.gitignore

-# This file is used to ignore files which are generated
-# ----------------------------------------------------------------------------
-
-*~
-*.autosave
-*.a
-*.core
-*.moc
-*.o
-*.obj
-*.orig
-*.rej
-*.so
-*.so.*
-*_pch.h.cpp
-*_resource.rc
-*.qm
-.#*
-*.*#
-core
-!core/
-tags
 .DS_Store
-.directory
-*.debug
-Makefile*
-*.prl
-*.app
-moc_*.cpp
-ui_*.h
-qrc_*.cpp
-Thumbs.db
-*.res
-*.rc
-/.qmake.cache
-/.qmake.stash
-
-# qtcreator generated files
-*.pro.user*
-CMakeLists.txt.user
-
-# xemacs temporary files
-*.flc
-
-# Vim temporary files
-.*.swp
-
-# Visual Studio generated files
-*.ib_pdb_index
-*.idb
-*.ilk
-*.pdb
-*.sln
-*.suo
-*.vcproj
-*vcproj.*.*.user
-*.ncb
-*.sdf
-*.opensdf
-*.vcxproj
-*vcxproj.*
-
-# MinGW generated files
-*.Debug
-*.Release
-
-# Python byte code
-*.pyc
-
-# Binaries
-# --------
-*.dll
-*.exe
-
-# Generated directories
-bin
-build
-lib
+/build*
 
 # Meson WrapDB stuff
-subprojects/packagecache/
-subprojects/googletest*
+/subprojects/*
+!/subprojects/*.wrap

CHANGELOG.md

@@ -2,8 +2,43 @@
 
 ## Active
 
-### TODO
-- Initial sequence-related data structures
+## [1.3.0] - 2019-07-11
+
+### Added
+ - Alignment algorithms from unanimity (local alignment, semi-global, affine, etc)
+
+### Removed
+ - Unused CallbackTimer
+ - Unused PacBio::Stream utilities
+
+## [1.2.0] - 2019-05-03
+
+### Changed
+ - CLI_v2::Results::NumProcessors() changed to CLI_v2::Results::NumThreads() for clarity.
+
+### Added
+ - Convenience methods for CLI_v2 clients: default log level override, explicit access to built-ins, built-in 'num-threads' option.
+
+## [1.1.0] - 2019-04-29
+
+### Added
+ - Reports module
+
+## [1.0.0] - 2019-04-23
+
+### Changed
+ - C++14 is now a *hard* minimum.
+
+### Removed
+ - Headers emulating C++14 features for C++11.
+
+### Added
+ - New (opt-in) CLI version 2.
+
+## [0.5.0] - 2019-04-11
+
+### Changed
+ - Requires C++14 at minimum.
 
 ## [0.3.0] - 2018-04-30
 

CMakeLists.txt

-########################################################################
-# CMake build script for PacBio pbcopper library.
-########################################################################
-cmake_policy(SET CMP0048 NEW)  # lets us set version in project()
-cmake_minimum_required(VERSION 3.2)
-
-project(pbcopper VERSION 0.4.0 LANGUAGES CXX C)
-enable_testing()
-
-# project options
-option(pbcopper_build_shared    "Build pbcopper as a shared library."         OFF)
-option(pbcopper_use_ccache      "Build pbcopper using ccache, if available."  ON)
-option(pbcopper_build_tests     "Build pbcopper tests."                       ON)
-option(pbcopper_build_docs      "Build pbcopper docs."                        ON)
-option(pbcopper_build_examples  "Build pbcopper examples."                    ON)
-
-# project paths
-set(pbcopper_RootDir       ${CMAKE_CURRENT_LIST_DIR})
-set(pbcopper_DocsDir       ${pbcopper_RootDir}/docs)
-set(pbcopper_IncludeDir    ${pbcopper_RootDir}/include)
-set(pbcopper_SourceDir     ${pbcopper_RootDir}/src)
-set(pbcopper_TestsDir      ${pbcopper_RootDir}/tests)
-set(pbcopper_ThirdPartyDir ${pbcopper_RootDir}/third-party)
-
-if(NOT pbcopper_OutputDir)
-    set(pbcopper_OutputDir ${CMAKE_CURRENT_BINARY_DIR})
-endif()
-
-set(pbcopper_LibDir  ${pbcopper_OutputDir}/lib)
-file(MAKE_DIRECTORY  ${pbcopper_LibDir})
-
-# project configuration
-set(CMAKE_MODULE_PATH ${CMAKE_CURRENT_LIST_DIR}/cmake ${CMAKE_MODULE_PATH})
-include(pbcopper-compilerflags)
-include(pbcopper-ccache)
-include(pbcopper-dependencies)
-include(pbcopper-libtype)
-
-# config generation
-include(pbcopper-gitsha1)
-find_git_sha1(COPPER_GIT_SHA1)
-configure_file(
-    ${pbcopper_SourceDir}/utility/PbcopperGitHash.cpp.in
-    ${CMAKE_BINARY_DIR}/generated/utility/PbcopperGitHash.cpp
-)
-configure_file(
-    ${pbcopper_SourceDir}/utility/PbcopperVersion.cpp.in
-    ${CMAKE_BINARY_DIR}/generated/utility/PbcopperVersion.cpp
-)
-
-# main library
-add_subdirectory(src)
-
-# project extras - only build on demand
-#
-if (pbcopper_build_docs)
-    add_subdirectory(docs)      # build with 'make doc' or 'make docs'
-endif()
-
-if (pbcopper_build_examples)
-    add_subdirectory(examples)  # build with 'make examples'
-endif()
-
-if (pbcopper_build_tests)
-    add_subdirectory(tests)
-endif()

