update tests

include/determine_bounds_type.hpp

@@ -47,9 +47,7 @@ determine_bounds_type(const bool vals_bound, const int n_vals, const arma::vec&
             } else if ( !std::isfinite(lower_bounds(i)) && std::isfinite(upper_bounds(i)) ) {
                 // upper bound only
                 ret_vec(i) = 3;
-            } else {
-                printf("determine_bounds_type: unknown error\n");
-            }
+            } // if both are infinite, this is covered by the base case
         }
     }
     //

tests/cov_setup

@@ -5,10 +5,16 @@ export CXXCOV=gcov
 export LD_LIBRARY_PATH="$PWD":$LD_LIBRARY_PATH
 cd tests
 
+cd examples
 ./configure -b dev -c
 make
 ./cov_check
 
-cd ..
+cd ../unit_tests
+./configure -b dev -c
+make
+./cov_check
+
+cd ../..
 rm -rf ./include/armadillo*
 cd tests

tests/configure → tests/examples/configure

@@ -62,7 +62,7 @@ MCMC_SHLIB_NAME="mcmc"
 
 if [[ "${MCMC_BUILD}" == "dev" ]]; then
     echo "MCMC: dev version"
-    cd ..
+    cd ../..
     MCMC_INCLUDE_PATH=${PWD}/include
     MCMC_INSTALL_PATH=${PWD}
     cd ${WDIR}

tests/unit_tests/Makefile.in

@@ -0,0 +1,38 @@
+
+# core compiling options
+CC  = @CC@
+CXX = @CXX@
+FC  = @FC@
+
+CXX_STD = -std=c++11
+OPT_FLAGS = @MCMC_OPT_FLAGS@
+
+ARMA_INCLUDE_PATH = @ARMA_INCLUDE_PATH@
+
+# install location
+INSTALL_PATH=@MCMC_INSTALL_PATH@
+
+# source directories
+SDIR = ./..
+MCMC_DIR = $(SDIR)
+MCMC_HEADER_DIR = @MCMC_INCLUDE_PATH@
+MCMC_TEST_DIR = .
+
+# general flags
+CXXFLAGS = $(CXX_STD) -Wall $(OPT_FLAGS) -I$(ARMA_INCLUDE_PATH) -I$(MCMC_HEADER_DIR)
+LIBS= -L@MCMC_INSTALL_PATH@ -l@MCMC_SHLIB_NAME@ @MCMC_BLAS_LAPACK@
+
+# TraME Test Files
+SOURCES_MCMC= $(MCMC_TEST_DIR)/determine_bounds_type.cpp $(MCMC_TEST_DIR)/log_jacobian.cpp $(MCMC_TEST_DIR)/rwmh.cpp $(MCMC_TEST_DIR)/transform_vals.cpp
+OBJECTS_MCMC= $(SOURCES_MCMC:.cpp=.test)
+
+all: $(OBJECTS_MCMC)
+
+# core TraME files
+$(MCMC_TEST_DIR)/%.test: $(MCMC_TEST_DIR)/%.cpp
+	$(CXX) $(CXXFLAGS) $< -o $@ $(LIBS)
+
+# cleanup and install
+.PHONY: clean
+clean:
+	@rm -rf *.so ./*.gcov ./*.gcno ./*.gcda ./*.dSYM ./*.test

tests/unit_tests/configure

@@ -0,0 +1,92 @@
+#!/bin/bash
+## MCMC tests config script
+
+while getopts b:c option
+do
+    case "${option}"
+    in
+    b) MCMC_BUILD=${OPTARG};;
+    c) MCMC_COVERAGE="y";;
+    esac
+done
+
+if [ -z ${CC+x} ]; then 
+    CC=gcc
+fi
+if [ -z ${CXX+x} ]; then 
+    CXX=g++
+fi
+if [ -z ${FC+x} ]; then 
+    FC=gfortran
+fi
+
+if [[ !(-z ${KEITH_DEV_SETTINGS+x}) ]]; then
+    CC=gcc-mp-7
+    CXX=g++-mp-7
+    FC=gfortran-mp-7
+fi
+
+WDIR=${PWD}
+
+if [ -z ${ARMA_INCLUDE_PATH+x} ]; then 
+    echo "MCMC: ARMA_INCLUDE_PATH not set"
+    if [ -f /usr/include/armadillo ]; then
+        ARMA_INCLUDE_PATH="/usr/include"
+    elif [ -f /usr/local/include/armadillo ]; then
+        ARMA_INCLUDE_PATH="/usr/local/include"
+    elif [ -f /opt/include/armadillo ]; then
+        ARMA_INCLUDE_PATH="/opt/include"
+    elif [ -f /opt/local/include/armadillo ]; then
+        ARMA_INCLUDE_PATH="/opt/local/include"
+    else 
+        echo "MCMC tests: cannot find the armadillo library."
+        echo ""
+        exit 1
+    fi
+fi
+
+echo "MCMC tests: ARMA_INCLUDE_PATH set to ${ARMA_INCLUDE_PATH}"
+
+# coverage build? used for codecov
+
+if [[ "${MCMC_COVERAGE}" == "y" ]]; then 
+    echo "MCMC tests: coverage build"
+    MCMC_OPT_FLAGS="-g -O0 -Wall --coverage -fno-inline -fno-inline-small-functions -fno-default-inline"
+else
+    MCMC_OPT_FLAGS="-O3 -Wall"
+fi
+
+MCMC_SHLIB_NAME="mcmc"
+
+# dev build
+
+if [[ "${MCMC_BUILD}" == "dev" ]]; then
+    echo "MCMC: dev version"
+    cd ../..
+    MCMC_INCLUDE_PATH=${PWD}/include
+    MCMC_INSTALL_PATH=${PWD}
+    cd ${WDIR}
+else
+    MCMC_INSTALL_PATH="/usr/local"
+fi
+
+# BLAS and LAPACK settings
+
+if [[ $OSTYPE == darwin* ]] ; then
+        MCMC_BLAS_LAPACK="-framework Accelerate"
+elif [[ $OSTYPE == *linux* ]] ; then
+    MCMC_BLAS_LAPACK="-lblas -llapack"
+else
+    MCMC_BLAS_LAPACK="-lblas -llapack"
+fi
+
+sed -e "s|@CC@|${CC}|" \
+    -e "s|@CXX@|${CXX}|" \
+    -e "s|@FC@|${FC}|" \
+    -e "s|@ARMA_INCLUDE_PATH@|${ARMA_INCLUDE_PATH}|" \
+    -e "s|@MCMC_BLAS_LAPACK@|${MCMC_BLAS_LAPACK}|" \
+    -e "s|@MCMC_OPT_FLAGS@|${MCMC_OPT_FLAGS}|" \
+    -e "s|@MCMC_SHLIB_NAME@|${MCMC_SHLIB_NAME}|" \
+    -e "s|@MCMC_INCLUDE_PATH@|${MCMC_INCLUDE_PATH}|" \
+    -e "s|@MCMC_INSTALL_PATH@|${MCMC_INSTALL_PATH}|" \
+    Makefile.in > Makefile

