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Jamroot.jam
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Jamroot.jam
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#
# $Id$
#
#
# Original author: Darren Kessner <darren@proteowizard.org>
#
# Copyright 2008 Spielberg Family Center for Applied Proteomics
# Cedars-Sinai Medical Center, Los Angeles, California 90048
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, software
# distributed under the License is distributed on an "AS IS" BASIS,
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
# See the License for the specific language governing permissions and
# limitations under the License.
if ( "--help" in [ modules.peek : ARGV ] )
{ # slip our own help text in here
ECHO
################################
## Targets and Related Options #
################################
# build Build ProteoWizard applications
# =====
# --libraries-path=<DIR> Find libraries directory here.
# Default: "./libraries"
#
# --boost-src=<DIR> Find Boost source distribution here.
# Default: "<libraries-path>/boost_*"
#
# --zlib-src=<DIR> Find zlib source distribution here.
# Default: "<libraries-path>/zlib-1.23.0"
#
# --i-agree-to-the-vendor-licenses For windows builds, indicates
# your willingness to comply with
# license terms of the vendor DLLs
# that enable reading of proprietary
# binary data formats. Without this
# switch your build will not include
# support for reading vendor binary
# files.
#
# --incremental Skip the checks for extracting external library
# tarballs - useful after your initial build
#
# --without-mz5 Build without mz5 support
# --without-agilent Build without Agilent support
# --without-bruker Build without Bruker support
# --without-sciex Build without Sciex support
# --without-shimadzu Build without Shimadzu support
# --without-thermo Build without Thermo support
# --without-waters Build without Waters support
#
# --without-binary-msdata Build with support for mass spec text formats only
# (mzML, mzXML, MGF, etc - no binary formats
# like mz5 or vendor-specifics )
#
# There are some aliases to build commonly used subsets of pwiz:
#
# msconvert (just the command-line executable, copied to <BUILD_DIR>/<TOOLSET_DIR>)
# executables (all the pwiz core tools, copied to <BUILD_DIR>/<TOOLSET_DIR>)
#
# If you just want to build a specific subset of pwiz, add a target to
# your command line. For example to build just the msdata file
# read/write stuff, add:
#
# pwiz/data/msdata
#
# Or to build a particular item of that subset, such as a test,
# you could add (note the double slashes!) :
#
# pwiz/data/msdata//MSDataFileTest
#
; # end of our own help text
}
.os = [ modules.peek : OS ] ; # NT, LINUX, MACOSX
.platform = [ modules.peek : OSPLAT ] ; # X86, X86_64, POWERPC
# set up explicit 32-bit or 64-bit builds
if "address-model=64" in [ modules.peek : ARGV ] || ( ! ( $(.os) = "NT" ) && $(.platform:L) = "x86_64" )
{
constant PROCESSOR_ARCHITECTURE : "AMD64" ;
constant PLATFORM : "x64" ;
}
else if "address-model=32" in [ modules.peek : ARGV ] || $(.platform:L) = "x86" || $(.os) = "NT"
{
constant PROCESSOR_ARCHITECTURE : "x86" ;
constant PLATFORM : "x86" ;
}
else
{
echo "Unable to determine address-model for platform $(.platform:L). The only supported platforms are x86 and x86_64." ;
exit ;
}
local default_libraries_path = "./libraries" ;
local libraries_path = [ MATCH --libraries-path=(.*) : [ modules.peek : ARGV ] ] ;
libraries_path ?= $(default_libraries_path) ; # set default path in absence of command-line path
local default_boost_src = "$(libraries_path)/boost_1_67_0" ;
local boost_src = [ MATCH --boost-src=(.*) : [ modules.peek : ARGV ] ] ;
boost_src ?= $(default_boost_src) ; # set default path in absence of command-line path
local default_zlib_src = "$(libraries_path)/zlib-1.2.3" ;
local zlib_src = [ MATCH --zlib-src=(.*) : [ modules.peek : ARGV ] ] ;
zlib_src ?= $(default_zlib_src) ; # set default path in absence of command-line path
# TODO: get version from boost/version.hpp
import regex ;
local boost_version_suffix = [ MATCH "boost_(._..(_.)?)" : $(boost_src:L) ] ;
if ! $(boost_version_suffix) { errors.user-error "Unable to determine version from external Boost source; expected x_xx[_xx] format." ; }
constant BOOST_VERSION : [ regex.split $(boost_version_suffix[1]) _ ] ;
import path ;
import feature ;
# declare a feature indicating vendor API support is desired (but not necessarily possible on the current platform)
if [ modules.peek : NT ] && --i-agree-to-the-vendor-licenses in [ modules.peek : ARGV ]
{
feature.feature vendor-api-support : on off : incidental propagated ; # on is the default
}
else
{
feature.feature vendor-api-support : off on : incidental propagated ; # off is the default
}
rule vendor-api-support ( properties * )
{
if [ modules.peek : NT ] && --i-agree-to-the-vendor-licenses in [ modules.peek : ARGV ]
{
return <vendor-api-support>on ;
}
else
{
return <vendor-api-support>off ;
}
}
if ( "--without-binary-msdata" in [ modules.peek : ARGV ] ) # support only text formats like mzML, mzXML, MGF etc
{
echo "NOTICE: building without support for binary msdata formats as requested" ;
}
else if ( "--without-mz5" in [ modules.peek : ARGV ] )
{
echo "NOTICE: building without mz5 support as requested" ;
}
# do we want to skip mz5 support?
rule without-mz5 ( properties * )
{
if --without-mz5 in [ modules.peek : ARGV ]
{
return <location-prefix>without-mz5 <define>WITHOUT_MZ5 ;
}
else
{
return [ without-binary-msdata $(properties) ] ;
}
}
# do we want to skip all binary file formats (vendors and mz5)?
rule without-binary-msdata ( properties * )
{
if --without-binary-msdata in [ modules.peek : ARGV ]
{
return <location-prefix>without-binary-msdata <define>WITHOUT_MZ5 <vendor-api-support>off ;
}
}
path-constant PWIZ_ROOT_PATH : . ;
path-constant PWIZ_BUILD_PATH : build-$(.os:L)-$(.platform:L) ;
path-constant PWIZ_LIBRARIES_PATH : $(libraries_path) ;
import testing ; # needed to enable unit-test rule
import package ; # needed for package install
import path ; # needed for glob, exists, etc.
