Merge pull request #19 from jougs/remove-sibling-container

Remove sibling container
hakonsbm · Aug 10, 2017 · 8c13a40 · 8c13a40
2 parents da95f77 + 0752fec
commit 8c13a40
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diff --git a/.travis.yml b/.travis.yml
@@ -21,12 +21,13 @@
 # This is the Travis CI top-level script to setup and run the NEST build and test environment. 
 
 
-language: generic
+language: minimal
 
 # Required for Ubuntu Trusty (14.04 LTS).
 sudo: required
 dist: trusty
-
+#https://blog.travis-ci.com/2017-06-19-trusty-updates-2017-Q2
+group: edge
 env:
   matrix:
     # We don't have to run a full matrix here, because most of the options are

diff --git a/CMakeLists.txt b/CMakeLists.txt
@@ -97,6 +97,12 @@ if ( "${CMAKE_INSTALL_PREFIX}" STREQUAL "/usr/local" )
                     "Please set -DCMAKE_INSTALL_PREFIX:PATH=<install prefix>." )
 endif ()
 
+################################################################################
+#################    Use absolute path for CMAKE_NEST_PREFIX   #################
+################################################################################
+
+get_filename_component(CMAKE_NEST_PREFIX ${CMAKE_INSTALL_PREFIX} REALPATH BASE_DIR "${CMAKE_BINARY_DIR}")
+
 ################################################################################
 ##################           Find utility programs            ##################
 ################################################################################

diff --git a/INSTALL b/INSTALL
@@ -11,9 +11,9 @@ NEST is installed with `cmake` (at least v2.8.12). In the simplest case, the com
     make
     make install
 
-should build and install NEST to <install-path>. Detailed installation 
-instructions can be found below, including instructions for macOS, BlueGene/Q
-and Fujitsu Sparc64 systems.
+should build and install NEST to `/install/path`, which should be an absolute
+path. Detailed installation  instructions can be found below, including 
+instructions for macOS, BlueGene/Q and Fujitsu Sparc64 systems.
 
 Choice of CMake Version
 =======================

diff --git a/build.sh b/build.sh
@@ -144,29 +144,40 @@ if [ "$xSTATIC_ANALYSIS" = "1" ] ; then
     done
   done
   echo "MSGBLD0100: Retrieving changed files completed."
-
-  printf '%s\n' "$file_names" | while IFS= read -r line
-  do
-    echo "MSGBLD0095: File changed: $line"
-  done
-  echo "MSGBLD0100: Retrieving changed files completed."
   echo
 
-  sudo chmod +x ./extras/static_code_analysis.sh
 
-  RUNS_ON_TRAVIS=true
-  INCREMENTAL=false
-  VERA=vera++
+  # Set the command line arguments for the static code analysis script and execute it.
+
+  # The names of the static code analysis tools executables.
+  VERA=vera++                   
   CPPCHECK=cppcheck
   CLANG_FORMAT=clang-format
   PEP8=pep8
-  PERFORM_VERA=false
-  PERFORM_CPPCHECK=false
+
+  # Perform or skip a certain analysis.
+  PERFORM_VERA=true
+  PERFORM_CPPCHECK=true
   PERFORM_CLANG_FORMAT=true
   PERFORM_PEP8=true
 
-  ./extras/static_code_analysis.sh "$RUNS_ON_TRAVIS" "$INCREMENTAL" "$file_names" "$NEST_VPATH" "$VERA" "$CPPCHECK" "$CLANG_FORMAT" "$PEP8" \
-  "$PERFORM_VERA" "$PERFORM_CPPCHECK" "$PERFORM_CLANG_FORMAT" "$PERFORM_PEP8"
+  # The following command line parameters indicate whether static code analysis error messages
+  # will cause the Travis CI build to fail or are ignored.
+  IGNORE_MSG_VERA=true
+  IGNORE_MSG_CPPCHECK=true
+  IGNORE_MSG_CLANG_FORMAT=false
+  IGNORE_MSG_PEP8=false
+
+  # The script is called within the Travis CI environment and cannot be run incremental.
+  RUNS_ON_TRAVIS=true
+  INCREMENTAL=false
+
+  sudo chmod +x ./extras/static_code_analysis.sh
+  ./extras/static_code_analysis.sh "$RUNS_ON_TRAVIS" "$INCREMENTAL" "$file_names" "$NEST_VPATH" \
+  "$VERA" "$CPPCHECK" "$CLANG_FORMAT" "$PEP8" \
+  "$PERFORM_VERA" "$PERFORM_CPPCHECK" "$PERFORM_CLANG_FORMAT" "$PERFORM_PEP8" \
+  "$IGNORE_MSG_VERA" "$IGNORE_MSG_CPPCHECK" "$IGNORE_MSG_CLANG_FORMAT" "$IGNORE_MSG_PEP8"
+
 fi   # Static code analysis.
 
