.clang-format

+BasedOnStyle:  Google
+BreakBeforeBraces: Mozilla
+
+AllowShortLoopsOnASingleLine: false
+AccessModifierOffset: -4
+BreakConstructorInitializersBeforeComma: true
+ColumnLimit: 100
+IndentWidth: 4
+PointerAlignment: Left
+TabWidth: 4
+
+ReflowComments: false  # protect ASCII art in comments
+KeepEmptyLinesAtTheStartOfBlocks: true

.gitignore

@@ -76,3 +76,7 @@ CMakeLists.txt.user
 bin
 build
 lib
+
+# Meson WrapDB stuff
+subprojects/packagecache/
+subprojects/googletest*

CHANGELOG.md

@@ -3,9 +3,25 @@
 ## Active
 
 ### TODO
-- Interface groups
 - Initial sequence-related data structures
 
+## [0.3.0] - 2018-04-30
+
+### Changed
+- Minor ToolContract::Config API change.
+
+## [0.2.0] - 2017-12-03
+
+### Added
+- WorkQueue for parallel execution
+
+## [0.1.1] - 2017-09-26
+
+### Changed
+- UNUSED macro to no-op method
+
+## [0.1.0] - 2017-01-13
+
 ### Added
 - Encapsulate project version and git sha1
 - RSMovieName & RSReadName: Sequel and RSII movie names are composed of
@@ -13,6 +29,10 @@ different data, and thus need to be handled separately. MovieName & ReadName
 handle Sequel-style data as the default.
 - GoogleTest/GoogleMock in third-party/googletest
 - Access to input command line from PacBio::CLI::Results
+- QGramIndex & seed results
+- Added support for new tool contract data model: option choices & modified JSON
+format.
+- Added basic option groups to CLI::Interface.
 
 ## [0.0.1] - 2016-06-22
 

CMakeLists.txt

@@ -2,9 +2,9 @@
 # CMake build script for PacBio pbcopper library.
 ########################################################################
 cmake_policy(SET CMP0048 NEW)  # lets us set version in project()
-cmake_minimum_required(VERSION 3.0)
+cmake_minimum_required(VERSION 3.2)
 
-project(pbcopper VERSION 0.0.1 LANGUAGES CXX C)
+project(pbcopper VERSION 0.4.0 LANGUAGES CXX C)
 enable_testing()
 
 # project options
@@ -40,8 +40,12 @@ include(pbcopper-libtype)
 include(pbcopper-gitsha1)
 find_git_sha1(COPPER_GIT_SHA1)
 configure_file(
-    ${pbcopper_IncludeDir}/pbcopper/utility/Version.h.in
-    ${CMAKE_BINARY_DIR}/generated/pbcopper/utility/Version.h
+    ${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

LICENSE.txt

-Copyright (c) 2016, Pacific Biosciences of California, Inc.
+Copyright (c) 2016-2018, Pacific Biosciences of California, Inc.
 
 All rights reserved.
 

README.md

@@ -66,3 +66,7 @@ make docs
 ## License
 
  - [PacBio open source license](https://github.com/PacificBiosciences/pbcopper/blob/master/LICENSE.txt)
+
+DISCLAIMER
+----------
+THIS WEBSITE AND CONTENT AND ALL SITE-RELATED SERVICES, INCLUDING ANY DATA, ARE PROVIDED "AS IS," WITH ALL FAULTS, WITH NO REPRESENTATIONS OR WARRANTIES OF ANY KIND, EITHER EXPRESS OR IMPLIED, INCLUDING, BUT NOT LIMITED TO, ANY WARRANTIES OF MERCHANTABILITY, SATISFACTORY QUALITY, NON-INFRINGEMENT OR FITNESS FOR A PARTICULAR PURPOSE. YOU ASSUME TOTAL RESPONSIBILITY AND RISK FOR YOUR USE OF THIS SITE, ALL SITE-RELATED SERVICES, AND ANY THIRD PARTY WEBSITES OR APPLICATIONS. NO ORAL OR WRITTEN INFORMATION OR ADVICE SHALL CREATE A WARRANTY OF ANY KIND. ANY REFERENCES TO SPECIFIC PRODUCTS OR SERVICES ON THE WEBSITES DO NOT CONSTITUTE OR IMPLY A RECOMMENDATION OR ENDORSEMENT BY PACIFIC BIOSCIENCES.