import project ; # needed for project.current
import errors ;
modules.poke : BOOST_BUILD_PATH : [ modules.peek : BOOST_BUILD_PATH ] $(PWIZ_LIBRARIES_PATH)/predef/check ;
import $(PWIZ_LIBRARIES_PATH)/predef/check/predef : require check : predef-require predef-check ;
if --teamcity-test-decoration in [ modules.peek : ARGV ]
{
if [ modules.peek : NT ]
{
TEST_PRECOMMAND = "set pp=##\necho %pp%teamcity[testStarted name='%name%']" ;
TEST_POSTCOMMAND =
"set pp=##\n"
"IF %status% NEQ 0"
"(echo %pp%teamcity[testFailed name='%name%' message='Exit status: %status%'] )\n" # TODO: does testFailed go to stderr? 1>&2
"echo %pp%teamcity[testFinished name='%name%']" ;
TEST_POSTCOMMAND = $(TEST_POSTCOMMAND:J=" ") ;
}
else
{
TEST_PRECOMMAND = "pp=##\necho $pp\"teamcity[testStarted name='$name']\"" ;
TEST_POSTCOMMAND =
"pp=##"
"if test $status -ne 0 ; then"
"echo $pp\"teamcity[testFailed name='$name' message='Exit status: $status']\" ;"
"fi"
"echo $pp\"teamcity[testFinished name='$name']\"" ;
TEST_POSTCOMMAND = $(TEST_POSTCOMMAND:J=\n) ;
}
# put raw commands in global module
modules.poke : TEST_PRECOMMAND : $(TEST_PRECOMMAND) ;
modules.poke : TEST_POSTCOMMAND : $(TEST_POSTCOMMAND) ;
TEAMCITY_TEST_DECORATION = <testing.arg>--teamcity-test-decoration ;
}
# return the itemname if textonly build is off (the default)
rule binary-readers-build ( itemname )
{
if ( ! [ without-binary-msdata ] )
{
return $(itemname) ; # do build binary readers
}
}
# return the itemname if mz5 build is on (the default)
rule mz5-build ( itemname )
{
if ( ! [ without-mz5 ] )
{
return $(itemname) ; # do build mz5
}
}
if ! [ modules.peek : NT ]
{
# make msbuild targets a no-op
rule msbuild ( name : sources * : requirements * : default-build * : usage-requirements * )
{
}
PREDEF_CHECKS =
# starting with gcc 4.8, gcc is extremely verbose about unused typedefs; heavily used in Boost concept checks
[ predef-check "BOOST_COMP_GNUC >= 4.8" : : <cxxflags>-Wno-unused-local-typedefs ]
# starting with gcc 4.9, gcc offers colored diagnostic messages, helpful when looking for an elusive "error" message in a sea of warning spam
[ predef-check "BOOST_COMP_GNUC >= 4.9" : : <cxxflags>-fdiagnostics-color=always ]
;
}
project pwiz
: requirements
<include>$(PWIZ_ROOT_PATH)
<include>$(PWIZ_LIBRARIES_PATH)/boost_aux
<include>$(boost_src)
<include>$(zlib_src)
<toolset>gcc,<link>shared:<runtime-link>shared
<toolset>darwin:<runtime-link>shared
# any module which links with .NET (either dynamically or statically) must use the shared runtime
<toolset>msvc:<runtime-link>shared
# SEH exceptions crossing native/managed boundaries are problematic with this set to off;
# also, catch(...) will catch SEH exceptions with this on
<toolset>msvc:<asynch-exceptions>on
# avoid deprecation warnings
<define>BOOST_NO_AUTO_PTR
# special msvc hacks
<toolset>msvc:<define>WIN32 # windows
<toolset>msvc:<define>_CRT_SECURE_NO_DEPRECATE # don't deprecate the standard library
<toolset>msvc:<define>_SCL_SECURE_NO_DEPRECATE # don't deprecate the standard library
<toolset>msvc:<define>_USE_MATH_DEFINES # for M_PI in <cmath>
<toolset>msvc:<define>BOOST_ALL_NO_LIB # disable auto-link
<toolset>msvc:<cxxflags>/wd4100 # warning: unreferenced formal parameter
<toolset>msvc:<cxxflags>/wd4512 # warning: assignment operator could not be generated
<toolset>msvc:<cxxflags>/wd4127 # warning: conditional expression is constant (boost::lexical_cast)
<toolset>msvc:<cxxflags>/wd4701 # warning: potentially uninitialized local variable 'result' used (boost::lexical_cast, debug)
<toolset>msvc:<cxxflags>/wd4245 # warning: conversion from 'type1' to 'type2', signed/unsigned mismatch (boost/filesystem/convenience.hpp)
<toolset>msvc:<cxxflags>/wd4251 # warning: class needs to have dll-interface to be used by clients of class
<toolset>msvc:<cxxflags>/wd4267 # warning: conversion from 'type1' to 'type2', possible loss of data (boost::lexical_cast)
<toolset>msvc:<cxxflags>/wd4244 # warning: conversion from 'int' to 'unsigned short', possible loss of data (boost/date_time/microsec_time_clock.hpp)
<toolset>msvc:<cxxflags>/wd4275 # warning: non dll-interface class 'base' used as base for dll-interface class 'derived'
<toolset>msvc:<cxxflags>/wd4702 # warning: unreachable code (boost::lexical_cast)
