[med-svn] [Git][med-team/libbioparser-dev][master] 4 commits: Really drop libbiosoup headers by removing the patch
Andreas Tille (@tille)
gitlab at salsa.debian.org
Wed Dec 1 07:36:59 GMT 2021
Andreas Tille pushed to branch master at Debian Med / libbioparser-dev
Commits:
58b172b3 by Andreas Tille at 2021-12-01T08:12:52+01:00
Really drop libbiosoup headers by removing the patch
- - - - -
1a3abaae by Andreas Tille at 2021-12-01T08:22:40+01:00
Do not try to install biosoup
- - - - -
d791aa0d by Andreas Tille at 2021-12-01T08:35:33+01:00
Install cmake files to /usr/share/cmake to reflect the Architecture: all nature of the package
- - - - -
b36af389 by Andreas Tille at 2021-12-01T08:36:23+01:00
Upload to unstable
- - - - -
5 changed files:
- debian/changelog
- debian/install
- − debian/patches/biosoup
- − debian/patches/series
- debian/rules
Changes:
=====================================
debian/changelog
=====================================
@@ -1,3 +1,12 @@
+libbioparser-dev (3.0.15-2) unstable; urgency=medium
+
+ * Really drop libbiosoup headers by removing the patch
+ Closes: #1000856
+ * Install cmake files to /usr/share/cmake to reflect the Architecture: all
+ nature of the package
+
+ -- Andreas Tille <tille at debian.org> Wed, 01 Dec 2021 08:35:40 +0100
+
libbioparser-dev (3.0.15-1) unstable; urgency=medium
[ Michael R. Crusoe ]
=====================================
debian/install
=====================================
@@ -1,2 +1 @@
include usr
-vendor/biosoup/include usr
=====================================
debian/patches/biosoup deleted
=====================================
@@ -1,213 +0,0 @@
-Description: snapshot of https://github.com/rvaser/biosoup/tree/4be6880b62a8e9fc2322ede3f69f82384f99499e
-Forwarded: not-needed
---- /dev/null
-+++ libbioparser-dev/vendor/biosoup/CMakeLists.txt
-@@ -0,0 +1,33 @@
-+cmake_minimum_required(VERSION 3.9)
-+
-+project(biosoup VERSION 0.8.1
-+ LANGUAGES CXX
-+ DESCRIPTION "Biosoup is a c++ collection of header only data structures used for storage and logging in bioinformatics tools.")
-+
-+set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -Wall -Wextra -pedantic")
-+set(CMAKE_CXX_STANDARD 11)
-+set(CMAKE_CXX_STANDARD_REQUIRED ON)
-+set(CMAKE_CXX_EXTENSIONS OFF)
-+
-+set(CMAKE_ARCHIVE_OUTPUT_DIRECTORY ${PROJECT_BINARY_DIR}/lib)
-+set(CMAKE_LIBRARY_OUTPUT_DIRECTORY ${PROJECT_BINARY_DIR}/lib)
-+set(CMAKE_RUNTIME_OUTPUT_DIRECTORY ${PROJECT_BINARY_DIR}/bin)
-+
-+add_library(${PROJECT_NAME} INTERFACE)
-+
-+target_include_directories(${PROJECT_NAME} INTERFACE
-+ $<BUILD_INTERFACE:${CMAKE_CURRENT_SOURCE_DIR}/include>)
-+
-+option(biosoup_build_tests "Build biosoup unit tests" OFF)
-+if (biosoup_build_tests)
-+ find_package(GTest REQUIRED)
-+ add_executable(${PROJECT_NAME}_test
-+ test/nucleic_acid_test.cpp
-+ test/overlap_test.cpp
-+ test/progress_bar_test.cpp
-+ test/sequence_test.cpp