bamboo_build.sh

+#!/usr/bin/env bash
+set -vex
+
+################
+# DEPENDENCIES #
+################
+
+## Load modules
+type module >& /dev/null || . /mnt/software/Modules/current/init/bash
+
+module purge
+
+module load meson
+module load ninja
+
+module load boost
+module load doxygen
+
+
+BOOST_ROOT="${BOOST_ROOT%/include}"
+# unset these variables to have meson discover all
+# boost-dependent variables from BOOST_ROOT alone
+unset BOOST_INCLUDEDIR
+unset BOOST_LIBRARYDIR
+
+export CC="ccache gcc"
+export CXX="ccache g++"
+export CCACHE_BASEDIR="${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
+
+  module unload ccache gtest
+  [[ ${i} != system-gcc ]] && module unload gcc
+done
+
+# create symlink so Bamboo can find the xunit output
+ln -s "${CURRENT_BUILD_DIR}" build
+
+if [[ -z ${PREFIX_ARG+x} ]]; 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 [[ ${BUILD_NUMBER} == 0 ]]; then
+  echo "Build number is 0, hence not creating artifact"
+  exit 0
+fi
+
+## Creating artifact
+# install into staging dir with --prefix /usr/local
+# in order to sidestep all the artifact policy
+rm -rf staging
+meson configure -Dprefix=/usr/local -Dtests=false "${CURRENT_BUILD_DIR}"
+DESTDIR="${PWD}/staging" ninja -C "${CURRENT_BUILD_DIR}" -v install
+
+( cd staging && tar zcf ../pbcopper-SNAPSHOT.tgz . )
+md5sum  pbcopper-SNAPSHOT.tgz | awk -e '{print $1}' >| pbcopper-SNAPSHOT.tgz.md5
+sha1sum pbcopper-SNAPSHOT.tgz | awk -e '{print $1}' >| pbcopper-SNAPSHOT.tgz.sha1
+
+UNSUPPORTED_URL=http://ossnexus.pacificbiosciences.com/repository/unsupported
+curl -vn --upload-file pbcopper-SNAPSHOT.tgz      $UNSUPPORTED_URL/gcc-6.4.0/pbcopper-SNAPSHOT.tgz
+curl -vn --upload-file pbcopper-SNAPSHOT.tgz.md5  $UNSUPPORTED_URL/gcc-6.4.0/pbcopper-SNAPSHOT.tgz.md5
+curl -vn --upload-file pbcopper-SNAPSHOT.tgz.sha1 $UNSUPPORTED_URL/gcc-6.4.0/pbcopper-SNAPSHOT.tgz.sha1

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

@@ -3,7 +3,8 @@
 echo "# DEPENDENCIES"
 echo "## Load modules"
 source /mnt/software/Modules/current/init/bash
-module load gcc/5.3.0 cmake ccache ninja boost doxygen
+module load gcc cmake ccache ninja boost doxygen
+export CC=gcc CXX=g++
 
 echo "# BUILD"
 echo "## Create build directory "

cmake/pbcopper-compilerflags.cmake

 
 include(CheckCXXCompilerFlag)
 
-# shared CXX flags for all source code & tests
-if (MSVC)
-    set(pbcopper_CXX_FLAGS "/Wall")
-else()
-    set(pbcopper_CXX_FLAGS "-std=c++11 -Wall")
-endif()
+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)

debian/changelog

+pbcopper (0.4.1+dfsg-1) unstable; urgency=medium
+
+  * Team upload.
+  * New upstream version
+  * d/watch: Upstream is now using release tags
+  * debhelper 11
+  * Point Vcs fields to salsa.debian.org
+  * Standards-Version: 4.2.0
+  * Respect DEB_BUILD_OPTIONS in dh_auto_test
+
+ -- Andreas Tille <tille@debian.org>  Fri, 17 Aug 2018 15:22:14 +0200
+
 pbcopper (0.0.1+20161202-2) unstable; urgency=medium
 
   * build with -fPIC

debian/compat

-10
+11

debian/control

 Source: pbcopper
-Priority: optional
 Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
 Uploaders: Afif Elghraoui <afif@debian.org>
-Build-Depends:
-	debhelper (>=10),
+Section: libs
+Priority: optional
+Build-Depends: debhelper (>= 11~),
                dh-exec,
                cmake,
-	libboost-dev,
-Standards-Version: 3.9.8
-Section: libs
+               libboost-dev
+Standards-Version: 4.2.0
+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
-Vcs-Git: https://anonscm.debian.org/git/debian-med/pbcopper.git
-Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/pbcopper.git
 
 Package: libpbcopper-dev
-Section: libdevel
 Architecture: any
-Depends:
-	${misc:Depends},
-	${shlibs:Depends},
+Section: libdevel
+Depends: ${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
  for use by applications of the Pacific Biosciences SMRT Analysis

debian/copyright

 Format: https://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
 Upstream-Name: pbcopper
 Source: https://github.com/PacificBiosciences/pbcopper
+Files-Excluded: tools/Darwin
+                tools/Linux
+                tools/win32
 
 Files: *
 Copyright: 2016, Pacific Biosciences of California, Inc.

debian/patches/git-version.patch

@@ -2,7 +2,7 @@ Description: Don't add git SHA hash to version
  We don't have the upstream git history for this to work.
  If we really want to be able to add it here, we should allow
  taking an environment variable as input. We can then get the git SHA
- from the version in debian/changelog and and pass it via debian/rules.
+ from the version in debian/changelog and pass it via debian/rules.
 Author: Afif Elghraoui <afif@debian.org>
 Forwarded: not-needed
 Last-Update: 2016-12-14

debian/rules

@@ -11,4 +11,6 @@ export DEB_CXXFLAGS_MAINT_APPEND=-fPIC
 
 # debhelper's cmake action is to run `make test`, which won't work
 override_dh_auto_test:
+ifeq (,$(filter nocheck,$(DEB_BUILD_OPTIONS)))
 	cd build && $(MAKE) check
+endif

debian/watch

 version=4
 
-# Upsteam does not tag releases.
-# Check the git annotations for the upstream changelog file to find the snapshot corresponding to a version number.
+opts="repacksuffix=+dfsg,dversionmangle=s/\+dfsg//g,repack,compression=xz" \
+  https://github.com/PacificBiosciences/pbcopper/releases .*/archive/@ANY_VERSION@@ARCHIVE_EXT@

docs/meson.build

+error('pbcopper doesn\'t support Doxygen yet')