<toolset>msvc:<cxxflags>/wd4714 # warning: marked as __forceinline not inlined (boost::spirit::karma::sequence)
<toolset>msvc:<cxxflags>/wd4456 # warning: declaration of 'type' hides previous local declaration
<toolset>msvc:<cxxflags>/wd4459 # warning: declaration of 'type' hides global declaration
<toolset>msvc:<cxxflags>/wd4458 # warning: declaration of 'type' hides class member
<toolset>msvc,<debug-symbols>off:<linkflags>"/OPT:REF,ICF"
<toolset>msvc,<toolset-msvc:version>12.0:<define>_HAS_TR1
<toolset>msvc,<toolset-msvc:version>14.0:<define>_HAS_TR1
<toolset>msvc,<toolset-msvc:version>14.1:<define>_HAS_TR1
<conditional>@secure-scl-throws
# special gcc hack - Cygwin gcc 3.4.4, Ubuntu gcc 4.1.2
# warning: '__cur' might be used uninitialized in this function
<toolset>gcc:<cxxflags>-Wno-uninitialized
# set standard to C++11
<toolset>gcc:<cxxflags>-std=c++11
# avoid warnings like concept_check.hpp ... warning: unused typedef 'boost_concept_check'
<toolset>clang:<cxxflags>-Wno-unused-local-typedef
<toolset>darwin:<cxxflags>-Wno-unused-local-typedef
# avoid C++1x deprecation warnings
<toolset>gcc:<cxxflags>-Wno-deprecated-declarations
<toolset>clang:<cxxflags>-Wno-deprecated-declarations
$(PREDEF_CHECKS)
# special Cygwin gcc-3.4.4 hack
# linker "multiple definition" error on inclusion of boost-1.34.1 filesystem headers
<toolset>gcc-3.4.4:<linkflags>-Wl,--allow-multiple-definition
<toolset>gcc-mingw-3.4.5:<linkflags>-Wl,--allow-multiple-definition
<toolset-gcc:flavor>mingw:<linkflags>-Wl,--allow-multiple-definition
# allow "long long" even with -pedantic
<toolset>gcc:<cxxflags>-Wno-long-long
<toolset>darwin:<cxxflags>-Wno-long-long
<toolset>darwin:<cxxflags>-std=c++11
<toolset>clang:<cxxflags>-std=c++11
# any GCC executable that uses shared libraries must have all its code built with -fPIC
<conditional>@static-with-fpic
# mz5 support?
<conditional>@without-mz5
# msdata text only?
<conditional>@without-binary-msdata
# don't call 'strip' -- causes 'Bus error' in some cases
# e.g. find_if with inline predicate
<toolset>darwin:<debug-symbols>on
# use of boost::thread requires multithreaded runtime
<threading>multi
# change boost debug assertions to exceptions by force including Exception.hpp
<variant>debug,<toolset>msvc:<cxxflags>/FIpwiz/utility/misc/Exception.hpp
<variant>debug,<toolset>gcc:<cxxflags>"-include pwiz/utility/misc/Exception.hpp"
<variant>debug,<toolset>darwin:<cxxflags>"-include pwiz/utility/misc/Exception.hpp"
<toolset>msvc,<debug-symbols>on:<preserve-test-targets>off # save space on debug builds by deleting test artifacts which run successfully
$(TEAMCITY_TEST_DECORATION)
: build-dir $(PWIZ_BUILD_PATH)
: usage-requirements
<include>.
: default-build
release
<link>static
<runtime-link>static
#<warnings-as-errors>on
<warnings>all
<threading>multi
;
# external library declarations
lib pthread
: # sources
: # requirements
<name>pthread
<link>shared
<toolset>gcc:<linkflags>-pthread # sometimes segfault without this -- dk
: # default-build
: # usage-requirements
<toolset>gcc:<linkflags>-pthread # sometimes segfault without this -- dk
;
lib fftw3 : : <threading>multi <search>$(PWIZ_LIBRARIES_PATH)/fftw-3.1.2/.libs : : <include>$(PWIZ_LIBRARIES_PATH)/fftw-3.1.2/api ;
lib fftw3 : : <threading>multi <toolset>msvc <name>libfftw3-3 <search>$(PWIZ_LIBRARIES_PATH) : : <include>$(PWIZ_LIBRARIES_PATH)/fftw-3.1.2/api ;
alias svm : $(PWIZ_LIBRARIES_PATH)/libsvm-3.0//svm ;
modules.poke : BOOST_BUILD_PATH : [ modules.peek : BOOST_BUILD_PATH ] $(PWIZ_LIBRARIES_PATH) ;
import numbers ;
rule is_leap_year ( year )
{
if [ CALC $(year) % 100 ] = 0
{
if [ CALC $(year) % 400 ] = 0 { return 1 ; }
else { return 0 ; }
}
else
{
if [ CALC $(year) % 4 ] = 0 { return 1 ; }
else { return 0 ; }
}
}
# given year, month, day return day of year
# Astronomical Algorithms, Jean Meeus, 2d ed, 1998, chap 7
rule day_of_year ( Y M D )
{
local K ;
if [ is_leap_year $(Y) ] = 1 { K = 1 ; }
else { K = 2 ; }
local a = [ CALC 275 * $(M) ] ;
local b = [ CALC $(M) + 9 ] ;
local c = [ CALC $(b) / 12 ] ;
local d = [ CALC $(K) * $(c) ] ;
local e = [ CALC $(a) / 9 ] ;
local f = [ CALC $(e) - $(d) ] ;
local g = [ CALC $(f) + $(D) ] ;
local N = [ CALC $(g) - 30 ] ;
if [ numbers.less $(N) 100 ]
{
N = "0" $(N) ;
return $(N:J=) ;
}
else
{
return $(N) ;