 
@@ -217,11 +228,13 @@ make installcheck
 echo "MSGBLD0300: Make installcheck completed."
 
 if [ "$TRAVIS_PULL_REQUEST" != "false" ]; then
-  echo "MSGBLD0310: This build was triggered by a pull request." >&2
-  echo "MSGBLD0330: (WARNING) Build artifacts not uploaded to Amazon S3." >&2
+  echo "MSGBLD0310: This build was triggered by a pull request."
+  echo "MSGBLD0330: (WARNING) Build artifacts not uploaded to Amazon S3."
 fi
 
 if [ "$TRAVIS_REPO_SLUG" != "nest/nest-simulator" ] ; then
-  echo "MSGBLD0320: This build was from a forked repository and not from nest/nest-simulator." >&2
-  echo "MSGBLD0330: (WARNING) Build artifacts not uploaded to Amazon S3." >&2
+  echo "MSGBLD0320: This build was from a forked repository and not from nest/nest-simulator."
+  echo "MSGBLD0330: (WARNING) Build artifacts not uploaded to Amazon S3."
 fi
+
+echo "MSGBLD0340: Build completed."
diff --git a/conngen/cg_connect.cpp b/conngen/cg_connect.cpp
@@ -63,8 +63,10 @@ cg_connect( ConnectionGeneratorDatum& cg,
   {
     if ( not params_map->known( names::weight )
       || not params_map->known( names::delay ) )
+    {
       throw BadProperty(
         "The parameter map has to contain the indices of weight and delay." );
+    }
 
     long w_idx = ( *params_map )[ names::weight ];
     long d_idx = ( *params_map )[ names::delay ];
@@ -128,8 +130,10 @@ cg_connect( ConnectionGeneratorDatum& cg,
   {
     if ( not params_map->known( names::weight )
       || not params_map->known( names::delay ) )
+    {
       throw BadProperty(
         "The parameter map has to contain the indices of weight and delay." );
+    }
 
     long w_idx = ( *params_map )[ names::weight ];
     long d_idx = ( *params_map )[ names::delay ];
@@ -234,7 +238,9 @@ cg_create_masks( std::vector< ConnectionGenerator::Mask >* masks,
     for ( size_t proc = 0; proc
             < static_cast< size_t >( kernel().mpi_manager.get_num_processes() );
           ++proc )
+    {
       ( *masks )[ proc ].sources.insert( cg_idx_left, right );
+    }
     cg_idx_left += num_elements + 1;
   }
 
@@ -296,7 +302,9 @@ cg_get_right_border( index left, size_t step, std::vector< long >& gids )
   // Check if left is already the index of the last element in
   // gids. If yes, return left as the right border
   if ( left == gids.size() - 1 )
+  {
     return left;
+  }
 
   // leftmost_r is the leftmost right border during the search
   long leftmost_r = -1;
@@ -316,7 +324,9 @@ cg_get_right_border( index left, size_t step, std::vector< long >& gids )
     if ( ( i == static_cast< long >( gids.size() ) - 1
            && gids[ i ] - gids[ left ] == i - static_cast< long >( left ) )
       || i == leftmost_r )
+    {
       return last_i;
+    }
 
     // Store the current value of i in last_i. This is the current
     // candidate for the right border of the range.
@@ -327,7 +337,9 @@ cg_get_right_border( index left, size_t step, std::vector< long >& gids )
     // for leftmost_r to the current i (i.e. the known leftmost
     // position) and set i to the left by step steps.
     if ( gids[ i ] - gids[ left ] == i - static_cast< long >( left ) )
+    {
       i += step;
+    }
     else
     {
       leftmost_r = i;
@@ -337,7 +349,9 @@ cg_get_right_border( index left, size_t step, std::vector< long >& gids )
     // Reduce the search interval by half its size if it is > 1.
     // This adaptation is the basis of the binary search.
     if ( step != 1 )
+    {
       step /= 2;
+    }
   }
 
