librg-blast-parser-perl (0.03-8) unstable; urgency=medium

  * Upstream download vanished
  * Standards-Version: 4.6.0 (routine-update)
  * Add missing build dependency on dh addon.
  * Versioned (Build-)Depends: librostlab-blast0-dev (>= 1.0.1-12)
  * Avoid clash between Perl headers' definition of YYEMPTY as a
    macro and Rost Lab headers' use of it as an enum name

[dgit import unpatched librg-blast-parser-perl 0.03-8]

13 files changed, 405 insertions, 0 deletions

diff --git a/debian/README.test b/debian/README.test
new file mode 100644
index 0000000..9f162fc
--- /dev/null
+++ b/debian/README.test
@@ -0,0 +1,17 @@
+Notes on how this package can be tested.
+────────────────────────────────────────
+
+This package uses `autopkgtest-pkg-perl` as a default testsuite.
+Read more at https://pkg-perl.alioth.debian.org/autopkgtest.html
+
+To test manually, run:
+
+  perl /usr/share/doc/librg-blast-parser-perl/01RG-Blast-Parser.t
+  
+Another test (02test.t) uses example files. 
+To run it, cd to some dir where you have write permissions and do
+    
+    cp -r /usr/share/doc/librg-blast-parser-perl/examples .
+    gunzip examples/*.gz
+    perl /usr/share/doc/librg-blast-parser-perl/02test.t
+  
diff --git a/debian/changelog b/debian/changelog
new file mode 100644
index 0000000..8fdf482
--- /dev/null
+++ b/debian/changelog
@@ -0,0 +1,97 @@
+librg-blast-parser-perl (0.03-8) unstable; urgency=medium
+
+  * Upstream download vanished
+  * Standards-Version: 4.6.0 (routine-update)
+  * Add missing build dependency on dh addon.
+  * Versioned (Build-)Depends: librostlab-blast0-dev (>= 1.0.1-12)
+  * Avoid clash between Perl headers' definition of YYEMPTY as a
+    macro and Rost Lab headers' use of it as an enum name
+
+ -- Andreas Tille <tille@debian.org>  Mon, 24 Jan 2022 16:20:30 +0100
+
+librg-blast-parser-perl (0.03-7) unstable; urgency=medium
+
+  [ Debian Janitor ]
+  * Use secure URI in Homepage field.
+  * Bump debhelper from old 11 to 12.
+  * Set debhelper-compat version in Build-Depends.
+
+  [ Andreas Tille ]
+  * Standards-Version: 4.5.1 (routine-update)
+  * debhelper-compat 13 (routine-update)
+  * Remove trailing whitespace in debian/copyright (routine-update)
+  * Add salsa-ci file (routine-update)
+  * Rules-Requires-Root: no (routine-update)
+  * watch file standard 4 (routine-update)
+
+ -- Andreas Tille <tille@debian.org>  Fri, 27 Nov 2020 18:53:13 +0100
+
+librg-blast-parser-perl (0.03-6) unstable; urgency=medium
+
+  * debhelper 11
+  * Point Vcs fields to salsa.debian.org
+  * Standards-Version: 4.2.1
+  * Drop useless get-orig-source target
+
+ -- Andreas Tille <tille@debian.org>  Fri, 26 Oct 2018 11:00:43 +0200
+
+librg-blast-parser-perl (0.03-5) unstable; urgency=medium
+
+  * Moved packaging from SVN to Git
+  * debhelper 10
+  * Standards-Version: 4.1.1
+
+ -- Andreas Tille <tille@debian.org>  Tue, 28 Nov 2017 08:18:22 +0100
+
+librg-blast-parser-perl (0.03-4) unstable; urgency=medium
+
+  * Team upload.
+  * Force -std=c++03, because of #829604, Closes: #811702
+
+ -- Gert Wollny <gw.fossdev@gmail.com>  Fri, 22 Jul 2016 17:21:09 +0000
+
+librg-blast-parser-perl (0.03-3) unstable; urgency=medium
+
+  * Team upload.
