Subject: [PATCH] gnu: Add python-cnmf.
From: Sharlatan Hellseher <[email-masked]>
To: [email-masked]
Date: Wed, 05 Feb 2025 17:52:34 +0000
List-Id: <debbugs-submit.debbugs.gnu.org>

Hi,

Thank you for the patch.

I've applied some cosmetic adjustments:

--8<---------------cut here---------------start------------->8---
@@ -2596,34 +2596,36 @@ (define-public python-cnmf
     (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))
+      #:tests? #f ; no tests in git checkout and PyPI archive
+      #:phases
+      #~(modify-phases %standard-phases
+          (add-after 'unpack 'set-envs
+            (lambda _
+              (setenv "MPLCONFIGDIR" "/tmp")
+              ;; Numba needs a writable dir to cache functions.
+              (setenv "NUMBA_CACHE_DIR" "/tmp"))))))
+    (native-inputs
+     (list python-setuptools
+           python-wheel))
+    (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))
     (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.")
+     "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)))
--8<---------------cut here---------------end--------------->8---

Pushed to master as 985c0fd63c1f0c1f2ab8adaac3109ccdad258a28

--
Oleg