Merge branch 'master' into remove_nest_vars_sh

Author: terhorstd

libnestutil/iterator_pair.h

@@ -170,7 +170,7 @@ struct rightshift_iterator_pair
   }
 
   template < typename T >
-  inline int
+  inline size_t
   operator()( boost::tuples::tuple< nest::Source&, T& > s, unsigned offset )
   {
     return boost::get< 0 >( s ).get_node_id() >> offset;

models/ht_synapse.h

@@ -45,11 +45,16 @@ Synaptic dynamics are given by
 
 .. math::
 
-    P'(t) = ( 1 - P ) / \tau_P  \\
-    P(T+) = (1 - \delta_P) P(T-)    \text{ for T : time of a spike } \\
-    P(t=0) = 1
+    \frac{dP(t)}{dt} &= \frac{1}{\tau_\mathrm{P}} \left( 1 - P \right)  \\
+    P(t=0) &= 1 \\
 
-:math:`w(t) = w_{max} \cdot P(t)`   is the resulting synaptic weight
+Upon the arrival of a presynaptic spike at time :math:`t_\mathrm{sp}`, the value of :math:`P` is updated as follows:
+
+.. math::
+
+    P \leftarrow (1 - \delta_\mathrm{P}) P
+
+:math:`w(t) = w_\mathrm{max} \cdot P(t)` is the resulting synaptic weight.
 
 For implementation details see:
 `HillTononi_model <../model_details/HillTononiModels.ipynb>`_
@@ -70,7 +75,7 @@ The following parameters can be set in the status dictionary:
  tau_P    ms      Synaptic vesicle pool recovery time constant
  delta_P  real    Fractional change in vesicle pool on incoming spikes
                   (unitless)
- P        real    Current size of the vesicle pool [unitless, 0 <= P <= 1]
+ P        real    Current size of the vesicle pool (unitless, 0 <= P <= 1)
 ========  ======  =========================================================
 
 References

nestkernel/source.h

@@ -40,20 +40,20 @@ namespace nest
 class Source
 {
 private:
-  uint64_t node_id_ : NUM_BITS_NODE_ID;  //!< node ID of source
-  bool processed_ : 1;                   //!< whether this target has already been moved
-                                         //!< to the MPI buffer
-  bool primary_ : 1;                     //!< source of primary connection
-  bool disabled_ : 1;                    //!< connection has been disabled
+  size_t node_id_ : NUM_BITS_NODE_ID;  //!< node ID of source
+  bool processed_ : 1;                 //!< whether this target has already been moved
+                                       //!< to the MPI buffer
+  bool primary_ : 1;                   //!< source of primary connection
+  bool disabled_ : 1;                  //!< connection has been disabled
 
 public:
   Source();
-  explicit Source( const uint64_t node_id, const bool primary );
+  explicit Source( const size_t node_id, const bool primary );
 
   /**
    * Returns this Source's node ID.
    */
-  uint64_t get_node_id() const;
+  size_t get_node_id() const;
 
   void set_processed( const bool processed );
   bool is_processed() const;
@@ -91,7 +91,7 @@ inline Source::Source()
 {
 }
 
-inline Source::Source( const uint64_t node_id, const bool is_primary )
+inline Source::Source( const size_t node_id, const bool is_primary )
   : node_id_( node_id )
   , processed_( false )
   , primary_( is_primary )
@@ -100,7 +100,7 @@ inline Source::Source( const uint64_t node_id, const bool is_primary )
   assert( node_id <= MAX_NODE_ID );
 }
 
-inline uint64_t
+inline size_t
 Source::get_node_id() const
 {
   return node_id_;

testsuite/CMakeLists.txt

@@ -37,6 +37,6 @@ install( PROGRAMS
 )
 
 install( FILES
-    junit_xml.sh run_test.sh summarize_tests.py
+    junit_xml.sh summarize_tests.py
     DESTINATION ${CMAKE_INSTALL_DATADIR}/testsuite
 )

testsuite/do_tests.sh

@@ -111,8 +111,6 @@ NEST_PY_PATH="$(${PYTHON} -c "import sysconfig; print(sysconfig.get_path('platli
 PYTHONPATH="${NEST_PY_PATH}${PYTHONPATH:+:$PYTHONPATH}"
 # shellcheck source=testsuite/junit_xml.sh
 . "$(dirname "$0")/junit_xml.sh"
-# shellcheck source=testsuite/run_test.sh
-. "$(dirname "$0")/run_test.sh"
 
 # Directory containing installed tests
 TEST_BASEDIR="${PREFIX}/share/nest/testsuite"
@@ -124,8 +122,6 @@ REPORTDIR="${PWD}/$(mktemp -d test_report_XXX)"
 
 TEST_LOGFILE="${REPORTDIR}/installcheck.log"
 TEST_OUTFILE="${REPORTDIR}/output.log"
-TEST_RETFILE="${REPORTDIR}/output.ret"
-TEST_RUNFILE="${REPORTDIR}/runtest.sh"
 
 get_build_info ()
 {