guix_mirror_bot pushed a commit to branch python-team
in repository guix.
commit 4e7bf086d29241c44108d57b71783106c54be765
Author: Sharlatan Hellseher <[email protected]>
AuthorDate: Fri Jan 2 22:02:42 2026 +0000
gnu: python-cellbender: Update to 0.3.2.
* gnu/packages/bioinformatics.scm (python-cellbender): Update to 0.3.2.
[arguments] <phases>: Add 'relax-requirements.
[propagated-inputs]: Remove python-scikit-learn, python-sphinx,
python-sphinx-argparse, python-sphinx-autodoc-typehints,
python-sphinx-rtd-theme, and python-sphinxcontrib-programoutput; add
python-loompy, python-lxml-html-clean, python-nbconvert,
python-notebook, python-psutil, and python-pytorch.
[native-inputs]: Add python-setuptools.
Change-Id: I79473da4ca33b648fd9bd19f21dc91edb4a12cc3
---
gnu/packages/bioinformatics.scm | 35 ++++++++++++++++++++++++-----------
1 file changed, 24 insertions(+), 11 deletions(-)
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 30f958ab69..689d79cf54 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -2495,33 +2495,46 @@ cell types. Cell2cell is suitable for single-cell RNA
sequencing
(define-public python-cellbender
(package
(name "python-cellbender")
- (version "0.2.2")
+ (version "0.3.2")
(source
(origin
(method git-fetch)
(uri (git-reference
- (url "https://github.com/broadinstitute/CellBender";)
- (commit (string-append "v" version))))
+ (url "https://github.com/broadinstitute/CellBender";)
+ (commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
(base32
- "0h9d9pznffdbya631hkk7b7jwjrgx5saqssar1d42qbyvdji3hgy"))))
+ "1sdw4dv881ll8ylxcp06xa74c3wvrdyzpwfilzk8i1pwgrdrgb3f"))))
(build-system pyproject-build-system)
(arguments
- (list #:tests? #false)) ;there are none
+ (list
+ #:tests? #f ;there are none
+ #:phases
+ #~(modify-phases %standard-phases
+ (add-after 'unpack 'relax-requirements
+ (lambda _
+ ;; See:
+ ;; <https://github.com/broadinstitute/CellBender/issues/426>,
+ ;; <https://github.com/broadinstitute/CellBender/issues/416>.
+ (substitute* "requirements.txt"
+ (("(notebook|ipython|jupyter.*)")"")
+ (("<.*") "\n")))))))
+ (native-inputs
+ (list python-setuptools))
(propagated-inputs
(list python-anndata
+ python-loompy
+ python-lxml-html-clean
python-matplotlib
+ python-nbconvert
+ python-notebook
python-numpy
python-pandas
+ python-psutil
python-pyro-ppl
- python-scikit-learn
+ python-pytorch
python-scipy
- python-sphinx
- python-sphinx-argparse
- python-sphinx-autodoc-typehints
- python-sphinx-rtd-theme
- python-sphinxcontrib-programoutput
python-tables))
(home-page "https://cellbender.rtfd.io/";)
(synopsis "Eliminate technical artifacts from single-cell RNA-seq data")
