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Here's a 245-line SConstruct file that I'm currently trying to organize for a project that's roughly as complex:

Here's a 245-line SConstruct file that I'm currently trying to organize for a project that's roughly as complex:

I've added two examples below, roughly in the 250-line range. The problem for me is generally a lack of modularity. Some of these projects can be organized into modular units, and it'd be nice to abstract the parts of the build along those lines to make it easier for me and future maintainers to keep track of. Breaking each script up into multiple files has been one solution I've been toying around with in my head.

The second example is particularly important, because I'm going to have to a large number of files to it soon.

Edit: As Thorbjørn has pointed out, I should add some context and usage examples. I'm finishing up my PhD in chemical engineering and I do research in computational science. (I'm a pro tem mod over at SciComp.SE, for those of you who visit.) My projects typically involve a mix of compiled languages (C, C++, Fortran) that do some of the heavy lifting, scripting languages (Python, Perl) for prototyping, and occasionally, domain-specific languages for prototyping or technical purposes.

Here's what a 265-line Makefile might look like for me, taken from an actual project, and organized as best I can:

#!/usr/bin/make
#Directory containing DAEPACK library folder
daepack_root = .
library = $(daepack_root)/lib
wrappers = $(daepack_root)/Wrappers/DSL48S
c_headers = parser.h problemSizes.h
f77_headers=problemSizes.f commonParam.f
f90_headers=problemSizes.f commonParam.f90
includes = -I. -Iinclude -I/usr/include/glib-2.0 \
    -I/usr/lib/glib-2.0/include -I/usr/include/libxml2 \
    -I/usr/include/libgdome -I/usr/include/gtest/

#Fortran 77 environment variables
f77=gfortran
fflags=-ggdb -cpp -fno-second-underscore --coverage -falign-commons \
    -mcmodel=large -fbacktrace -pg 
flibs=

#Fortran 90 environment variables
f90=gfortran
f90flags=-ggdb -cpp -fno-second-underscore --coverage -falign-commons \
    -mcmodel=large -fbacktrace -pg 
f90libs=

#C environment flags
cc=gcc
cflags=-ggdb --coverage $(includes) -mcmodel=large 
clibs=

#Libraries for linking
libs=-L$(library) -ldaepack_sparse -lblas -llapack -ldl -lg2c \
    -lgdome -lxml2 -lgtest -lcunit -lcholmod -lamd -lcolamd -lccolamd \
    -lmetis -lspqr -lm -lblas -llapack -lstdc++ -lpcre

#Object files
objs=main.o $(dsl48sObjs) $(gdxObjs)
gdxObjs = gdxf9def.o gdxf9glu.o gamsglobals_mod.o 
commonObjs=libdsl48s_model.sl cklib.o parser.o $(gdxObjs)
originalModelObjs=originalModel.o dsl48sChemkinModule.o $(commonObjs)
cspSlowModelObjs=cspSlowModel.o dsl48sChemkinModuleSlow.o cspModule.o \
    $(commonObjs)
orthoProjModelObjs=orthoProjModel.o dsl48sChemkinModuleOrthoProj.o \
    orthoProjModule.o basisModule.o spqrUtility.o $(commonObjs)

#Shell environment variable definitions for FUnit
FCFLAGS := $(f90flags)
LDFLAGS := libdsl48s_model.sl cklib.o gdxf9glu.o parser.o spqrUtility.o \
    $(libs)

misc=*table *size.f 
output=*.out

#Ftncheck flags for static analysis of Fortran 77 code
ftnchekflags= -declare -include=. -library -style=block-if,distinct-do,do-enddo,end-name,goto,labeled-stmt,structured-end