   // The border should always be found and returned during the while
@@ -370,9 +384,14 @@ cg_get_ranges( RangeSet& ranges, std::vector< long >& gids )
     right = cg_get_right_border( left, ( gids.size() - left ) / 2, gids );
     ranges.push_back( Range( gids[ left ], gids[ right ] ) );
     if ( right == gids.size() - 1 ) // We're at the end of gids and stop
+    {
       break;
+    }
     else
-      left = right + 1; // The new left border is one after the old right
+    {
+      // The new left border is one after the old right
+      left = right + 1;
+    }
   }
 }
 

diff --git a/conngen/conngen.cpp b/conngen/conngen.cpp
@@ -32,7 +32,6 @@
 #include "exceptions.h"
 #include "kernel_manager.h"
 #include "modelrange.h"
-#include "nest_datums.h"
 
 // Includes from sli:
 #include "token.h"
@@ -91,7 +90,9 @@ nest::cg_connect( nest::ConnectionGeneratorDatum& cg,
   const Token synmodel =
     kernel().model_manager.get_synapsedict()->lookup( synmodel_name );
   if ( synmodel.empty() )
+  {
     throw UnknownSynapseType( synmodel_name.toString() );
+  }
   const index synmodel_id = static_cast< index >( synmodel );
 
   const modelrange source_range =
@@ -129,7 +130,9 @@ nest::cg_connect( nest::ConnectionGeneratorDatum& cg,
   const Token synmodel =
     kernel().model_manager.get_synapsedict()->lookup( synmodel_name );
   if ( synmodel.empty() )
+  {
     throw UnknownSynapseType( synmodel_name.toString() );
+  }
   const index synmodel_id = static_cast< index >( synmodel );
 
   RangeSet source_ranges;

diff --git a/doc/CMakeLists.txt b/doc/CMakeLists.txt
@@ -19,28 +19,44 @@
 
 if ( NOT CMAKE_CROSSCOMPILING )
   add_custom_target( generate_help ALL )
-  # Extract help from all source files in the source code, put them in
-  # doc/help and generate a local help index in the build directory containing 
-  # links to the help files.
-  add_custom_command( TARGET generate_help POST_BUILD
-    COMMAND python -B generate_help.py "${PROJECT_SOURCE_DIR}" "${PROJECT_BINARY_DIR}"
-    COMMAND python -B generate_helpindex.py "${PROJECT_BINARY_DIR}/doc"
-    WORKING_DIRECTORY "${PROJECT_SOURCE_DIR}/extras/help_generator"
-    COMMENT "Extracting help information; this may take a litte while."
-    )
-  # Copy the local doc/help directory to the global installation
-  # directory for documentation.
-  install( DIRECTORY "${CMAKE_CURRENT_BINARY_DIR}/help"
-    DESTINATION "${CMAKE_INSTALL_DOCDIR}"
-    )
-  # Update the global help index to contain all help files that are
-  # located in the global installation directory for documentation.
-  install( CODE
-    "execute_process(
-      COMMAND python -B generate_helpindex.py \"${CMAKE_INSTALL_PREFIX}/${CMAKE_INSTALL_DOCDIR}\"
-      WORKING_DIRECTORY \"${PROJECT_SOURCE_DIR}/extras/help_generator\"
-    )"
-    )
+
+    # Python is needed to generate the help. If Python does not exist, there are
+    # problems with the following.
+    # See https://github.com/nest/nest-simulator/issues/678.
+    find_package( PythonInterp )
+    if ( PYTHONINTERP_FOUND )
+
+      # Because of problems of help generation with the implementation of 're'
+      # in Python older than 2.7.8, the production of the help is skipped
+      # completely for these versions.
+      if(${PYTHON_VERSION_STRING} VERSION_GREATER "2.7.7")
+          # Extract help from all source files in the source code, put them in
+          # doc/help and generate a local help index in the build directory containing
+          # links to the help files.
+          add_custom_command( TARGET generate_help POST_BUILD
+            COMMAND ${PYTHON_EXECUTABLE} -B generate_help.py "${PROJECT_SOURCE_DIR}"
+            "${PROJECT_BINARY_DIR}"
+            COMMAND ${PYTHON_EXECUTABLE} -B generate_helpindex.py "${PROJECT_BINARY_DIR}/doc"
+            WORKING_DIRECTORY "${PROJECT_SOURCE_DIR}/extras/help_generator"
+            COMMENT "Extracting help information; this may take a litte while."
+            )
+          # Copy the local doc/help directory to the global installation
+          # directory for documentation.
+          install( DIRECTORY "${CMAKE_CURRENT_BINARY_DIR}/help"
+            DESTINATION "${CMAKE_INSTALL_DOCDIR}"
+            )
+          # Update the global help index to contain all help files that are
+          # located in the global installation directory for documentation.
+          install( CODE
+            "execute_process(
+              COMMAND ${PYTHON_EXECUTABLE} -B generate_helpindex.py \"${CMAKE_INSTALL_PREFIX}/${CMAKE_INSTALL_DOCDIR}\"
+              WORKING_DIRECTORY \"${PROJECT_SOURCE_DIR}/extras/help_generator\"
+            )"
+            )
+      endif ()
+
+    endif ()
+
 endif ()
 
