From 5107a8a1a394fef300c2d98d36b1bd92122ecf39 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?M=C4=83d=C4=83lin=20Ionel=20Patra=C8=99cu?=
 <madalinionel.patrascu@mdc-berlin.de>
Date: Fri, 21 Apr 2023 10:16:38 +0200
Subject: [PATCH] gnu: bpp-phyl: Update to 2.4.1.
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* gnu/packages/bioinformatics.scm (bpp-phyl): Update to 2.4.1.

[source]: Remove the commit and use the release version. Changed to the github
repo.
[arguments]: Remove the disabled parallel-build and out-of-source.
[home-page]: Changed to new host Université Claude-Bernard Lyon 1.
[synopsis]: Use proper capitalization.
---
 gnu/packages/bioinformatics.scm | 49 ++++++++++++++-------------------
 1 file changed, 20 insertions(+), 29 deletions(-)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 232d0e42c6..ad61b979dd 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -2244,37 +2244,28 @@ (define-public bpp-core
       (license license:cecill-c)))
 
 (define-public bpp-phyl
-  ;; The last release was in 2014 and the recommended way to install from source
-  ;; is to clone the git repository, so we do this.
-  ;; http://biopp.univ-montp2.fr/wiki/index.php/Main_Page
-  (let ((commit "0c07167b629f68b569bf274d1ad0c4af83276ae2"))
-    (package
-      (name "bpp-phyl")
-      (version (string-append "2.2.0-1." (string-take commit 7)))
-      (source (origin
-                (method git-fetch)
-                (uri (git-reference
-                      (url "http://biopp.univ-montp2.fr/git/bpp-phyl")
-                      (commit commit)))
-                (file-name (string-append name "-" version "-checkout"))
-                (sha256
-                 (base32
-                  "1ssjgchzwj3iai26kyly7gwkdv8sk59nqhkb1wpap3sf5m6kyllh"))))
-      (build-system cmake-build-system)
-      (arguments
-       `(#:parallel-build? #f
-         ;; If out-of-source, test data is not copied into the build directory
-         ;; so the tests fail.
-         #:out-of-source? #f))
-      (inputs
-       (list bpp-core bpp-seq))
-      (home-page "http://biopp.univ-montp2.fr")
-      (synopsis "Bio++ phylogenetic Library")
-      (description
-       "Bio++ is a set of C++ libraries for Bioinformatics, including sequence
+  (package
+    (name "bpp-phyl")
+    (version "2.4.1")
+    (source (origin
+              (method git-fetch)
+              (uri (git-reference
+                    (url "https://github.com/BioPP/bpp-phyl")
+                    (commit (string-append "v" version))))
+              (file-name (git-file-name name version))
+              (sha256
+               (base32
+                "192zks6wyk903n06c2lbsscdhkjnfwms8p7jblsmk3lvjhdipb20"))))
+    (build-system cmake-build-system)
+    (inputs
+     (list bpp-core bpp-seq))
+    (home-page "https://pbil.univ-lyon1.fr/bpp-doc/bpp-phyl/html/")
+    (synopsis "Bio++ phylogenetic library")
+    (description
+     "Bio++ is a set of C++ libraries for Bioinformatics, including sequence
 analysis, phylogenetics, molecular evolution and population genetics.  This
 library provides phylogenetics-related modules.")
-      (license license:cecill-c))))
+    (license license:cecill-c)))
 
 (define-public bpp-popgen
   ;; The last release was in 2014 and the recommended way to install from source