}
}
# YMMDD in UTC where Y is number of years since 2016, optionally suffixed with HH (hour)
rule MAKE_BUILD_TIMESTAMP ( )
{
local utc = [ modules.peek : JAMDATE ] ;
local ymd = [ MATCH "([0-9][0-9][0-9][0-9])-([0-9][0-9])-([0-9][0-9])" : $(utc) ] ;
local d = [ MATCH "[0-9][0-9]([0-9][0-9])" : $(ymd[0]) ] [ day_of_year $(ymd) ] ;
return $(d:J=) ;
}
local rev = [ MATCH "([a-f0-9]*)" : [ SHELL "git rev-parse --short HEAD" ] ] ;
local branch = [ MATCH "\\* ([^\r\n]*)" : [ SHELL "git branch" ] ] ;
local args = [ modules.peek : ARGV ] ;
constant PWIZ_MAJOR : 3 ;
constant PWIZ_MINOR : 0 ;
constant PWIZ_BUILD_TIMESTAMP : [ MAKE_BUILD_TIMESTAMP ] ;
constant PWIZ_GIT_REV : $(rev:E=0) ;
constant PWIZ_GIT_BRANCH : $(branch:E=master) ;
numeric-version-tag = $(PWIZ_MAJOR) $(PWIZ_MINOR) $(PWIZ_BUILD_TIMESTAMP) ;
version-tag = $(numeric-version-tag) $(PWIZ_GIT_REV) ;
constant PWIZ_NUMERIC_VERSION_TAG : $(numeric-version-tag:J=.) ;
constant PWIZ_VERSION_TAG : $(version-tag:J=.) ;
echo ProteoWizard $(version-tag:J=.) $(PWIZ_GIT_BRANCH) $(PLATFORM) $(PROCESSOR_ARCHITECTURE) ;
import generate-version ;
generate-version.cpp $(PWIZ_ROOT_PATH)/pwiz/data/msdata/Version.cpp : pwiz msdata : $(PWIZ_MAJOR) : $(PWIZ_MINOR) : $(PWIZ_BUILD_TIMESTAMP) : $(PWIZ_GIT_REV) : $(PWIZ_GIT_BRANCH) ;
generate-version.cpp $(PWIZ_ROOT_PATH)/pwiz/analysis/Version.cpp : pwiz analysis : $(PWIZ_MAJOR) : $(PWIZ_MINOR) : $(PWIZ_BUILD_TIMESTAMP) : $(PWIZ_GIT_REV) : $(PWIZ_GIT_BRANCH) ;
generate-version.cpp $(PWIZ_ROOT_PATH)/pwiz/data/identdata/Version.cpp : pwiz identdata : $(PWIZ_MAJOR) : $(PWIZ_MINOR) : $(PWIZ_BUILD_TIMESTAMP) : $(PWIZ_GIT_REV) : $(PWIZ_GIT_BRANCH) ;
generate-version.cpp $(PWIZ_ROOT_PATH)/pwiz/data/tradata/Version.cpp : pwiz tradata : $(PWIZ_MAJOR) : $(PWIZ_MINOR) : $(PWIZ_BUILD_TIMESTAMP) : $(PWIZ_GIT_REV) : $(PWIZ_GIT_BRANCH) ;
generate-version.cpp $(PWIZ_ROOT_PATH)/pwiz/data/proteome/Version.cpp : pwiz proteome : $(PWIZ_MAJOR) : $(PWIZ_MINOR) : $(PWIZ_BUILD_TIMESTAMP) : $(PWIZ_GIT_REV) : $(PWIZ_GIT_BRANCH) ;
generate-version.cpp $(PWIZ_ROOT_PATH)/pwiz/Version.cpp : pwiz : $(PWIZ_MAJOR) : $(PWIZ_MINOR) : $(PWIZ_BUILD_TIMESTAMP) : $(PWIZ_GIT_REV) : $(PWIZ_GIT_BRANCH) ;
# create a VERSION file which can be used by TC to parse the canonical pwiz version
make VERSION : : @make_VERSION : <location>$(PWIZ_BUILD_PATH) ;
actions make_VERSION { @($(STDOUT):E=$(version-tag:]=.)) > "$(<)" }
#actions make_VERSION { @($(STDOUT):E=$(version-tag:]=.)) > "$(<)" ; @($(STDOUT):E=<version>$(version-tag:J=.)</version>) > "$(PWIZ_BUILD_PATH)/VERSION.xml" }
import tar ;
using tar ;
if ! [ without-mz5 ]
{
tar.extract $(PWIZ_LIBRARIES_PATH)/hdf5-1.8.7.tar.bz2 : *.c* *.h* *.jam *.settings : <location>$(PWIZ_LIBRARIES_PATH) ;
}
path-constant BOOST_SOURCE : $(boost_src) ;
path-constant ZLIB_SOURCE : $(zlib_src) ;
path-constant GD_SOURCE : $(PWIZ_LIBRARIES_PATH)/libgd-2.1.0alpha ;
path-constant PNG_SOURCE : $(PWIZ_LIBRARIES_PATH)/libpng-1.5.6 ;
path-constant FREETYPE_SOURCE : $(PWIZ_LIBRARIES_PATH)/freetype-2.4.7 ;
path-constant EXPAT_SOURCE : $(PWIZ_LIBRARIES_PATH)/expat-2.0.1 ;
using ext-boost : $(BOOST_VERSION:J=.) : $(BOOST_SOURCE) : <zlib-src-location>$(ZLIB_SOURCE) ;
if [ modules.peek : NT ]
{
import path ;
if ( ! --incremental in $(args) ) && ! [ without-binary-msdata ]
{
# extract the vendor APIs if the user agrees to the licenses
if --i-agree-to-the-vendor-licenses in $(args)
{
echo "Extracting vendor APIs..." ;
if ! --without-sciex in $(args) { SHELL "$(PWIZ_LIBRARIES_PATH)\\7za.exe x -aoa -pi-agree-to-the-vendor-licenses -o$(PWIZ_ROOT_PATH)\\pwiz_aux\\msrc\\utility $(PWIZ_ROOT_PATH)\\pwiz_aux\\msrc\\utility\\vendor_api_ABI.7z" ; }
if ! --without-agilent in $(args) { SHELL "$(PWIZ_LIBRARIES_PATH)\\7za.exe x -aoa -pi-agree-to-the-vendor-licenses -o$(PWIZ_ROOT_PATH)\\pwiz_aux\\msrc\\utility $(PWIZ_ROOT_PATH)\\pwiz_aux\\msrc\\utility\\vendor_api_Agilent.7z" ; }
if ! --without-bruker in $(args) { SHELL "$(PWIZ_LIBRARIES_PATH)\\7za.exe x -aoa -pi-agree-to-the-vendor-licenses -o$(PWIZ_ROOT_PATH)\\pwiz_aux\\msrc\\utility $(PWIZ_ROOT_PATH)\\pwiz_aux\\msrc\\utility\\vendor_api_Bruker.7z" ; }
if ! --without-shimadzu in $(args) { SHELL "$(PWIZ_LIBRARIES_PATH)\\7za.exe x -aoa -pi-agree-to-the-vendor-licenses -o$(PWIZ_ROOT_PATH)\\pwiz_aux\\msrc\\utility $(PWIZ_ROOT_PATH)\\pwiz_aux\\msrc\\utility\\vendor_api_Shimadzu.7z" ; }
