Subject: [PATCH 1/2] bioinformatics: Add python-mofapy2

From: [email-masked]
Date: Thu, 20 Jun 2024 08:50:03 +0000

Change-Id: Ide92878258511b3daf4e56d5faa94d190fdee62f
---
 gnu/packages/bioinformatics.scm | 38 +++++++++++++++++++++++++++++++++
 1 file changed, 38 insertions(+)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index cdda029809..37fa1727cb 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -4443,6 +4443,44 @@ (define-public python-mudata
 omics data.")
     (license license:bsd-3)))
 
+(define-public python-mofapy2
+  (package
+    (name "python-mofapy2")
+    (version "0.7.1")
+    (source
+     (origin
+       ;; The tarball from PyPi doesn't include tests.
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://github.com/bioFAM/mofapy2")
+             (commit (string-append "v" version))))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32
+         "0ahhnqk6gjrhyq286mrd5n7mxcv8l6040ffsawbjx9maqx8wbam0"))))
+    (build-system pyproject-build-system)
+    (arguments
+     (list
+      #:phases
+      #~(modify-phases %standard-phases
+          (add-before 'check 'disable-failing-tests
+            (lambda _
+              ;; cupy is an optional dependency, which
+              ;; itself has nonfree dependencies (CUDA)
+              (delete-file "mofapy2/notebooks/test_cupy.py"))))))
+    (propagated-inputs (list python-anndata
+                             python-pandas
+                             python-scipy
+                             python-numpy
+                             python-scikit-learn
+                             python-h5py))
+    (native-inputs (list python-poetry-core
+                         python-pytest))
+    (home-page "https:/biofam.github.io/MOFA2/")
+    (synopsis "Multi-omics factor analysis")
+    (description "Multi-omics factor analysis.")
+    (license license:lgpl3)))
+
 (define-public python-pyega3
   (deprecated-package "python-pyega3" python-ega-download-client))
 
-- 
2.45.1