+  * add hardening
+  * cme fix dpkg-control
+  * add autopkgtest-pkg-perl to debian/control
+  * add `tests/pkg-perl/smoke-files` file, as described here:
+    http://pkg-perl.alioth.debian.org/autopkgtest.html#smoke
+    - to enable using files from `examples` folder while running tests
+  * add debian/README.test and package tests to debian/docs
+
+ -- Tatiana Malygina <merlettaia@gmail.com>  Wed, 22 Jun 2016 11:38:12 +0300
+
+librg-blast-parser-perl (0.03-2) unstable; urgency=medium
+
+  * debian/control
+    - cme fix dpkg-control
+    - Priority: optional
+    - debhelper 9
+    - Build-Depends: librostlab3-dev
+      Closes: #746071
+
+ -- Andreas Tille <tille@debian.org>  Sun, 27 Apr 2014 17:35:52 +0200
+
+librg-blast-parser-perl (0.03-1) unstable; urgency=low
+
+  * New upstream release.
+  * Added hardening flags.
+
+ -- Laszlo Kajan <lkajan@rostlab.org>  Mon, 24 Sep 2012 10:17:26 +0200
+
+librg-blast-parser-perl (0.02-2) unstable; urgency=low
+
+  * [Andreas Tille <tille@debian.org>]
+    debian/control: Restored control file from Laszlo with better
+    description which I accidentially ignored in the initial
+    upload
+
+ -- Laszlo Kajan <lkajan@rostlab.org>  Wed, 11 Apr 2012 09:19:39 +0200
+
+librg-blast-parser-perl (0.02-1) unstable; urgency=low
+
+  * Initial release in Debian (Closes: #666194)
+
+ -- Laszlo Kajan <lkajan@rostlab.org>  Thu, 29 Mar 2012 12:52:29 +0200
diff --git a/debian/control b/debian/control
new file mode 100644
index 0000000..4bec298
--- /dev/null
+++ b/debian/control
@@ -0,0 +1,30 @@
+Source: librg-blast-parser-perl
+Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
+Uploaders: Laszlo Kajan <lkajan@rostlab.org>,
+           Andreas Tille <tille@debian.org>
+Section: perl
+Testsuite: autopkgtest-pkg-perl
+Priority: optional
+Build-Depends: debhelper-compat (= 13),
+               libextutils-xspp-perl,
+               librostlab-blast0-dev (>= 1.0.1-12),
+               librostlab3-dev,
+               debhelper
+Standards-Version: 4.6.0
+Vcs-Browser: https://salsa.debian.org/med-team/librg-blast-parser-perl
+Vcs-Git: https://salsa.debian.org/med-team/librg-blast-parser-perl.git
+Homepage: https://rostlab.org/
+Rules-Requires-Root: no
+
+Package: librg-blast-parser-perl
+Architecture: any
+Depends: ${shlibs:Depends},
+         ${misc:Depends},
+         ${perl:Depends}
+Description: very fast NCBI BLAST parser - binding for Perl
+ This package contains Perl binding for a very fast C++ library that parses
+ the default output of NCBI BLAST programs.  BLAST results are returned in a
+ convenient hash structure.
+ .
+ Evaluated on a very small test set, this parser is considerably faster
+ than Zerg::Report from libzerg-perl.
diff --git a/debian/copyright b/debian/copyright
new file mode 100644
index 0000000..56a43b2
--- /dev/null
+++ b/debian/copyright
@@ -0,0 +1,215 @@
+Format: https://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+Upstream-Name: librg-blast-parser-perl
+Upstream-Contact: Laszlo Kajan <lkajan@rostlab.org>
+Source: http://rostlab.org/
+
+Files: *
+Copyright: 2012 Laszlo Kajan <lkajan@rostlab.org>, Technical University of Munich, Germany
+License: Artistic-2
+
+Files: debian/*
+Copyright: 2012 Laszlo Kajan <lkajan@rostlab.org>, Technical University of Munich, Germany
+License: Artistic-2
+
+License: Artistic-2
+ The Artistic License 2.0
+ .
