Merge pull request #29 from KineticPreProcessor/dev

KPP version 2.4.0 release

.ci-pipelines/Dockerfile

@@ -17,6 +17,10 @@ ENV KPP_HOME=/kpp
 ENV CC=gcc CXX=g++ FC=gfortran
 ENV F90=$FC F9X=$FC F77=$FC
 
+# for CI, MAX_EQN and MAX_SPECIES must be < 1024:
+RUN sed -i 's/#define MAX_EQN .*/#define MAX_EQN 1023/g' /kpp/src/gdata.h \
+    && sed -i 's/#define MAX_SPECIES .*/#define MAX_SPECIES 1023/g' /kpp/src/gdata.h
+
 # switch compiler to use gfortran instead of ifort
 RUN sed -i 's/COMPILER = INTEL/#COMPILER = INTEL/g' /kpp/util/Makefile.f90 \
     && sed -i 's/#COMPILER = GFORTRAN/COMPILER = GFORTRAN/g' /kpp/util/Makefile.f90

.ci-pipelines/build-testing.yml

@@ -13,6 +13,7 @@ trigger:
       - dev*
       - patch*
       - bugfix*
+      - MECCA*
 pr:
   branches:
     include:

.ci-pipelines/ci-manual-cleanup-script.sh

@@ -0,0 +1,31 @@
+#!/bin/sh
+
+########################################################################
+### CI tests for github.com/KineticPreProcessor/KPP                  ###
+### NOTE: This script runs CI-tests manually (for testing/debugging) ###
+########################################################################
+
+# List of tests (add more as necessary; separate each with a space)
+all_tests="radau90 rk rktlm ros rosadj rosenbrock90 rostlm saprc2006 sd sdadj small_f90"
+
+# Run each test
+# Check status of each individual operation and exit if any do not complete
+for this_test in $all_tests; do
+
+    cd ../ci-tests/$this_test
+    [ $? -ne 0 ] && exit 1
+
+    echo ""
+    echo ">>>>>>>> Making clean for $this_test <<<<<<<<"
+    echo ""
+    make -f Makefile_$this_test distclean
+
+    # Also remove other output files from the tests
+    rm -f *.m
+
+    cd ..
+
+done
+
+# Return w/ success
+exit 0

.ci-pipelines/ci-manual-testing-script.sh

@@ -0,0 +1,45 @@
+#!/bin/sh
+
+########################################################################
+### CI tests for github.com/KineticPreProcessor/KPP                  ###
+### NOTE: This script runs CI-tests manually (for testing/debugging) ###
+########################################################################
+
+# List of tests (add more as necessary; separate each with a space)
+all_tests="radau90 rk rktlm ros rosadj rosenbrock90 rostlm saprc2006 sd sdadj small_f90"
+
+# Run each test
+# Check status of each individual operation and exit if any do not complete
+for this_test in $all_tests; do
+
+    cd ../ci-tests/$this_test
+    [ $? -ne 0 ] && exit 1
+
+    echo ""
+    echo ">>>>>>>> Generating $this_test mechanism with KPP <<<<<<<<"
+    echo ""
+    ../../bin/kpp $this_test.kpp
+    [ $? -ne 0 ] && exit 1
+
+    echo ""
+    echo ">>>>>>>> Building the $this_test test executable <<<<<<<<<"
+    echo ""
+    make -f Makefile_$this_test COMPILER=GFORTRAN
+    [ $? -ne 0 ] && exit 1
+
+    echo ""
+    echo ">>>>>>>> Running the $this_test test <<<<<<<<"
+    echo ""
+    ./$this_test.exe
+    [ $? -ne 0 ] && exit 1
+
+    echo ""
+    echo ">>>>>>>> $this_test test was successful! <<<<<<<<"
+    echo ""
+
+    cd ..
+
+done
+
+# Return w/ success
+exit 0

.ci-pipelines/ci-testing-script.sh

@@ -1,4 +1,42 @@
 #!/bin/sh
-cd /kpp/examples
-../bin/kpp small_f90.kpp
-make -f Makefile_small_f90
+
+########################################################################
+### CI tests for github.com/KineticPreProcessor/KPP                  ###
+########################################################################
+
+# List of tests (add more as necessary; separate each with a space)
+all_tests="radau90 rk rktlm ros rosadj rosenbrock90 rostlm saprc2006 sd sdadj small_f90"
+
+# Run each test
+# Check status of each individual operation and exit if any do not complete
+for this_test in $all_tests; do
+
+    cd /kpp/ci-tests/$this_test
+    [ $? -ne 0 ] && exit 1
+
+    echo ""
+    echo ">>>>>>>> Generating $this_test mechanism with KPP <<<<<<<<"
+    echo ""
+    ../../bin/kpp $this_test.kpp
+    [ $? -ne 0 ] && exit 1
+
+    echo ""
+    echo ">>>>>>>> Building the $this_test test executable <<<<<<<<<"
+    echo ""
+    make -f Makefile_$this_test COMPILER=GFORTRAN
+    [ $? -ne 0 ] && exit 1
+
+    echo ""
+    echo ">>>>>>>> Running the $this_test test <<<<<<<<"
+    echo ""
+    ./$this_test.exe
+    [ $? -ne 0 ] && exit 1
+
+    echo ""
+    echo ">>>>>>>> $this_test test was successful! <<<<<<<<"
+    echo ""
+
+done
+
+# Return w/ success
+exit 0

.gitignore

@@ -1,12 +1,60 @@
-# OS generated files
-.DS_Store
+# https://www.atlassian.com/git/tutorials/saving-changes/gitignore
+# https://linuxize.com/post/gitignore-ignoring-files-in-git
 
-# generated output files
-*.log
+# temporary files:
+*.~*
+*~
+.\#*
+\#*
+
+# files generated by bison:
+/src/lex.yy.c
+/src/y.tab.c
+/src/y.tab.h
+
+# from compiler:
+*.mod
 *.o
-src/y.tab.h
-src/y.tab.c
-src/lex.yy.c
 
-# executables
-bin/
+# results from ci-tests:
+/ci-tests/**/*.m
+/ci-tests/**/*results*
+
+# keep empty directory for executables, but not its contents:
+/bin/*
+!/bin/.gitkeep
+
+# KPP-generated files:
+*_Function*
+*_Global*
+*_Hessian*
+*_HessianSP*
+*_Initialize*
+*_Integrator*
+*_Jacobian*
+*_JacobianSP*
+*_LinearAlgebra*
+*_Main*
+*.map
+*_mex_Fun*
+*_mex_Hessian*
+*_mex_Jac_SP*
+*_Model*
+*_Monitor*
+*_Parameters*
+*_Precision*
+*_Rates*
+*_Stoichiom*
+*_StoichiomSP*
+*_Util*
+Makefile_*
+
+# LaTeX and BibTeX files:
+/manual/*.aux
+/manual/*.bbl
+/manual/*.blg
+/manual/*.log
+/manual/*.toc
+
+# are there any *.dat files to exclude?
+*.dat