Reorganize test utilities, add unit tests.

.github/workflows/merge-gate.yml

@@ -41,6 +41,7 @@ jobs:
     steps:
       - name: Install prerequisite packages
         run: |
+          sudo apt update
           sudo apt-get install gfortran \
                                libbz2-dev \
                                libblas-dev \

Jenkinsfile

@@ -40,6 +40,22 @@ pipeline {
                 }
             }
             parallel {
+              stage("Linux GNU Unit Tests") {
+                    agent {
+                        docker {
+                            image 'ambermd/cpu-build:latest'
+                            alwaysPull true
+                        }
+                    }
+
+                    steps {
+                        unstash "source"
+                        sh "./configure --with-netcdf --with-fftw3 gnu"
+                        sh "cd unitTests && make test.all"
+                    }
+
+                    post { cleanup { deleteDir() } }
+                }
                 stage("Linux GNU serial build") {
                     agent {
                         docker {

Makefile

@@ -21,10 +21,14 @@ libstatic: config.h
 check: config.h
 	cd test && $(MAKE) test.complete summary
 
+unittest: config.h
+	cd unitTests && $(MAKE) test.complete summary
+
 # Clean up
 clean: config.h
 	cd src && $(MAKE) clean
 	cd test && $(MAKE) clean
+	cd unitTests && $(MAKE) clean
 
 docs: src/cpptraj.Doxyfile
 	cd src && doxygen cpptraj.Doxyfile

configure

@@ -114,7 +114,7 @@ EXE=''                    # Binary executable suffix
 REBUILDOPT=''             # Can be set to --rebuild and passed to get_library.sh
 BUILDTESTOPT='silent'     # Set to blank to avoid asking about building libraries
 INSTALL_DAT='install_dat' # Target for installing data directory
-CPPTRAJSRC=''             # CPPTRAJ source directory
+#CPPTRAJSRC=''             # CPPTRAJ source directory
 COMPERR='cpptrajcfg.compile.err'
 COMPOUT='cpptrajcfg.compile.out'
 
@@ -2260,7 +2260,7 @@ fi
 if [ "$WORKDIR" != '.' ] ; then
   Err "CPPTRAJ configure must be executed from the source directory."
 fi
-CPPTRAJSRC=$CURRENTDIR
+#CPPTRAJSRC=$CURRENTDIR
 
 # Basic checks and directives
 BasicChecks
@@ -2406,11 +2406,6 @@ if [ $USE_SHARED -eq 1 ] ; then
 else
   LIBCPPTRAJ_TARGET='nolibcpptraj'
 fi
-# Only build nproc for MPI
-if [ $USE_MPI -ne 0 ] ; then
-  NPROC_TARGET=nproc
-  INSTALL_TARGETS=$INSTALL_TARGETS" $NPROC_TARGET"
-fi
 # CUDA
 if [ $USE_CUDA -eq 1 ] ; then
   CUDA_TARGET='cuda_kernels/libcpptraj_cuda.a'
@@ -2532,7 +2527,6 @@ if [ "$PERFORM_CHECKS" = 'yes' ] ; then
     RFILE=$CPPTRAJHOME/cpptraj.sh
     cat > $RFILE <<EOF
 export CPPTRAJHOME="$CPPTRAJHOME"
-export CPPTRAJSRC="$CPPTRAJSRC"
 export PATH=$CPPTRAJBIN:\${PATH}
 EOF
     if [ "$PLATFORM" != "Darwin" ] ; then
@@ -2543,7 +2537,6 @@ EOF
     RFILE=$CPPTRAJHOME/cpptraj.csh
     cat > $RFILE <<EOF
 setenv CPPTRAJHOME "$CPPTRAJHOME"
-setenv CPPTRAJSRC "$CPPTRAJSRC"
 setenv PATH "$CPPTRAJBIN:\${PATH}"
 EOF
     if [ "$PLATFORM" != "Darwin" ] ; then

lgtm.yml

@@ -2,6 +2,7 @@ path_classifiers:
   test:
     - "src/readline/*"
     - "src/tng/*"
+    - "unitTests/*/*"
 extraction:
   cpp:
     prepare:

