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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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@ -2026,71 +2026,62 @@ (define-public python-cyvcf2
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(license license:expat)))
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(define-public python-decoupler-py
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;; This latest commit fixes a bug in test_omnip.py.
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(let ((commit "459b235348ddd9135217a3722d9dd1caa9a14ace")
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(revision "1"))
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(package
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(name "python-decoupler-py")
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(version (git-version "1.5.0" revision commit))
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(source (origin
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(method git-fetch)
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(uri (git-reference
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(url "https://github.com/saezlab/decoupler-py")
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(commit commit)))
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(file-name (git-file-name name version))
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(sha256
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(base32
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"1c0xk006iilyffdaqar2d05qdhik22fbkny387zx0bndkgqifxhl"))))
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(build-system pyproject-build-system)
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(arguments
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(list
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#:test-flags
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'(list "-k"
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;; These tests require internet access
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(string-append "not test_get_resource"
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" and not test_show_resources"
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" and not test_get_dorothea"
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" and not test_get_progeny"
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" and not test_get_ksn_omnipath"
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;; XXX module 'omnipath.interactions' has no
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;; attribute 'CollecTRI'
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" and not test_get_collectri"
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;; XXX This one fails because the "texts" list
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;; is empty, so there are no texts to adjust.
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;; It is not clear whether this a compatibility
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;; problem with our adjusttext package.
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" and not test_plot_volcano"))
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#:phases
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'(modify-phases %standard-phases
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(add-before 'check 'set-home
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;; Some tests require a home directory to be set.
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(lambda _ (setenv "HOME" "/tmp")))
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;; Numba needs a writable dir to cache functions.
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(add-before 'build 'set-numba-cache-dir
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(lambda _ (setenv "NUMBA_CACHE_DIR" "/tmp"))))))
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(propagated-inputs (list python-adjusttext
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python-anndata
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python-ipython
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python-matplotlib
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python-nbsphinx
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python-numba
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python-numpy
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python-numpydoc
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python-omnipath
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python-scanpy
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python-scikit-learn
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python-scipy
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python-skranger
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python-tqdm
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python-typing-extensions))
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(native-inputs (list python-pytest))
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(home-page "https://github.com/saezlab/decoupler-py")
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(synopsis
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"Framework for modeling, analyzing and interpreting single-cell RNA-seq data")
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(description
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"This package provides different statistical methods to extract
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(package
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(name "python-decoupler-py")
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(version "1.6.0")
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(source (origin
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(method git-fetch)
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(uri (git-reference
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(url "https://github.com/saezlab/decoupler-py")
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(commit (string-append "v" version))))
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(file-name (git-file-name name version))
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(sha256
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(base32
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"1mqkp0i8k5hzhfnka4nc2f0phmrs0k404ynbl1lqfjzywx25y75h"))))
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(build-system pyproject-build-system)
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(arguments
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(list
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#:test-flags
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'(list "-k"
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;; These tests require internet access
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(string-append "not test_get_resource"
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" and not test_show_resources"
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" and not test_get_dorothea"
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" and not test_get_progeny"
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" and not test_get_ksn_omnipath"
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;; This attempts to download things for Omnipath
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" and not test_get_collectri"))
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#:phases
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'(modify-phases %standard-phases
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(add-before 'check 'set-home
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;; Some tests require a home directory to be set.
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(lambda _ (setenv "HOME" "/tmp")))
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;; Numba needs a writable dir to cache functions.
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(add-before 'build 'set-numba-cache-dir
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(lambda _ (setenv "NUMBA_CACHE_DIR" "/tmp"))))))
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(propagated-inputs (list python-adjusttext
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python-anndata
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python-ipython
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python-matplotlib
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python-nbsphinx
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python-numba
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python-numpy
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python-numpydoc
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python-omnipath
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python-scanpy
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python-scikit-learn
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python-scipy
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python-skranger
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python-tqdm
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python-typing-extensions))
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(native-inputs (list python-pytest))
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(home-page "https://github.com/saezlab/decoupler-py")
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(synopsis
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"Framework for modeling, analyzing and interpreting single-cell RNA-seq data")
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(description
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"This package provides different statistical methods to extract
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biological activities from omics data within a unified framework.")
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(license license:gpl3+))))
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(license license:gpl3+)))
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(define-public python-demuxem
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(package
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