Merge branch 'main' into nondefault-settings

.gitignore

@@ -0,0 +1,5 @@
+.python-version
+.ipynb_checkpoints/
+spatio_flux.egg-info/
+__pycache__/
+out/

spatio_flux/__init__.py

@@ -4,9 +4,7 @@
 """
 
 from process_bigraph import ProcessTypes
-
-# make type system
-core = ProcessTypes()
+from spatio_flux.processes import register_processes
 
 
 def apply_non_negative(schema, current, update, core):
@@ -17,13 +15,26 @@ def apply_non_negative(schema, current, update, core):
 positive_float = {
     '_type': 'positive_float',
     '_inherit': 'float',
-    '_apply': apply_non_negative
-}
-core.register('positive_float', positive_float)
+    '_apply': apply_non_negative}
+
 
 bounds_type = {
     'lower': 'maybe[float]',
-    'upper': 'maybe[float]'
+    'upper': 'maybe[float]'}
+
+
+particle_type = {
+    'id': 'string',
+    'position': 'tuple[float,float]',
+    'size': 'float',
+    'local': 'map[float]',
+    'exchange': 'map[float]',    # {mol_id: delta_value}
 }
-core.register_process('bounds', bounds_type)
 
+
+def register_types(core):
+    core.register('positive_float', positive_float)
+    core.register('bounds', bounds_type)
+    core.register('particle', particle_type)
+
+    return register_processes(core)

spatio_flux/processes/__init__.py

@@ -0,0 +1,13 @@
+from spatio_flux.processes.dfba import DynamicFBA
+from spatio_flux.processes.diffusion_advection import DiffusionAdvection
+from spatio_flux.processes.particles import Particles, MinimalParticle
+
+
+def register_processes(core):
+    core.register_process('DynamicFBA', DynamicFBA)
+    core.register_process('DiffusionAdvection', DiffusionAdvection)
+    core.register_process('Particles', Particles)
+    core.register_process('MinimalParticle', MinimalParticle)
+
+    return core
+

spatio_flux/processes/comets.py

@@ -20,6 +20,36 @@
     'initial_min_max': {'glucose': (0, 10), 'acetate': (0, 0), 'biomass': (0, 0.1)},
 }
 
+## TODO -- maybe we need to make specific composites
+class COMETS(Composite):
+    """
+    This needs to declare what types of processes are in the composite.
+    """
+    config_schema = {
+        'n_bins': 'tuple',
+    }
+
+    def __init__(self, config, core=None):
+        # set up the document here
+        state = {
+            'dFBA': {
+                'config': {
+                    'n_bins': config['n_bins'],
+                }
+            },
+            'diffusion': {
+                'config': {
+                    'something_else': config['n_bins'],
+                }
+            }
+        }
+
+        super().__init__(config, core=core)
+
+    # TODO -- this could be in Process.
+    def get_default(self):
+        return self.core.default(self.config_schema)
+
 
 def run_comets(
         total_time=10.0,