Add support for GitLab CI

There is a lingering issue with the *_host* tests.
Their failure will not be reported correctly by the ci_print_failing.py
script, since error messages are going to stderr and not to the output
file.

Author: robertodr

.gitignore

@@ -28,7 +28,7 @@
 *.app
 
 # Build directories
-*build*
+*build*/
 
 # Python stuff
 *.pyc

.gitlab-ci.yml

@@ -1,16 +1,25 @@
 before_script:
-    - ls -la
-    - apt-get update -y
-    - apt-get install gcc g++ gfortran make cmake zlib1g-dev python-dateutil python-pyparsing python-numpy python-matplotlib python-pip python-setuptools python-dev -y
-gcc_debug:
-    script:
-        - "python setup.py --cxx=g++ --cc=gcc --fc=gfortran --type=debug"
-        - cd build
-        - make
-        - ctest
-gcc_debug_nocxx11:
-    script:
-        - "python setup.py --cxx=g++ --cc=gcc --fc=gfortran --type=debug --cmake-options='-DENABLE_CXX11_SUPPORT=OFF'"
-        - cd build
-        - make
-        - ctest
+  - ls -la
+  - apt-get update -y
+  - apt-get install cmake zlib1g-dev libboost-all-dev python-dateutil python-pyparsing python-numpy python-matplotlib python-pip python-setuptools python-dev -y
+  - python -V
+  - cmake --version
+  - g++ --version
+  - gcc --version
+  - gfortran --version
+
+variables:
+  CTEST_COMMAND: "ctest --parallel 2 --output-on-failure --verbose --dashboard Experimental --track GitLabCI"
+
+gcc:
+  image: gcc:5.4
+  script:
+    - python setup.py --cxx=g++ --cc=gcc --fc=gfortran --type=release
+    - cd build
+    - ../.scripts/ci_build.sh
+    - python ../.scripts/ci_test.py ${CTEST_COMMAND}
+    - python ../.scripts/ci_print_failing.py
+  artifacts:
+    paths:
+      - build.log
+      - full_ctest_output.dat

.scripts/ci_build.sh

@@ -0,0 +1,14 @@
+#!/usr/bin/env bash
+
+# The return code will capture an error from ANY of the functions in the pipe
+set -o pipefail
+cmake --build . -- --jobs=2 VERBOSE=1 | tee build.log | grep "Building"
+RESULT=$?
+
+if [ $RESULT -eq 0 ]; then
+  echo build succeeded
+else
+  echo build failed
+  cat build.log
+  exit 1
+fi

.scripts/ci_print_failing.py

@@ -0,0 +1,29 @@
+#!/usr/bin/env python
+import re
+import sys
+
+badtests = []
+testfail = re.compile(r'^\s*(?P<num>\d+) - (?P<name>\w+(?:-\w+)*) \(Failed\)\s*$')
+
+with open('full_ctest_output.dat', 'r') as outfile:
+    ctestout = outfile.readlines()
+
+ctest_exit_status = int(ctestout[0])
+if len(ctestout[1:]) == 0:
+    sys.stdout.write('\n  <<<  All test cases have passed!  >>>\n\n')
+else:
+    sys.stdout.write('\n  <<<  Failing outputs follow.  >>>\n\n')
+
+for line in ctestout[1:]:
+    linematch = testfail.match(line)
+    if linematch:
+        bad = linematch.group('name')
+        sys.stdout.write('\n\n {} failed. Here is the output:\n'.format(bad))
+
+        badoutfile = 'tests/' + bad + '.log'
+
+        with open(badoutfile, 'r') as ofile:
+            sys.stdout.write(ofile.read())
+
+# <<<  return ctest error code  >>>
+sys.exit(ctest_exit_status)

