Unverified Commit 58710a43 authored by Tyler Wilson's avatar Tyler Wilson Committed by GitHub
Browse files

Merge pull request #485 from ihumphrey-usgs/cmake 

Cmake integration with dev, preparing for release branch off
parents bb9542ad 8a4c96dc

.gitignore

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@@ -42,4 +42,12 @@ print.prt 
*/tsts/*/input/*

*/tsts/*/truth/*

*/tsts/*/output/*

data/
 
*/build/

*/install/

Jenkinsfile

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pipeline { 

    agent none 

    environment {

        ISISROOT="${workspace}" + "/build/"

        ISIS3TESTDATA="/usgs/cpkgs/isis3/testData/"

        ISIS3DATA="/usgs/cpkgs/isis3/data/"

    }

    stages {

        stage('Fedora25') {

            agent {

                docker {

                    label 'cmake'

                    image 'chrisryancombs/docker_isis'

                    args  '''\

                            -v /usgs/cpkgs/isis3/data:/usgs/cpkgs/isis3/data \

                            -v /usgs/cpkgs/isis3/testData:/usgs/cpkgs/isis3/testData\

                            -v /usgs/cpkgs/isis3/isis3mgr_scripts:/usgs/cpkgs/isis3/isis3mgr_scripts

                          '''  

                }

            }

            steps { 

                sh """

                    conda env create -n isis3 -f environment.yml

                    source activate isis3

                    mkdir -p ./install ./build && cd build

                    source /usgs/cpkgs/isis3/isis3mgr_scripts/initIsisCmake.sh .

                    cmake -GNinja -DJP2KFLAG=OFF -Dpybindings=OFF -DCMAKE_INSTALL_PREFIX=../install -Disis3Data=/usgs/cpkgs/isis3/data -Disis3TestData=/usgs/cpkgs/isis3/testData ../isis

                    set +e

                    ninja -j8 && ninja install

                    source /usgs/cpkgs/isis3/isis3mgr_scripts/initIsisCmake.sh .

                    ctest -V -R _unit_ --timeout 500

                    ctest -V -R _app_ --timeout 500

                    ctest -V -R _module_ --timeout 500

                    """

            }

        }

        stage('CentOS7') {

            agent {

                docker {

                    label 'cmake_cool'

                    image 'chrisryancombs/docker_isis_centos'

                    args  '''\

                            -v /usgs/cpkgs/isis3/data:/usgs/cpkgs/isis3/data \

                            -v /usgs/cpkgs/isis3/testData:/usgs/cpkgs/isis3/testData\

                            -v /usgs/cpkgs/isis3/isis3mgr_scripts:/usgs/cpkgs/isis3/isis3mgr_scripts

                          '''  

                }

            }

            steps {

                sh """

                    conda env create -n isis3 -f environment.yml

                    source activate isis3

                    cd build

                    set +e

                    source /usgs/cpkgs/isis3/isis3mgr_scripts/initIsisCmake.sh .

                    ctest -V -R _unit_ --timeout 500

                    ctest -V -R _app_ --timeout 500

                    ctest -V -R _module_ --timeout 500

                """

            }

        }

    }

//    post {

//        success {

//            sh 'pwd && ls'

//            archiveArtifacts artifacts: "build/objects/*.o"

//        }

//        always {

//            mail to: 'ccombs@usgs.gov',

//                    subject: "Build Finished: ${currentBuild.fullDisplayName}",

//                    body: "Link: ${env.BUILD_URL}"

//            sh "rm -rf build/* && rm -rf install/*"

//            cleanWs()

//        }

//    }

}

README.md

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# ISIS3



[![Join the chat at https://gitter.im/USGS-Astrogeology/isis3_cmake](https://badges.gitter.im/USGS-Astrogeology/isis3_cmake.svg)](https://gitter.im/USGS-Astrogeology/isis3_cmake?utm_source=badge&utm_medium=badge&utm_campaign=pr-badge&utm_content=badge)



Integrated Software for Imagers and Spectrometers ISIS3 public release site

configure.py

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import os

import sys

import sipconfig

import sipdistutils

import PyQt5

import subprocess

import argparse



from os.path import splitext

from os.path import dirname

from glob import glob

from distutils.spawn import find_executable



from PyQt5.QtCore import PYQT_CONFIGURATION

from plio.utils.utils import find_in_dict

from PyQt5.QtCore import PYQT_CONFIGURATION as qtconfigdict

from sipconfig import ModuleMakefile



def main (module):

    # The name of the SIP build file generated by SIP and used by the build

    # system.

    sipy_sip_dir = "sipfiles/"

    module = sipy_sip_dir+module + '.sip'

    build_file = "bundle"+".sbf"

    target = module+".so"