-+ test/timer_test.cpp)
-+ target_link_libraries(${PROJECT_NAME}_test
-+ ${PROJECT_NAME}
-+ GTest::Main)
-+endif ()
---- /dev/null
-+++ libbioparser-dev/vendor/biosoup/include/biosoup/sequence.hpp
-@@ -0,0 +1,89 @@
-+// Copyright (c) 2020 Robert Vaser
-+
-+#ifndef BIOSOUP_SEQUENCE_HPP_
-+#define BIOSOUP_SEQUENCE_HPP_
-+
-+#include <algorithm>
-+#include <atomic>
-+#include <cctype>
-+#include <cstdint>
-+#include <string>
-+
-+namespace biosoup {
-+
-+struct Sequence {
-+ public:
-+ Sequence() = default;
-+
-+ Sequence(const std::string& name, const std::string& data)
-+ : Sequence(name.c_str(), name.size(), data.c_str(), data.size()) {}
-+
-+ Sequence(
-+ const char* name, std::uint32_t name_len,
-+ const char* data, std::uint32_t data_len)
-+ : id(num_objects++),
-+ name(name, name_len),
-+ data(data, data_len),
-+ quality() {}
-+
-+ Sequence(
-+ const std::string& name,
-+ const std::string& data,
-+ const std::string& quality)
-+ : Sequence(
-+ name.c_str(), name.size(),
-+ data.c_str(), data.size(),
-+ quality.c_str(), quality.size()) {}
-+
-+ Sequence(
-+ const char* name, std::uint32_t name_len,
-+ const char* data, std::uint32_t data_len,
-+ const char* quality, std::uint32_t quality_len)
-+ : id(num_objects++),
-+ name(name, name_len),
-+ data(data, data_len),
-+ quality(quality, quality_len) {}
-+
-+ Sequence(const Sequence&) = default;
-+ Sequence& operator=(const Sequence&) = default;
-+
-+ Sequence(Sequence&&) = default;
-+ Sequence& operator=(Sequence&&) = default;
-+
-+ ~Sequence() = default;
-+
-+ void ReverseAndComplement() { // (optional) Watson-Crick base pairing
-+ for (auto& it : data) {
-+ switch (static_cast<char>(std::toupper(static_cast<unsigned char>(it)))) {
-+ case 'A': it = 'T'; break;
-+ case 'C': it = 'G'; break;
-+ case 'G': it = 'C'; break;
-+ case 'T': case 'U': it = 'A'; break;
-+ case 'R': it = 'Y'; break; // A || G
-+ case 'Y': it = 'R'; break; // C || T (U)
-+ case 'K': it = 'M'; break; // G || T (U)
-+ case 'M': it = 'K'; break; // A || C
-+ case 'S': break; // C || G
-+ case 'W': break; // A || T (U)
-+ case 'B': it = 'V'; break; // !A
-+ case 'D': it = 'H'; break; // !C
-+ case 'H': it = 'D'; break; // !G
-+ case 'V': it = 'B'; break; // !T (!U)
-+ default: break; // N || -
-+ }
-+ }
-+ std::reverse(data.begin(), data.end());
-+ std::reverse(quality.begin(), quality.end());
-+ }
-+
-+ static std::atomic<std::uint32_t> num_objects;
-+
-+ std::uint32_t id; // (optional) initialize num_objects to 0
-+ std::string name;
-+ std::string data;
-+ std::string quality; // (optional) Phred quality scores
-+};
-+
-+} // namespace biosoup
-+
-+#endif // BIOSOUP_SEQUENCE_HPP_
---- /dev/null
-+++ libbioparser-dev/vendor/biosoup/include/biosoup/overlap.hpp
-@@ -0,0 +1,80 @@
-+// Copyright (c) 2020 Robert Vaser
-+
-+#ifndef BIOSOUP_OVERLAP_HPP_
-+#define BIOSOUP_OVERLAP_HPP_
-+
-+#include <cstdint>