all: ckinterp.exe parserTest.exe originalModel.exe cspSlowModel.exe \
    orthoProjModel.exe spqrUtilityTest.exe
#Check code style with lexical analyzer
    @echo Checking program style...
    ftnchek $(ftnchekflags) rhs.f
    ftnchek $(ftnchekflags) resorig.f
    ftnchek $(ftnchekflags) res.f
#   ftnchek $(ftnchekflags) cklib.f
#   ftnchek $(ftnchekflags) ckinterp.f
#Set up baseline coverage data file
    @echo Set up baseline coverage data file
    lcov -c -i -d . -o conpDSL48Sbase.info
#Run unit test on cspModule.f90
    @echo Running unit tests on cspModule.f90...
    funit cspModule
#Generate test coverage data for cspModule.f90
    @echo Generating test coverage data from cspModule.f90 tests...
    lcov -c -d . -o conpDSL48ScspTest.info
#Run unit test on orthoProjModule.f90
    @echo Running unit tests on orthoProjModule.f90...
    funit orthoProjModule
#Generate test coverage data for orthoProjModule.f90
    @echo Generating test coverage data from orthoProjModule.f90 tests...
    lcov -c -d . -o conpDSL48SgenProjTest.info
#Run unit tests on the parser C library
    @echo Running unit tests on parser in C...
    -G_SLICE=always-malloc G_DEBUG=gc-friendly valgrind -v --tool=memcheck \
    --leak-check=full --show-reachable=yes --leak-resolution=high \
    --num-callers=20 --log-file=parserTest.vgdump \
    ./parserTest.exe > parserTest.log
#Generate test coverage data for the parser wrapper C library
    @echo Generating test coverage data for the parser in C...
    lcov -c -d . -o conpDSL48SparserTest.info
#Run unit tests on the SparseQR C library
    @echo Running unit tests on SparseQR library in C...
    ./spqrUtilityTest.exe
#Generate test coverage data for the SparseQR C library
    @echo Generating test coverage data for the SparseQR C library...
    lcov -c -d . -o conpDSL48SsparseTest.info
#Run unit test on basisModule.f90
    @echo Running unit tests on basisModule.f90...
    funit basisModule
#Generate test coverage data for basisModule.f90
    @echo Generating test coverage data from basisModule.f90 tests...
    lcov -c -d . -o conpDSL48SbasisMod.info
#Combine test coverage data
    @echo Combine baseline and test coverage data...
    lcov -a conpDSL48Sbase.info \
    -a conpDSL48ScspTest.info \
    -a conpDSL48SgenProjTest.info \
    -a conpDSL48SbasisMod.info \
    -a conpDSL48SparserTest.info \
    -a conpDSL48SsparseTest.info \
    -o conpDSL48Stotal.info
#Post-process to remove coverage statistics from automatically 
#generated source code.
    @echo Removing coverage statistics for automatically generated source...
    lcov -r conpDSL48Stotal.info basisModule_fun.f90 \
    ckinterp.f cklib.f cspModule_fun.f90 davisSkodjeAd.f90 \
    davisSkodjeJac.f90 davisSkodjeRes.f90 davisSkodjeRhs.f90 \
    davisSkodjeSp.f90 gdxf9def.f90 gdxf9glu.c orthoProjModule_fun.f90 \
    jac.f jacorig.f resad.f resadp.f resorigad.f resorigadp.f ressp.f \
    resorigsp.f senrhs.f senrhsorig.f TestRunner.f90 \
    -o conpDSL48Stotal.info
#Generate HTML report of coverage data
    @echo Generate HTML report of coverage data...
    genhtml conpDSL48Stotal.info
    @echo Open "index.html" in browser for coverage results!