    # Get the extra SIP flags needed by the imported qt module.  Note that

    # this normally only includes those flags (-x and -t) that relate to SIP's

    # versioning system.

    qt_sip_flags = qtconfigdict["sip_flags"]



    # sip_bin = current_env_path + "/bin/sip"

    sip_bin = find_executable('sip')

    pyqt_sip_dir = dirname(dirname(sip_bin)) + "/share/sip/PyQt5"



    # Get the PyQt configuration information.

    config = sipconfig.Configuration()



    # Run SIP to generate the code.  Note that we tell SIP where to find the qt

    # module's specification files using the -I flag.



    errcode = os.system(" ".join([sip_bin, "-e","-c", ".", "-b", build_file, "-I",

        pyqt_sip_dir, qt_sip_flags, module]))



    if errcode != 0:

        print('sip exited with non zero error code: {}'.format(errcode))



    # We are going to install the SIP specification file for this module and

    # its configuration module.

    installs = []

    installs.append([module, os.path.join(pyqt_sip_dir, "isis3")])



    isis_root = os.getenv("ISISROOT")

    if not isis_root:

        raise("Please set ISIS")



    extra_libs = ["$(ALLLIBS)", "-Wl,-rpath,"+isis_root+"/lib", "-Wl,-rpath,"+isis_root+"/3rdParty/lib"]



    makefile = ModuleMakefile(configuration=config, build_file=build_file, installs=installs)

    makefile.extra_cxxflags = ["$(ALLINCDIRS)", "-Wstrict-aliasing=0", "-Wno-unused-variable"]

    makefile.extra_lflags =  ["$(ALLLIBDIRS)"]

    makefile.extra_include_dirs = [x[0] for x in os.walk('incs/')]

    makefile.extra_lib_dirs = [isis_root + '/3rdParty/lib', isis_root + 'lib']

    makefile.generate()



    # add import line for isismake.os

    isis_makefile = "include " + isis_root + "/make/isismake.os"



    with open("Makefile", 'r+') as f:

        content = f.read()

        content = content.replace("LIBS =", "LIBS = " + ' '.join(extra_libs))

        f.seek(0, 0)

        f.write(isis_makefile + '\n\n' + content)



if __name__ == "__main__":

    clean = ['cpp', 'c', 'h', 'hpp', 'o', 'sbf']



    # If clean is passed in, clear up all the files genreated by the scripts

    if len(sys.argv) > 1 and sys.argv[1] == 'clean':

        files = []

        for filetype in clean:

            files.extend(glob('*.{}'.format(filetype)))



        for f in files:

            os.remove(f)

        exit()



    main('master')

environment.yml

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channels:

  - usgs-astrogeology

  - conda-forge

  - probcomp

  - anaconda

  - defaults



dependencies:

  - armadillo==8.200.0

  - blas==1.1=openblas

  - bullet==2.86.1=0

  - bz2file==0.98

  - bzip2==1.0.6=1

  - cmake==3.9.1=0

  - cspice==66=h470a237_3

  - curl==7.60.0=0

  - doxygen==1.8.14=0

  - eigen==3.3.3=0

  - embree==2.14.0=0

  - geos==3.5.1

  - geotiff==1.4.2=1

  - gmm==5.0

  - gmp==6.1.2=0

  - gsl==2.2.1=blas_openblas_3

  - hdf5==1.8.18=2

  - icu==58.2=0

  - jama==125

  - jpeg==9b=2

  - kakadu==1

  - krb5==1.14.2=0

  - libpng>=1.6.34

  - libprotobuf==3.5.2

  - libtiff==4.0.9=0

  - libxml2==2.9.7=0

  - make

  - mesalib==17.2.0=0

  - mysql==5.7.20

  - mysql-connector-c==6.1.6=0

  - nanoflann==1.2.2

  - ninja==1.7.2=0

  - conda-forge/label/gcc7::nn

  # - numpy==1.13.3=py36_blas_openblas_200

  - openblas==0.2.19=2

  - opencv

  - openssl==1.0.2n=0

  - patchelf==0.9

  - pcl==1.8.1

  - pip==9.0.1

  - protobuf==3.5.2

  # - pyqt==5.6.0

  - python==3.6

  - qhull==7.2.0=0

  - qt=5.9.6

  - qwt=6.1.3

  - setuptools=38.5.1

  - sip==4.18

  - sqlite==3.13.0=1

  - suitesparse==4.5.4=blas_openblas_200

  - superlu==5.2.1=blas_openblas_201

  - tnt==126=0

  - wheel==0.30.0

  - x264==20131218

  - xalan-c==1.11

  - xerces-c==3.1.4=0

  - xorg-kbproto==1.0.7=1

  - xorg-libice

  - xorg-libsm

  - xorg-libx11==1.6.4=6

  - xorg-libxi

  - zlib==1.2.11=0



prefix: /scratch/anaconda3/envs/isis