if ! --without-thermo in $(args) { SHELL "$(PWIZ_LIBRARIES_PATH)\\7za.exe x -aoa -pi-agree-to-the-vendor-licenses -o$(PWIZ_ROOT_PATH)\\pwiz_aux\\msrc\\utility $(PWIZ_ROOT_PATH)\\pwiz_aux\\msrc\\utility\\vendor_api_Thermo.7z" ; }
#if ! --without-unifi in $(args) { SHELL "$(PWIZ_LIBRARIES_PATH)\\7za.exe x -aoa -pi-agree-to-the-vendor-licenses -o$(PWIZ_ROOT_PATH)\\pwiz_aux\\msrc\\utility $(PWIZ_ROOT_PATH)\\pwiz_aux\\msrc\\utility\\vendor_api_UNIFI.7z" ; }
if ! --without-waters in $(args) { SHELL "$(PWIZ_LIBRARIES_PATH)\\7za.exe x -aoa -pi-agree-to-the-vendor-licenses -o$(PWIZ_ROOT_PATH)\\pwiz_aux\\msrc\\utility $(PWIZ_ROOT_PATH)\\pwiz_aux\\msrc\\utility\\vendor_api_Waters.7z" ; }
RESCAN ;
}
else
{
echo "NOTICE: not extracting vendor APIs; use --i-agree-to-the-vendor-licenses to extract and use them." ;
}
}
# overwrite the original header files because of MSVC looking in the current header's path with #include "foo"
# HACK: bug in boost::interprocess (up to at least 1.55) requires a patch to support opening memory-mapped files with UTF-8 filenames
# Boost bug ticket: https://svn.boost.org/trac/boost/ticket/4335
#SHELL "@IF NOT EXIST $(BOOST_SOURCE)\\boost\\interprocess\\detail\\os_file_functions.hpp.bak rename $(BOOST_SOURCE)\\boost\\interprocess\\detail\\os_file_functions.hpp os_file_functions.hpp.bak" ;
#SHELL "@IF NOT EXIST $(BOOST_SOURCE)\\boost\\interprocess\\detail\\win32_api.hpp.bak rename $(BOOST_SOURCE)\\boost\\interprocess\\detail\\win32_api.hpp win32_api.hpp.bak" ;
#SHELL "@copy /Y $(PWIZ_LIBRARIES_PATH)\\boost_aux\\boost\\interprocess\\detail\\os_file_functions.hpp $(BOOST_SOURCE)\\boost\\interprocess\\detail" ;
#SHELL "@copy /Y $(PWIZ_LIBRARIES_PATH)\\boost_aux\\boost\\interprocess\\detail\\win32_api.hpp $(BOOST_SOURCE)\\boost\\interprocess\\detail" ;
}
rule project-exists ( project-path )
{
if [ path.exists $(project-path) ] &&
[ path.glob $(project-path) : "[Jj]amroot.jam" "[Jj]amfile.jam" "[Jj]amroot" "[Jj]amfile" ]
{
return true ;
}
else
{
return ;
}
}
# to make subsetting the source tree much easier,
# use these rules to test that a sub-project path exists before building it
rule build-project-if-exists ( project-path )
{
local project = [ project.current ] ;
local p = [ path.native [ path.join [ $(project).location ] $(project-path) ] ] ;
if [ project-exists $(p) ]
{
local attributes = [ project.attributes [ $(project).name ] ] ;
local now = [ $(attributes).get projects-to-build ] ;
$(attributes).set projects-to-build : $(now) $(project-path) ;
}
}
rule run-if-exists ( sources + : args * : input-files * : requirements * : target-name ? : default-build * )
{
local project = [ project.current ] ;
local full-path = [ path.native [ path.join [ $(project).location ] $(project-path) $(sources[1]) ] ] ;
if [ path.exists $(full-path) ]
{
return [ run $(sources) : $(args) : $(input-files) : $(requirements) : $(target-name) : $(default-build) ] ;
}
}
rule run-fail-if-exists ( sources + : args * : input-files * : requirements * : target-name ? : default-build * )
{
local project = [ project.current ] ;
local full-path = [ path.native [ path.join [ $(project).location ] $(project-path) $(sources[1]) ] ] ;
if [ path.exists $(full-path) ]
{
return [ run-fail $(sources) : $(args) : $(input-files) : $(requirements) : $(target-name) : $(default-build) ] ;
}
}
rule unit-test-if-exists ( target : sources + : properties * )
{
local project = [ project.current ] ;
local full-path = [ path.native [ path.join [ $(project).location ] $(project-path) $(sources[1]) ] ] ;
if [ path.exists $(full-path) ]
{
return [ unit-test $(target) : $(sources) : $(properties) ] ;
}
}
rule doctest ( name : sources + : requirements * )
{
unit-test-if-exists $(name) : $(sources) : $(requirements) <define>PWIZ_DOCTEST <location-prefix>doctest ;
}
# build/install
build-project-if-exists pwiz ;
build-project-if-exists pwiz_aux ;
build-project-if-exists pwiz_tools ;
rule install-location ( properties * )
{
local toolsets = [ feature.get-values <toolset> : $(properties) ] ;
local variants = [ feature.get-values <variant> : $(properties) ] ;
local location = [ path.make $(PWIZ_BUILD_PATH)/$(toolsets[1])-$(variants[1]) ] ;
