[med-svn] [Git][med-team/libbiod][master] Remove unused old patches, fix linking of zlib
Andreas Tille
gitlab at salsa.debian.org
Tue Mar 19 13:46:50 GMT 2019
Andreas Tille pushed to branch master at Debian Med / libbiod
Commits:
2ed0b22f by Andreas Tille at 2019-03-19T13:46:29Z
Remove unused old patches, fix linking of zlib
- - - - -
7 changed files:
- Makefile
- − debian/patches/001_fix_unit_tests.patch
- − debian/patches/002_include_bio2.patch
- − debian/patches/003_modernize_meson.patch
- debian/patches/fix_clean_target.patch
- + debian/patches/fix_linking_zlib.patch
- debian/patches/series
Changes:
=====================================
Makefile
=====================================
@@ -42,5 +42,5 @@ check: $(BIN)
clean:
rm -vf $(OBJ)
- rm -vf $(BIN)
+ rm -v $(BIN)
# find -name '*.o' -exec rm \{\} \;
=====================================
debian/patches/001_fix_unit_tests.patch deleted
=====================================
@@ -1,21 +0,0 @@
-Origin: https://github.com/biod/BioD/pull/38/commits/643b454f04f36d66c34304b7186a3d2c24fdf783
-From: Matthias Klumpp <matthias at tenstral.net>
-Date: Thu, 4 Oct 2018 14:33:37 +0200
-Subject: [PATCH] trivial: Fix unittests
-
----
- test/unittests.d | 1 +
- 1 file changed, 1 insertion(+)
-
-diff --git a/test/unittests.d b/test/unittests.d
-index d52fb687..263662af 100644
---- a/test/unittests.d
-+++ b/test/unittests.d
-@@ -22,6 +22,7 @@
-
- */
-
-+import bio.bam.cigar;
- import bio.bam.reader;
- import bio.bam.writer;
- import bio.sam.reader;
=====================================
debian/patches/002_include_bio2.patch deleted
=====================================
@@ -1,66 +0,0 @@
-Origin: https://github.com/biod/BioD/pull/38/commits/ee9428fea0d240ad6a65892346ddc051e086af16
-From: Matthias Klumpp <matthias at tenstral.net>
-Date: Thu, 4 Oct 2018 14:35:02 +0200
-Subject: [PATCH] meson: Include bio2 in libbiod build
-
----
- meson.build | 21 +++++++++++++++++++--
- 1 file changed, 19 insertions(+), 2 deletions(-)
-
-diff --git a/meson.build b/meson.build
-index 76da2a00..88f3bcc7 100644
---- a/meson.build
-+++ b/meson.build
-@@ -89,19 +89,33 @@ biod_src = [
- 'bio/sam/utils/recordparser.d',
- 'bio/sam/reader.d',
- 'bio/sam/header.d'
-+
-+bio2_src = [
-+ 'bio2/bam/header.d',
-+ 'bio2/bam/reader.d',
-+ 'bio2/bam/writer.d',
-+ 'bio2/bgzf.d',
-+ 'bio2/bgzf_writer.d',
-+ 'bio2/constants.d',
-+ 'bio2/hashing.d',
-+ 'bio2/logger.d',
-+ 'bio2/pileup.d',
-+ 'bio2/reads.d',
-+ 'bio2/unpack.d'
- ]
-
- #
- # Includes
- #
--install_subdir('bio/', install_dir: 'include/d/')
-+install_subdir('bio/', install_dir: 'include/d/bio/')
-+install_subdir('bio2/', install_dir: 'include/d/bio/')
-
- #
- # Library and pkg-config
- #
- biod_lib = library('biod',
-- [biod_src],
- include_directories: [src_dir],
-+ [biod_src, bio2_src],
- dependencies: [undead_dep, zlib_dep],
- install: true,
- version: project_version,
-@@ -111,6 +125,7 @@ pkgc.generate(name: 'biod',
- libraries: biod_lib,
- subdirs: 'd/',
- version: project_version,
-+ subdirs: 'd/bio/',
- description: 'Bioinformatics library in D (utils for working with SAM, BAM, SFF formats).'
- )
-
-@@ -121,6 +136,8 @@ biod_test_exe = executable('biod_test',
- ['test/unittests.d',
- biod_src],
- include_directories: [src_dir],
-+ biod_src,
-+ bio2_src],
- dependencies: [undead_dep, zlib_dep],
- d_args: meson.get_compiler('d').unittest_args()
- )
=====================================
debian/patches/003_modernize_meson.patch deleted
=====================================
@@ -1,197 +0,0 @@
-From c059165f359327c5a67aadabe18d6016efb58780 Mon Sep 17 00:00:00 2001
-From: Matthias Klumpp <matthias at tenstral.net>
-Date: Thu, 4 Oct 2018 14:35:24 +0200
-Subject: [PATCH] meson: Modernize Meson build definition
-Origin: https://github.com/biod/BioD/pull/38/commits/c059165f359327c5a67aadabe18d6016efb58780
-
----
- meson.build | 131 +++++++++++++++++++++++++++-------------------------
- 1 file changed, 67 insertions(+), 64 deletions(-)
-
---- libbiod.orig/meson.build
-+++ libbiod/meson.build
-@@ -1,6 +1,9 @@
--project('BioD', 'd')
-+project('BioD', 'd',
-+ meson_version : '>=0.46',
-+ license : 'MIT',
-+ version : '0.2.2'
-+)
-
--project_version = '0.1.0'
- project_soversion = '0'
-
- src_dir = include_directories('.')