originalModel.exe: $(originalModelObjs) $(f90_headers) $(f77_headers) \
    $(c_headers)
    $(f90) $(f90flags) -o originalModel.exe $(originalModelObjs) $(libs)

originalModel.o: dsl48sChemkinModule.o $(commonObjs) $(f77_headers) \
    $(f90_headers) $(c_headers)
    $(f90) $(f90flags) -c -o originalModel.o originalModel.f90

cspSlowModel.exe: $(cspSlowModelObjs) $(f90_headers) $(f77_headers) \
    $(c_headers)
    $(f90) $(f90flags) -o cspSlowModel.exe $(cspSlowModelObjs) $(libs)

cspSlowModel.o: dsl48sChemkinModuleSlow.o cspModule.o $(commonObjs) \
    $(c_headers) $(f77_headers)
    $(f90) $(f90flags) -c -o cspSlowModel.o cspSlowModel.f90

orthoProjModel.exe: $(orthoProjModelObjs) $(f90_headers) $(f77_headers) \
    $(c_headers) resOrthoFast.o
    $(f90) $(f90flags) -o orthoProjModel.exe $(orthoProjModelObjs) \
    resOrthoFast.o $(libs)

orthoProjModel.o: dsl48sChemkinModuleOrthoProj.o orthoProjModule.o $(commonObjs) \
    $(c_headers) $(f90_headers) $(f77_headers) resOrthoFast.o basisModule.o
    $(f90) $(f90flags) -c -o orthoProjModel.o orthoProjModel.f90

dsl48sChemkinModule.o: dsl48sChemkinModule.f90 cklib.o problemSizes.h \
    parser.o $(c_headers) $(f90_headers)
    $(f90) $(f90flags) -c -o dsl48sChemkinModule.o dsl48sChemkinModule.f90 

dsl48sChemkinModuleSlow.o: dsl48sChemkinModuleSlow.f90 cspModule.o cklib.o \
    problemSizes.h parser.o $(c_headers) $(f90_headers)
    $(f90) $(f90flags) -c -o dsl48sChemkinModuleSlow.o \
    dsl48sChemkinModuleSlow.f90

dsl48sChemkinModuleOrthoProj.o: dsl48sChemkinModuleOrthoProj.f90 \
    orthoProjModule.o basisModule.o cklib.o problemSizes.h \
    parser.o $(c_headers) $(f90_headers)
    $(f90) $(f90flags) -c -o dsl48sChemkinModuleOrthoProj.o \
    dsl48sChemkinModuleOrthoProj.f90

basisModule.o: basisModule.f90 cklib.o spqrUtility.o commonParam.f90
    $(f90) $(f90flags) -c -o basisModule.o basisModule.f90

spqrUtility.o: spqrUtility.h spqrUtility.c
    $(cc) $(cflags) -c -o spqrUtility.o spqrUtility.c

spqrUtilityTest.exe: spqrUtilityTest.o spqrUtility.o
    $(cc) $(cflags) -o spqrUtilityTest.exe spqrUtilityTest.o \
    spqrUtility.o $(libs)

spqrUtilityTest.o: spqrUtilityTest.c spqrUtility.o
    $(cc) $(cflags) -c -o spqrUtilityTest.o spqrUtilityTest.c

cklib.o: cklib.f ckstrt.f
    $(f77) $(fflags) -c -o cklib.o cklib.f

ckinterp.exe: ckinterp.o
    $(f77) $(fflags) -o ckinterp.exe ckinterp.o

ckinterp.o: ckinterp.f
    $(f77) $(fflags) -c -o ckinterp.o ckinterp.f

#Recursive makefile inherited from previous graduate students
libdsl48s_model.sl: $(f77_headers) cklibDAEPACK.f
    cp $(wrappers)/makefile model.mk
    make -f model.mk

resOrthoFast.o: libdsl48s_model.sl
    $(f90) $(f90flags) -c -o resOrthoFast.o resOrthoFast.f90

problemSizes.f: problemSizes.fpp problemSizes.h
    cpp problemSizes.fpp problemSizes.f
    perl -p -i.bak -we 's/# /! /;' problemSizes.f

commonParam.f90: commonParam.f
    perl -p -i.bak -we 's/^#/!/;' commonParam.f
    echo "commonParam t f t fpp" | pref77tof90
    echo "commonParam /" | f77tof90
    perl -p -i.bak -we 's/integer a/!integer a/;' commonParam.f
    perl -p -i.bak -we 's/END   //;' commonParam.f90

