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gnu: pyscenic: Update to 0.11.2-1.5f170fd.

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* gnu/packages/bioinformatics.scm (pyscenic): Update to 0.11.2-1.5f170fd.
[build-system]: Use pyproject-build-system.
[arguments]: Patch setup.py.
[propagated-inputs]: Add python-pyarrow.

Change-Id: I3acd7c921c2c44741c0afd0bbda011f63ed14c42
This commit is contained in:
Ricardo Wurmus 2023-12-15 15:34:35 +01:00
parent 46b1e717cf
commit 93597fc39c
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GPG key ID: 197A5888235FACAC
1 changed files with 68 additions and 58 deletions
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@ -18066,30 +18066,39 @@ tree-based ensemble regressors.")
(license license:bsd-3))) (license license:bsd-3)))
(define-public pyscenic (define-public pyscenic
;; Latest commit from the update-pyarrow branch
(let ((commit "5f170fdf474548c37ab381d1849c662820d658ee")
(revision "1"))
(package (package
(name "pyscenic") (name "pyscenic")
(version "0.11.2") (version (git-version "0.11.2" revision commit))
(source (source
(origin (origin
(method git-fetch) (method git-fetch)
(uri (git-reference (uri (git-reference
(url "https://github.com/aertslab/pySCENIC") (url "https://github.com/aertslab/pySCENIC")
(commit version))) (commit commit)))
(file-name (git-file-name name version)) (file-name (git-file-name name version))
(sha256 (sha256
(base32 (base32
"0pbmmr1zdb1vbbs6wx357s59d13pna6x03wq8blj6ckjws8bbq73")))) "03qkvy400rjndg2ds6bhcaprir71mqr2v3yv9vd77lcnzxgw3s0z"))))
(build-system python-build-system) (build-system pyproject-build-system)
(arguments (arguments
`(#:phases (list
(modify-phases %standard-phases #:phases
'(modify-phases %standard-phases
;; The cli modules referenced here have been removed, so this
;; breaks the sanity check.
(add-after 'unpack 'do-not-reference-deleted-modules
(lambda _
(substitute* "setup.py"
(("'db2feather = .*',") "")
(("'invertdb = .*',") "")
(("'gmt2regions = pyscenic.cli.gmt2regions:main'") ""))))
;; Numba needs a writable dir to cache functions. ;; Numba needs a writable dir to cache functions.
(add-before 'check 'set-numba-cache-dir (add-before 'check 'set-numba-cache-dir
(lambda _ (lambda _
(setenv "NUMBA_CACHE_DIR" "/tmp"))) (setenv "NUMBA_CACHE_DIR" "/tmp"))))))
(replace 'check
(lambda _
(invoke "pytest" "-v"))))))
(propagated-inputs (propagated-inputs
(list python-ctxcore (list python-ctxcore
python-cytoolz python-cytoolz
@ -18102,6 +18111,7 @@ tree-based ensemble regressors.")
python-pandas python-pandas
python-cloudpickle python-cloudpickle
python-dask python-dask
python-pyarrow ;XXX for dask
python-distributed python-distributed
python-arboreto python-arboreto
python-boltons python-boltons
@ -18126,7 +18136,7 @@ tree-based ensemble regressors.")
rEgulatory Network Inference and Clustering) which enables biologists to infer rEgulatory Network Inference and Clustering) which enables biologists to infer
transcription factors, gene regulatory networks and cell types from transcription factors, gene regulatory networks and cell types from
single-cell RNA-seq data.") single-cell RNA-seq data.")
(license license:gpl3+))) (license license:gpl3+))))
(define-public python-ikarus (define-public python-ikarus
(package (package