+ Copyright (c) 2000-2006, The Perl Foundation.
+ .
+ Everyone is permitted to copy and distribute verbatim copies
+ of this license document, but changing it is not allowed.
+ .
+ Preamble
+ .
+ This license establishes the terms under which a given free software
+ Package may be copied, modified, distributed, and/or redistributed.
+ The intent is that the Copyright Holder maintains some artistic
+ control over the development of that Package while still keeping the
+ Package available as open source and free software.
+ .
+ You are always permitted to make arrangements wholly outside of this
+ license directly with the Copyright Holder of a given Package.  If the
+ terms of this license do not permit the full use that you propose to
+ make of the Package, you should contact the Copyright Holder and seek
+ a different licensing arrangement.
+ .
+ Definitions
+ .
+     "Copyright Holder" means the individual(s) or organization(s)
+     named in the copyright notice for the entire Package.
+ .
+     "Contributor" means any party that has contributed code or other
+     material to the Package, in accordance with the Copyright Holder's
+     procedures.
+ .
+     "You" and "your" means any person who would like to copy,
+     distribute, or modify the Package.
+ .
+     "Package" means the collection of files distributed by the
+     Copyright Holder, and derivatives of that collection and/or of
+     those files. A given Package may consist of either the Standard
+     Version, or a Modified Version.
+ .
+     "Distribute" means providing a copy of the Package or making it
+     accessible to anyone else, or in the case of a company or
+     organization, to others outside of your company or organization.
+ .
+     "Distributor Fee" means any fee that you charge for Distributing
+     this Package or providing support for this Package to another
+     party.  It does not mean licensing fees.
+ .
+     "Standard Version" refers to the Package if it has not been
+     modified, or has been modified only in ways explicitly requested
+     by the Copyright Holder.
+ .
+     "Modified Version" means the Package, if it has been changed, and
+     such changes were not explicitly requested by the Copyright
+     Holder.
+ .
+     "Original License" means this Artistic License as Distributed with
+     the Standard Version of the Package, in its current version or as
+     it may be modified by The Perl Foundation in the future.
+ .
+     "Source" form means the source code, documentation source, and
+     configuration files for the Package.
+ .
+     "Compiled" form means the compiled bytecode, object code, binary,
+     or any other form resulting from mechanical transformation or
+     translation of the Source form.
+ .
+ .
+ Permission for Use and Modification Without Distribution
+ .
+ (1)  You are permitted to use the Standard Version and create and use
+ Modified Versions for any purpose without restriction, provided that
+ you do not Distribute the Modified Version.
+ .
+ .
+ Permissions for Redistribution of the Standard Version
+ .
+ (2)  You may Distribute verbatim copies of the Source form of the
+ Standard Version of this Package in any medium without restriction,
+ either gratis or for a Distributor Fee, provided that you duplicate
+ all of the original copyright notices and associated disclaimers.  At
+ your discretion, such verbatim copies may or may not include a
+ Compiled form of the Package.
+ .
+ (3)  You may apply any bug fixes, portability changes, and other
+ modifications made available from the Copyright Holder.  The resulting
+ Package will still be considered the Standard Version, and as such
+ will be subject to the Original License.
+ .
+ .
+ Distribution of Modified Versions of the Package as Source
+ .
+ (4)  You may Distribute your Modified Version as Source (either gratis
+ or for a Distributor Fee, and with or without a Compiled form of the
+ Modified Version) provided that you clearly document how it differs
+ from the Standard Version, including, but not limited to, documenting
+ any non-standard features, executables, or modules, and provided that
+ you do at least ONE of the following:
+ .
+     (a)  make the Modified Version available to the Copyright Holder
+     of the Standard Version, under the Original License, so that the
+     Copyright Holder may include your modifications in the Standard
+     Version.
+ .
+     (b)  ensure that installation of your Modified Version does not
+     prevent the user installing or running the Standard Version. In
+     addition, the Modified Version must bear a name that is different
+     from the name of the Standard Version.
+ .
