[med-svn] [Git][med-team/metaphlan][master] 6 commits: d/copyright: bring up the header paragraph.

[Étienne Mollier (@emollier)]

Étienne Mollier pushed to branch master at Debian Med / metaphlan


Commits:
895336df by Étienne Mollier at 2025-05-22T21:47:30+02:00
d/copyright: bring up the header paragraph.

- - - - -
7b5d5743 by Étienne Mollier at 2025-05-22T21:48:55+02:00
d/control: declare compliance to standards version 4.7.2.

- - - - -
394278ae by Étienne Mollier at 2025-05-22T22:07:44+02:00
d/rules: fix calculate_diversity.R script not executable.

- - - - -
4cdabfb3 by Étienne Mollier at 2025-05-22T22:09:28+02:00
d/copyright: clarify the need for repack.

Gbp-Dch: ignore

- - - - -
d9884854 by Étienne Mollier at 2025-05-22T22:29:54+02:00
d/control: metaphlan depends on r-base-core.

- - - - -
85c192c4 by Étienne Mollier at 2025-05-22T22:31:50+02:00
d/changelog: ready for upload to unstable.

- - - - -


4 changed files:

- debian/changelog
- debian/control
- debian/copyright
- debian/rules


Changes:

=====================================
debian/changelog
=====================================
@@ -1,18 +1,22 @@
-metaphlan (4.0.4+ds-1) UNRELEASED; urgency=medium
+metaphlan (4.0.4+ds-1) unstable; urgency=medium
+
+  * Team upload.
 
   [ Harish chavre ]
-  * patch added Replace distutils.version with packaging.version for Python 3.12+ compatibility
+  * patch added Replace distutils.version with packaging.version for
+    Python 3.12+ compatibility
   * Add autopkgtest for metaphlan
+    Closes: #1035175
   * Add copyright info for autopkgtest data in debian/copyright
   * created  gbp.conf to embed the test data
-  * New upstream version 4.0.4
-  * New upstream version 4.0.4
   * move large test data to separate debian-tests-data component
-  * modify copyright to add debian-tests data in files
-  * patch added Replace distutils.version with packaging.version for Python 3.12+ compatibility
-  Closes: #1035175
 
- -- Harish <harrych_1 at yahoo.com>  Thu, 22 May 2025 04:43:07 +0000
+  [ Étienne Mollier ]
+  * d/rules: fix calculate_diversity.R script not executable.
+  * d/control: metaphlan depends on r-base-core.
+  * d/control: declare compliance to standards version 4.7.2.
+
+ -- Étienne Mollier <emollier at debian.org>  Thu, 22 May 2025 22:30:27 +0200
 
 metaphlan (4.0.4-1) unstable; urgency=medium
 


=====================================
debian/control
=====================================
@@ -10,7 +10,7 @@ Build-Depends: debhelper-compat (= 13),
                bowtie2,
                python3-setuptools,
                python3-biopython <!nocheck>
-Standards-Version: 4.6.2
+Standards-Version: 4.7.2
 Vcs-Browser: https://salsa.debian.org/med-team/metaphlan
 Vcs-Git: https://salsa.debian.org/med-team/metaphlan.git
 Homepage: https://github.com/biobakery/MetaPhlAn
@@ -25,6 +25,7 @@ Depends: ${python3:Depends},
          python3-msgpack,
          python3-pandas,
          python3-packaging,
+         r-base-core,
          bowtie2
 Conflicts: metaphlan2
 Provides: metaphlan2


=====================================
debian/copyright
=====================================
@@ -1,23 +1,26 @@
-Files: debian-tests-data/*
-Copyright: 2024 Segata Lab
-License: Expat
-Comment: This test data was obtained from the MetaPhlAn4 upstream database at
- http://cmprod1.cibio.unitn.it/biobakery4/metaphlan_databases/
-
 Format: https://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
 Upstream-Name: MetaPhlAn
 Upstream-Contact:  Nicola Segata <nicola.segata at unitn.it>
 Source: https://github.com/biobakery/MetaPhlAn
+Comment: Repack suffix may be dropped on next upstream release.
+ It was introduced to differentiate upstream 4.0.4 without and with test
+ data.
 
 Files: *
 Copyright: 2012-2022 Duy Tin Truong, Nicola Segata and Curtis Huttenhower
-License: expat
+License: Expat
+
+Files: debian-tests-data/*
+Copyright: 2024 Segata Lab
+License: Expat
+Comment: This test data was obtained from the MetaPhlAn4 upstream database at
+ http://cmprod1.cibio.unitn.it/biobakery4/metaphlan_databases/
 
 Files: debian/*
 Copyright: 2016-2022 Andreas Tille <tille at debian.org>
-License: expat
+License: Expat
 
-License: expat
+License: Expat
  Permission is hereby granted, free of charge, to any person obtaining a
  copy of this software and associated documentation files (the
  "Software"), to deal in the Software without restriction, including


=====================================
debian/rules
=====================================
@@ -18,3 +18,5 @@ override_dh_installchangelogs:
 override_dh_fixperms:
 	dh_fixperms
 	find debian/$(DEB_SOURCE) -name "*.txt" -exec chmod -x \{\} \;
+	find debian/$(DEB_SOURCE) -name "calculate_diversity.R" \
+		-exec chmod +x \{\} \;



View it on GitLab: https://salsa.debian.org/med-team/metaphlan/-/compare/eae87a24ac582ef7e35110bd5c5851d708e4706e...85c192c417bb69d1211a8ab6517d5c0a157f2b71

-- 
View it on GitLab: https://salsa.debian.org/med-team/metaphlan/-/compare/eae87a24ac582ef7e35110bd5c5851d708e4706e...85c192c417bb69d1211a8ab6517d5c0a157f2b71
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