Merge pull request #454 from jgonin/issue67

Issue67 (Move the `max_delay` argument of `setup()` into `extra_params`)

pyNN/brian/__init__.py

@@ -28,13 +28,15 @@ def list_standard_models():
 
 
 def setup(timestep=DEFAULT_TIMESTEP, min_delay=DEFAULT_MIN_DELAY,
-          max_delay=DEFAULT_MAX_DELAY, **extra_params):
+          **extra_params):
     """
     Should be called at the very beginning of a script.
     extra_params contains any keyword arguments that are required by a given
     simulator but not by others.
     """
-    common.setup(timestep, min_delay, max_delay, **extra_params)
+
+    max_delay = extra_params.get('max_delay', DEFAULT_MAX_DELAY)
+    common.setup(timestep, min_delay, **extra_params)
     simulator.state.clear()
     brian.set_global_preferences(**extra_params)
     simulator.state.dt = timestep  # move to common.setup?

pyNN/common/control.py

@@ -31,7 +31,7 @@ def __init__(self):
 
 
 def setup(timestep=DEFAULT_TIMESTEP, min_delay=DEFAULT_MIN_DELAY,
-          max_delay=DEFAULT_MAX_DELAY, **extra_params):
+           **extra_params):
     """
     Initialises/reinitialises the simulator. Any existing network structure is
     destroyed.
@@ -41,6 +41,7 @@ def setup(timestep=DEFAULT_TIMESTEP, min_delay=DEFAULT_MIN_DELAY,
     `extra_params` contains any keyword arguments that are required by a given
     simulator but not by others.
     """
+    max_delay = extra_params.get('max_delay', DEFAULT_MAX_DELAY)
     invalid_extra_params = ('mindelay', 'maxdelay', 'dt', 'time_step')
     for param in invalid_extra_params:
         if param in extra_params:

pyNN/core.py

@@ -90,3 +90,4 @@ def projection(self, projection):
 
     def __call__(self, i, j):
         raise NotImplementedError
+

pyNN/mock/__init__.py

@@ -29,8 +29,10 @@ def list_standard_models():
 
 
 def setup(timestep=DEFAULT_TIMESTEP, min_delay=DEFAULT_MIN_DELAY,
-          max_delay=DEFAULT_MAX_DELAY, **extra_params):
-    common.setup(timestep, min_delay, max_delay, **extra_params)
+          **extra_params):
+
+    max_delay = extra_params.get('max_delay', DEFAULT_MAX_DELAY)
+    common.setup(timestep, min_delay, **extra_params)
     simulator.state.clear()
     simulator.state.dt = timestep  # move to common.setup?
     simulator.state.min_delay = min_delay

pyNN/moose/__init__.py

@@ -30,13 +30,14 @@
 # ==============================================================================
 
 
-def setup(timestep=0.1, min_delay=0.1, max_delay=10.0, **extra_params):
+def setup(timestep=0.1, min_delay=0.1, **extra_params):
     """
     Should be called at the very beginning of a script.
     extra_params contains any keyword arguments that are required by a given
     simulator but not by others.
     """
-    common.setup(timestep, min_delay, max_delay, **extra_params)
+    max_delay = extra_params.get('max_delay', 10.0)
+    common.setup(timestep, min_delay, **extra_params)
     simulator.state.dt = timestep
     if not os.path.exists(temporary_directory):
         os.mkdir(temporary_directory)

pyNN/nemo/__init__.py

@@ -41,7 +41,7 @@ def list_standard_models():
 # ==============================================================================
 
 
-def setup(timestep=1, min_delay=1, max_delay=10.0, **extra_params):
+def setup(timestep=1, min_delay=1, **extra_params):
     """
     Should be called at the very beginning of a script.
     extra_params contains any keyword arguments that are required by a given
@@ -52,7 +52,8 @@ def setup(timestep=1, min_delay=1, max_delay=10.0, **extra_params):
     if (min_delay < 1):
         raise Exception("It is not currently possible to have a min_delay less than 1ms with this simulator")
 
-    common.setup(timestep, min_delay, max_delay, **extra_params)
+    max_delay = extra_params.get('max_delay', 10.0)
+    common.setup(timestep, min_delay, **extra_params)
     simulator.state = simulator._State(timestep, min_delay, max_delay)
     simulator.spikes_array_list = []
     simulator.recorder_list = []

pyNN/nest/__init__.py

@@ -86,7 +86,7 @@ def _discrepancy_due_to_rounding(parameters, output_values):
 
 
 def setup(timestep=DEFAULT_TIMESTEP, min_delay=DEFAULT_MIN_DELAY,
-          max_delay=DEFAULT_MAX_DELAY, **extra_params):
+          **extra_params):
     """
     Should be called at the very beginning of a script.
 
@@ -110,7 +110,8 @@ def setup(timestep=DEFAULT_TIMESTEP, min_delay=DEFAULT_MIN_DELAY,
     `rng_seeds_seed`:
         a single seed that will be used to generate random values for `rng_seeds`
     """
-    common.setup(timestep, min_delay, max_delay, **extra_params)
+    max_delay = extra_params.get('max_delay', DEFAULT_MAX_DELAY)
+    common.setup(timestep, min_delay, **extra_params)
     simulator.state.clear()
     for key in ("verbosity", "spike_precision", "recording_precision",
                 "threads"):

pyNN/neuron/__init__.py

@@ -51,8 +51,7 @@ def list_standard_models():
 # ==============================================================================
 
 
-def setup(timestep=DEFAULT_TIMESTEP, min_delay=DEFAULT_MIN_DELAY,
-          max_delay=DEFAULT_MAX_DELAY, **extra_params):
+def setup(timestep=DEFAULT_TIMESTEP, min_delay=DEFAULT_MIN_DELAY, **extra_params):
     """
     Should be called at the very beginning of a script.
 
@@ -72,12 +71,12 @@ def setup(timestep=DEFAULT_TIMESTEP, min_delay=DEFAULT_MIN_DELAY,
     returns: MPI rank
 
     """
-    common.setup(timestep, min_delay, max_delay, **extra_params)
+    common.setup(timestep, min_delay, **extra_params)
     simulator.initializer.clear()
     simulator.state.clear()
     simulator.state.dt = timestep
     simulator.state.min_delay = min_delay
-    simulator.state.max_delay = max_delay
+    simulator.state.max_delay = extra_params.get('max_delay', DEFAULT_MAX_DELAY)
     if 'use_cvode' in extra_params:
         simulator.state.cvode.active(int(extra_params['use_cvode']))
         if 'rtol' in extra_params:

pyNN/nineml/__init__.py

@@ -24,12 +24,12 @@ def list_standard_models():
     return [obj.__name__ for obj in globals().values() if isinstance(obj, type) and issubclass(obj, std.StandardCellType)]
 
 
-def setup(timestep=0.1, min_delay=0.1, max_delay=10.0, **extra_params):
-    common.setup(timestep, min_delay, max_delay, **extra_params)
+def setup(timestep=0.1, min_delay=0.1, **extra_params):
+    common.setup(timestep, min_delay, **extra_params)
     simulator.state.clear()
     simulator.state.dt = timestep  # move to common.setup?
     simulator.state.min_delay = min_delay
-    simulator.state.max_delay = max_delay
+    simulator.state.max_delay = extra_params.get('max_delay', 10.0)
     simulator.state.mpi_rank = extra_params.get('rank', 0)
     simulator.state.num_processes = extra_params.get('num_processes', 1)
     simulator.state.output_filename = extra_params.get("filename", "PyNN29ML.xml")