Merge branch 'v2.1'

Conflicts:
	.travis.yml

.travis.install.cppcheck

+#! /bin/bash
+
+set -e
+set -x
+
+
+git clone https://github.com/danmar/cppcheck.git
+cd cppcheck
+
+if [ -n "$1" ] ; then
+  echo "installing cppcheck $version"
+  version=$1
+else
+  echo "installing latest doxygen"
+  version=$(git tag | tail -n 1)
+fi
+
+
+git checkout $tag
+sudo make -j 4 install CFGDIR=/usr/share/cppcheck/
+cd ../
+
+

.travis.yml

@@ -15,6 +15,13 @@ env:
   - PLUMED_CC=clang PLUMED_CXX=clang++ PLUMED_CXXFLAGS=-O3 LAPACK=yes
   - PLUMED_CC=gcc   PLUMED_CXX=g++     PLUMED_CXXFLAGS=-O3 LAPACK=yes
   - PLUMED_CC=mpicc PLUMED_CXX=mpic++  PLUMED_CXXFLAGS=-O3 LAPACK=yes
+# cppcheck
+# in principle we should make only "cppcheck" here
+# to avoid to many if's below, I also make a quick test with -O0 here
+  - PLUMED_CC=gcc   PLUMED_CXX=g++     PLUMED_CXXFLAGS=-O0 CPPCHECK=yes
+matrix:
+  allow_failures:
+    - env: PLUMED_CC=gcc   PLUMED_CXX=g++     PLUMED_CXXFLAGS=-O0 CPPCHECK=yes
 # Possible additional variables:
 #   VALGRIND=yes to make valgrind tests, only when log contains string [valgrind]
 install:
@@ -26,10 +33,11 @@ install:
 # install some package - these are fast, we install them anyway
   - sudo apt-get update -qq
   - sudo apt-get install -y libmatheval-dev
-# this is not needed (will be used in 2.2)
   - ./.travis.install.xdrfile
   - LIBRARY_PATH="$LIBRARY_PATH:/usr/local/lib"
   - LD_LIBRARY_PATH="$LD_LIBRARY_PATH:/usr/local/lib"
+# cppcheck:
+  - test "$CPPCHECK" == yes && ./.travis.install.cppcheck 1.69 || true
 # installation of these packages takes a lot of time
 # we do it only when needed
   - test "$PLUMED_CXX" == "mpic++" && sudo apt-get install -y libopenmpi1.5-dev openmpi1.5-bin || true
@@ -56,10 +64,12 @@ script:
   - make -j 2
 # we install plumed so that it is in the path
   - sudo make install
+# run static analyzer
   - test "$VALGRIND" == yes && OPT=valgrind || OPT=""
   - make -C regtest $OPT
   - test "$MAKEDOC" == yes && make -C regtest copytodoc || true
   - test "$MAKEDOC" == yes && make doc >/dev/null || true
   - make -C regtest checkfail
+  - if test "$CPPCHECK" == yes ; then make cppcheck ; fi
 after_success:
   - test "$MAKEDOC" == yes && ./.travis.pushdoc

Makefile

@@ -7,7 +7,7 @@ SUBDIRS := $(SRCDIRS) user-doc developer-doc regtest
 SUBDIRSCLEAN:=$(addsuffix .clean,$(SUBDIRS))
 
      
-.PHONY: all lib clean $(SRCDIRS) doc docclean check
+.PHONY: all lib clean $(SRCDIRS) doc docclean check cppcheck
 
 # if machine dependent configuration has been found:
 ifdef GCCDEP
@@ -67,5 +67,8 @@ docclean:
 	cd user-doc && make clean
 	cd developer-doc && make clean
 
+cppcheck:
+	$(MAKE) -C src cppcheck
+
 
 

src/Makefile

@@ -20,13 +20,14 @@ SUBDIRSCLEAN :=$(addsuffix .clean,$(SUBDIRS))
 
 # this is cleaning all subdirectories
 clean: $(SUBDIRSCLEAN)
+	rm -f cppcheck.log cppcheck.fatal
 
 $(SUBDIRSCLEAN): %.clean:
 	$(MAKE) -C $* clean
 
 .PHONY: cppcheck
 cppcheck:
-	cppcheck --std=c++03 --std=posix -j 4 --platform=unix64 -q --enable=all --force */*.{h,cpp}
+	maketools/cppcheck
 