commonParam.f: commonParam.fpp problemSizes.h
    cpp commonParam.fpp commonParam.f
    perl -p -i.bak -we 's/^#/!/;' commonParam.f

cspModule.o: cspModule.f90
    $(f90) $(f90flags) -c -o cspModule.o cspModule.f90

orthoProjModule.o: gamsglobals_mod.o gdxf9def.o gdxf9glu.o orthoProjModule.f90 \
    formatLabels.f90
    $(f90) $(f90flags) -c -o orthoProjModule.o orthoProjModule.f90

gdxf9def.o: gdxf9def.f90
    $(f90) $(f90flags) -c -o gdxf9def.o gdxf9def.f90

gdxf9glu.o: gdxf9glu.c gdxf9def.o
#64-bit version of wrappers (with underscores)
    $(cc) $(cflags) -DCIA_LEX -DAPIWRAP_LCASE_DECOR -c -o \
    gdxf9glu.o gdxf9glu.c
#64-bit version of wrappers (without underscores, for C interoperability)
#   $(cc) $(cflags) -DCIA_LEX -DAPIWRAP_LCASE_NODECOR -c gdxf9glu.c
#32-bit version of wrappers
#   $(cc) $(cflags) -DAPIWRAP_LCASE_DECOR -c gdxf9glu.c -Iinclude

gamsglobals_mod.o: gamsglobals_mod.f90 gdxf9def.o gdxf9glu.o
    $(f90) $(f90flags) -c gamsglobals_mod.f90

parser.o: parser.c $(c_headers)
    $(cc) $(cflags) -c -o parser.o parser.c 

parserTest.exe: parserTest.o parser.o
    $(cc) $(cflags) -o parserTest.exe parser.o \
    parserTest.o $(libs)

parserTest.o: parserTest.cpp parser.o
    $(cc) $(cflags) -c -o parserTest.o parserTest.cpp

clean:
    -rm *.bak
    -rm *.f77
    -rm *.log
    -rm commonParam.f90
    -rm problemSizes.f
    -rm commonParam.f
    -make clean -f model.mk
    -rm model.mk
    -rm *.o
    -rm *.mod
    -rm $(misc)
    -rm *.exe
    -funit --clean
    -rm *.gcno
    -rm *.gcda
    -rm *.info
    -rm *.png
    -rm *.html
    -rm *.css
    -rm -rf html
    -rm *.pyc
    -rm *.lst

Here's a 245-line SConstruct file that I'm currently trying to organize for a project that's roughly as complex:

## \file SConstruct
#  \brief Compiles the library and compiles tests.
#

import SCons

## \brief Build up directory names of each COIN library from package names
#         and versions.
#

## Overall SCons environment
#
env = Environment();

flags = []

## Compile using debug versions?
#
debug = True
debugString = '-debug'
debugFlags = ['-ggdb']

dynamicLinkFlag = '-Wl,-rpath,'

if debug:
    flags += debugFlags

## Compile Google Test from scratch.
#
GTestVersion = '1.6.0'
GTestStem = 'gtest-' + GTestVersion
GTestBuildIncDir = [GTestStem,
                    GTestStem + '/include',
                    ]
GTestAllLib = env.Library('lib/libgtest.a', 'gtest-1.6.0/src/gtest-all.cc',
                      CPPPATH = GTestBuildIncDir,
                      CXXFLAGS = flags)
GTestMainLib = env.Library('lib/libgtest_main.a',
                           'gtest-1.6.0/src/gtest_main.cc',
                           CPPPATH = GTestBuildIncDir,
                           CXXFLAGS = flags)

GTestIncDir = GTestStem + '/include/gtest'
GTestLibDir = 'lib'
GTestLibFlags = ['gtest', 'gtest_main', 'pthread']