if <link>shared in $(properties) { location = $(location)-shared ; }
if <address-model>64 in $(properties) { location = $(location)-x86_64 ; }
return <location>$(location) ;
}
rule install-type ( properties * )
{
local result = <install-type>EXE ;
if <link>shared in $(properties)
{
result += <install-dependencies>on <install-type>SHARED_LIB <install-type>MANIFEST ;
}
return $(result) ;
}
import string ;
rule install-vendor-api-dependencies ( properties * )
{
properties = $(properties) [ vendor-api-support $(properties) ] ;
local location = [ feature.get-values <location> : $(properties) ] ;
if $(location) { location = [ string.join <location> [ path.make $(location[1]) ] ] ; }
location ?= [ install-location $(properties) ] ;
local dependencies ;
if <toolset>msvc in $(properties) && <link>static in $(properties) && ! [ without-binary-msdata ]
{
if [ path.exists pwiz_aux/msrc/utility/vendor_api/ABI ] { dependencies += <dependency>$(PWIZ_ROOT_PATH)/pwiz_aux/msrc/utility/vendor_api/ABI//install_pwiz_vendor_api_abi_dlls/$(location) ; }
if [ path.exists pwiz_aux/msrc/utility/vendor_api/ABI ] { dependencies += <dependency>$(PWIZ_ROOT_PATH)/pwiz_aux/msrc/utility/vendor_api/ABI//install_pwiz_vendor_api_abi_sqlite/$(location) ; }
if [ path.exists pwiz_aux/msrc/utility/vendor_api/ABI/T2D ] { dependencies += <dependency>$(PWIZ_ROOT_PATH)/pwiz_aux/msrc/utility/vendor_api/ABI/T2D//install_pwiz_vendor_api_abi_t2d/$(location) ; }
if [ path.exists pwiz_aux/msrc/utility/vendor_api/Agilent ] { dependencies += <dependency>$(PWIZ_ROOT_PATH)/pwiz_aux/msrc/utility/vendor_api/Agilent//install_pwiz_vendor_api_agilent/$(location) ; }
if [ path.exists pwiz_aux/msrc/utility/vendor_api/Bruker ] { dependencies += <dependency>$(PWIZ_ROOT_PATH)/pwiz_aux/msrc/utility/vendor_api/Bruker//install_pwiz_vendor_api_bruker/$(location) ; }
if [ path.exists pwiz_aux/msrc/utility/vendor_api/Shimadzu ] { dependencies += <dependency>$(PWIZ_ROOT_PATH)/pwiz_aux/msrc/utility/vendor_api/Shimadzu//install_pwiz_vendor_api_shimadzu_core/$(location) ; }
if [ path.exists pwiz_aux/msrc/utility/vendor_api/Shimadzu ] { dependencies += <dependency>$(PWIZ_ROOT_PATH)/pwiz_aux/msrc/utility/vendor_api/Shimadzu//install_pwiz_vendor_api_shimadzu_platform/$(location) ; }
if [ path.exists pwiz_aux/msrc/utility/vendor_api/thermo ] { dependencies += <dependency>$(PWIZ_ROOT_PATH)/pwiz_aux/msrc/utility/vendor_api/thermo//install_pwiz_vendor_api_thermo/$(location) ; }
if [ path.exists pwiz_aux/msrc/utility/vendor_api/UIMF ] { dependencies += <dependency>$(PWIZ_ROOT_PATH)/pwiz_aux/msrc/utility/vendor_api/UIMF//install_pwiz_vendor_api_uimf/$(location) ; }
if [ path.exists pwiz_aux/msrc/utility/vendor_api/UNIFI ] { dependencies += <dependency>$(PWIZ_ROOT_PATH)/pwiz_aux/msrc/utility/vendor_api/UNIFI//install_pwiz_vendor_api_unifi/$(location) ; }
if [ path.exists pwiz_aux/msrc/utility/vendor_api/Waters ] { dependencies += <dependency>$(PWIZ_ROOT_PATH)/pwiz_aux/msrc/utility/vendor_api/Waters//install_pwiz_vendor_api_waters/$(location) ; }
if <vendor-api-support>on in $(properties) { dependencies += <dependency>$(PWIZ_ROOT_PATH)/pwiz_tools/prototype//ThermoRawMetaDumpInstall/$(location) ; }
}
return $(dependencies) ;
}
rule install-identdata-dependencies ( properties * )
{
local location = [ feature.get-values <location> : $(properties) ] ;
if $(location) { location = [ string.join <location> [ path.make $(location[1]) ] ] ; }
location ?= [ install-location $(properties) ] ;
local dependencies ;
if [ path.exists pwiz/data/identdata ] { dependencies += <dependency>$(PWIZ_ROOT_PATH)/pwiz/data/identdata//install_pwiz_identdata/$(location) ; }
return $(dependencies) ;
}
rule pwiz-bindings-dependency ( properties * )
{
if <toolset>msvc in $(properties)
{
local variants = [ feature.get-values <variant> : $(properties) ] ;
local location = <location>$(PWIZ_BUILD_PATH)/obj/$(PLATFORM)/$(variants[1]) ;
return <assembly>$(PWIZ_ROOT_PATH)/pwiz/utility/bindings/CLI//pwiz_bindings_cli
<dependency>$(PWIZ_ROOT_PATH)/pwiz/utility/bindings/CLI//pwiz_bindings_cli/$(location)
<dependency>$(PWIZ_ROOT_PATH)/pwiz/utility/bindings/CLI//pwiz_bindings_cli.xml/$(location) ;
}
}
rule dotNET-dependencies ( properties * )
{
if <toolset-msvc:version>12.0 in $(properties) || <toolset-msvc:version>14.0 in $(properties) || <toolset-msvc:version>14.1 in $(properties)