src/Makefile

@@ -62,10 +62,6 @@ nolibcpptraj:
 	@echo ""
 	@exit 1
 
-# nproc --------------------------------
-nproc:
-	cd ../util && $(MAKE)
-
 # Internal object/library targets
 pub_fft.o:  pub_fft.F90
 	$(FC) $(FPPFLAGS) -c $(FFLAGS) -o $@ pub_fft.F90

test/MasterTest.sh

@@ -611,7 +611,7 @@ SetNthreads() {
       export N_THREADS=1
       return 1
     fi
-    export N_THREADS=`$DO_PARALLEL $CPPTRAJ_NPROC`
+    export N_THREADS=`$CPPTRAJ_NPROC`
     echo "  $N_THREADS MPI threads."
   fi
   return 0
@@ -835,13 +835,7 @@ SetBinaries() {
   fi
   # Determine location of ndiff.awk
   if [ -z "$CPPTRAJ_NDIFF" ] ; then
-    if [ $STANDALONE -eq 0 ] ; then
-      CPPTRAJ_NDIFF=$DIRPREFIX/test/ndiff.awk
-    elif [ ! -z "$CPPTRAJSRC" ] ; then
-      CPPTRAJ_NDIFF=$CPPTRAJSRC/util/ndiff/ndiff.awk
-    else
-      CPPTRAJ_NDIFF=$CPPTRAJ_TEST_ROOT/../util/ndiff/ndiff.awk
-    fi
+    CPPTRAJ_NDIFF=$CPPTRAJ_TEST_ROOT/utilities/ndiff/ndiff.awk
     if [ ! -f "$CPPTRAJ_NDIFF" ] ; then
       ErrMsg "'ndiff.awk' not present: $CPPTRAJ_NDIFF"
       exit 1
@@ -851,14 +845,8 @@ SetBinaries() {
   # Determine location of nproc/numprocs
   if [ -z "$CPPTRAJ_NPROC" ] ; then
     if [ ! -z "$DO_PARALLEL" ] ; then
-      if [ $STANDALONE -eq 0 ] ; then
-        CPPTRAJ_NPROC=$DIRPREFIX/AmberTools/test/numprocs
-      elif [ ! -z "$CPPTRAJSRC" ] ; then
-        CPPTRAJ_NPROC=$CPPTRAJSRC/test/nproc
-      else
-        CPPTRAJ_NPROC=$CPPTRAJ_TEST_ROOT/nproc
-      fi
-      if [ -z "$CPPTRAJ_NPROC" ] ; then
+      CPPTRAJ_NPROC=$CPPTRAJ_TEST_ROOT/utilities/nproc.sh
+      if [ ! -f "$CPPTRAJ_NPROC" ] ; then
         ErrMsg "Error: nproc $CPPTRAJ_NPROC not found."
         exit 1
       fi

test/utilities/nproc.sh

@@ -0,0 +1,21 @@
+#!/bin/bash
+
+# Assuming DO_PARALLEL is set with the command to execute mpirun,
+# determine how many processes.
+
+if [ -z "`which grep`" ] ; then
+  >&2 echo "Error: nproc.sh relies on grep"
+  exit 1
+fi
+if [ -z "`which wc`" ] ; then
+  >&2 echo "Error: nproc.sh relies on wc"
+  exit 1
+fi
+
+NPROC=0
+
+if [ ! -z "$DO_PARALLEL" ] ; then
+  NPROC=`$DO_PARALLEL echo "cpptraj_nproc_test" | grep "cpptraj_nproc_test" | wc -l`
+fi
+echo $NPROC
+exit 0

unitTests/ArgList/UnitTest.sh

@@ -0,0 +1,13 @@
+#!/bin/bash
+
+. ../UnitMaster.sh
+
+CleanFiles Makefile main.o ArgList.o a.out CpptrajStdio.o StringRoutines.o
+
+UNITSOURCES='ArgList.cpp CpptrajStdio.cpp StringRoutines.cpp'
+
+CreateMakefile
+
+RunMake "ArgList class unit test."
+
+EndTest

