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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
This commit is contained in:
Sharlatan Hellseher
parent
018b8a474e
commit
962948f2a4
1 changed files with 54 additions and 35 deletions
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@ -79,6 +79,7 @@
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#:use-module (gnu packages bison)
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#:use-module (gnu packages bioconductor)
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#:use-module (gnu packages boost)
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#:use-module (gnu packages certs)
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#:use-module (gnu packages check)
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#:use-module (gnu packages code)
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#:use-module (gnu packages cmake)
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@ -2836,41 +2837,51 @@ specifying the usage of each program for each cell in the data.")
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parsing of Variant Call Format (VCF) files.")
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(license license:expat)))
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(define-public python-decoupler-py
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(define-public python-decoupler
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(package
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(name "python-decoupler-py")
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;; Upstream places release on a new branch, see
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;; <https://github.com/saezlab/decoupler-py/issues/175>.
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(version "1.8.0")
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(name "python-decoupler")
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(version "2.1.1")
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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 version)))
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(url "https://github.com/scverse/decoupler")
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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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"0c3yg7jjb1nxb6hsh9wn7wr8w0ba55gixdbf5fp443nhv1cwlajj"))))
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"0b15n5sq940sn29jsgmdkkm4fcpzfq1n221scfwhjxb4ybdpsz4v"))))
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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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'(list "-k" (string-join
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;; Tests requiring internet access to reach out
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;; <datasets.cellxgene.cziscience.com>, <ftp.ebi.ac.uk>,
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;; <omnipathdb.org>, <raw.githubusercontent.com>,
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;; <static.omnipathdb.org>, <www.ensembl.org>,
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;; <www.ncbi.nlm.nih.gov>, and <zenodo.org>.
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(list "not test_collectri"
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"test_covid5k"
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"test_dorothea"
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"test_download"
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"test_download_anndata"
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"test_ensmbl_to_symbol"
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"test_erygast1k"
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"test_hallmark"
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"test_hsctgfb"
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"test_knocktf"
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"test_msvisium"
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"test_pbmc3k"
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"test_progeny"
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"test_resource"
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"test_show_resources"
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"test_translate"
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;; XXX: Some precision mismatched.
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"test_func_gsea"
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"test_net_corr")
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" and not "))
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#:phases
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'(modify-phases %standard-phases
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(add-after 'unpack 'relax-requirements
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(lambda _
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(substitute* "pyproject.toml"
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;; numba = "^0.60.0"; all tests passed.
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(("0.60.0") "0.61.0"))))
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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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@ -2879,27 +2890,35 @@ parsing of Variant Call Format (VCF) files.")
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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-dcor
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python-docrep
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python-igraph
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python-ipywidgets
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python-marsilea
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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-requests
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python-scipy
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python-skranger
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python-session-info2
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python-tqdm
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python-typing-extensions))
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(native-inputs (list python-poetry-core python-pytest))
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(home-page "https://github.com/saezlab/decoupler-py")
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python-xgboost))
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(native-inputs
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(list nss-certs-for-test
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python-hatchling
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python-gseapy
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python-memory-profiler
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python-pytest
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python-scanpy))
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(home-page "https://github.com/scverse/decoupler")
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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:bsd-3)))
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;; See: <https://github.com/scverse/decoupler/blob/main/CHANGELOG.md#200>
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(define-public python-decoupler-py
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(deprecated-package "python-decoupler-py" python-decoupler))
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(define-public python-demuxem
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(package
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