@@ 29,8 29,8 @@
;;; Copyright © 2024 Spencer King <spencer.king@geneoscopy.com>
;;; Copyright © 2025 nomike Postmann <nomike@nomike.com>
;;; Copyright © 2025 Janneke Nieuwenhuizen <janneke@gnu.org>
-;;; Copyright © 2025 Sharlatan Hellseher <sharlatanus@gmail.com>
;;; Copyright © 2026 Hartmut Goebel <h.goebel@crazy-compilers.com>
+;;; Copyright © 2025-2026 Sharlatan Hellseher <sharlatanus@gmail.com>
;;;
;;; This file is part of GNU Guix.
;;;
@@ 3998,6 3998,108 @@ sequencing data and the end result are tables of UMI-unique DamID and CEL-Seq
counts.")
(license license:expat)))
+(define-public python-scprep
+ (package
+ (name "python-scprep")
+ (version "1.2.3")
+ (source
+ (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/KrishnaswamyLab/scprep")
+ (commit (string-append "v" version))))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32 "1dbmaix4bqaf9p1zw1fvk5a64kwdbg015q3ykc6rsmdwrcd2g5cz"))))
+ (build-system pyproject-build-system)
+ (arguments
+ (list
+ ;; tests: 344 passed
+ #:test-flags
+ ;; XXX: Mixture of remote data download and some assertion errors.
+ ;;
+ ;; Tests from "test/test_io.py" download data files from
+ ;; <https://raw.githubusercontent.com/KrishnaswamyLab/scprep/>.
+ #~(list "--ignore-files=test_io.py"
+ (string-join
+ (list "--exclude=(test.*dyngen.*" ;TODO: they need R packages
+ "test_slingshot.*" ;
+ "test_splatter_.*" ;
+ "test_builtins"
+ "test_combine_batches_errors"
+ "test_conversion_sce"
+ "test_conversion_spmatrix"
+ "test_differential_expression"
+ "test_differential_expression_error"
+ "test_fcs"
+ "test_fcs_PnN"
+ "test_fcs_header_error"
+ "test_fcs_reformat_meta"
+ "test_generate_colorbar_dict"
+ "test_install_bioc"
+ "test_install_github_dependencies_None"
+ "test_install_github_dependencies_True"
+ "test_install_github_lib"
+ "test_is_sparse_series"
+ "test_builtins"
+ "test_mtx"
+ "test_scatter_rotate_mp4"
+ "test_sparse_svd"
+ "test_to_array_or_spmatrix_list_of_strings"
+ "test_unzip_no_destination)")
+ "|")
+ "test")
+ #:phases
+ #~(modify-phases %standard-phases
+ (add-after 'unpack 'relax-requirements
+ (lambda _
+ (substitute* "setup.py"
+ ;; "pandas>=0.25,<2.1",
+ ((",<2.1") ""))))
+ (add-before 'check 'pre-check
+ (lambda _
+ (setenv "HOME" "/tmp"))))))
+ (native-inputs
+ (list python-fcsparser
+ python-anndata
+ python-h5py
+ python-matplotlib
+ python-parameterized
+ python-nose2
+ python-pynose
+ python-requests
+ python-rpy2
+ python-setuptools
+ python-tables))
+ ;; Used by rpy2
+ (inputs
+ (list bash-minimal
+ r-apeglm
+ r-deseq2
+ r-drimseq
+ r-ggplot2
+ r-lazyeval
+ r-minimal
+ r-qqman
+ r-renv
+ r-rlang
+ r-slingshot
+ #;r-splatter)) ;https://github.com/Oshlack/splatter
+ (propagated-inputs
+ (list python-decorator
+ python-numpy
+ python-packaging
+ python-pandas
+ python-scikit-learn
+ python-scipy))
+ (home-page "https://github.com/KrishnaswamyLab/scprep")
+ (synopsis "Tools for loading, processing, and handling single cell data")
+ (description
+ "@code{scprep} provides an all-in-one framework for loading,
+ preprocessing, and plotting matrices in Python, with a focus on single-cell
+genomics.")
+ (license license:expat)))
+
(define-public python-snaptools
(package
(name "python-snaptools")
@@ 19654,7 19756,7 @@ implementation differs in these ways:
;; XXX: When python-dask is added some tests fail with error:
;; ImportError: cannot import name 'as_sparse_dask_array' from
;; 'anndata.tests.helpers'.
- ;;
+ ;;
;; That functionality was removed from anndata: see
;; <https://github.com/scverse/anndata/pull/2201>.
#$@(map (lambda (test) (string-append "--deselect=tests/"