Process keywords

vivarium/composites/toys.py

@@ -263,7 +263,7 @@ def next_update(self, timestep, states):
 class Proton(Process):
     name = 'proton'
     defaults = {
-        'time_step': 1.0,
+        'timestep': 1.0,
         'radius': 0.0}
 
     def ports_schema(self):
@@ -314,7 +314,7 @@ def next_update(self, timestep, states):
 class Electron(Process):
     name = 'electron'
     defaults = {
-        'time_step': 1.0,
+        'timestep': 1.0,
         'spin': electron_spins[0]}
 
     def ports_schema(self):
@@ -667,10 +667,10 @@ def test_composite_parameters() -> None:
     composer_parameters = bb_composer.get_parameters()
     composite_parameters = bb_composite.get_parameters()
     expected_parameters = {
-        'a1': {'time_step': 1.0},
-        'a2': {'time_step': 1.0},
+        'a1': {'timestep': 1.0},
+        'a2': {'timestep': 1.0},
         'a3_store': {
-            'a3': {'time_step': 1.0}}}
+            'a3': {'timestep': 1.0}}}
     assert composite_parameters == composer_parameters
     assert composite_parameters == expected_parameters
 

vivarium/core/process.py

@@ -82,43 +82,51 @@ def _get_parameters(
 
 
 class Process(metaclass=abc.ABCMeta):
+    """Process parent class.
+
+      All :term:`process` classes must inherit from this class. Each
+      class can provide a ``defaults`` class variable to specify the
+      process defaults as a dictionary.
+
+      Note that subclasses should call the superclass init function
+      first. This allows the superclass to correctly save the initial
+      parameters before they are mutated by subclass constructor code.
+      We need access to the original parameters for serialization to
+      work properly.
+
+      Args:
+          parameters: Override the class defaults. This dictionary may
+              also contain the following special keys:
+
+              * ``name``: Saved to ``self.name``.
+              * ``_original_parameters``: Returned by
+                ``__getstate__()`` for serialization.
+              * ``_no_original_parameters``: If specified with a value
+                of ``True``, original parameters will not be copied
+                during initialization, and ``__getstate__()`` will
+                instead return ``self.parameters``. This puts the
+                responsibility on the user to not mutate process
+                parameters.
+              * ``_schema``: Overrides the schema.
+              * ``_parallel``: Indicates that the process should be
+                parallelized. ``self.parallel`` will be set to True.
+              * ``_condition``: Path to a variable whose value will be
+                returned by
+                :py:meth:`vivarium.core.process.Process.update_condition`.
+              * ``time_step``: Returned by
+                :py:meth:`vivarium.core.process.Process.calculate_timestep`.
+      """
+
     defaults: Dict[str, Any] = {}
 
     def __init__(self, parameters: Optional[dict] = None) -> None:
-        """Process parent class.
-
-        All :term:`process` classes must inherit from this class. Each
-        class can provide a ``defaults`` class variable to specify the
-        process defaults as a dictionary.
-
-        Note that subclasses should call the superclass init function
-        first. This allows the superclass to correctly save the initial
-        parameters before they are mutated by subclass constructor code.
-        We need access to the original parameters for serialization to
-        work properly.
+        self.initialize_parameters(parameters)
 
-        Args:
-            parameters: Override the class defaults. This dictionary may
-                also contain the following special keys:
-
-                * ``name``: Saved to ``self.name``.
-                * ``_original_parameters``: Returned by
-                  ``__getstate__()`` for serialization.
-                * ``_no_original_parameters``: If specified with a value
-                  of ``True``, original parameters will not be copied
-                  during initialization, and ``__getstate__()`` will
-                  instead return ``self.parameters``. This puts the
-                  responsibility on the user to not mutate process
-                  parameters.
-                * ``_schema``: Overrides the schema.
-                * ``_parallel``: Indicates that the process should be
-                  parallelized. ``self.parallel`` will be set to True.
-                * ``_condition``: Path to a variable whose value will be
-                  returned by
-                  :py:meth:`vivarium.core.process.Process.update_condition`.
-                * ``time_step``: Returned by
-                  :py:meth:`vivarium.core.process.Process.calculate_timestep`.
-        """
+    def initialize_parameters(
+            self,
+            parameters: Optional[dict] = None,
+            **kwargs
+    ) -> None:
         parameters = parameters or {}
         if '_original_parameters' in parameters:
             original_parameters = parameters.pop('_original_parameters')
@@ -155,9 +163,28 @@ class can provide a ``defaults`` class variable to specify the
                 '_emit': True,
                 '_updater': 'set'}))
 