README.md

@@ -9,27 +9,14 @@ Download repo & compile library:
 
 ```sh
 git clone https://github.com/PacificBiosciences/pbcopper.git && cd pbcopper
-mkdir build && cd build
-cmake ..
-make
+meson build .
+ninja -C build
 ```
 
 To build & run tests:
 
 ```sh
-make check
-```
-
-To build examples:
-
-```sh
-make examples
-```
-
-To build Doxygen API documentation: (**not yet available**)
-
-```sh
-make docs
+ninja -C build test
 ```
 
 ## API Overview - main modules

bamboo_build.sh

@@ -23,72 +23,27 @@ BOOST_ROOT="${BOOST_ROOT%/include}"
 unset BOOST_INCLUDEDIR
 unset BOOST_LIBRARYDIR
 
-export CC="ccache gcc"
-export CXX="ccache g++"
-export CCACHE_BASEDIR="${PWD}"
-
-if [[ $USER == bamboo ]]; then
-  export CCACHE_DIR=/mnt/secondary/Share/tmp/bamboo.${bamboo_shortPlanKey}.ccachedir
-  export CCACHE_TEMPDIR=/scratch/bamboo.ccache_tempdir
-fi
-
-case "${bamboo_planRepository_branchName}" in
-  develop|master)
-    export PREFIX_ARG="/mnt/software/p/pbcopper/${bamboo_planRepository_branchName}"
-    export BUILD_NUMBER="${bamboo_globalBuildNumber:-0}"
-    ;;
-  *)
-    export BUILD_NUMBER="0"
-    ;;
-esac
-
 # in order to make shared libraries consumable
 # by conda and other package managers
-export LDFLAGS="-static-libstdc++ -static-libgcc"
-
-for i in "system-gcc" "gcc/8.1.0" "gcc"; do
-  # 1. load either current MOBS GCC or RHEL-default GCC
-  if [[ ${i} == system-gcc ]]; then
-    module load gtest/gcc48
-  else
-    module load ${i} gtest
-  fi
-  module load ccache
-
-  export CURRENT_BUILD_DIR="build_gcc=${i/\//_}"
-  export ENABLED_TESTS="true"
-
-  bash scripts/ci/build.sh
-  bash scripts/ci/test.sh
+export LDFLAGS=${LDFLAGS:-"-fuse-ld=gold -static-libstdc++ -static-libgcc"}
 
-  module unload ccache gtest
-  [[ ${i} != system-gcc ]] && module unload gcc
-done
+source scripts/ci/setup.sh
+source scripts/ci/build.sh
+source scripts/ci/test.sh
 
-# create symlink so Bamboo can find the xunit output
-ln -s "${CURRENT_BUILD_DIR}" build
-
-if [[ -z ${PREFIX_ARG+x} ]]; then
+if [[ ${BUILD_NUMBER} == 0 ]]; then
   echo "Not installing anything (branch: ${bamboo_planRepository_branchName}), exiting."
   exit 0
 fi
 
-# reload GCC to prevent default `g++` from mis-linking
-module load gcc
-
-bash scripts/ci/install.sh
-
-if [[ ${BUILD_NUMBER} == 0 ]]; then
-  echo "Build number is 0, hence not creating artifact"
-  exit 0
-fi
+source scripts/ci/install.sh
 
 ## Creating artifact
 # install into staging dir with --prefix /usr/local
 # in order to sidestep all the artifact policy
 rm -rf staging
-meson configure -Dprefix=/usr/local -Dtests=false "${CURRENT_BUILD_DIR}"
-DESTDIR="${PWD}/staging" ninja -C "${CURRENT_BUILD_DIR}" -v install
+meson configure -Dprefix=/usr/local "${CURRENT_BUILD_DIR:-build}"
+DESTDIR="${PWD}/staging" ninja -C "${CURRENT_BUILD_DIR:-build}" -v install
 