 .PHONY: mod-light mod-heavy mod-reset
 mod-light:

src/lib/Makefile

@@ -98,7 +98,7 @@ install-do:
 # copy inc files changing the path
 	for file in Plumed.inc* Plumed.cmake* ; do sed "s| $(realpath ../../)| $(PLUMED_INSTALL_ROOT)/|g" $$file > $(PLUMED_INSTALL_ROOT)/src/lib/$$file ; done
 # modulefile
-	@sed "s|@_PREFIX_@|$(PLUMED_INSTALL_PREFIX)|" modulefile.in | sed "s|@_SOEXT_@|$(SOEXT)|"> $(PLUMED_INSTALL_ROOT)/src/lib/modulefile
+	@sed "s|@_PREFIX_@|$(PLUMED_INSTALL_PREFIX)|" modulefile.in | sed "s|@_SOEXT_@|$(SOEXT)|" | sed "s|@_SUFFIX_@|$(PLUMED_INSTALL_LIBSUFFIX)|" > $(PLUMED_INSTALL_ROOT)/src/lib/modulefile
 # install links
 	ln -s $(PLUMED_INSTALL_ROOT)/src/lib/plumed $(PLUMED_INSTALL_PREFIX)/bin/plumed$(PLUMED_INSTALL_LIBSUFFIX)
 	for file in $(PLUMED_SCRIPTS) ; do ln -s $(PLUMED_INSTALL_ROOT)/src/lib/plumed-$$file $(PLUMED_INSTALL_PREFIX)/bin/plumed$(PLUMED_INSTALL_LIBSUFFIX)-$$file ; done

src/lib/modulefile.in

@@ -7,6 +7,9 @@ set prefix "@_PREFIX_@"
 # this is the extension for dynamic libraries
 # if set to empty, switches off plumed library
 set soext  "@_SOEXT_@"
+# this is the suffix to plumed executable and library
+# could be set to plumed version, but is usually blank
+set suffix "@_SUFFIX_@"
 
 # everything past this line should not need any editing
 
@@ -36,5 +39,5 @@ if { [module-info mode load] && [ info exists ::env(PLUMED_KERNEL) ] } {
 prepend-path  LIBRARY_PATH       $prefix/lib/
 prepend-path  LD_LIBRARY_PATH    $prefix/lib/
 prepend-path  DYLD_LIBRARY_PATH  $prefix/lib/
-setenv        PLUMED_KERNEL      $prefix/lib/libplumedKernel.$soext
+setenv        PLUMED_KERNEL      $prefix/lib/libplumed${suffix}Kernel.$soext
 }

src/maketools/cppcheck

+#! /bin/bash
+
+set -e
+
+# I use a "tee" here so that errors qre written both immediately (to see progress)
+# and on a file (for later report)
+
+cppcheck --std=c++03 --std=posix -j 4 --platform=unix64 -q \
+  --template='[{file}:{line}] ({severity}) :{id}: {message}' --enable=all --inline-suppr --force \
+  */*.{h,cpp} 2> >(tee cppcheck.log >&2)
+
+## this part could be useful to clean the code
+# echo "+++++++ THIS IS A COMPLETE LIST OF ERRORS +++++++"
+# cat cppcheck.log
+# echo "+++++++++++++++++++++++++++++++++++++"
+# echo "summary from cppcheck report:
+# for t in error warning performance portability style
+# do
+#   echo "$t: $(cat cppcheck.log | grep "($t)" | wc -l)"
+# done
+# echo "+++++++++++++++++++++++++++++++++++++"
+
+
+## I exclude src/molfile which is full of warnings
+## I also exclude (style) messages
+## perhaps we could keep some of them to make to code cleaner at some point
+##
+## (the "true" command is necessary so that the script does not fail if some string is not found)
+grep -v "(style)" cppcheck.log | grep -v "\[molfile/" > cppcheck.fatal || true
+count=$(cat cppcheck.fatal | wc -l)
+echo 
+echo "++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++"
+if ((count==0))
+then
+  echo "      cppcheck did not find any fatal error"
+  echo "      (fatal here means: excluding style and excluding molfile/)"
+echo "++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++"
+  exit 0
+fi
+
+echo "      cppcheck reported the following fatal errors:"
+echo "      (fatal here means: excluding style and excluding molfile/)"
+echo
+cat cppcheck.fatal
+echo
+echo "++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++"
+echo
+
+exit 1
+