Refactor C-I test scripts and update Dockerfile to avoid issues

.ci-pipelines/ci-common-defs.sh
- Abstracted reusable code into this script, which is sourced
  by the other C-I test scripts.
- Renamed ALL_TESTS to GENERAL_TESTS
- Now put the X_minver test in the MINVERSION_TEST variable

.ci-pipelines/ci-cleanup-script.sh
.ci-pipelines/ci-testing-script.sh
- Now gets common variables & functions from ci-common-defs.sh
- Now execute the test for #MINVERSION separately
- Now uses #!/bin/bash instead of #!/bin/sh
- Now uses absolute paths instead of relative paths

./ci-manual-cleanup-script.sh
./ci-manual-testing-script.sh
- Removed

./ci-pipelines/Dockerfile
- Updated comments
- Add commands to make sure ci-common-defs.sh and ci-testing-script.sh
  are made executable

Signed-off-by: Bob Yantosca <yantosca@seas.harvard.edu>

.ci-pipelines/Dockerfile

@@ -3,20 +3,20 @@
 # `docker build -f ./.ci-pipelines/Dockerfile --platform=amd64 -t kpp-build .` from top level of project
 # To exec into the container run: `docker run -it --entrypoint /bin/bash kpp-build`
 
-# Set platform/OS, a reference to maintainers, and the working directory.
+# Set OS, a reference to maintainers, and the working directory.
 #
-# NOTE: The --platform=amd64 will make sure that the C-I tests will always
-# run with AMD64 hardware.  Otherwise, Docker will use the architecture
-# of your current hardware, which might cause differences in library paths
+# NOTE: Add --platform=amd64 (in .build-testing.yml and in your local
+# aliases for 'docker build'.  This will make sure that the C-I tests always
+# run on AMD64 hardware.  Otherwise, Docker will use the architecture of
+# your current hardware, which might cause differences in library paths
 # (e.g. /lib/aarch64-linux-gnu on Mac/M1 vs. /lib/x86_64-linux-gnu on Linux).
 #   -- Lucas Estrada & Bob Yantosca (06 Jul 2022)
 FROM ubuntu:20.04
 LABEL maintainer="GEOS-Chem Support Team <geos-chem-support@g.harvard.edu>"
 WORKDIR /kpp
 
 # Install KPP software dependencies
-RUN apt-get update && apt-get install -y \
-    git gcc gfortran make flex bison
+RUN apt-get update && apt-get install -y git gcc gfortran make flex bison
 
 COPY . .
 
@@ -35,7 +35,9 @@ RUN sed -i 's/#define MAX_EQN .*/#define MAX_EQN 1023/g' /kpp/src/gdata.h \
 RUN sed -i 's/FLEX_LIB_DIR = \/usr\/lib/FLEX_LIB_DIR = \/lib\/x86_64-linux-gnu/' /kpp/src/Makefile.defs
 
 # Build KPP executable and ensure testing scripts are executable
-RUN cd /kpp/src/ && make && chmod +x /kpp/.ci-pipelines/ci-*.sh
+RUN cd /kpp/src/ && make
+RUN chmod +x /kpp/.ci-pipelines/ci-common-defs.sh
+RUN chmod +x /kpp/.ci-pipelines/ci-testing-script.sh
 
 # Run C-I tests
 RUN /kpp/.ci-pipelines/ci-testing-script.sh

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

@@ -0,0 +1,26 @@
+#!/bin/bash
+
+########################################################################
+### C-I test cleanup script for github.com/KineticPreProcessor/KPP   ###
+###                                                                  ###
+### Use this if you have run the C-I tests manually, and wish to     ###
+### remove compiled files (*.o, *.mod, *.exe) from C-I test folders. ###
+########################################################################
+
+# Load common variables and functions
+. ${KPP_HOME}/.ci-pipelines/ci-common-defs.sh
+
+# Current directory
+cwd=$(pwd -P)
+
+# Clean up files in each C-I test folder
+for this_test in ${GENERAL_TESTS}; do
+    clean_ci_test_folder "${this_test}" "${cwd}"
+done
+
+# Remove any log files used to store C-I test results
+cd $cwd
+rm -fv *log*
+
+# Return w/ success
+exit 0

