guix_mirror_bot pushed a commit to branch master
in repository guix.
commit 962948f2a46b870a438fd7f8cf6ac9734853f466
Author: Sharlatan Hellseher <[email protected]>
AuthorDate: Thu Aug 7 17:06:40 2025 +0100
gnu: Add python-decoupler.
This package is a successor of python-decoupler-py with reworked tests
and inputs. Project has changed the license from GPL3+ to BSD-3.
See: <https://github.com/scverse/decoupler/blob/main/CHANGELOG.md#200>
* gnu/packages/bioinformatics.scm (python-decoupler): New variable based
on python-decoupler-py.
[source] <url>: Fix permanent redirect.
[arguments] <test-flags>: Rework skipped tests.
<phases>: Remove 'relax-requirements.
[propagated-inputs]: Remove python-ipython, python-matplotlib,
python-nbsphinx, python-numpy, python-numpydoc, python-omnipath,
python-scanpy, python-scikit-learn, python-skranger, and
python-typing-extensions; add python-dcor, python-docrep,
python-igraph, python-ipywidgets, python-marsilea, python-requests,
python-session-info2, and python-xgboost.
[native-inputs]: Remove python-poetry-core; add nss-certs-for-test,
python-hatchling, python-gseapy, python-memory-profiler, and
python-scanpy.
[home-page]: Fix permanent redirect.
[licenses]: Switch to bsd-3.
(python-decoupler-py): Deprecate package.
Change-Id: Ia517db074c7ac405408731c9a8cfe00e56b8107b
---
gnu/packages/bioinformatics.scm | 89 +++++++++++++++++++++++++----------------
1 file changed, 54 insertions(+), 35 deletions(-)
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 1332a1b68d..0d3395cdeb 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -79,6 +79,7 @@
#:use-module (gnu packages bison)
#:use-module (gnu packages bioconductor)
#:use-module (gnu packages boost)
+ #:use-module (gnu packages certs)
#:use-module (gnu packages check)
#:use-module (gnu packages code)
#:use-module (gnu packages cmake)
@@ -2836,41 +2837,51 @@ specifying the usage of each program for each cell in
the data.")
parsing of Variant Call Format (VCF) files.")
(license license:expat)))
-(define-public python-decoupler-py
+(define-public python-decoupler
(package
- (name "python-decoupler-py")
- ;; Upstream places release on a new branch, see
- ;; <https://github.com/saezlab/decoupler-py/issues/175>.
- (version "1.8.0")
+ (name "python-decoupler")
+ (version "2.1.1")
(source (origin
(method git-fetch)
(uri (git-reference
- (url "https://github.com/saezlab/decoupler-py";)
- (commit version)))
+ (url "https://github.com/scverse/decoupler";)
+ (commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
(base32
- "0c3yg7jjb1nxb6hsh9wn7wr8w0ba55gixdbf5fp443nhv1cwlajj"))))
+ "0b15n5sq940sn29jsgmdkkm4fcpzfq1n221scfwhjxb4ybdpsz4v"))))
(build-system pyproject-build-system)
(arguments
(list
#:test-flags
- '(list "-k"
- ;; These tests require internet access
- (string-append "not test_get_resource"
- " and not test_show_resources"
- " and not test_get_dorothea"
- " and not test_get_progeny"
- " and not test_get_ksn_omnipath"
- ;; This attempts to download things for Omnipath
- " and not test_get_collectri"))
+ '(list "-k" (string-join
+ ;; Tests requiring internet access to reach out
+ ;; <datasets.cellxgene.cziscience.com>, <ftp.ebi.ac.uk>,
+ ;; <omnipathdb.org>, <raw.githubusercontent.com>,
+ ;; <static.omnipathdb.org>, <www.ensembl.org>,
+ ;; <www.ncbi.nlm.nih.gov>, and <zenodo.org>.
+ (list "not test_collectri"
+ "test_covid5k"
+ "test_dorothea"
+ "test_download"
+ "test_download_anndata"
+ "test_ensmbl_to_symbol"
+ "test_erygast1k"
+ "test_hallmark"
+ "test_hsctgfb"
+ "test_knocktf"
+ "test_msvisium"
+ "test_pbmc3k"
+ "test_progeny"
+ "test_resource"
+ "test_show_resources"
+ "test_translate"
+ ;; XXX: Some precision mismatched.
+ "test_func_gsea"
+ "test_net_corr")
+ " and not "))
#:phases
'(modify-phases %standard-phases
- (add-after 'unpack 'relax-requirements
- (lambda _
- (substitute* "pyproject.toml"
- ;; numba = "^0.60.0"; all tests passed.
- (("0.60.0") "0.61.0"))))
(add-before 'check 'set-home
;; Some tests require a home directory to be set.
(lambda _ (setenv "HOME" "/tmp")))
@@ -2879,27 +2890,35 @@ parsing of Variant Call Format (VCF) files.")
(lambda _ (setenv "NUMBA_CACHE_DIR" "/tmp"))))))
(propagated-inputs (list python-adjusttext
python-anndata
- python-ipython
- python-matplotlib
- python-nbsphinx
+ python-dcor
+ python-docrep
+ python-igraph
+ python-ipywidgets
+ python-marsilea
python-numba
- python-numpy
- python-numpydoc
- python-omnipath
- python-scanpy
- python-scikit-learn
+ python-requests
python-scipy
- python-skranger
+ python-session-info2
python-tqdm
- python-typing-extensions))
- (native-inputs (list python-poetry-core python-pytest))
- (home-page "https://github.com/saezlab/decoupler-py";)
+ python-xgboost))
+ (native-inputs
+ (list nss-certs-for-test
+ python-hatchling
+ python-gseapy
+ python-memory-profiler
+ python-pytest
+ python-scanpy))
+ (home-page "https://github.com/scverse/decoupler";)
(synopsis
"Framework for modeling, analyzing and interpreting single-cell RNA-seq
data")
(description
"This package provides different statistical methods to extract
biological activities from omics data within a unified framework.")
- (license license:gpl3+)))
+ (license license:bsd-3)))
+
+;; See: <https://github.com/scverse/decoupler/blob/main/CHANGELOG.md#200>
+(define-public python-decoupler-py
+ (deprecated-package "python-decoupler-py" python-decoupler))
(define-public python-demuxem
(package