tests/unit_tests/cov_check

@@ -0,0 +1,16 @@
+
+if [ -z ${CXXCOV+x} ]; then 
+    CXXCOV=gcov
+fi
+
+if [[ !(-z ${KEITH_DEV_SETTINGS+x}) ]]; then
+    CXXCOV=gcov-mp-7
+fi
+
+for t in ./*.test; do
+   "$t"
+done
+
+for t in ./*.cpp; do
+   $CXXCOV "$t"
+done

tests/unit_tests/determine_bounds_type.cpp

@@ -0,0 +1,51 @@
+/*################################################################################
+  ##
+  ##   Copyright (C) 2011-2017 Keith O'Hara
+  ##
+  ##   This file is part of the MCMC C++ library.
+  ##
+  ##   MCMC is free software: you can redistribute it and/or modify
+  ##   it under the terms of the GNU General Public License as published by
+  ##   the Free Software Foundation, either version 2 of the License, or
+  ##   (at your option) any later version.
+  ##
+  ##   MCMC is distributed in the hope that it will be useful,
+  ##   but WITHOUT ANY WARRANTY; without even the implied warranty of
+  ##   MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+  ##   GNU General Public License for more details.
+  ##
+  ################################################################################*/
+
+/*
+ * unit test
+ *
+ * Keith O'Hara
+ * 08/12/2017
+ *
+ * This version:
+ * 08/12/2017
+ */
+
+#include "mcmc.hpp"
+
+int main()
+{   
+    const bool vals_bound = true;
+    const int n_vals = 4;
+
+    arma::vec lb(n_vals);
+    lb(0) = 1;
+    lb(1) = 1;
+    lb(2) = -arma::datum::inf;
+    lb(3) = -arma::datum::inf;
+
+    arma::vec ub(n_vals);
+    ub(0) = 2;
+    ub(1) = arma::datum::inf;
+    ub(2) = 2;
+    ub(4) = arma::datum::inf;
+
+    arma::uvec bounds_type = determine_bounds_type(vals_bound,n_vals,lb,ub);
+
+    return 0;
+}

tests/unit_tests/log_jacobian.cpp

@@ -0,0 +1,57 @@
+/*################################################################################
+  ##
+  ##   Copyright (C) 2011-2017 Keith O'Hara
+  ##
+  ##   This file is part of the MCMC C++ library.
+  ##
+  ##   MCMC is free software: you can redistribute it and/or modify
+  ##   it under the terms of the GNU General Public License as published by
+  ##   the Free Software Foundation, either version 2 of the License, or
+  ##   (at your option) any later version.
+  ##
+  ##   MCMC is distributed in the hope that it will be useful,
+  ##   but WITHOUT ANY WARRANTY; without even the implied warranty of
+  ##   MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+  ##   GNU General Public License for more details.
+  ##
+  ################################################################################*/
+
+/*
+ * unit test
+ *
+ * Keith O'Hara
+ * 08/12/2017
+ *
+ * This version:
+ * 08/12/2017
+ */
+
+#include "mcmc.hpp"
+
+int main()
+{   
+    const bool vals_bound = true;
+    const int n_vals = 4;
+
+    arma::vec lb(n_vals);
+    lb(0) = 0;
+    lb(1) = 0;
+    lb(2) = -arma::datum::inf;
+    lb(3) = -arma::datum::inf;
+
+    arma::vec ub(n_vals);
+    ub(0) = 2;
+    ub(1) = arma::datum::inf;
+    ub(2) = 2;
+    ub(4) = arma::datum::inf;
+
+    arma::uvec bounds_type = mcmc::determine_bounds_type(vals_bound,n_vals,lb,ub);
+
+    arma::vec initial_vals = arma::ones(n_vals,1);
+
+    arma::vec vals_trans = mcmc::transform(initial_vals,bounds_type,lb,ub);
+
+    double lj_val = log_jacobian(vals_trans,bounds_type,lb,ub);
+
+    return 0;
+}