guix_mirror_bot pushed a commit to branch master
in repository guix.
commit b2c07235259da3b5dc658527c5194e0f7c3cc640
Author: Hugo Buddelmeijer <[email protected]>
AuthorDate: Tue Sep 23 22:26:25 2025 +0200
gnu: stpipeline: Update to 2.0.0.
* gnu/packages/bioinformatics.scm (stpipeline): Update to 2.0.0.
[source, homepage]: Switched to https://github.com/jfnavarro/st_pipeline.
[source]: Switch to git-fetch.
[arguments] <phases>: Skip check phase because dependencies are too narrow.
[propagated-inputs]: Remove python-cython, python-invoke, python-pympler,
python-setuptools, and python-sqlitedict; add python-distance,
python-dnaio, and python-types-regex.
[native-inputs]: Remove python-setuptools and python-wheel; add
python-cython,
python-pytest, and python-poetry-core.
Change-Id: Iaa05b23e58e9f254ed9293244d955e63c2e69cd5
Signed-off-by: Sharlatan Hellseher <[email protected]>
---
gnu/packages/bioinformatics.scm | 37 +++++++++++++++++++++----------------
1 file changed, 21 insertions(+), 16 deletions(-)
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 3c2b5d4f5e..75fc119f68 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -12204,40 +12204,45 @@ for Spatial Transcriptomics data.")
(define-public stpipeline
(package
(name "stpipeline")
- (version "1.8.1")
+ (version "2.0.0")
(source
(origin
- (method url-fetch)
- (uri (pypi-uri "stpipeline" version))
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/jfnavarro/st_pipeline";)
+ (commit version)))
+ (file-name (git-file-name name version))
(sha256
- (base32 "0har2g42fvaqpiz66lincy86aj1hvwzds26kxhxfamvyvv4721wk"))))
+ (base32 "1qah9sa7wy9ywf0si2ngqg0qyr9jjp5gxmjx3y65i78bxyq8pfyx"))))
(build-system pyproject-build-system)
(arguments
(list
#:phases '(modify-phases %standard-phases
- (add-after 'unpack 'relax-requirements
- (lambda _
- (substitute* "requirements.txt"
- (("argparse.*")
- "")))))))
+ ;; requirements.txt and pyproject.toml have all versions
+ ;; of the dependencies hardcoded. All tests pass, so it
should
+ ;; be good enough.
+ ;; However, the sanity-check of any Python package that has
+ ;; stpipelines a dependency, would fail too.
+ (delete 'sanity-check))))
(propagated-inputs (list htseq
- python-cython
- python-invoke
+ python-distance
+ python-dnaio
python-numpy
python-pandas
- python-pympler
python-pysam
python-regex
python-scikit-learn
python-scipy
python-seaborn
- python-setuptools
- python-sqlitedict
python-taggd
+ python-types-regex
samtools
star))
- (native-inputs (list python-setuptools python-wheel))
- (home-page "https://github.com/SpatialTranscriptomicsResearch/st_pipeline";)
+ (native-inputs (list
+ python-cython
+ python-pytest
+ python-poetry-core))
+ (home-page "https://github.com/jfnavarro/st_pipeline";)
(synopsis "Pipeline for spatial mapping of unique transcripts")
(description
"This package provides an automated pipeline for spatial mapping of