.scripts/ci_test.py

@@ -0,0 +1,52 @@
+#!/usr/bin/env python
+import sys
+import time
+import subprocess
+
+def run_ctest(command):
+    """
+    Execute CTest command
+    """
+    return subprocess.Popen(command,
+                            bufsize=0,
+                            stdout=subprocess.PIPE,
+                            universal_newlines=True)
+
+ctest_command = sys.argv[1:]
+print("CTest command \"{}\"".format(' '.join(ctest_command)))
+retcode = run_ctest(ctest_command)
+print_all = False
+ctestout = ''
+while True:
+    data = retcode.stdout.readline()
+#    print(data.split())
+    if not data:
+        break
+
+    if '% tests passed,' in data:
+        print_all = True
+
+    sdata = data.split()
+    test_line = ('Test' in sdata) and ('sec' in sdata)
+    start_line = ('Start' in sdata)
+    if test_line or start_line or print_all:
+        sys.stdout.write(data)  # screen
+    #print sys.stdout.write(data)
+    ctestout += data  # string
+
+while True:
+    retcode.poll()
+    exstat = retcode.returncode
+    if exstat is not None:
+        ctest_exit_status = exstat
+        break
+    time.sleep(0.1)
+
+# <<<  identify failed tests and cat their output  >>>
+sys.stdout.write("""\n  <<<  CTest complete with status %d.  >>>\n\n""" %
+                 (ctest_exit_status))
+
+ctestout = str(ctest_exit_status) + "\n" + ctestout
+
+with open('full_ctest_output.dat', 'w') as outfile:
+    outfile.write(ctestout)

.travis.yml

@@ -349,8 +349,10 @@ before_script:
 - ${Fortran_COMPILER} --version
 - python setup.py --cxx=${CXX_COMPILER} --cc=${C_COMPILER} --fc=${Fortran_COMPILER} --type=${BUILD_TYPE} --cmake-options='-Hprojects/CMake' ${STATIC} ${COVERAGE}
 - cd build
+- ../.scripts/ci_build.sh
 script:
-- ctest --parallel 2 --output-on-failure --verbose --dashboard Experimental --track TravisCI
+- python ../.scripts/ci_test.py ctest --parallel 2 --output-on-failure --verbose --dashboard Experimental --track TravisCI
+- python ../.scripts/ci_print_failing.py
 after_success:
 - |
   if [[ "${COVERAGE}" = true ]]; then

cmake/custom/test.cmake

@@ -9,10 +9,9 @@ macro(add_Catch_test _name _labels)
   endforeach()
   unset(_labels)
 
-  # This is the unit tests runner
-  set(RUNNER ${PROJECT_BINARY_DIR}/tests/unit_tests --success)
-
-  add_test(NAME ${_name} COMMAND ${RUNNER} [${_name}])
+  add_test(NAME ${_name}
+           COMMAND ${PROJECT_BINARY_DIR}/tests/unit_tests [${_name}] --success --out ${PROJECT_BINARY_DIR}/tests/${_name}.log --durations yes
+           WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR})
 
   if(labels)
     set_tests_properties(${_name} PROPERTIES LABELS "${labels}")

src/interface/Input.hpp

@@ -38,7 +38,6 @@ struct BIOperatorData;
 struct CavityData;
 struct GreenData;
 struct SolverData;
-struct TDSolverData;
 } // namespace pcm
 
 #include "utils/Molecule.hpp"

src/utils/Atom.hpp

@@ -85,7 +85,7 @@ struct Atom {
         symbol(sym) {}
 };
 
-typedef tuple<std::string, std::vector<Atom> > RadiiSet;
+typedef pcm::tuple<std::string, std::vector<Atom> > RadiiSet;
 
 namespace detail {
 /*! \brief Returns a vector<Atom> containing Bondi van der Waals

tests/C_host/C_host.c

@@ -39,7 +39,7 @@ void host_writer(const char * message) { fprintf(output, "%s\n", message); }
 
