorDate: Mon Mar 31 08:18:33 2025 +0200
gnu: python-pyvcf: Use the fork python-pyvcf3.
* gnu/packages/bioinformatics.scm (python-pyvcf): Define in terms of
'deprecated-package'.
(python-pyvcf3): New variable.
(python-nanosv): Replace python-pyvcf by python-pyvcf3.
Signed-off-by: Sharlatan Hellseher <sharlata...@gmail.com>
---
gnu/packages/bioinformatics.scm | 46 +++++++++++++----------------------------
1 file changed, 14 insertions(+), 32 deletions(-)
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 6274b2d868..659e7cfea0 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -23917,51 +23917,33 @@ for the analysis and visualization of raw nanopore
signal.")
;; Some parts may be BSD-3-licensed.
(license license:mpl2.0)))
-(define-public python-pyvcf
- (let ((commit "476169cd457ba0caa6b998b301a4d91e975251d9")
+;; This is a fork of the original unmaintained python-pyvcf.
+(define-public python-pyvcf3
+ (let ((commit "1fb3789153d1d8e28e2cedf121399f276b5f312a")
(revision "0"))
(package
- (name "python-pyvcf")
- (version (git-version "0.6.8" revision commit))
- ;; Use git, because the PyPI tarballs lack test data.
+ (name "python-pyvcf3")
+ (version (git-version "1.0.3" revision commit))
(source
(origin
(method git-fetch)
(uri (git-reference
- (url "https://github.com/jamescasbon/PyVCF.git";)
- ;; Latest release is not tagged.
+ (url "https://github.com/dridk/PyVCF3";)
(commit commit)))
(file-name (git-file-name name version))
(sha256
- (base32
- "0qf9lwj7r2hjjp4bd4vc7nayrhblfm4qcqs4dbd43a6p4bj2jv5p"))))
- (build-system python-build-system)
- (arguments
- `(#:phases
- (modify-phases %standard-phases
- (add-after 'unpack 'patch-sample-script
- (lambda _
- ;; Add Python 3 compatibility to this sample script.
- (substitute* "scripts/vcf_sample_filter.py"
- (("print (.*)\n" _ arg)
- (string-append "print(" arg ")\n")))))
- (add-after 'install 'remove-installed-tests
- ;; Do not install test files.
- (lambda* (#:key inputs outputs #:allow-other-keys)
- (delete-file-recursively (string-append
- (site-packages inputs outputs)
- "/vcf/test")))))))
- (native-inputs
- ;; Older setuptools is needed for use_2to3.
- (list python-cython python-setuptools-57))
- (propagated-inputs
- (list python-pysam python-rpy2))
- (home-page "https://github.com/jamescasbon/PyVCF";)
+ (base32 "0i4j5bq5q32q216ja7yvg0mpww5j0b9p8ky5bya4d31wqmygal8z"))))
+ (build-system pyproject-build-system)
+ (propagated-inputs (list python-setuptools))
+ (native-inputs (list python-setuptools python-wheel))
+ (home-page "https://github.com/dridk/PyVCF3";)
(synopsis "Variant Call Format parser for Python")
(description "This package provides a @acronym{VCF,Variant Call Format}
parser for Python.")
(license license:expat))))
+(define-deprecated/public-alias python-pyvcf python-pyvcf3)
+
(define-public nanosv
(package
(name "nanosv")
@@ -23974,7 +23956,7 @@ parser for Python.")
"1wl2daj0bwrl8fx5xi8j8hfs3mp3vg3qycy66538n032v1qkc6xg"))))
(build-system python-build-system)
(inputs
- (list python-configparser python-pysam python-pyvcf))
+ (list python-configparser python-pysam python-pyvcf3))
(home-page "https://github.com/mroosmalen/nanosv";)
(synopsis "Structural variation detection tool for Oxford Nanopore data")
(description "NanoSV is a software package that can be used to identify