 install( DIRECTORY conngen model_details

diff --git a/examples/MyModule/drop_odd_spike_connection.h b/examples/MyModule/drop_odd_spike_connection.h
@@ -183,7 +183,9 @@ DropOddSpikeConnection< targetidentifierT >::send( nest::Event& e,
   const CommonPropertiesType& props )
 {
   if ( e.get_stamp().get_steps() % 2 ) // stamp is odd, drop it
+  {
     return;
+  }
 
   // Even time stamp, we send the spike using the normal sending mechanism
   // send the spike to the target

diff --git a/examples/MyModule/pif_psc_alpha.cpp b/examples/MyModule/pif_psc_alpha.cpp
@@ -110,21 +110,25 @@ mynest::pif_psc_alpha::Parameters_::set( const DictionaryDatum& d )
   updateValue< double >( d, names::V_th, V_th );
   updateValue< double >( d, names::V_reset, V_reset );
   updateValue< double >( d, names::t_ref, t_ref );
-
   if ( C_m <= 0 )
+  {
     throw nest::BadProperty(
       "The membrane capacitance must be strictly positive." );
-
+  }
   if ( tau_syn <= 0 )
+  {
     throw nest::BadProperty(
       "The synaptic time constant must be strictly positive." );
-
+  }
   if ( V_reset >= V_th )
+  {
     throw nest::BadProperty( "The reset potential must be below threshold." );
-
+  }
   if ( t_ref < 0 )
+  {
     throw nest::BadProperty(
       "The refractory time must be at least one simulation step." );
+  }
 }
 
 void
@@ -240,10 +244,15 @@ mynest::pif_psc_alpha::update( Time const& slice_origin,
 
     // update membrane potential
     if ( S_.refr_count == 0 ) // neuron absolute not refractory
+    {
       S_.V_m +=
         V_.P30 * ( S_.I_ext + P_.I_e ) + V_.P31 * S_.dI_syn + V_.P32 * S_.I_syn;
+    }
     else
-      --S_.refr_count; // count down refractory time
+    {
+      // count down refractory time
+      --S_.refr_count;
+    }
 
     // update synaptic currents
     S_.I_syn = V_.P21 * S_.dI_syn + V_.P22 * S_.I_syn;

diff --git a/examples/MyModule/pif_psc_alpha.h b/examples/MyModule/pif_psc_alpha.h
@@ -347,7 +347,9 @@ mynest::pif_psc_alpha::handles_test_event( nest::SpikeEvent&,
   // to handle @c SpikeEvent on port 0. You need to extend the function
   // if you want to differentiate between input ports.
   if ( receptor_type != 0 )
+  {
     throw nest::UnknownReceptorType( receptor_type, get_name() );
+  }
   return 0;
 }
 
@@ -360,7 +362,9 @@ mynest::pif_psc_alpha::handles_test_event( nest::CurrentEvent&,
   // to handle @c CurrentEvent on port 0. You need to extend the function
   // if you want to differentiate between input ports.
   if ( receptor_type != 0 )
+  {
     throw nest::UnknownReceptorType( receptor_type, get_name() );
+  }
   return 0;
 }
 
@@ -374,7 +378,9 @@ mynest::pif_psc_alpha::handles_test_event( nest::DataLoggingRequest& dlr,
   // The function also tells the built-in UniversalDataLogger that this node
   // is recorded from and that it thus needs to collect data during simulation.
   if ( receptor_type != 0 )
+  {
     throw nest::UnknownReceptorType( receptor_type, get_name() );
+  }
 
   return B_.logger_.connect_logging_device( dlr, recordablesMap_ );
 }

diff --git a/examples/MyModule/step_pattern_builder.cpp b/examples/MyModule/step_pattern_builder.cpp
@@ -129,7 +129,9 @@ mynest::StepPatternBuilder::connect_()
             for ( nest::GIDCollection::const_iterator sgid = sources_->begin();
                   sgid < sources_->end();
                   ++sgid )
+            {
               skip_conn_parameter_( tid );
+            }
             continue;
           }
           nest::Node* const target =