 int main() {
 
-  output = fopen("C_host.log", "w+");
+  output = fopen("C_host.out", "w+");
   if (!pcmsolver_is_compatible_library()) {
     fprintf(stderr, "%s\n", "PCMSolver library not compatible");
     exit(EXIT_FAILURE);
@@ -48,17 +48,36 @@ int main() {
   fprintf(output, "%s\n", "Starting a PCMSolver calculation");
   // Use C2H4 in D2h symmetry
   double charges[NR_NUCLEI] = {6.0, 1.0, 1.0, 6.0, 1.0, 1.0};
-  double coordinates[3 * NR_NUCLEI] = {
-      0.0, 0.000000, 1.257892,  0.0, 1.745462, 2.342716,  0.0, -1.745462, 2.342716,
-      0.0, 0.000000, -1.257892, 0.0, 1.745462, -2.342716, 0.0, -1.745462, -2.342716};
+  double coordinates[3 * NR_NUCLEI] = {0.0,
+                                       0.000000,
+                                       1.257892,
+                                       0.0,
+                                       1.745462,
+                                       2.342716,
+                                       0.0,
+                                       -1.745462,
+                                       2.342716,
+                                       0.0,
+                                       0.000000,
+                                       -1.257892,
+                                       0.0,
+                                       1.745462,
+                                       -2.342716,
+                                       0.0,
+                                       -1.745462,
+                                       -2.342716};
   // This means the molecular point group has three generators:
   // the Oxy, Oxz and Oyz planes
   int symmetry_info[4] = {3, 4, 2, 1};
   struct PCMInput host_input = pcmsolver_input();
 
-  pcmsolver_context_t * pcm_context =
-      pcmsolver_new(PCMSOLVER_READER_HOST, NR_NUCLEI, charges, coordinates,
-                    symmetry_info, &host_input, host_writer);
+  pcmsolver_context_t * pcm_context = pcmsolver_new(PCMSOLVER_READER_HOST,
+                                                    NR_NUCLEI,
+                                                    charges,
+                                                    coordinates,
+                                                    symmetry_info,
+                                                    &host_input,
+                                                    host_writer);
 
   pcmsolver_print(pcm_context);
 
@@ -89,8 +108,8 @@ int main() {
   // This is the B3g irreducible representation
   irrep = 3;
   pcmsolver_compute_response_asc(pcm_context, mep_lbl, asc_neq_B3g_lbl, irrep);
-  pcmsolver_get_surface_function(pcm_context, grid_size, asc_neq_B3g,
-                                 asc_neq_B3g_lbl);
+  pcmsolver_get_surface_function(
+      pcm_context, grid_size, asc_neq_B3g, asc_neq_B3g_lbl);
 
   // Equilibrium ASC in B3g symmetry.
   // This is an internal check: the relevant segment of the vector
@@ -104,33 +123,39 @@ int main() {
   // Cavity size
   const int ref_size = 576;
   if (grid_size != ref_size) {
-    fprintf(stderr, "%s\n", "Error in the cavity size, please file an issue on: "
-                            "https://github.com/PCMSolver/pcmsolver");
+    fprintf(stderr,
+            "%s\n",
+            "Error in the cavity size, please file an issue on: "
+            "https://github.com/PCMSolver/pcmsolver");
     exit(EXIT_FAILURE);
   } else {
     fprintf(output, "%s\n", "Test on cavity size: PASSED");
   }
   // Irreducible cavity size
   const int ref_irr_size = 72;
   if (irr_grid_size != ref_irr_size) {
-    fprintf(stderr, "%s\n", "Error in the irreducible cavity size, please file an "
-                            "issue on: https://github.com/PCMSolver/pcmsolver");
+    fprintf(stderr,
+            "%s\n",
+            "Error in the irreducible cavity size, please file an "
+            "issue on: https://github.com/PCMSolver/pcmsolver");
     exit(EXIT_FAILURE);
   } else {
     fprintf(output, "%s\n", "Test on irreducible cavity size: PASSED");
   }
   // Polarization energy
   const double ref_energy = -0.437960027982;
   if (!check_unsigned_error(energy, ref_energy, 1.0e-7)) {
-    fprintf(stderr, "%s\n", "Error in the polarization energy, please file an issue "
-                            "on: https://github.com/PCMSolver/pcmsolver");
+    fprintf(stderr,
+            "%s\n",
+            "Error in the polarization energy, please file an issue "
+            "on: https://github.com/PCMSolver/pcmsolver");
     exit(EXIT_FAILURE);
   } else {
     fprintf(output, "%s\n", "Test on polarization energy: PASSED");
   }
   // Surface functions
-  test_surface_functions(output, grid_size, mep, asc_Ag, asc_B3g, asc_neq_B3g,
-                         areas);
+  test_surface_functions(
+      output, grid_size, mep, asc_Ag, asc_B3g, asc_neq_B3g, areas);
 
   pcmsolver_write_timings(pcm_context);