Make btllib an external dependency (#464)

* remove btllib header files

* RAlgorithmsShort.cpp: use ssytem btllib

* RResolver/Makefile.am: compiled with system btllib

* configure.ac: set up btllib compile

* azure: use conda to compile

* gtest-1.7.0/Makefile.am: disable specific warning

* azure: download and compile btllib on the fly

* azure: remove ninja

* azure: remove security

* azure: old install

* azure: use full btllib path

* azure: export dist check fig

* azure: compile btllib with specific version of gxx

* azure: set up env variable for btllib

* azure: export gxx variable

* azure: compile with non-deprecated gxx

* azure: macOS with default clang and gxx

* azure: update btllib path for macOS

* azure: install via brew

* azure: use container

* azure: remove pool for gcc-12

* azure: change job parameter

* azure: try unbuntu 22.04

* azure: install via apt

* azure: install ABySS with clang

* azure: add cmake to installation

* azure: export cmake flags

* azure: fix export syntax

* azure: correct export statement

* azure: install llvm

* azure: install libs

* azure: build libcxx

* azure: fix spacing

* azure: try clang on macOS

* azure: remove btllib from brew install

* Azure: remove clang suffix

* azure: try brew paths

* azure: use clang14

* azure: try calling clang with subversion

* azure: check install dir

* azure: use keg path

* azure: compile with different clang

* azure: try libc++ flag

* azure: test

* azure: dont use extra flags

* azure: test

* azure: test installation

* makefile.am: disable deprecated declaration

* Test updates

* Try installing btllib from source for clang12

* Bugfix

* azure: include all tests

* Change bionic to focal, VMs for mac

* Remove gcc-7 test

- As per documentation, the charcov header now in btllib is only supported by gcc-8+

* Troubleshooting

* Update flags, add clang-format, update path to llvm

* Add dependencies for compilers-12 and macos_default_clang

* Fix naming for compilers-12 and macos_default_clang dependencies

* compilers-12 - activate conda environment

* Add CXXFLAG for ubuntu-latest, print message for macos_default_clang

* Try btllib brew install for macos_default_clang, add libomp to macos_def_gcc

* tap brewsci/bio

* Organize and only retain needed/important tests

* For mac, move away from using brew for most tests

* Formatting fixes

* Move clang-format to gcc-10, add paths to mac_gcc install

* Troubleshooting mac gcc

* Fix for sparsehash

* See if btllib path is wrong

* Fix path to btllib install

* Add DISTCHECK flags

* Change VM image for mac

* Clean-up azure-pipelines.yml, remove circleCI tests, update README.md

---------

Co-authored-by: Johnathan Wong <jowong@jowong07.phage.bcgsc.ca>
Co-authored-by: Johnathan Wong <34543031+jowong4@users.noreply.github.com>
Co-authored-by: JW <34543031+jwcodee@users.noreply.github.com>

README.md

@@ -120,11 +120,12 @@ The following libraries are required:
 * [Boost](http://www.boost.org/)
 * [Open MPI](http://www.open-mpi.org)
 * [sparsehash](https://code.google.com/p/sparsehash/)
+* [btllib](https://github.com/bcgsc/btllib)
 
 Conda:
 
 	conda install -c conda-forge boost openmpi
-	conda install -c bioconda google-sparsehash
+	conda install -c bioconda google-sparsehash btllib
 
 It is also helpful to install the compilers Conda package that automatically passes the correct compiler flags to use the available Conda packages:
 
@@ -152,6 +153,7 @@ You may also pass the following flags to `configure` script:
 	--with-mpi=PATH
 	--with-sqlite=PATH
 	--with-sparsehash=PATH
+	--with-btllib=PATH
 
 Where PATH is the path to the directory containing the corresponding dependencies. This should only be necessary if `configure` doesn't find the dependencies by default. If you are using Conda, PATH would be the path to the Conda installation. SQLite and MPI are optional dependencies.
 

RResolver/Makefile.am

@@ -1,4 +1,5 @@
 bin_PROGRAMS = abyss-rresolver-short
+AM_CXXFLAGS += $(PTHREAD_CFLAGS) -Wno-deprecated-declarations
 
 abyss_rresolver_short_CXXFLAGS = \
 	$(AM_CXXFLAGS) $(OPENMP_CXXFLAGS) \
@@ -13,7 +14,8 @@ LDFLAGS += -pthread
 abyss_rresolver_short_LDADD = \
 	$(top_builddir)/DataLayer/libdatalayer.a \
 	$(top_builddir)/Common/libcommon.a \
-	libralgorithmsshort.a
+	libralgorithmsshort.a \
+	-lbtllib
 
 noinst_LIBRARIES = libralgorithmsshort.a
 
@@ -32,4 +34,3 @@ libralgorithmsshort_a_LIBADD = \
 	$(top_builddir)/DataLayer/libdatalayer.a \
 	$(top_builddir)/Common/libcommon.a
 
-EXTRA_DIST = btllib

RResolver/RAlgorithmsShort.cpp

@@ -3,7 +3,7 @@
 #include "RUtils.h"
 #include "SequenceTree.h"
 
-#include "btllib/include/btllib/seq_reader.hpp"
+#include <btllib/seq_reader.hpp>
 
 #if _OPENMP
 #include <omp.h>