+     (c)  allow anyone who receives a copy of the Modified Version to
+     make the Source form of the Modified Version available to others
+     under
+ .
+         (i)  the Original License or
+ .
+         (ii)  a license that permits the licensee to freely copy,
+         modify and redistribute the Modified Version using the same
+         licensing terms that apply to the copy that the licensee
+         received, and requires that the Source form of the Modified
+         Version, and of any works derived from it, be made freely
+         available in that license fees are prohibited but Distributor
+         Fees are allowed.
+ .
+ .
+ Distribution of Compiled Forms of the Standard Version
+ or Modified Versions without the Source
+ .
+ (5)  You may Distribute Compiled forms of the Standard Version without
+ the Source, provided that you include complete instructions on how to
+ get the Source of the Standard Version.  Such instructions must be
+ valid at the time of your distribution.  If these instructions, at any
+ time while you are carrying out such distribution, become invalid, you
+ must provide new instructions on demand or cease further distribution.
+ If you provide valid instructions or cease distribution within thirty
+ days after you become aware that the instructions are invalid, then
+ you do not forfeit any of your rights under this license.
+ .
+ (6)  You may Distribute a Modified Version in Compiled form without
+ the Source, provided that you comply with Section 4 with respect to
+ the Source of the Modified Version.
+ .
+ .
+ Aggregating or Linking the Package
+ .
+ (7)  You may aggregate the Package (either the Standard Version or
+ Modified Version) with other packages and Distribute the resulting
+ aggregation provided that you do not charge a licensing fee for the
+ Package.  Distributor Fees are permitted, and licensing fees for other
+ components in the aggregation are permitted. The terms of this license
+ apply to the use and Distribution of the Standard or Modified Versions
+ as included in the aggregation.
+ .
+ (8) You are permitted to link Modified and Standard Versions with
+ other works, to embed the Package in a larger work of your own, or to
+ build stand-alone binary or bytecode versions of applications that
+ include the Package, and Distribute the result without restriction,
+ provided the result does not expose a direct interface to the Package.
+ .
+ .
+ Items That are Not Considered Part of a Modified Version
+ .
+ (9) Works (including, but not limited to, modules and scripts) that
+ merely extend or make use of the Package, do not, by themselves, cause
+ the Package to be a Modified Version.  In addition, such works are not
+ considered parts of the Package itself, and are not subject to the
+ terms of this license.
+ .
+ .
+ General Provisions
+ .
+ (10)  Any use, modification, and distribution of the Standard or
+ Modified Versions is governed by this Artistic License. By using,
+ modifying or distributing the Package, you accept this license. Do not
+ use, modify, or distribute the Package, if you do not accept this
+ license.
+ .
+ (11)  If your Modified Version has been derived from a Modified
+ Version made by someone other than you, you are nevertheless required
+ to ensure that your Modified Version complies with the requirements of
+ this license.
+ .
+ (12)  This license does not grant you the right to use any trademark,
+ service mark, tradename, or logo of the Copyright Holder.
+ .
+ (13)  This license includes the non-exclusive, worldwide,
+ free-of-charge patent license to make, have made, use, offer to sell,
+ sell, import and otherwise transfer the Package with respect to any
+ patent claims licensable by the Copyright Holder that are necessarily
+ infringed by the Package. If you institute patent litigation
+ (including a cross-claim or counterclaim) against any party alleging
+ that the Package constitutes direct or contributory patent
+ infringement, then this Artistic License to you shall terminate on the
+ date that such litigation is filed.
+ .
