Annual copyright update 2025

Copyright optimisation

missing deps

- centralised copyright information into NOTICE file
- added NOTICE file
- restored standard LICENSE file
- added test for checking license and copyright headers
- updated MANIFEST and MANIFEST.SKIP files
- added missing license and copyright headers

TravisCI optimisations

- added unexpected missing header file package

- added forced install of XML::LibXML because of a bug in its test suite
- added version constraint to BioPerl in cpanfile

- updated Perl versions 5.26, 5.32
- updated HTSLIB versions 1.9-1.13
- removed COVERALLS reporting
- moved Perl dependencies into `cpanfile`
- installed Perl dependencies using cpanm
- updated `harness.sh`

Yearly copyright update 2024

Copyright update 2023

master branch has become main

Yearly copyright update - 2022

Remove perl 5.10 testing in travis

Yearly copyright update

Delete DISCLAIMER

This file talks about the old licence and a somewhat questionable one (it contains an indemnity clause) as well. Simply remove it so that it is clear Bio::DB::HTS is now licensed wholly under Apache-2.0.

Yearly copyright update

Build.PL: Improve pkgconfig integration

The old way of using pkgconfig in Build.PL has got a few shortcomings:
 - instead of retrieving both libdir and includedir, it only retrieves
   the former and transforms it into what it expects includedir to be
   (assuming in the process that libdir is .../lib and not e.g.
   .../lib64) - i.e. does the same as for all other ways of specifying
   location of htslib;
 - it directly accesses variables in htslib.pc instead of using --cflags
   and --libs, which is the recommended way;
 - it works by running the pkg-config executable so extending this would
   likely require processing the output of this command;
 - it still checks for the presence of hts.h and libhts.a/so, even
   though pkgconfig is supposed to return valid locations.

This commit adds an alternative implementation of pkgconfig-based
detection of htslib which retrieves both includedir and libdir, uses
--cflags and --libs instead of accessing variables directly, and which
avoids custom implementation of the handling of pkg-config output by
using an existing Perl module designed for that purpose. It also extends
set_include_and_compiler_flags() to handle the scenario of $hts_include
and $hts_lib being empty, which is the case when --cflags/--libs are
used and htslib has been installed to a standard prefix such as /usr.

In order to retain backward compatibility, for the time being the new
implementation is only invoked after all earlier attempts of locating
htslib - including the old way of invoking pkg-config - have failed.
Will leave it to the maintainers to decide whether to move this
implementation up in the queue and/or retire any old detection modes.

Note that this adds an optional build-time dependency on
ExtUtils::PkgConfig.

Build.PL: allow explicit definition of hts_include and hts_lib

Release 3.01.

copyright update

Documentation fixes

These are described in HTSlib as of samtools/htslib@445b0d721eb391e8825b5f07b9ebf8f72ef93367.