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| author | Ricardo Wurmus <rekado@elephly.net> | 2024-12-21 17:35:56 +0100 |
|---|---|---|
| committer | Ricardo Wurmus <rekado@elephly.net> | 2025-01-20 21:37:26 +0100 |
| commit | ae63ff8dca9ca2a2c2f900099affa65b41584273 (patch) | |
| tree | b35c97b8f7f95bae33adeab195e9bc22a0a05f55 /gnu | |
| parent | 43b061aaf6fbf4c03d61abb2e0a2611c41ba5f5e (diff) | |
| download | guix-ae63ff8dca9ca2a2c2f900099affa65b41584273.tar.gz guix-ae63ff8dca9ca2a2c2f900099affa65b41584273.zip | |
gnu: pyscenic: Update to 0.12.1-1.eaf23eb.
* gnu/packages/bioinformatics.scm (pyscenic): Update to 0.12.1-1.eaf23eb.
[arguments]: Update phase 'do-not-reference-deleted-modules.
[propagated-inputs]: Add python-numexpr.
[native-inputs]: Add python-wheel.
Change-Id: Ib1b5a7d36a24b280160befe579057a241d69455d
Diffstat (limited to 'gnu')
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 58 |
1 files changed, 31 insertions, 27 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 449e6dd5f2..433e60a47c 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -21123,12 +21123,14 @@ tree-based ensemble regressors.") (license license:bsd-3))) (define-public pyscenic - ;; Latest commit from the update-pyarrow branch - (let ((commit "5f170fdf474548c37ab381d1849c662820d658ee") + ;; We use this commit because the last release is not compatible with the + ;; current version of numpy. See + ;; https://github.com/aertslab/pySCENIC/issues/579#issuecomment-2405207860 + (let ((commit "eaf23eb1fdcaae79b273de56b374b71aa8afde5a") (revision "1")) (package (name "pyscenic") - (version (git-version "0.11.2" revision commit)) + (version (git-version "0.12.1" revision commit)) (source (origin (method git-fetch) @@ -21138,7 +21140,7 @@ tree-based ensemble regressors.") (file-name (git-file-name name version)) (sha256 (base32 - "03qkvy400rjndg2ds6bhcaprir71mqr2v3yv9vd77lcnzxgw3s0z")))) + "1si2ifmj0cy2yba8lw5m7mg97iqaxi0cwhy3j43rz5bzkp0cah8n")))) (build-system pyproject-build-system) (arguments (list @@ -21149,43 +21151,45 @@ tree-based ensemble regressors.") (add-after 'unpack 'do-not-reference-deleted-modules (lambda _ (substitute* "setup.py" - (("'db2feather = .*',") "") - (("'invertdb = .*',") "") - (("'gmt2regions = pyscenic.cli.gmt2regions:main'") "")))) + (("\"db2feather = .*\",") "") + (("\"csv2loom = .*\",") "") + (("\"invertdb = .*\",") "") + (("\"gmt2regions = .*\",") "")))) ;; Numba needs a writable dir to cache functions. (add-before 'check 'set-numba-cache-dir (lambda _ (setenv "NUMBA_CACHE_DIR" "/tmp")))))) (propagated-inputs - (list python-ctxcore - python-cytoolz - python-multiprocessing-on-dill - python-llvmlite - python-numba + (list python-aiohttp + python-arboreto python-attrs - python-frozendict - python-numpy - python-pandas + python-boltons python-cloudpickle + python-ctxcore + python-cytoolz python-dask - python-pyarrow ;XXX for dask python-distributed - python-arboreto - python-boltons - python-setuptools - python-pyyaml - python-tqdm + python-frozendict + python-fsspec python-interlap - python-umap-learn + python-llvmlite python-loompy + python-multiprocessing-on-dill python-networkx - python-scipy - python-fsspec + python-numba + python-numexpr + python-numpy + python-pandas + python-pyarrow ;XXX for dask + python-pyyaml python-requests - python-aiohttp - python-scikit-learn)) + python-scikit-learn + python-scipy + python-setuptools + python-tqdm + python-umap-learn)) (native-inputs - (list python-pytest)) + (list python-pytest python-wheel)) (home-page "https://scenic.aertslab.org/") (synopsis "Single-Cell regulatory network inference and clustering") (description |