-@@ -16,79 +19,83 @@
- # Sources
- #
- biod_src = [
-- 'bio/bam/utils/value.d',
-- 'bio/bam/utils/samheadermerger.d',
-- 'bio/bam/utils/array.d',
-- 'bio/bam/utils/graph.d',
-- 'bio/bam/pileup.d',
-- 'bio/bam/readrange.d',
-- 'bio/bam/reader.d',
-- 'bio/bam/thirdparty/msgpack.d',
-+ 'bio/bam/abstractreader.d',
-+ 'bio/bam/bai/bin.d',
- 'bio/bam/baifile.d',
-+ 'bio/bam/bai/indexing.d',
-+ 'bio/bam/baseinfo.d',
-+ 'bio/bam/cigar.d',
-+ 'bio/bam/constants.d',
- 'bio/bam/iontorrent/flowcall.d',
- 'bio/bam/iontorrent/flowindex.d',
-- 'bio/bam/splitter.d',
-- 'bio/bam/abstractreader.d',
-- 'bio/bam/bai/indexing.d',
-- 'bio/bam/bai/bin.d',
-- 'bio/bam/multireader.d',
-- 'bio/bam/reference.d',
-- 'bio/bam/md/operation.d',
- 'bio/bam/md/core.d',
-+ 'bio/bam/md/operation.d',
- 'bio/bam/md/parse.d',
- 'bio/bam/md/reconstruct.d',
-- 'bio/bam/tagvalue.d',
-- 'bio/bam/validation/alignment.d',
-- 'bio/bam/validation/samheader.d',
-- 'bio/bam/region.d',
-+ 'bio/bam/multireader.d',
-+ 'bio/bam/pileup.d',
- 'bio/bam/randomaccessmanager.d',
-+ 'bio/bam/read.d',
-+ 'bio/bam/reader.d',
-+ 'bio/bam/readrange.d',
-+ 'bio/bam/reference.d',
- 'bio/bam/referenceinfo.d',
-- 'bio/bam/constants.d',
-+ 'bio/bam/region.d',
- 'bio/bam/snpcallers/maq.d',
- 'bio/bam/snpcallers/simple.d',
-- 'bio/bam/read.d',
-+ 'bio/bam/splitter.d',
-+ 'bio/bam/tagvalue.d',
-+ 'bio/bam/thirdparty/msgpack.d',
-+ 'bio/bam/utils/array.d',
-+ 'bio/bam/utils/graph.d',
-+ 'bio/bam/utils/samheadermerger.d',
-+ 'bio/bam/utils/value.d',
-+ 'bio/bam/validation/alignment.d',
-+ 'bio/bam/validation/samheader.d',
- 'bio/bam/writer.d',
-- 'bio/bam/baseinfo.d',
-- 'bio/maf/reader.d',
-- 'bio/maf/parser.d',
-- 'bio/maf/block.d',
-- 'bio/core/utils/memoize.d',
-- 'bio/core/utils/algo.d',
-- 'bio/core/utils/stream.d',
-- 'bio/core/utils/zlib.d',
-- 'bio/core/utils/tmpfile.d',
-- 'bio/core/utils/roundbuf.d',
-- 'bio/core/utils/format.d',
-- 'bio/core/utils/bylinefast.d',
-- 'bio/core/utils/range.d',
-- 'bio/core/utils/switchendianness.d',
-- 'bio/core/utils/outbuffer.d',
-- 'bio/core/genotype.d',
-- 'bio/core/fasta.d',
- 'bio/core/base.d',
-- 'bio/core/kmer.d',
-- 'bio/core/region.d',
-- 'bio/core/tinymap.d',
-- 'bio/core/sequence.d',
-- 'bio/core/bgzf/outputstream.d',
-+ 'bio/core/bgzf/block.d',
- 'bio/core/bgzf/chunk.d',
-- 'bio/core/bgzf/inputstream.d',
-+ 'bio/core/bgzf/compress.d',
- 'bio/core/bgzf/constants.d',
-- 'bio/core/bgzf/block.d',
-+ 'bio/core/bgzf/inputstream.d',
-+ 'bio/core/bgzf/outputstream.d',
- 'bio/core/bgzf/virtualoffset.d',
-- 'bio/core/bgzf/compress.d',
- 'bio/core/call.d',
-- 'bio/sff/utils/roundup.d',
-- 'bio/sff/index.d',
-- 'bio/sff/readrange.d',
-- 'bio/sff/reader.d',
-- 'bio/sff/constants.d',
-- 'bio/sff/read.d',
-- 'bio/sff/writer.d',
-+ 'bio/core/fasta.d',
-+ 'bio/core/fastq.d',
-+ 'bio/core/genotype.d',
-+ 'bio/core/kmer.d',
-+ 'bio/core/region.d',
-+ 'bio/core/sequence.d',
-+ 'bio/core/tinymap.d',
-+ 'bio/core/utils/algo.d',
-+ 'bio/core/utils/bylinefast.d',
-+ 'bio/core/utils/exception.d',
