[med-svn] [Git][med-team/libbio-db-hts-perl][master] Fix find of htslib, change upstream links, and other small fixes.

[David Miguel Susano Pinto]

David Miguel Susano Pinto pushed to branch master at Debian Med / libensembl-bio-db-hts


Commits:
8835cdb8 by David Miguel Susano Pinto at 2019-11-21T14:59:10Z
Fix find of htslib, change upstream links, and other small fixes.

* d/rules: fix finding htslib by not attempting to manually
  specify its location and leaving pkg-config to do its job.

* d/compat: add file and set to 11 because my system is too old.

* d/control: this fits better in the science section than perl; set
  debhelper to 11 because my build system is too old; add the
  libextutils-cbuilder-perl build dependency; use metacpan as the
  upstream location.

* d/copyright: upstream releases to metacpan.

* d/libbio-db-hts-perl.lintian-overrides: silence lintian about this
  package not being in the perl section.

* d/upstream/metadata: remove empty sections and fill what I know
  about.

* d/watch: releases to CPAN will appear on metacpan not github so
  watch metacpan for new releases not github.

- - - - -


7 changed files:

- + debian/compat
- debian/control
- debian/copyright
- + debian/libbio-db-hts-perl.lintian-overrides
- debian/rules
- debian/upstream/metadata
- debian/watch


Changes:

=====================================
debian/compat
=====================================
@@ -0,0 +1 @@
+11


=====================================
debian/control
=====================================
@@ -1,26 +1,24 @@
 Source: libbio-db-hts-perl
-Section: perl
+Section: science
 Priority: optional
 Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
 Uploaders: Andreas Tille <tille at debian.org>
-Testsuite: autopkgtest-pkg-perl
-Build-Depends: debhelper-compat (= 12),
-               libmodule-build-perl,
-               libextutils-pkgconfig-perl,
-               libhts-dev
-Build-Depends-Indep: perl,
-                     libbio-perl-perl,
-                     pkg-config
+Build-Depends: debhelper (>= 11),
+ libbio-perl-perl,
+ libextutils-cbuilder-perl,
+ libextutils-pkgconfig-perl,
+ libhts-dev,
+ libmodule-build-perl,
+ perl
 Standards-Version: 4.4.1
 Vcs-Browser: https://salsa.debian.org/med-team/libbio-db-hts-perl
 Vcs-Git: https://salsa.debian.org/med-team/libbio-db-hts-perl.git
-Homepage: https://github.com/Ensembl/Bio-DB-HTS
+Homepage: https://metacpan.org/release/Bio-DB-HTS
+Testsuite: autopkgtest-pkg-perl
 
 Package: libbio-db-hts-perl
 Architecture: any
-Depends: ${perl:Depends},
-         ${shlibs:Depends},
-         ${misc:Depends}
+Depends: ${perl:Depends}, ${misc:Depends}
 Description: Perl interface to the HTS library
  HTSlib is an implementation of a unified C library for accessing common file
  formats, such as SAM (Sequence Alignment/Map), CRAM and VCF (Variant Call
@@ -29,7 +27,7 @@ Description: Perl interface to the HTS library
  compatible with gcc, g++ and clang.
  .
  HTSlib implements a generalized BAM (binary SAM) index, with file extension
- ‘csi’ (coordinate-sorted index). The HTSlib file reader first looks for the
+ 'csi' (coordinate-sorted index). The HTSlib file reader first looks for the
  new index and then for the old if the new index is absent.
  .
  This package provides a Perl interface to the HTS library.


=====================================
debian/copyright
=====================================
@@ -1,6 +1,6 @@
 Format: https://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+Source: https://metacpan.org/release/Bio-DB-HTS
 Upstream-Name: Bio-DB-HTS
-Source: https://github.com/Ensembl/Bio-DB-HTS
 
 Files: *
 Copyright: 2015-2019 EMBL-European Bioinformatics Institute


=====================================
debian/libbio-db-hts-perl.lintian-overrides
=====================================
@@ -0,0 +1,3 @@
+## Even though this is a perl library, its use cases are so specific
+## that science is a better fit.
+libbio-db-hts-perl: wrong-section-according-to-package-name libbio-db-hts-perl => perl


=====================================
debian/rules
=====================================
@@ -1,11 +1,4 @@
 #!/usr/bin/make -f
 
-# DH_VERBOSE := 1
-
 %:
 	dh $@
-
-override_dh_auto_configure:
-	# dh_auto_configure -- --prefix=/usr
-	# dh_auto_configure -- --htslib-includedir=/usr/include
-	HTSLIB_DIR=/usr/include dh_auto_configure


=====================================
debian/upstream/metadata
=====================================
@@ -1,12 +1,6 @@
-Reference:
-  Author: 
-  Title: 
-  Journal: 
-  Year: 
-  Volume: 
-  Number: 
-  Pages: 
-  DOI: 
-  PMID:
-  URL: 
-  eprint: 
+---
+Archive: CPAN
+Bug-Database: https://github.com/Ensembl/Bio-DB-HTS/issues
+Name: Bio-DB-HTS
+Repository: https://github.com/Ensembl/Bio-DB-HTS.git
+Repository-Browse: https://github.com/Ensembl/Bio-DB-HTS


=====================================
debian/watch
=====================================
@@ -1,4 +1,3 @@
-version=4
-
-opts="mode=git,pretty=98+git%cd.%h" \
-    https://github.com/Ensembl/Bio-DB-HTS.git HEAD
+version=3
+https://metacpan.org/release/Bio-DB-HTS \
+  .*/Bio-DB-HTS-v?(\d[\d.-]*)\.(?:tar(?:\.gz|\.bz2)?|tgz|zip)$



View it on GitLab: https://salsa.debian.org/med-team/libbio-db-hts-perl/commit/8835cdb8c66fadc5ca141767d093761fc1919c44

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View it on GitLab: https://salsa.debian.org/med-team/libbio-db-hts-perl/commit/8835cdb8c66fadc5ca141767d093761fc1919c44
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