GNU bug report logs - #76073
[PATCH] gnu: Add python-cnmf.

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From: help-debbugs <at> gnu.org (GNU bug Tracking System)
To: Sharlatan Hellseher <sharlatanus <at> gmail.com>
Cc: tracker <at> debbugs.gnu.org
Subject: bug#76073: closed ([PATCH] gnu: Add python-cnmf.)
Date: Wed, 05 Feb 2025 17:53:02 +0000

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Your message dated Wed, 05 Feb 2025 17:52:34 +0000
with message-id <874j18i8il.fsf <at> gmail.com>
and subject line [PATCH] gnu: Add python-cnmf.
has caused the debbugs.gnu.org bug report #76073,
regarding [PATCH] gnu: Add python-cnmf.
to be marked as done.

(If you believe you have received this mail in error, please contact
help-debbugs <at> gnu.org.)


-- 
76073: https://debbugs.gnu.org/cgi/bugreport.cgi?bug=76073
GNU Bug Tracking System
Contact help-debbugs <at> gnu.org with problems

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From: Navid Afkhami <navid.afkhami <at> mdc-berlin.de>
To: <guix-patches <at> gnu.org>
Cc: Navid Afkhami <navid.afkhami <at> mdc-berlin.de>
Subject: [PATCH] gnu: Add python-cnmf.
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

[Message part 3 (message/rfc822, inline)]

From: Sharlatan Hellseher <sharlatanus <at> gmail.com>
To: 76073-done <at> debbugs.gnu.org
Subject: [PATCH] gnu: Add python-cnmf.
Date: Wed, 05 Feb 2025 17:52:34 +0000

[Message part 4 (text/plain, inline)]

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

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