## Armadillo matrix library
#
ArmadilloLibFlags = ['armadillo'];

## Quick reminder of SCons flags:
#  CPPPATH = path of headers (include directories)
#  LIBPATH = path of libraries
#  LIBS = flags of libraries
#  CXXFLAGS = C++ compilation flags
#




## Locations of libraries installed on system in standard locations
#
StdIncDir = '/usr/include'
StdLibDir = '/usr/lib'

## Configuration information for COIN libraries
#
CoinUtilsVersion = '2.6.4'
ClpVersion = '1.12.0'
OsiVersion = '0.103.0'
CbcVersion = '2.5.0'

## Some standard directory locations of COIN libraries, with slashes added for
#  for convenience.
#
CoinLibLocation = '/usr/local/COIN/'
StdCoinIncDir = '/include/coin'
StdCoinLibDir = '/lib'

CoinUtilsStem = 'CoinUtils-' + CoinUtilsVersion
ClpStem = 'Clp-' + ClpVersion
OsiStem = 'Osi-' + OsiVersion
CbcStem = 'Cbc-' + CbcVersion

if debug:
    CoinUtilsStem += debugString
    CbcStem += debugString
    ClpStem += debugString
    OsiStem += debugString

    
## Build up include directory names for COIN projects from constituent parts.
#
CoinUtilsIncDir = CoinLibLocation + CoinUtilsStem + StdCoinIncDir
ClpIncDir = CoinLibLocation + ClpStem + StdCoinIncDir
OsiIncDir = CoinLibLocation + OsiStem + StdCoinIncDir
CbcIncDir = CoinLibLocation + CbcStem + StdCoinIncDir

## Build up library names from COIN projects from constituent parts
#
CoinUtilsLibDir = CoinLibLocation + CoinUtilsStem + StdCoinLibDir
ClpLibDir = CoinLibLocation + ClpStem + StdCoinLibDir
OsiLibDir = CoinLibLocation + OsiStem + StdCoinLibDir
CbcLibDir = CoinLibLocation + CbcStem + StdCoinLibDir

## CPLEX
#
CpxStem = '/opt/ibm/ILOG/CPLEX_Studio_Academic123/cplex/'
CpxIncDir = CpxStem + 'include/ilcplex'
CpxLibDir = CpxStem + 'lib/x86-64_sles10_4.1/static_pic'

## Gurobi
# 
GrbStem = '/opt/gurobi460/linux64/'
GrbIncDir = GrbStem + 'include'
GrbLibDir = GrbStem + 'lib'

OsiLibFlags = ['Osi', 'CoinUtils']
ClpLibFlags = ['Clp', 'OsiClp']
CbcLibFlags = ['Cbc', 'Cgl']
OsiCpxLibFlags = ['OsiCpx']
OsiGrbLibFlags = ['OsiGrb']
CpxLibFlags = ['cplex', 'ilocplex', 'pthread', 'm']
GrbLibFlags = ['gurobi_c++', 'gurobi46', 'pthread', 'm']

milpIncDirs = [CoinUtilsIncDir,
               ClpIncDir,
               OsiIncDir,
               CbcIncDir,
               CpxIncDir,
               GrbIncDir,
            GTestIncDir,
               ]
milpLibDirs = [CoinUtilsLibDir,
               ClpLibDir,
               OsiLibDir,
               CbcLibDir,
               CpxLibDir,
               GrbLibDir,
               GTestLibDir,
            ]
milpLibFlags = [OsiCpxLibFlags,
                OsiGrbLibFlags,
                CbcLibFlags,
                ClpLibFlags,
                OsiLibFlags,
                CpxLibFlags,
                GrbLibFlags,
                GTestLibFlags,
                ]
##milpSolver = env.Object('milpSolver.cpp',
            ##                         CPPPATH = milpIncDirs,
##                         LIBPATH = milpLibDirs,
##                         CXXFLAGS = flags)
milpSolverTest = env.Program('milpSolverUnitTest',
                                  ['milpSolverTest.cpp',
                                   'milpSolver.cpp'],
                                  CPPPATH = milpIncDirs,
                                  LIBPATH = milpLibDirs,
                                  LIBS = milpLibFlags,
                                  CXXFLAGS = flags,
                                  LINKFLAGS = ['-Wl,-rpath,' + OsiLibDir])
env.Depends(milpSolverTest, [GTestAllLib, GTestMainLib])