-        self.parameters.setdefault('time_step', DEFAULT_TIME_STEP)
+        self._set_timestep()
+
         self.schema: Optional[dict] = None
 
+    def initialize(
+            self,
+            parameters: Optional[dict] = None,
+            base_parameters: Optional[dict] = None
+    ) -> None:
+        # base_parameters = parameters.pop('base_parameters')
+
+        for local in ['self', '__class__', 'ipdb']:
+            if local in parameters:
+                del parameters[local]
+        parameters.update(base_parameters)
+        self.initialize_parameters(parameters)
+
+    def _set_timestep(self) -> None:
+        self.parameters.setdefault('timestep', DEFAULT_TIME_STEP)
+        if self.parameters.get('time_step'):
+            self.parameters['timestep'] = self.parameters['time_step']
+
     def __getstate__(self) -> dict:
         """Return parameters
 
@@ -275,10 +302,10 @@ def calculate_timestep(self, states: Optional[State]) -> Union[float, int]:
         """Return the next process time step
 
         A process subclass may override this method to implement
-        adaptive timesteps. By default it returns self.parameters['time_step'].
+        adaptive timesteps. By default it returns self.parameters['timestep'].
         """
         _ = states
-        return self.parameters['time_step']
+        return self.parameters['timestep']
 
     def default_state(self) -> State:
         """Get the default values of the variables in each port.

vivarium/core/serialize_test.py

@@ -115,7 +115,7 @@ def test_serialization_full() -> None:
         serialized.pop('function'))
     expected_serialized = {
         'process': (
-            "!ProcessSerializer[{'time_step': 1.0, '_name': "
+            "!ProcessSerializer[{'timestep': 1.0, '_name': "
             "'SerializeProcess'}]"
         ),
         '1': True,

vivarium/processes/growth_rate.py

@@ -22,11 +22,22 @@ class GrowthRate(Process):
     """ A Vivarium process that models exponential growth of biomass """
 
     name = NAME
-    defaults = {
-        'default_growth_rate': 0.0005,
-        'default_growth_noise': 0.0,
-        'variables': ['mass']
-    }
+    # defaults = {
+    #     'default_growth_rate': 0.0005,
+    #     'default_growth_noise': 0.0,
+    #     'variables': ['mass']
+    # }
+
+    def __init__(
+            self,
+            default_growth_rate=0.0005,
+            default_growth_noise=0.0,
+            variables=('mass',),
+            **base_parameters):
+
+        parameters = locals().copy()
+        base_parameters = parameters.pop('base_parameters')
+        self.initialize(parameters, base_parameters)
 
     def ports_schema(self):
         return {
@@ -73,13 +84,16 @@ def next_update(self, timestep, states):
 def test_growth_rate(total_time=1350):
     initial_mass = 100
     growth_rate = 0.0005
-    config = {
-        'variables': ['mass'],
-        'default_growth_rate': growth_rate,
-        'time_step': 2,
-    }
-
-    growth_rate_process = GrowthRate(config)
+    # config = {
+    #     'variables': ['mass'],
+    #     'default_growth_rate': growth_rate,
+    #     'timestep': 2,
+    # }
+
+    growth_rate_process = GrowthRate(
+        default_growth_rate=growth_rate,
+        timestep=5.0,
+        variables=('mass',))
     initial_state = {'variables': {'mass': initial_mass}}
     experiment = process_in_experiment(
         growth_rate_process,