New upstream version 1.3.0+dfsg

# 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

## 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

########################################################################

# 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()

```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

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