From 389e9019a754d4a4151634d865fa0780c5f85b9c Mon Sep 17 00:00:00 2001
From: Nicolas Graves <ngraves@ngraves.fr>
Date: Sun, 26 Oct 2025 01:24:14 +0200
Subject: [PATCH] gnu: python-illumina-utils: Update to 2.13.

* gnu/packages/bioinformatics.scm (python-illumina-utils): Update to 2.13.
<#:phases>: In phase 'adjust-requirements, add python-levenshtein patch.

Change-Id: I03cafaea1f73206bb5cfc887b9b4d0df7d959fca
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
---
 gnu/packages/bioinformatics.scm | 32 ++++++++++++++++++++++----------
 1 file changed, 22 insertions(+), 10 deletions(-)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 013354c4561246bafc0f48fd7f70fd3163c6ab7f..4e7950c32f7434dd82dac740f6efe0e874670b28 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -8134,17 +8134,29 @@ exploration.")
 (define-public python-illumina-utils
   (package
     (name "python-illumina-utils")
-    (version "2.12")
-    (source (origin
-              (method url-fetch)
-              (uri (pypi-uri "illumina-utils" version))
-              (sha256
-               (base32
-                "0z9g0prj7pmgl5z4vdpxv3v30grzhc194801qnf0wqzgy7w3aj2s"))))
+    (version "2.13")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://github.com/meren/illumina-utils")
+             (commit (string-append "v" version))))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32 "15cyb5slw07va5siq8nzc0nwcgnvx1hmqqrgwk2v0fxy250fp9v4"))))
     (build-system pyproject-build-system)
-    (arguments (list #:tests? #false))  ;there are none
-    (propagated-inputs (list python-matplotlib python-numpy python-levenshtein))
-    (native-inputs (list python-setuptools python-wheel python-pip))
+    (arguments
+     (list
+      #:tests? #f                       ;there are none
+      #:phases
+      #~(modify-phases %standard-phases
+          (add-after 'unpack 'adjust-requirements
+            (lambda _
+              (substitute* "requirements.txt"
+                (("python-Levenshtein")
+                 "levenshtein")))))))
+    (propagated-inputs (list python-levenshtein python-matplotlib python-numpy))
+    (native-inputs (list python-pip python-setuptools))
     (home-page "https://github.com/meren/illumina-utils")
     (synopsis "Library and scripts to work with Illumina paired-end data")
     (description