-+#include <string>
-+
-+namespace biosoup {
-+
-+struct Overlap {
-+ public:
-+ Overlap() = default;
-+
-+ Overlap(
-+ std::uint64_t lhs_id, std::uint32_t lhs_begin, std::uint32_t lhs_end,
-+ std::uint64_t rhs_id, std::uint32_t rhs_begin, std::uint32_t rhs_end,
-+ std::uint32_t score,
-+ bool strand = true)
-+ : lhs_id(lhs_id),
-+ lhs_begin(lhs_begin),
-+ lhs_end(lhs_end),
-+ rhs_id(rhs_id),
-+ rhs_begin(rhs_begin),
-+ rhs_end(rhs_end),
-+ score(score),
-+ strand(strand),
-+ alignment() {}
-+
-+ Overlap(
-+ std::uint64_t lhs_id, std::uint32_t lhs_begin, std::uint32_t lhs_end,
-+ std::uint64_t rhs_id, std::uint32_t rhs_begin, std::uint32_t rhs_end,
-+ std::uint32_t score,
-+ const std::string& alignment,
-+ bool strand = true)
-+ : Overlap(
-+ lhs_id, lhs_begin, lhs_end,
-+ rhs_id, rhs_begin, rhs_end,
-+ score,
-+ alignment.c_str(), alignment.size(),
-+ strand) {}
-+
-+ Overlap(
-+ std::uint64_t lhs_id, std::uint32_t lhs_begin, std::uint32_t lhs_end,
-+ std::uint64_t rhs_id, std::uint32_t rhs_begin, std::uint32_t rhs_end,
-+ std::uint32_t score,
-+ const char* alignment, std::uint32_t alignment_len,
-+ bool strand = true)
-+ : lhs_id(lhs_id),
-+ lhs_begin(lhs_begin),
-+ lhs_end(lhs_end),
-+ rhs_id(rhs_id),
-+ rhs_begin(rhs_begin),
-+ rhs_end(rhs_end),
-+ score(score),
-+ strand(strand),
-+ alignment(alignment, alignment_len) {}
-+
-+ Overlap(const Overlap&) = default;
-+ Overlap& operator=(const Overlap&) = default;
-+
-+ Overlap(Overlap&&) = default;
-+ Overlap& operator=(Overlap&&) = default;
-+
-+ ~Overlap() = default;
-+
-+ std::uint32_t lhs_id;
-+ std::uint32_t lhs_begin;
-+ std::uint32_t lhs_end;
-+ std::uint32_t rhs_id;
-+ std::uint32_t rhs_begin;
-+ std::uint32_t rhs_end;
-+ std::uint32_t score; // based on k-mer matches or alignment score
-+ bool strand; // (optional) Watson-Crick strand
-+ std::string alignment; // (optional) cigar string
-+};
-+
-+} // namespace biosoup
-+
-+#endif // BIOSOUP_OVERLAP_HPP_
=====================================
debian/patches/series deleted
=====================================
@@ -1 +0,0 @@
-biosoup
=====================================
debian/rules
=====================================
@@ -14,3 +14,8 @@ override_dh_auto_test:
ifeq (,$(filter nocheck,$(DEB_BUILD_OPTIONS)))
set -e -x; for f in obj-*/bin/*_test; do [ ! -x $$f ] || $$f; done
endif
+
+override_dh_install:
+ dh_install
+ mv debian/`dh_listpackages`/usr/lib/*/cmake debian/`dh_listpackages`/usr/share
+ rm -rf debian/`dh_listpackages`/usr/lib
View it on GitLab: https://salsa.debian.org/med-team/libbioparser-dev/-/compare/e2222d604033ec469ab8ace1995bf1f12bfcf7fb...b36af389919113ce7da1248b6801e2a9ba783406
--
View it on GitLab: https://salsa.debian.org/med-team/libbioparser-dev/-/compare/e2222d604033ec469ab8ace1995bf1f12bfcf7fb...b36af389919113ce7da1248b6801e2a9ba783406
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