{
local location = [ install-location $(properties) ] ;
return <dependency>$(PWIZ_ROOT_PATH)/pwiz_tools/MSConvertGUI//MSConvertGUI.exe/$(location)
<dependency>$(PWIZ_ROOT_PATH)/pwiz_tools/SeeMS//seems/$(location) ;
}
}
rule gcc-install-dll-path ( properties * )
{
if <toolset>gcc in $(properties) && <link>shared in $(properties) && <target-os>linux in $(properties)
{
return <dll-path>'$ORIGIN' ;
}
}
install executables
: pwiz_tools/commandline
pwiz_tools/sld//sldout
pwiz_tools/examples//example_tools
: <conditional>@install-type
<conditional>@install-location
<conditional>@install-identdata-dependencies
<conditional>@install-vendor-api-dependencies
<conditional>@dotNET-dependencies
<conditional>@gcc-install-dll-path
<dependency>VERSION
;
install gui_tools
: VERSION
: <conditional>@install-type
<conditional>@install-location
<conditional>@install-identdata-dependencies
<conditional>@install-vendor-api-dependencies
<conditional>@dotNET-dependencies
<conditional>@gcc-install-dll-path
;
install package_docs
: doc/package/readme.txt
: <conditional>@install-location
;
# convenient test targets
install msconvert
: pwiz_tools/commandline//msconvert
: <conditional>@install-type
<conditional>@install-location
<conditional>@install-identdata-dependencies
<conditional>@install-vendor-api-dependencies
<conditional>@gcc-install-dll-path
;
explicit msconvert ;
install msbenchmark
: pwiz_tools/examples//msbenchmark
: <conditional>@install-type
<conditional>@install-location
<conditional>@install-vendor-api-dependencies
<conditional>@gcc-install-dll-path
;
explicit msbenchmark ;
install idconvert
: pwiz_tools/commandline//idconvert
: <conditional>@install-type
<conditional>@install-location
<conditional>@install-identdata-dependencies
<conditional>@install-vendor-api-dependencies
<conditional>@gcc-install-dll-path
;
explicit idconvert ;
alias all-tests : pwiz pwiz_tools pwiz_aux ;
# for copying all libraries and headers to one dir each
alias libraries : install-pwiz-lib install-boost-headers ;
explicit libraries ;
# default install location
local default-prefix = /usr/local ; # LINUX, MACOS
if [ modules.peek : NT ] { default-prefix = "C:\\" ; }
# set the default option value to be used when building the lib tarball
option.set prefix : $(default-prefix) ;
local headers = [ path.glob-tree pwiz : *.h *.hpp : .svn ] ;
package.install install-pwiz-lib
: <install-source-root>$(PWIZ_ROOT_PATH)
: # executables
: pwiz
: $(headers)
;
explicit install-pwiz-lib ;
# move boost headers separately because install-source-root is different
local boost_headers = [ path.glob-tree $(BOOST_SOURCE)/boost : *.h *.hpp : .svn ] ;
package.install install-boost-headers
: <install-source-root>$(BOOST_SOURCE)
: # exe
: # lib
: $(boost_headers)
;
explicit install-boost-headers ;
# warning: _SECURE_SCL_THROWS is deprecated
# checked iterators throw instead of crash
rule secure-scl-throws ( properties * )
{
if <toolset>msvc in $(properties) &&
! ( <toolset-msvc:version>11.0 in $(properties) ) &&
! ( <toolset-msvc:version>12.0 in $(properties) ) &&
! ( <toolset-msvc:version>14.0 in $(properties) ) &&
! ( <toolset-msvc:version>14.1 in $(properties) )
{
return <define>_SILENCE_DEPRECATION_OF_SECURE_SCL_THROWS
<define>_SECURE_SCL_THROWS=1 ;
}
}
# any GCC executable that uses shared libraries must have all its code built with -fPIC
rule static-with-fpic ( properties * )
{
if ( <toolset>gcc in $(properties) || <toolset>darwin in $(properties) ) &&
<link>static in $(properties)
{
return <cflags>-fPIC <cxxflags>-fPIC <linkflags>-fPIC ;
}
}
# predicate for use as a <conditional> requirement of targets that must only build with MSVC
rule msvc-requirement ( properties * )
{
if ! <toolset>msvc in $(properties) { return <build>no ; }
}
# predicate for use as a <conditional> requirement of targets that must only build with MSVC and current .NET Framework
rule msvc-dotnet-requirement ( properties * )
{
# require VS 2013 because of .NET Framework version
if ! ( <toolset-msvc:version>12.0 in $(properties) ||
<toolset-msvc:version>14.0 in $(properties) ||
<toolset-msvc:version>14.1 in $(properties) )
{ return <build>no ; }
}
