Subject: [PATCH] gnu: Add python-cnmf.

From: Navid Afkhami <[email-masked]>
Date: Wed, 5 Feb 2025 16:20:58 +0000

* gnu/packages/bioinformatics.scm (python-cnmf): New variable.

Change-Id: I8a4f2293bde59b10e7b673025bbb4c5a8420738b
---
 gnu/packages/bioinformatics.scm | 43 +++++++++++++++++++++++++++++++++
 1 file changed, 43 insertions(+)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 317c15817e..7566346df1 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -2581,6 +2581,49 @@ (define-public python-cmseq
 and sequence consensus.")
     (license license:expat)))
 
+(define-public python-cnmf
+  (package
+    (name "python-cnmf")
+    (version "1.6.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (pypi-uri "cnmf" version))
+       (sha256
+        (base32 "0aic8cwj6riykcfgl6v2x3si5z04gaknkh5a8lcyv1qh4s1gx3d3"))))
+    (build-system pyproject-build-system)
+    (arguments
+     (list
+      #:tests? #f ;There are no tests
+      #:phases '(modify-phases %standard-phases
+                  (add-before 'check 'pre-check
+                    (lambda _
+                      (setenv "MPLCONFIGDIR" "/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-anndata
+                             python-fastcluster
+                             python-matplotlib
+                             python-numba
+                             python-numpy
+                             python-palettable
+                             python-pandas
+                             python-pyyaml
+                             python-scanpy
+                             python-scikit-learn
+                             python-scipy))
+    (native-inputs (list python-setuptools python-wheel))
+    (home-page "https://github.com/dylkot/cNMF")
+    (synopsis "Consensus NMF for scRNA-Seq data")
+    (description
+     "This tool offers a pipeline for inferring gene expression programs from scRNA-Seq.
+It takes a count matrix (N cells X G genes) as input and produces a (K x G) matrix of
+gene expression programs (GEPs) and a (N x K) matrix specifying the usage of each
+program for each cell in the data.")
+    (license license:expat)))
+
 (define-public python-cyvcf2
   (package
     (name "python-cyvcf2")

base-commit: 49a113e3fc618d6f6bd5000c164a1d33701a30c4
-- 
2.43.0