+ (14)  Disclaimer of Warranty:
+ THE PACKAGE IS PROVIDED BY THE COPYRIGHT HOLDER AND CONTRIBUTORS "AS
+ IS' AND WITHOUT ANY EXPRESS OR IMPLIED WARRANTIES. THE IMPLIED
+ WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE, OR
+ NON-INFRINGEMENT ARE DISCLAIMED TO THE EXTENT PERMITTED BY YOUR LOCAL
+ LAW. UNLESS REQUIRED BY LAW, NO COPYRIGHT HOLDER OR CONTRIBUTOR WILL
+ BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, OR CONSEQUENTIAL
+ DAMAGES ARISING IN ANY WAY OUT OF THE USE OF THE PACKAGE, EVEN IF
+ ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
diff --git a/debian/docs b/debian/docs
new file mode 100644
index 0000000..63cb579
--- /dev/null
+++ b/debian/docs
@@ -0,0 +1,3 @@
+README
+debian/README.test
+t/*
diff --git a/debian/examples b/debian/examples
new file mode 100644
index 0000000..e7f0698
--- /dev/null
+++ b/debian/examples
@@ -0,0 +1 @@
+examples/*.ali
diff --git a/debian/patches/no_clash_YYEMPTY.patch b/debian/patches/no_clash_YYEMPTY.patch
new file mode 100644
index 0000000..502fb61
--- /dev/null
+++ b/debian/patches/no_clash_YYEMPTY.patch
@@ -0,0 +1,18 @@
+Author: Andreas Tille <tille@debian.org>
+        Aaron M. Ucko <ucko@debian.org>
+Last-Update: Sat, 22 Jan 2022 07:13:18 +0100
+Origin: https://lists.debian.org/debian-med/2022/01/msg00080.html
+Description: Avoid clash between Perl headers' definition of
+ YYEMPTY as a macro and Rost Lab headers' use of it as an enum name
+
+--- a/Parser.xs
++++ b/Parser.xs
+@@ -11,6 +11,8 @@ extern "C" {
+ }
+ #endif
+ 
++/* Do not clash with /usr/lib/x86_64-linux-gnu/perl/5.32/CORE/parser.h */
++#undef YYEMPTY
+ /* include your class headers here */
+ #include <rostlab/blast-parser-driver.h>
+ 
diff --git a/debian/patches/series b/debian/patches/series
new file mode 100644
index 0000000..381dfb7
--- /dev/null
+++ b/debian/patches/series
@@ -0,0 +1 @@
+no_clash_YYEMPTY.patch
diff --git a/debian/rules b/debian/rules
new file mode 100755
index 0000000..53b4f05
--- /dev/null
+++ b/debian/rules
@@ -0,0 +1,12 @@
+#!/usr/bin/make -f
+
+# Uncomment this to turn on verbose mode.
+#export DH_VERBOSE=1
+
+export DEB_BUILD_MAINT_OPTIONS = hardening=+all
+
+%:
+	dh $@
+
+override_dh_auto_configure:
+	dh_auto_configure --  LD="$(shell perl -V::ld:) $(LDFLAGS)" OPTIMIZE="$(CPPFLAGS) $(CFLAGS) -std=c++03"
diff --git a/debian/salsa-ci.yml b/debian/salsa-ci.yml
new file mode 100644
index 0000000..33c3a64
--- /dev/null
+++ b/debian/salsa-ci.yml
@@ -0,0 +1,4 @@
+---
+include:
+  - https://salsa.debian.org/salsa-ci-team/pipeline/raw/master/salsa-ci.yml
+  - https://salsa.debian.org/salsa-ci-team/pipeline/raw/master/pipeline-jobs.yml
diff --git a/debian/source/format b/debian/source/format
new file mode 100644
index 0000000..163aaf8
--- /dev/null
+++ b/debian/source/format
@@ -0,0 +1 @@
+3.0 (quilt)
diff --git a/debian/tests/pkg-perl/smoke-files b/debian/tests/pkg-perl/smoke-files
new file mode 100644
index 0000000..c9d8569
--- /dev/null
+++ b/debian/tests/pkg-perl/smoke-files
@@ -0,0 +1,2 @@
+examples
+t
diff --git a/debian/watch b/debian/watch
new file mode 100644
index 0000000..d26f1ea
--- /dev/null
+++ b/debian/watch
@@ -0,0 +1,4 @@
+version=4
+opts=dversionmangle=s/.*/0.No-Site/ \
+https://people.debian.org/~eriberto/ FakeWatchNoUpstreamSiteForThisPackage-(\d\S+)\.gz
+