 ( cd staging && tar zcf ../pbcopper-SNAPSHOT.tgz . )
 md5sum  pbcopper-SNAPSHOT.tgz | awk -e '{print $1}' >| pbcopper-SNAPSHOT.tgz.md5

bamboo_coverage.sh

-#!/usr/bin/env bash
-set -vex
-
-## Load modules
-type module >& /dev/null || . /mnt/software/Modules/current/init/bash
-
-module purge
-
-module load gcc
-module load ccache
-
-module load meson
-module load ninja
-
-module load boost
-module load doxygen
-module load gcov
-module load gtest
-
-#####################
-# BUILD & RUN TESTS #
-#####################
-
-rm -rf build
-mkdir build 
-cd build
-
-meson \
-  --werror \
-  --backend ninja \
-  --buildtype debug \
-  --default-library shared \
-  --libdir lib \
-  --wrap-mode nofallback \
-  --prefix "${PREFIX_ARG:-/usr/local}" \
-  -Db_coverage=true \
-  ..
-
-ninja test
-
-############
-# COVERAGE #
-############
-
-find . -type f -iname '*.o' | xargs gcov -acbrfu {} \; >/dev/null && \
-mkdir coverage && pushd coverage && mv ../*.gcov . && \
-sed -i -e 's@Source:@Source:../@' *.gcov && \
-sed -i -e 's@Graph:@Graph:../@' *.gcov && \
-sed -i -e 's@Data:@Data:../@' *.gcov 

bamboo_test.sh

-#!/usr/bin/env bash
-
-echo "################"
-echo "# DEPENDENCIES #"
-echo "################"
-
-echo "## Load modules"
-source /mnt/software/Modules/current/init/bash
-
-module load gcc meson ccache ninja gtest
-if [[ $USER == "bamboo" ]]; then
-  export CCACHE_DIR=/mnt/secondary/Share/tmp/bamboo.mobs.ccachedir
-  export CCACHE_TEMPDIR=/scratch/bamboo.ccache_tempdir
-fi
-export CCACHE_COMPILERCHECK='%compiler% -dumpversion'
-export CCACHE_BASEDIR=$PWD
-
-
-echo "#########"
-echo "# TESTS #"
-echo "#########"
-
-echo "## Unit tests"
-ninja -C build test

build.sh

-#!/bin/bash
-
-echo "# DEPENDENCIES"
-echo "## Load modules"
-source /mnt/software/Modules/current/init/bash
-module load gcc cmake ccache ninja boost doxygen
-export CC=gcc CXX=g++
-
-echo "# BUILD"
-echo "## Create build directory "
-if [ ! -d build ] ; then mkdir build ; fi
-
-echo "## Build source"
-( cd build &&\
-  rm -rf * &&\
-  CMAKE_BUILD_TYPE=ReleaseWithAssert cmake -GNinja .. )
-
-( cd build && ninja )
-
-echo "# TEST"
-echo "# Run unit tests"
-( cd build &&  ninja check-xunit )

cmake/pbcopper-ccache.cmake

-
-if(pbcopper_use_ccache)
-    find_program(CCACHE_FOUND ccache)
-    if(CCACHE_FOUND)
-        set_property(GLOBAL PROPERTY RULE_LAUNCH_COMPILE ccache)
-        set_property(GLOBAL PROPERTY RULE_LAUNCH_LINK    ccache)
-    endif()
-endif()

cmake/pbcopper-compilerflags.cmake

-
-include(CheckCXXCompilerFlag)
-
-set(CMAKE_CXX_STANDARD 11)
-set(CMAKE_CXX_STANDARD_REQUIRED ON)
-set(CMAKE_CXX_EXTENSIONS OFF)
-
-# NOTE: quash clang warnings w/ Boost
-check_cxx_compiler_flag("-Wno-unused-local-typedefs" HAS_NO_UNUSED_LOCAL_TYPEDEFS)
-if(HAS_NO_UNUSED_LOCAL_TYPEDEFS)
-    set(pbcopper_CXX_FLAGS "${pbcopper_CXX_FLAGS} -Wno-unused-local-typedefs")
-endif()
-

cmake/pbcopper-dependencies.cmake

-
-if(NOT Boost_INCLUDE_DIRS)
-    find_package(Boost REQUIRED)
-endif()

