gnu: python-decoupler-py: Update to 1.6.0.

* gnu/packages/bioinformatics.scm (python-decoupler-py): Update to 1.6.0.
[arguments]: Do not disable test_plot_volcano test.

Change-Id: I44a31d30e8a03d2d1ffd86383c8bc6db79628def
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Ricardo Wurmus 2024-05-03 10:55:57 +02:00
parent 0e24635033
commit cb9ec4c5c5
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@ -2026,71 +2026,62 @@ (define-public python-cyvcf2
(license license:expat)))
(define-public python-decoupler-py
;; This latest commit fixes a bug in test_omnip.py.
(let ((commit "459b235348ddd9135217a3722d9dd1caa9a14ace")
(revision "1"))
(package
(name "python-decoupler-py")
(version (git-version "1.5.0" revision commit))
(source (origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/saezlab/decoupler-py")
(commit commit)))
(file-name (git-file-name name version))
(sha256
(base32
"1c0xk006iilyffdaqar2d05qdhik22fbkny387zx0bndkgqifxhl"))))
(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"
;; XXX module 'omnipath.interactions' has no
;; attribute 'CollecTRI'
" and not test_get_collectri"
;; XXX This one fails because the "texts" list
;; is empty, so there are no texts to adjust.
;; It is not clear whether this a compatibility
;; problem with our adjusttext package.
" and not test_plot_volcano"))
#:phases
'(modify-phases %standard-phases
(add-before 'check 'set-home
;; Some tests require a home directory to be set.
(lambda _ (setenv "HOME" "/tmp")))
;; Numba needs a writable dir to cache functions.
(add-before 'build 'set-numba-cache-dir
(lambda _ (setenv "NUMBA_CACHE_DIR" "/tmp"))))))
(propagated-inputs (list python-adjusttext
python-anndata
python-ipython
python-matplotlib
python-nbsphinx
python-numba
python-numpy
python-numpydoc
python-omnipath
python-scanpy
python-scikit-learn
python-scipy
python-skranger
python-tqdm
python-typing-extensions))
(native-inputs (list python-pytest))
(home-page "https://github.com/saezlab/decoupler-py")
(synopsis
"Framework for modeling, analyzing and interpreting single-cell RNA-seq data")
(description
"This package provides different statistical methods to extract
(package
(name "python-decoupler-py")
(version "1.6.0")
(source (origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/saezlab/decoupler-py")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
(base32
"1mqkp0i8k5hzhfnka4nc2f0phmrs0k404ynbl1lqfjzywx25y75h"))))
(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"))
#:phases
'(modify-phases %standard-phases
(add-before 'check 'set-home
;; Some tests require a home directory to be set.
(lambda _ (setenv "HOME" "/tmp")))
;; Numba needs a writable dir to cache functions.
(add-before 'build 'set-numba-cache-dir
(lambda _ (setenv "NUMBA_CACHE_DIR" "/tmp"))))))
(propagated-inputs (list python-adjusttext
python-anndata
python-ipython
python-matplotlib
python-nbsphinx
python-numba
python-numpy
python-numpydoc
python-omnipath
python-scanpy
python-scikit-learn
python-scipy
python-skranger
python-tqdm
python-typing-extensions))
(native-inputs (list python-pytest))
(home-page "https://github.com/saezlab/decoupler-py")
(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:gpl3+)))
(define-public python-demuxem
(package