Improve Travis CI usage

Introduced MARBL_tools/run_test_suite.sh, a bash script that runs a series of
tests; Travis CI now tries to build the sphinx documentation and then runs this
test script. A few improvements to some python scripts along the way:

1. added a --no_pause option to bld_lib.py and bld_exe.py; if run with that
   flag, the user will not be prompted to press [return] between compilers
2. If a build fails, bld_lib.py and bld_exe.py exit immediately (rather than
   attempting to build with the next compiler and eventually returning a status
   of 0)
3. marbl_with_restore.input reflects tracers that are restored in POP

.travis.yml

@@ -4,23 +4,13 @@ before_install:
   - sudo apt-get install gfortran
 install:
   - pip install pyyaml
+  - pip install -r docs/py_requirements.txt
 python:
   - '2.7'
   - '3.6'
 script:
-  - cd MARBL_tools; ./yaml_to_json.py
-  - ./MARBL_generate_settings_file.py
-  - ./MARBL_generate_diagnostics_file.py
-  - cd ../tests/bld_tests; ./bld_exe.py
-  - cd ../unit_tests/get_put; ./get_put.py
-  - cd ../utils_routines; ./marbl_utils.py
-  - cd ../../regression_tests/init; ./init.py
-  - cd ../init-twice; ./init-twice.py
-  - cd ../gen_input_file; ./gen_input_file.py
-  - cd ../requested_diags; ./requested_diags.py
-  - cd ../requested_forcings; ./requested_forcings.py
-  - cd ../requested_restoring; ./requested_restoring.py
-  - cd ../requested_tracers; ./requested_tracers.py
+  - cd docs/src; make html
+  - cd ../../MARBL_tools; ./run_test_suite.sh
 
 branches:
   only:

MARBL_tools/run_test_suite.sh

@@ -0,0 +1,157 @@
+#!/bin/bash
+
+# Convert shell return code to "PASS" or "FAIL"
+# (0 = PASS, all other return codes = FAIL)
+function check_return() {
+  if [ $1 -eq 0 ]; then
+    echo "PASS"
+  else
+    echo "FAIL"
+  fi
+
+}
+
+#################################################
+
+# Output test results
+function print_status() {
+  TEST_CNT=$((TEST_CNT+1))
+  if [ "${STATUS}" == "FAIL" ]; then
+    FAIL_CNT=$((FAIL_CNT+1))
+  fi
+  echo "${TEST_CNT}. $1: ${STATUS}"
+}
+
+#################################################
+
+###############
+# Global Vars #
+###############
+
+MARBL_ROOT=`(cd ..; pwd -P)`
+OUTFILE=${MARBL_ROOT}/.test.out
+TEST_CNT=0
+FAIL_CNT=0
+echo "Test Results:" > $OUTFILE
+
+#########
+# TESTS #
+#########
+
+# Convert YAML to JSON
+cd ${MARBL_ROOT}/MARBL_tools
+echo "$ ./yaml_to_json.py"
+./yaml_to_json.py
+STATUS=$(check_return $?)
+print_status "yaml_to_json.py" >> $OUTFILE
+
+# Generate a settings file (python)
+cd ${MARBL_ROOT}/MARBL_tools
+echo "$ ./MARBL_generate_settings_file.py"
+./MARBL_generate_settings_file.py
+STATUS=$(check_return $?)
+print_status "MARBL_generate_settings_file.py" >> $OUTFILE
+
+# Test MARBL_generate_diagnostics_file.py
+cd ${MARBL_ROOT}/MARBL_tools
+echo "$ ./MARBL_generate_diagnostics_file.py"
+./MARBL_generate_diagnostics_file.py
+STATUS=$(check_return $?)
+print_status "MARBL_generate_diagnostics_file.py" >> $OUTFILE
+
+# Clean Fortran Code
+cd ${MARBL_ROOT}/tests/driver_src
+echo "$ make clean"
+make clean
+STATUS=$(check_return $?)
+print_status "make clean" >> $OUTFILE
+
+# Build libmarbl.a
+cd ${MARBL_ROOT}/tests/bld_tests
+echo "$ ./bld_lib.py --no_pause"
+./bld_lib.py --no_pause
+STATUS=$(check_return $?)
+print_status "bld_lib.py --no_pause" >> $OUTFILE
+
+# Build stand-alone executable (only if library built successfully)
+if [ "${STATUS}" == "PASS" ]; then
+  cd ${MARBL_ROOT}/tests/bld_tests
+  echo "$ ./bld_exe.py --no_pause"
+  ./bld_exe.py --no_pause
+  STATUS=$(check_return $?)
+  print_status "bld_exe.py --no_pause" >> $OUTFILE
+fi
+
+# Only test Fortran executable if build was successful
+if [ "${STATUS}" == "PASS" ]; then
+  # get_put unit test
+  cd ${MARBL_ROOT}/tests/unit_tests/get_put
+  echo "$ ./get_put.py"
+  ./get_put.py
+  STATUS=$(check_return $?)
+  print_status "get_put.py" >> $OUTFILE
+
+  # marbl_utils unit test
+  cd ${MARBL_ROOT}/tests/unit_tests/utils_routines
+  echo "$ ./marbl_utils.py"
+  ./marbl_utils.py
+  STATUS=$(check_return $?)
+  print_status "marbl_utils.py" >> $OUTFILE
+
+  # Initialize MARBL
+  cd ${MARBL_ROOT}/tests/regression_tests/init
+  echo "$ ./init.py"
+  ./init.py
+  STATUS=$(check_return $?)
+  print_status "init.py" >> $OUTFILE
+
+  # Initialize MARBL, clean up memory, initialize again
+  cd ${MARBL_ROOT}/tests/regression_tests/init-twice
+  echo "$ ./init-twice.py"
+  ./init-twice.py
+  STATUS=$(check_return $?)
+  print_status "init-twice.py" >> $OUTFILE
+
+  # Generate a settings file (Fortran)
+  cd ${MARBL_ROOT}/tests/regression_tests/gen_input_file
+  echo "$ ./gen_input_file.py"
+  ./gen_input_file.py
+  STATUS=$(check_return $?)
+  print_status "gen_input_file.py" >> $OUTFILE
+
+  # Print all diagnostics MARBL can provide
+  cd ${MARBL_ROOT}/tests/regression_tests/requested_diags
+  echo "$ ./requested_diags.py"
+  ./requested_diags.py
+  STATUS=$(check_return $?)
+  print_status "requested_diags.py" >> $OUTFILE
+
+  # Print all forcings MARBL requires
+  cd ${MARBL_ROOT}/tests/regression_tests/requested_forcings
+  echo "$ ./requested_forcings.py"
+  ./requested_forcings.py
+  STATUS=$(check_return $?)
+  print_status "requested_forcings.py" >> $OUTFILE
+
+  # Print all restoring fields being requested
+  cd ${MARBL_ROOT}/tests/regression_tests/requested_restoring
+  echo "$ ./requested_restoring.py"
+  ./requested_restoring.py -i ${MARBL_ROOT}/tests/input_files/marbl_with_restore.input
+  STATUS=$(check_return $?)
+  print_status "requested_restoring.py" >> $OUTFILE
+
+  # Print all tracers MARBL computes tendencies for
+  cd ${MARBL_ROOT}/tests/regression_tests/requested_tracers
+  echo "$ ./requested_tracers.py"
+  ./requested_tracers.py
+  STATUS=$(check_return $?)
+  print_status "requested_tracers.py" >> $OUTFILE
+fi
+
+echo "----"
+cat $OUTFILE
+rm -f $OUTFILE
+echo ""
+echo "${TEST_CNT} tests were run, and $FAIL_CNT failed."
+exit ${FAIL_CNT}
+

docs/py_requirements.txt

@@ -0,0 +1,3 @@
+Sphinx==1.7.5
+sphinx-rtd-theme==0.2.5b1
+sphinxcontrib-bibtex==0.4.0

tests/bld_tests/bld_exe.py

@@ -10,11 +10,12 @@
 from general import pause
 
 mt = MARBL_testcase()
-mt.parse_args(desc='Build marbl.exe with every supported compiler on specified machine', HaveCompiler=False, HaveInputFile=False)
+mt.parse_args(desc='Build marbl.exe with every supported compiler on specified machine', HaveCompiler=False,
+              HaveInputFile=False, HasPause=True)
 
