Merge pull request #749 from apdavison/update-ci

Use NEST v3.3 and NEURON v8.1 for CI

Author: apdavison

.gitignore

@@ -21,6 +21,7 @@
 x86_64
 i386
 i686
+arm64
 _build
 
 # Python files

.travis.yml

@@ -1,5 +1,5 @@
 language: python
-dist: bionic
+dist: focal
 matrix:
   include:
     - python: 3.7
@@ -17,7 +17,7 @@ after_success:
   - bash ci/upload_coveralls.sh
 cache:
   directories:
-    - $HOME/nest-3.0
-    - $HOME/nrn-8.0.0
-    - $HOME/build/nest-3.0
+    - $HOME/nest-simulator-3.3
+    - $HOME/nrn-8.1
+    - $HOME/build/nest-simulator-3.3
     - $HOME/.cache/pip

ci/install_nest.sh

@@ -6,7 +6,7 @@ if [ "$TRAVIS_PYTHON_VERSION" == "3.9" ]; then
     echo -e "\n========== Installing NEST ==========\n"
     # Specify which version of NEST to install
     #export NEST_VERSION="master"
-    export NEST_VERSION="3.1"
+    export NEST_VERSION="3.3"
 
     pip install cython
 

ci/install_neuron.sh

@@ -4,12 +4,12 @@ set -e  # stop execution in case of errors
 
 if [ "$TRAVIS_PYTHON_VERSION" == "3.9" ]; then
     echo -e "\n========== Installing NEURON ==========\n"
-    export NRN_VERSION="nrn-8.0.0"
+    export NRN_VERSION="nrn-8.1"
     export VENV=`python -c "import sys; print(sys.prefix)"`
 
     if [ ! -f "$HOME/$NRN_VERSION/build/CMakeCache.txt" ]; then
         echo 'Cloning NEURON sources from GitHub'
-        git clone https://github.com/neuronsimulator/nrn -b 8.0.0 $HOME/$NRN_VERSION
+        git clone https://github.com/neuronsimulator/nrn -b release/8.1 $HOME/$NRN_VERSION
         mkdir -p $HOME/$NRN_VERSION/build
     else
         echo 'Using cached NEURON build directory.'

pyNN/nest/populations.py

@@ -161,7 +161,7 @@ def _create_cells(self):
                                    size=self.size)
         try:
             self.node_collection = nest.Create(nest_model, self.size, params=params)
-        except nest.kernel.NESTError as err:
+        except nest.NESTError as err:
             if "UnknownModelName" in err.args[0] and "cond" in err.args[0]:
                 raise errors.InvalidModelError("%s Have you compiled NEST with the GSL (Gnu Scientific Library)?" % err)
             if "Spike times must be sorted in non-descending order" in err.args[0]:
@@ -212,7 +212,7 @@ def _set_initial_value_array(self, variable, value):
                 simulator.state.set_status(self.node_collection, variable, local_values)
             else:
                 simulator.state.set_status(self.node_collection[self._mask_local], variable, local_values)
-        except nest.kernel.NESTError as e:
+        except nest.NESTError as e:
             if "Unused dictionary items" in e.args[0]:
                 logger.warning("NEST does not allow setting an initial value for %s" % variable)
                 # should perhaps check whether value-to-be-set is the same as current value,

pyNN/nest/projections.py

@@ -306,7 +306,7 @@ def _convergent_connect(self, presynaptic_indices, postsynaptic_index,
                         if name in self._common_synapse_property_names:
                             self._set_common_synapse_property(name, value)
 
-            except nest.kernel.NESTError as e:
+            except nest.NESTError as e:
                 errmsg = "%s. presynaptic_cells=%s, postsynaptic_cell=%s, weights=%s, delays=%s, synapse model='%s'" % (
                     e, presynaptic_cells, postsynaptic_cell,
                     weights, delays, self.nest_synapse_model)

pyNN/nest/recording.py

@@ -27,8 +27,8 @@ def _set_status(obj, parameters):
     """Wrapper around nest.SetStatus() to add a more informative error message."""
     try:
         nest.SetStatus(obj, parameters)
-    except nest.kernel.NESTError as e:
-        raise nest.kernel.NESTError("%s. Parameter dictionary was: %s" % (e, parameters))
+    except nest.NESTError as e:
+        raise nest.NESTError("%s. Parameter dictionary was: %s" % (e, parameters))
 
 
 class RecordingDevice(object):

pyNN/nest/simulator.py

@@ -51,7 +51,7 @@ def _get(self):
     def _set(self, val):
         try:
             nest.SetKernelStatus({name: dtype(val)})
-        except nest.kernel.NESTError as e:
+        except nest.NESTError as e:
             reraise(e, "%s = %s (%s)" % (name, val, type(val)))
     return property(fget=_get, fset=_set)
 
@@ -76,7 +76,7 @@ def __init__(self):
         try:
             nest.Install('pynn_extensions')
             self.extensions_loaded = True
-        except nest.kernel.NESTError as err:
+        except nest.NESTError as err:
             self.extensions_loaded = False
         self.initialized = False
         self.optimize = False

pyNN/nest/standardmodels/synapses.py

@@ -53,7 +53,7 @@ def _get_nest_synapse_model(self):
             logger.warning(", ".join(model for model in base_model))
             base_model = list(base_model)[0]
             logger.warning("By default, %s is used" % base_model)
-        available_models = nest.Models(mtype='synapses')
+        available_models = nest.synapse_models
         if base_model not in available_models:
             raise ValueError("Synapse dynamics model '%s' not a valid NEST synapse model. "
                              "Possible models in your NEST build are: %s" % (base_model, available_models))

pyNN/nest/synapses.py

@@ -23,7 +23,7 @@ def get_synapse_defaults(model_name):
               'property_object', 'element_type', 'type', 'sizeof',
               'has_delay', 'synapse_model', 'requires_symmetric',
               'weight_recorder', 'init_flag', 'next_readout_time',
-              'synapse_id']
+              'synapse_id', 'synapse_modelid']
     default_params = {}
     for name, value in defaults.items():
         if name not in ignore:
@@ -44,7 +44,7 @@ def _get_nest_synapse_model(self):
         synapse_defaults.pop("tau_minus", None)
         try:
             nest.SetDefaults(self.nest_name + '_lbl', synapse_defaults)
-        except nest.lib.hl_api_exceptions.NESTError as err:
+        except nest.NESTError as err:
             if not state.extensions_loaded:
                 raise NoModelAvailableError(
                     "{self.__class__.__name__} is not available."