-+ 'bio/core/utils/format.d',
-+ 'bio/core/utils/memoize.d',
-+ 'bio/core/utils/outbuffer.d',
-+ 'bio/core/utils/range.d',
-+ 'bio/core/utils/roundbuf.d',
-+ 'bio/core/utils/stream.d',
-+ 'bio/core/utils/switchendianness.d',
-+ 'bio/core/utils/tmpfile.d',
-+ 'bio/core/utils/zlib.d',
-+ 'bio/maf/block.d',
-+ 'bio/maf/parser.d',
-+ 'bio/maf/reader.d',
-+ 'bio/sam/header.d',
-+ 'bio/sam/reader.d',
- 'bio/sam/utils/fastrecordparser.d',
- 'bio/sam/utils/recordparser.d',
-- 'bio/sam/reader.d',
-- 'bio/sam/header.d'
-+ 'bio/sff/constants.d',
-+ 'bio/sff/index.d',
-+ 'bio/sff/read.d',
-+ 'bio/sff/reader.d',
-+ 'bio/sff/readrange.d',
-+ 'bio/sff/utils/roundup.d',
-+ 'bio/sff/writer.d'
-+]
-
- bio2_src = [
- 'bio2/bam/header.d',
-@@ -114,18 +121,16 @@
- # Library and pkg-config
- #
- biod_lib = library('biod',
-- include_directories: [src_dir],
- [biod_src, bio2_src],
- dependencies: [undead_dep, zlib_dep],
- install: true,
-- version: project_version,
-+ version: meson.project_version(),
- soversion: project_soversion
- )
- pkgc.generate(name: 'biod',
- libraries: biod_lib,
-- subdirs: 'd/',
-- version: project_version,
- subdirs: 'd/bio/',
-+ version: meson.project_version(),
- description: 'Bioinformatics library in D (utils for working with SAM, BAM, SFF formats).'
- )
-
-@@ -134,11 +139,9 @@
- #
- biod_test_exe = executable('biod_test',
- ['test/unittests.d',
-- biod_src],
-- include_directories: [src_dir],
- biod_src,
- bio2_src],
- dependencies: [undead_dep, zlib_dep],
-- d_args: meson.get_compiler('d').unittest_args()
-+ d_unittest: true
- )
- test('biod_tests', biod_test_exe)
=====================================
debian/patches/fix_clean_target.patch
=====================================
@@ -1,3 +1,7 @@
+Author: Andreas Tille <tille at debian.org>
+Last-Update: Tue, 19 Mar 2019 09:18:43 +0100
+Description: Do not fail if file to be removed does not exist
+
--- a/Makefile
+++ b/Makefile
@@ -42,5 +42,5 @@ check: $(BIN)
=====================================
debian/patches/fix_linking_zlib.patch
=====================================
@@ -0,0 +1,15 @@
+Author: Andreas Tille <tille at debian.org>
+Last-Update: Tue, 19 Mar 2019 09:18:43 +0100
+Description: Link zlib dynamically
+
+--- a/Makefile
++++ b/Makefile
+@@ -1,7 +1,7 @@
+ # Simple Makefile
+
+ D_COMPILER=ldc2
+-DFLAGS = -wi -g -relocation-model=pic -unittest -main -Icontrib/undead
++DFLAGS = -wi -g -relocation-model=pic -unittest -main -Icontrib/undead -L-lz
+
+ ifndef GUIX
+ ifdef GUIX_ENVIRONMENT
=====================================
debian/patches/series
=====================================
@@ -1,4 +1,2 @@
-# 001_fix_unit_tests.patch
-# 002_include_bio2.patch
-# 003_modernize_meson.patch
fix_clean_target.patch
+fix_linking_zlib.patch
View it on GitLab: https://salsa.debian.org/med-team/libbiod/commit/2ed0b22f62e49616a6afa015c1f926ef5696b0ef
--
View it on GitLab: https://salsa.debian.org/med-team/libbiod/commit/2ed0b22f62e49616a6afa015c1f926ef5696b0ef
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