cmake/pbcopper-gitsha1.cmake

-
-if(__find_git_sha1)
-    return()
-endif()
-set(__find_git_sha1 YES)
-
-function(find_git_sha1 _GIT_SHA1)
-    find_package(Git QUIET REQUIRED)
-    execute_process(COMMAND
-        "${GIT_EXECUTABLE}" "describe" "--always" "--dirty=*"
-        WORKING_DIRECTORY "${CMAKE_CURRENT_SOURCE_DIR}"
-        RESULT_VARIABLE res
-        OUTPUT_VARIABLE out
-        ERROR_QUIET
-        OUTPUT_STRIP_TRAILING_WHITESPACE)
-    if (NOT res EQUAL 0)
-        message(FATAL_ERROR "Could not determine git sha1 via `git describe --always --dirty=*`")
-    endif()
-    set(${_GIT_SHA1} "${out}" PARENT_SCOPE)
-endfunction()

cmake/pbcopper-libtype.cmake

-
-if(pbcopper_build_shared)
-    set(BUILD_SHARED_LIBS    ON)
-    set(PBCOPPER_LIB_MODE    SHARED)
-    set(PBCOPPER_LIB_SUFFIX  ${CMAKE_SHARED_LIBRARY_SUFFIX})
-else()
-    set(BUILD_SHARED_LIBS    OFF)
-    set(PBCOPPER_LIB_MODE    STATIC)
-    set(PBCOPPER_LIB_SUFFIX  ${CMAKE_STATIC_LIBRARY_SUFFIX})
-endif()
-

debian/changelog

+pbcopper (1.3.0+dfsg-1) unstable; urgency=medium
+
+  * Fix watch file
+  * New upstream version
+  * debhelper-compat 12
+  * Standards-Version: 4.4.1
+  * Remove patch git-version.patch that is missing from
+    debian/patches/series.
+  * Build-Depends: meson, libgtest-dev
+  * Meson does not build static lib - leave this out for the moment
+  * Split binary packages into dynamic lib and development package
+
+ -- Andreas Tille <tille@debian.org>  Tue, 17 Dec 2019 11:16:46 +0100
+
 pbcopper (0.4.1+dfsg-3) unstable; urgency=medium
 
   [ Afif Elghraoui ]

debian/compat

-11

debian/control

@@ -3,19 +3,36 @@ Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.
 Uploaders: Andreas Tille <tille@debian.org>
 Section: libs
 Priority: optional
-Build-Depends: debhelper (>= 11~),
-               dh-exec,
+Build-Depends: debhelper-compat (= 12),
+#               dh-exec,
+               meson,
                cmake,
-               libboost-dev
-Standards-Version: 4.3.0
+               pkg-config,
+               libboost-dev,
+               googletest,
+               libgtest-dev
+Standards-Version: 4.4.1
 Vcs-Browser: https://salsa.debian.org/med-team/pbcopper
 Vcs-Git: https://salsa.debian.org/med-team/pbcopper.git
 Homepage: https://github.com/PacificBiosciences/pbcopper
 
+Package: libpbcopper1.3.0
+Architecture: any
+Section: libs
+Depends: ${misc:Depends},
+         ${shlibs:Depends}
+Description: data structures, algorithms, and utilities for C++ applications
+ pbcopper provides general tools for C++ applications. It is developed
+ for use by applications of the Pacific Biosciences SMRT Analysis
+ suite.
+ .
+ This package contains the dynamic library
+
 Package: libpbcopper-dev
 Architecture: any
 Section: libdevel
-Depends: ${misc:Depends},
+Depends: libpbcopper1.3.0 (= ${binary:Version}),
+         ${misc:Depends},
          ${shlibs:Depends}
 Description: data structures, algorithms, and utilities for C++ applications -- header files
  pbcopper provides general tools for C++ applications. It is developed

debian/copyright

@@ -13,10 +13,6 @@ Files: include/pbcopper/json/internal/json.hpp
 Copyright: 2013-2016 Niels Lohmann <http://nlohmann.me>
 License: MIT
 
-Files: third-party/googletest/*
-Copyright: 2005-2015, Google Inc.
-License: BSD-3-Clause-Google
-
 Files: debian/*
 Copyright: 2016 Afif Elghraoui <afif@debian.org>
 License: BSD-3-Clause

debian/install

-#!/usr/bin/dh-exec
-include/pbcopper	/usr/include
-*/lib/libpbcopper.a	/usr/lib/${DEB_HOST_MULTIARCH}

debian/libpbcopper-dev.install

+usr/include
+usr/lib/*/pkgconfig
+usr/lib/*/*.so

debian/libpbcopper1.3.0.install

+usr/lib/*/*.so.1*