# predicate for use as a <conditional> requirement of targets that must only build with non-express version of MSVC
rule no-express-requirement ( properties * )
{
# only the latest, non-express version of MSVC
if ! ( <toolset-msvc:version>12.0 in $(properties) ||
<toolset-msvc:version>14.0 in $(properties) ||
<toolset-msvc:version>14.1 in $(properties) )
{ return <build>no ; }
if 12.0express in $(properties:G=) { return <build>no ; }
}
# CONSIDER: would be nice to access msvc.jam's setup logic, but that would seem to require significant refactoring
constant MSVC_CURRENT_SETUP_SCRIPT : "CALL $(PWIZ_ROOT_PATH)\\libraries\\msvc_setup_script.bat $(PROCESSOR_ARCHITECTURE:L) >nul" ;
# special support for MSFileReader on Windows
if [ modules.peek : NT ]
{
# can't build or run 64-bit version on Windows 32-bit OS
import os ;
local ProgramFiles = [ os.environ ProgramFiles ] ;
local ProgramFilesX86 = [ os.environ "ProgramFiles(x86)" ] ;
ProgramFilesX86 = $(ProgramFilesX86:E=$(ProgramFiles)) ;
if ( [ MATCH (x64) : $(PLATFORM) ] )
{
# HACK: we can't just look at the PROCESSOR_ARCHITECTURE environment variable, because it is
# set to "x86" even on a 64-bit machine, probably because bjam is running in 32-bit mode
if ( ! $(ProgramFilesX86) && [ MATCH (x86) : $(ProgramFiles) ] ) # infer 64-bit machine from (x86) appended to ProgramFiles
{
EXIT "\n*** ERROR: It is not possible to build or run a 64-bit build on 32-bit Windows." ;
}
# MSFileReader install directory
constant ProgramFilesLibs : "C:\\Program Files" ;
constant MSFILEREADER_SUFFIX : "_x64" ;
}
else
{
# MSFileReader install directory
constant ProgramFilesLibs : "$(ProgramFilesX86)" ;
constant MSFILEREADER_SUFFIX : "" ;
}
constant MSFILEREADER_INSTALL_DIR : "$(ProgramFilesLibs)\\Thermo\\MSFileReader" ;
} # if NT
# HACK: find location of WiffFileDataReader DLLs (it must be in Jamroot so both vendor_readers and vendor_api can use it)
rule wiff-dll-location ( api-path : properties * )
{
# .NET 4 DLLs should work for anything .NET 4 or greater (hopefully); there's no Boost.Build property for .NET version
local result = $(api-path) ;
if --i-agree-to-the-vendor-licenses in [ modules.peek : ARGV ] &&
[ path.exists $(result)\\Clearcore2.Data.WiffReader.dll ]
{
return $(result) ;
}
}
rule unifi-dll-location ( api-path : properties * )
{
# .NET 4.5 DLLs should work for anything .NET 4 or greater (hopefully); there's no Boost.Build property for .NET version
local result = $(api-path) ;
if --i-agree-to-the-vendor-licenses in [ modules.peek : ARGV ] &&
[ path.exists $(result)\\unifi-protobuf-net.dll ]
{
return $(result) ;
}
}
rule bruker-dll-location ( api-path : properties * )
{
local result ;
if ( [ MATCH (x64) : $(PLATFORM) ] )
{
result = $(api-path)\\x64 ;
}
else
{
result = $(api-path)\\x86 ;
}
if --i-agree-to-the-vendor-licenses in [ modules.peek : ARGV ] &&
$(result) &&
[ path.exists $(result)\\CompassXtractMS.dll ]
{
return $(result) ;
}
}
rule shimadzu-dll-location ( api-path : properties * )
{
local result ;
if ( [ MATCH (x64) : $(PLATFORM) ] )
{
result = $(api-path)\\x64 ;
}
else
{
result = $(api-path)\\x86 ;
}
if --i-agree-to-the-vendor-licenses in [ modules.peek : ARGV ] &&
$(result) &&
[ path.exists $(result)\\DataReader.dll ]
{
return $(result) ;
}
}
rule mhdac-dll-location ( api-path : properties * )
{
local result ;
if ( [ MATCH (x64) : $(PLATFORM) ] )
{
result = $(api-path)\\x64 ;
}
else
{
result = $(api-path)\\x86 ;
}
if --i-agree-to-the-vendor-licenses in [ modules.peek : ARGV ] &&
$(result) &&
[ path.exists $(result)\\MassSpecDataReader.dll ]
{
return $(result) ;
}
}
rule uimf-dll-location ( api-path : properties * )
{
local result ;
if <toolset-msvc:version>9.0 in $(properties) ||
<toolset-msvc:version>9.0express in $(properties)
{
# not supported
}
else # VC10 DLLs should work for VC11 as well (it's dependent on .NET version)
{
if ( [ MATCH (x64) : $(PLATFORM) ] )
{
result = $(api-path)\\x64 ;
}
else
{
result = $(api-path)\\x86 ;
}
}
if --i-agree-to-the-vendor-licenses in [ modules.peek : ARGV ] &&
$(result) &&
[ path.exists $(result)\\UIMFLibrary.dll ]
{
return $(result) ;
}
}
rule masslynxraw-dll-location ( api-path : properties * )
{
local result ;
if <toolset>msvc in $(properties)
{
if ( [ MATCH (x64) : $(PLATFORM) ] )
{
result = $(api-path)\\vc12_x64 ;
}
else
{
result = $(api-path)\\vc12_x86 ;
}
}