GNU bug report logs - #62980
gnu: bpp-popgen and bppsuite: Update to 2.4.1.

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Message #5 received at submit <at> debbugs.gnu.org (full text, mbox):

From: "MadalinIonel.Patrascu <at> mdc-berlin.de"
 <MadalinIonel.Patrascu <at> mdc-berlin.de>
To: "guix-patches <at> gnu.org" <guix-patches <at> gnu.org>
Subject: gnu: bpp-popgen and bppsuite: Update to 2.4.1.
Date: Fri, 21 Apr 2023 00:00:37 +0000

[Message part 1 (text/plain, inline)]

[Message part 2 (text/html, inline)]

Message #8 received at 62980 <at> debbugs.gnu.org (full text, mbox):

From: Mădălin Ionel Patrașcu
 <madalinionel.patrascu <at> mdc-berlin.de>
To: <62980 <at> debbugs.gnu.org>
Subject: [PATCH 1/2] gnu: bpp-popgen: Update to 2.4.1.
Date: Fri, 21 Apr 2023 02:03:57 +0200

* gnu/packages/bioinformatics.scm (bpp-popgen): 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.
[home-page]: Changed to new host Université Claude-Bernard Lyon 1.
---
 gnu/packages/bioinformatics.scm | 49 +++++++++++++++------------------
 1 file changed, 22 insertions(+), 27 deletions(-)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index c4cea24632..3969e205b3 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -2296,35 +2296,30 @@ (define-public bpp-phyl-omics
     (license license:cecill)))
 
 (define-public bpp-popgen
-  ;; 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 "e472bac9b1a148803895d747cd6d0c5904f85d9f"))
-    (package
-      (name "bpp-popgen")
-      (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-popgen")
-                      (commit commit)))
-                (file-name (string-append name "-" version "-checkout"))
-                (sha256
-                 (base32
-                  "0yn82dzn1n5629nzja68xfrhi655709rjanyryb36vzkmymy6dw5"))))
-      (build-system cmake-build-system)
-      (arguments
-       `(#:parallel-build? #f
-         #:tests? #f)) ; There are no tests.
-      (inputs
-       (list bpp-core bpp-seq))
-      (home-page "http://biopp.univ-montp2.fr")
-      (synopsis "Bio++ population genetics library")
-      (description
-       "Bio++ is a set of C++ libraries for Bioinformatics, including sequence
+  (package
+    (name "bpp-popgen")
+    (version "2.4.1")
+    (source (origin
+              (method git-fetch)
+              (uri (git-reference
+                    (url "https://github.com/BioPP/bpp-popgen")
+                    (commit (string-append "v" version))))
+              (file-name (git-file-name name version))
+              (sha256
+               (base32
+                "0bz0fhrq3dri6a0hvfc3zlvrns8mrzzlnicw5pyfa812gc1qwfvh"))))
+    (build-system cmake-build-system)
+    (arguments
+     (list #:tests? #f)) ; There are no tests.
+    (inputs
+     (list bpp-core bpp-seq))
+    (home-page "https://pbil.univ-lyon1.fr/bpp-doc/bpp-popgen/html/")
+    (synopsis "Bio++ population genetics library")
+    (description
+     "Bio++ is a set of C++ libraries for Bioinformatics, including sequence
 analysis, phylogenetics, molecular evolution and population genetics.  This
 library provides population genetics-related modules.")
-      (license license:cecill-c))))
+    (license license:cecill-c)))
 
 (define-public bpp-seq
   (package

base-commit: 2d06dfc050114dba44e791d8decc8eaa705fee01
prerequisite-patch-id: 5853dbe5778b2160c2bf5dca3f01be75fcbb678c
prerequisite-patch-id: 4af2ed7c595ec571d717d161aff1ef51a8dfc365
prerequisite-patch-id: e460dac992e961a5f13af1ed99bfad48d2f0ceb5
prerequisite-patch-id: 4241e6e34dc593a321a69e135db83293eaf011f7
prerequisite-patch-id: 78c7d0a29aee256ae2df1759863ef7e6dc34102f
prerequisite-patch-id: 4dc46155f0d7730f6996403f20442c2892e08a7c
-- 
2.39.2

Message #11 received at 62980 <at> debbugs.gnu.org (full text, mbox):

From: Mădălin Ionel Patrașcu
 <madalinionel.patrascu <at> mdc-berlin.de>
To: <62980 <at> debbugs.gnu.org>
Subject: [PATCH 2/2] gnu: bppsuite: Update to 2.4.1.
Date: Fri, 21 Apr 2023 02:03:58 +0200

* gnu/packages/bioinformatics.scm (bppsuite): 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.
[inputs]: Use list.
[home-page]: Changed to github page.
---
 gnu/packages/bioinformatics.scm | 56 ++++++++++++++-------------------
 1 file changed, 24 insertions(+), 32 deletions(-)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 3969e205b3..625dd5a409 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -2367,40 +2367,32 @@ (define-public bpp-seq-omics
     (license license:cecill)))
 
 (define-public bppsuite
-  ;; 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 "c516147f57aa50961121cd505bed52cd7603698b"))
-    (package
-      (name "bppsuite")
-      (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/bppsuite")
-                      (commit commit)))
-                (file-name (string-append name "-" version "-checkout"))
-                (sha256
-                 (base32
-                  "1y87pxvw0jxjizhq2dr9g2r91md45k1p9ih2sl1yy1y3p934l2kb"))))
-      (build-system cmake-build-system)
-      (arguments
-       `(#:parallel-build? #f
-         #:tests? #f)) ; There are no tests.
-      (native-inputs
-       (list groff man-db texinfo))
-      (inputs
-       `(("bpp-core" ,bpp-core)
-         ("bpp-seq" ,bpp-seq)
-         ("bpp-phyl" ,bpp-phyl)
-         ("bpp-phyl" ,bpp-popgen)))
-      (home-page "http://biopp.univ-montp2.fr")
-      (synopsis "Bioinformatics tools written with the Bio++ libraries")
-      (description
-       "Bio++ is a set of C++ libraries for Bioinformatics, including sequence
+  (package
+    (name "bppsuite")
+    (version "2.4.1")
+    (source (origin
+              (method git-fetch)
+              (uri (git-reference
+                    (url "https://github.com/BioPP/bppsuite")
+                    (commit (string-append "v" version))))
+              (file-name (git-file-name name version))
+              (sha256
+               (base32
+                "1wdwcgczqbc3m116vakvi0129wm3acln3cfc7ivqnalwvi6lrpds"))))
+    (build-system cmake-build-system)
+    (arguments
+     (list #:tests? #f)) ; There are no tests.
+    (native-inputs
+     (list groff man-db texinfo))
+    (inputs
+     (list bpp-core bpp-seq bpp-phyl bpp-popgen))
+    (home-page "https://github.com/BioPP")
+    (synopsis "Bioinformatics tools written with the Bio++ libraries")
+    (description
+     "Bio++ is a set of C++ libraries for Bioinformatics, including sequence
 analysis, phylogenetics, molecular evolution and population genetics.  This
 package provides command line tools using the Bio++ library.")
-      (license license:cecill-c))))
+    (license license:cecill-c)))
 
 (define-public blast+
   (package
-- 
2.39.2

Message #18 received at 62980-done <at> debbugs.gnu.org (full text, mbox):

From: Ricardo Wurmus <rekado <at> elephly.net>
To: 62980-done <at> debbugs.gnu.org
Subject: gnu: bpp-popgen and bppsuite: Update to 2.4.1.
Date: Fri, 21 Apr 2023 14:04:41 +0200

Applied, thank you!

-- 
Ricardo

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