## Chemkin source directories and files
#
ChemkinSourceDir = '/mnt/hgfs/DataFromOldLaptop/Data/ModelReductionResearch/Papers/AdaptiveChemistryPaper/AdaptiveChemistry/NonOpenSource/ChemkinII/';
ChemkinSourceList = ['cklib.f', 'pcmach.f','tranlib.f']
ChemkinSourceList = [ChemkinSourceDir + FileName
                     for FileName in ChemkinSourceList]
env.Depends('cklib.f','ckstrt.f')

## Cantera include directorie
#
CanteraStem = '/usr/local/cantera'

if debug:
    CanteraStem += debugString

CanteraIncDir = CanteraStem + '/include/cantera'
CanteraLibDir = CanteraStem + '/lib'
CanteraTestingFlags = ['kinetics', 'thermo', 'tpx', 'ctbase', 'm',]
CanteraLibFlags = ['user', 'oneD', 'zeroD', 'equil', 'kinetics', 'transport',
                    'thermo', 'ctnumerics', 'ctmath', 'tpx', 'ctspectra',
                    'converters', 'ctbase', 'cvode', 'ctlapack', 'ctblas',
                    'ctf2c', 'ctcxx', 'ctf2c', 'm', 'm', 'stdc++']

CxxFortranFlags = ['g2c', 'gfortran']; 

chemSolverIncDir = [CanteraIncDir,
                    StdIncDir,
                    '/usr/local/include',
                    GTestIncDir,
                    ]
chemSolverLibDir = [StdLibDir,
                    CanteraLibDir,
                    GTestLibDir,
                    ]
chemSolverLibFlags = [GTestLibFlags,
                      CxxFortranFlags,
                      CanteraLibFlags,
                      ArmadilloLibFlags,
                      ]

chemSolverTest = env.Program('chemSolverUnitTest',
                        ['chemSolverTest.cpp',
                         'chemSolver.cpp',
                         'ckwrapper.f90'] + ChemkinSourceList,
                        CPPPATH = chemSolverIncDir,
                        LIBPATH = chemSolverLibDir,
                        LIBS = chemSolverLibFlags,
                        CXXFLAGS = flags,
                        FORTRANFLAGS = flags,
                        F90FLAGS = flags)
env.Depends(chemSolverTest, [GTestAllLib, GTestMainLib])

#env.AddPostAction(milpSolverTest, milpSolverTest[0].abspath)
testAlias = env.Alias('test', [milpSolverTest, chemSolverTest])
AlwaysBuild(testAlias)

ckInterp = env.Program('ckinterp', ChemkinSourceDir + 'ckinterp.f')

canteraGTestLibFlags = CanteraTestingFlags + GTestLibFlags

#canteraGTestLibFlags = ['kinetics', 'thermo', 'tpx',
#                        'ctbase',  'm', 'gtest', 'gtest_main', 'pthread']

canteraGTest = env.Program('canteraGTest',
                           'canteraGTest.cpp',
                           CPPPATH = chemSolverIncDir,
                           LIBPATH = chemSolverLibDir,
                           LIBS = canteraGTestLibFlags,
                           CXXFLAGS = flags)
env.Depends(canteraGTest, [GTestAllLib, GTestMainLib])

canteraMemTestLibFlags = CanteraTestingFlags

canteraMemTest = env.Program('canteraMemTest',
                             'canteraMemTest.cpp',
                             CPPPATH = chemSolverIncDir,
                             LIBPATH = chemSolverLibDir,
                             LIBS = canteraMemTestLibFlags,
                             CXXFLAGS = flags)