successfully loading a saved composite

vivarium-collective · Aug 28, 2024 · aa11888 · aa11888
1 parent 0d50bd4
commit aa11888
Show file tree

Hide file tree

Showing 2 changed files with 32 additions and 29 deletions.
diff --git a/process_bigraph/composite.py b/process_bigraph/composite.py
@@ -618,6 +618,7 @@ class Composite(Process):
     def load(cls, path, core=None):
         with open(path) as data:
             document = json.load(data)
+
             composite = cls(
                 document,
                 core=core)

diff --git a/process_bigraph/experiments/comets.py b/process_bigraph/experiments/comets.py
@@ -8,27 +8,12 @@
 from process_bigraph import Process, ProcessTypes, Composite
 from process_bigraph.experiments.parameter_scan import RunProcess
 
-core = ProcessTypes()
-
 
 # create new types
 def apply_non_negative(schema, current, update, core):
     new_value = current + update
     return max(0, new_value)
 
-positive_float = {
-    '_type': 'positive_float',
-    '_inherit': 'float',
-    '_apply': apply_non_negative
-}
-core.register('positive_float', positive_float)
-
-bounds_type = {
-    'lower': 'maybe[float]',
-    'upper': 'maybe[float]'
-}
-core.register_process('bounds', bounds_type)
-
 
 # TODO -- check the function signature of the apply method and report missing keys upon registration
 
@@ -76,7 +61,6 @@ def __init__(self, config, core):
             # error handling
             raise ValueError('Invalid model file')
 
-
         for reaction_id, bounds in self.config['bounds'].items():
             if bounds['lower'] is not None:
                 self.model.reactions.get_by_id(reaction_id).lower_bound = bounds['lower']
@@ -125,9 +109,6 @@ def update(self, state, interval):
             'substrates': substrate_update,
         }
 
-core.register_process('DynamicFBA', DynamicFBA)
-
-
 # Laplacian for 2D diffusion
 LAPLACIAN_2D = np.array([[0, 1, 0],
                          [1, -4, 1],
@@ -246,9 +227,6 @@ def diffusion_delta(self, state, interval, diffusion_coeff, advection_coeff):
 
         return updated_state - state
 
-core.register_process('DiffusionAdvection', DiffusionAdvection)
-
-
 def dfba_config(
         model_file='textbook',
         kinetic_params={
@@ -294,6 +272,27 @@ def run_process(
     return run.update(initial_state)
 
 
+def register_types(core):
+    core.register('positive_float', {
+        '_type': 'positive_float',
+        '_inherit': 'float',
+        '_apply': apply_non_negative})
+
+    core.register('bounds', {
+        'lower': 'maybe[float]',
+        'upper': 'maybe[float]'})
+
+    core.register_process(
+        'DynamicFBA',
+        DynamicFBA)
+
+    core.register_process(
+        'DiffusionAdvection',
+        DiffusionAdvection)
+
+    return core
+
+
 def run_dfba_spatial():
     n_bins = (2, 2)
 
@@ -396,7 +395,7 @@ def run_diffusion_process():
     print(data)
 
 
-def run_comets():
+def run_comets(core):
     n_bins = (6, 6)
 
     initial_glucose = np.random.uniform(low=0, high=20, size=n_bins)
@@ -495,15 +494,18 @@ def run_comets():
 
     other_results = load.gather_results()
 
-    assert results == other_results
-
-    import ipdb; ipdb.set_trace()
+    np.testing.assert_equal(
+        results[('emitter',)][-1]['fields'],
+        other_results[('emitter',)][-1]['fields'])
 
     print(results)
 
 
 
 if __name__ == '__main__':
-    # run_dfba_spatial()
-    # run_diffusion_process()
-    run_comets()
+    core = ProcessTypes()
+    core = register_types(core)
+
+    # run_dfba_spatial(core)
+    # run_diffusion_process(core)
+    run_comets(core)