unitTests/ArgList/main.cpp

@@ -0,0 +1,50 @@
+#include <cstdio>
+#include <cmath>
+#include "ArgList.h"
+
+static const int Err(const char* msg) {
+  fprintf(stderr, "Error: %s\n", msg);
+  return 1;
+}
+
+const double SMALL        = 0.00000000000001;
+
+bool f_not_equals(double d1, double d2) {
+  return (fabs(d1 - d2) > SMALL);
+}
+
+int main() {
+  //          7       6 6    4               1    1 2  3    3       5
+  ArgList a1("This is a test 3.14159 arglist with 4 45 darg 123.323 :12@H=");
+
+  int iarg = a1.getKeyInt("with", -1);
+  if (iarg != 4) return Err("getKeyInt() failed.");
+
+  iarg = a1.getNextInteger(-1);
+  if (iarg != 45) return Err("getNextInteger() failed.");
+
+  double darg = a1.getKeyDouble("darg", 0);
+  if (f_not_equals(darg, 123.323)) return Err("getKeyDouble() failed.");
+
+  darg = a1.getNextDouble(0);
+  if (f_not_equals(darg, 3.14159)) return Err("getNextDouble() failed.");
+
+  std::string sarg = a1.GetMaskNext();
+  if (sarg != ":12@H=") return Err("GetMaskNext() failed.");
+
+  sarg = a1.GetStringKey("a");
+  if (sarg != "test") return Err("GetStringKey() failed.");
+
+  sarg = a1.GetStringNext();
+  if (sarg != "This") return Err("GetStringKey() failed.");
+
+  ArgList r1 = a1.RemainingArgs();
+  if (a1.NremainingArgs() > 0) return Err("RemainingArgs() failed (# remaining args).");
+  if (r1.Nargs() != 2) return Err("RemainingArgs() failed (# new args).");
+
+  r1.MarkArg(0);
+  sarg = r1.GetStringNext();
+  if (sarg != "arglist") return Err("MarkArg() failed.");
+
+  return 0;
+}

unitTests/CpptrajTest.sh

@@ -0,0 +1,9 @@
+#!/bin/bash
+
+if [ ! -f 'UnitMaster.sh' ] ; then
+  echo "Fatal Error: UnitMaster.sh not present" > /dev/stderr
+  exit 1
+fi
+CPPTRAJ_TEST_MODE='master'
+. UnitMaster.sh
+exit 0

unitTests/Makefile

@@ -0,0 +1,36 @@
+# Makefile for unit tests
+
+test: test.all
+
+# ----- All unit tests go below ------------------
+
+unit.NameType:
+	@-cd NameType && ./UnitTest.sh $(OPT)
+
+unit.ArgList:
+	@-cd ArgList && ./UnitTest.sh $(OPT)
+
+# ----- Every unit test should go here -----------
+COMPLETETESTS= \
+  unit.NameType \
+  unit.ArgList
+
+test.cpptraj: $(COMPLETETESTS)
+
+# ------------------------------------------------
+
+test.complete: CpptrajTest.sh UnitMaster.sh
+	@./CpptrajTest.sh --target test.cpptraj $(OPT)
+
+test.all:
+	$(MAKE) test.complete summary
+
+test.showerrors:
+	$(MAKE) test.complete summary OPT="$(OPT) showerrors"
+
+summary: CpptrajTest.sh UnitMaster.sh 
+	@./CpptrajTest.sh summary $(OPT)
+
+clean:
+	@echo "Cleaning unit tests."
+	$(MAKE) test.complete OPT=clean

unitTests/NameType/UnitTest.sh

@@ -0,0 +1,13 @@
+#!/bin/bash
+
+. ../UnitMaster.sh
+
+CleanFiles Makefile main.o NameType.o a.out CpptrajStdio.o
+
+UNITSOURCES='NameType.cpp CpptrajStdio.cpp'
+
+CreateMakefile
+
+RunMake "NameType class unit test."
+
+EndTest