.ci-pipelines/ci-common-defs.sh

@@ -0,0 +1,128 @@
+########################################################################
+### Common variables and functions for the C-I tests                 ###
+########################################################################
+
+#=======================================================================
+# Lists of C-I tests
+#=======================================================================
+
+# Testing different mechanisms
+GENERAL_TESTS="C_rk
+C_rosadj
+C_sd
+C_sdadj
+C_small_strato
+F90_lsode
+F90_radau
+F90_rk
+F90_rktlm
+F90_ros
+F90_rosadj
+F90_ros_autoreduce
+F90_rosenbrock
+F90_ros_split
+F90_rostlm
+F90_ros_upcase
+F90_saprc_2006
+F90_sd
+F90_sdadj
+F90_seulex
+F90_small_strato
+"
+# Testing if #MINVERSION works
+MINVERSION_TEST="X_minver"
+
+#=======================================================================
+# Functions
+#=======================================================================
+
+# Returns the path to a C-I test folder
+function get_ci_test_path() {
+    echo "${KPP_HOME}/ci-tests/${1}"
+    return
+}
+
+# Run a C-I test
+function run_ci_test() {
+
+    # Arguments
+    this_test=${1}     # Name of test
+    return_dir=${2}    # Directory where we will return upon test completion
+
+    # Navigate to C-I test folder (or exit if error)
+    test_path=$(get_ci_test_path "${this_test}")
+    cd $test_path
+    [[ $? -ne 0 ]] && exit 1
+
+    echo ""
+    echo ">>>>>>>> Generating ${this_test} mechanism with KPP <<<<<<<<"
+    echo ""
+    ${KPP_HOME}/bin/kpp $this_test.kpp
+    [[ $? -ne 0 ]] && exit 1
+
+    echo ""
+    echo ">>>>>>>> Building the ${this_test} test executable <<<<<<<<<"
+    echo ""
+    make -j -f Makefile_$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 ""
+
+    # Navigate back to original path and return w/ success
+    cd $return_dir
+}
+
+# Test if the #MINVERSION command works
+function run_minversion_ci_test() {
+
+    # Arguments
+    this_test=${1}     # Name of test
+    return_dir=${2}    # Directory where we will return upon test completion
+
+    # Navigate to test folder (or exit if error)
+    test_path=$(get_ci_test_path "${MINVERSION_TEST}")
+    cd ${test_path}
+    [[ $? -ne 0 ]] && exit 1
+
+    # Build the mechanism with KPP
+    echo ""
+    echo ">>>>>>>> Generating ${this_test} mechanism with KPP <<<<<<<<"
+    echo ""
+    ${KPP_HOME}/bin/kpp ${MINVERSION_TEST}.kpp
+
+    # Navigate back to original path and return w/ success
+    cd $return_dir
+}
+
+# Removes compiled files in C-I test folders
+function clean_ci_test_folder()  {
+
+    # Arguments
+    this_test=${1}     # Name of test
+    return_dir=${2}    # Directory where we will return upon test completion
+
+    # Navigate to test folder (or exit if error)
+    test_path=$(get_ci_test_path "${this_test}")
+    cd ${test_path}
+    [[ $? -ne 0 ]] && exit 1
+
+    echo ""
+    echo ">>>>>>>> Making distclean for ${this_test} <<<<<<<<"
+    echo ""
+    make -f Makefile_${this_test} distclean
+
+    # Also remove other output files from the tests
+    rm -f *.m
+    rm -f Makefile.${this_test}
+
+    # Navigate back to original path and return w/ success
+    cd ${cwd}
+}

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

@@ -1,45 +1,27 @@
-#!/bin/sh
+#!/bin/bash
 
 ########################################################################
-### CI tests for github.com/KineticPreProcessor/KPP                  ###
+### C-I test script for github.com/KineticPreProcessor/KPP           ###
 ########################################################################
 
-# Get the list of CI test folders in ALL_TESTS
-source /kpp/.ci-pipelines/ci-testing-list.sh
+# Load common variables and functions
+. ${KPP_HOME}/.ci-pipelines/ci-common-defs.sh
 
-# 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 $this_test test executable <<<<<<<<<"
-    echo ""
-    make -j -f Makefile_$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 ">>>>>>>> $this_test test was successful! <<<<<<<<"
-    echo ""
+# Current directory
+cwd=$(pwd -P)
 
+# Run C-I tests with various mechanism + integrator combinations
+for this_test in ${GENERAL_TESTS}; do
+    run_ci_test "${this_test}" "${cwd}"
 done
 
+# Run a C-I test to see if the #MINVERSION command works as advertised
+run_minversion_ci_test "${MINVERSION_TEST}" "${cwd}"
+
 # Return w/ success
 echo ""
 echo ">>>>>>>> All tests finished succesfully! <<<<<<<<"
 echo ""
+
+# Return with success
 exit 0