 for i,compiler in enumerate(mt.supported_compilers):
   mt.build_exe(loc_compiler=compiler)
   logging.info("Done with %s build" % compiler)
-  if i != len(mt.supported_compilers)-1:
+  if (i != len(mt.supported_compilers)-1) and (mt.pause):
     pause()
 

tests/bld_tests/bld_lib.py

@@ -11,11 +11,12 @@
 from general import pause
 
 mt = MARBL_testcase()
-mt.parse_args(desc='Build lib-marbl.a with every supported compiler on specified machine', HaveCompiler=False, HaveInputFile=False, CleanLibOnly=True)
+mt.parse_args(desc='Build lib-marbl.a with every supported compiler on specified machine', HaveCompiler=False,
+              HaveInputFile=False, HasPause=True, CleanLibOnly=True)
 
 for i,compiler in enumerate(mt.supported_compilers):
   mt.build_lib(loc_compiler=compiler)
   logger.info("Done with %s build" % compiler)
-  if i != len(mt.supported_compilers)-1:
+  if i != len(mt.supported_compilers)-1 and (mt.pause):
     pause()
 

tests/input_files/marbl_with_restore.input

@@ -1,3 +1,5 @@
 tracer_restore_vars(1) = 'SiO3'
 tracer_restore_vars(2) = 'NO3'
 tracer_restore_vars(3) = 'PO4'
+tracer_restore_vars(4) = 'ALK'
+tracer_restore_vars(5) = 'ALK_ALT_CO2'

tests/python_for_tests/marbl_testing_class.py

@@ -27,7 +27,7 @@ def __init__(self):
   # Some tests will let you specify a compiler and / or input file
   # Some tests will require you to specify a machine
   def parse_args(self, desc, HaveCompiler=True, HaveInputFile=True,
-                 CleanLibOnly=False):
+                 HasPause=False, CleanLibOnly=False):
 
     import argparse
 
@@ -42,6 +42,10 @@ def parse_args(self, desc, HaveCompiler=True, HaveInputFile=True,
       parser.add_argument('-i', '--input_file', action='store', dest='input_file',
                           default=None, help='input file to read')
 
+    if HasPause:
+        parser.add_argument('--no_pause', action='store_true', dest='no_pause',
+                            help='do not pause between compilers')
+
     if CleanLibOnly:
       parser.add_argument('--clean', action='store_true',
              help='remove object, module, and library files for MARBL lib')
@@ -112,6 +116,9 @@ def parse_args(self, desc, HaveCompiler=True, HaveInputFile=True,
     self._mpitasks = int(args.mpitasks)
     sys.stdout.flush()
 
+    if HasPause:
+        self.pause = not args.no_pause
+
     # ERROR CHECKING
     if HaveCompiler:
       if not self._compiler in self.supported_compilers:
@@ -135,7 +142,10 @@ def build_lib(self, loc_compiler=None):
     makecmd = 'make %s' % loc_compiler
     if self._mpitasks > 0:
       makecmd += ' USEMPI=TRUE'
-    sh_command('cd %s; %s' % (src_dir, makecmd))
+    status_code = sh_command('cd %s; %s' % (src_dir, makecmd))
+    if status_code != 0:
+        logging.error("ERROR building MARBL library")
+        sys.exit(1)
 
   # -----------------------------------------------
 
@@ -153,7 +163,10 @@ def build_exe(self, loc_compiler=None):
     makecmd = 'make %s' % loc_compiler
     if self._mpitasks > 0:
       makecmd += ' USEMPI=TRUE'
-    sh_command('cd %s; %s' % (drv_dir, makecmd))
+    status_code = sh_command('cd %s; %s' % (drv_dir, makecmd))
+    if status_code != 0:
+        logging.error("ERROR building MARBL stand-alone driver")
+        sys.exit(1)
 
   # -----------------------------------------------
 
@@ -198,7 +211,7 @@ def run_exe(self):
     status_code = sh_command(execmd)
     if status_code != 0:
         logging.error("ERROR in executable")
-        sys.exit(status_code)
+        sys.exit(1)
 
   # -----------------------------------------------
   # PRIVATE ROUTINES