add processes module

process_bigraph/experiments/comets.py

@@ -1,12 +1,11 @@
 import numpy as np
 from pathlib import Path
-import matplotlib.pyplot as plt
 from scipy.ndimage import convolve
 import cobra
 from cobra.io import load_model
 
 from process_bigraph import Process, ProcessTypes, Composite
-from process_bigraph.experiments.parameter_scan import RunProcess
+from process_bigraph.processes.parameter_scan import RunProcess
 
 
 # create new types

process_bigraph/experiments/parameter_scan.py → process_bigraph/processes/parameter_scan.py

@@ -36,17 +36,14 @@ class ToySystem(Process):
                 'kdeg': 'float',
                 'ksynth': 'float'}}}
 
-
     def inputs(self):
         return {
             'species': 'map[float]'}
 
-
     def outputs(self):
         return {
             'species': 'map[float]'}
 
-
     def update(self, inputs, interval):
         species = {
             key: input * (self.config['rates'][key]['ksynth'] - self.config['rates'][key]['kdeg'])
@@ -59,7 +56,6 @@ def update(self, inputs, interval):
 class ODE(Process):
     config_schema = 'ode_config'
 
-
     def __init__(self, config, core):
         super().__init__(config, core)
 
@@ -72,17 +68,14 @@ def __init__(self, config, core):
             self.species_count,
             self.species_count)
 
-
     def inputs(self):
         return {
             'species': f'array[({self.species_count}), float]'}
 
-
     def outputs(self):
         return {
             'species': f'array[({self.species_count}), float]'}
 
-
     def update(self, state, interval):
         total = np.dot(
             self.config['rates'],
@@ -100,7 +93,6 @@ class RunProcess(Step):
         'timestep': 'float',
         'runtime': 'float'}
 
-
     def __init__(self, config, core):
         super().__init__(config, core)
 
@@ -187,18 +179,15 @@ def __init__(self, config, core):
 
         self.composite = Composite(composite_config, core=core)
 
-
     def inputs(self):
         return self.process.inputs()
 
-
     def outputs(self):
         return {
             'results': dict(
                 {'time': 'list[float]'},
                 **self.results_schema)}
 
-
     def update(self, inputs):
         # TODO: instead of the composite being a reference it is instead read through
         #   some port and lives in the state of the simulation (??)
@@ -265,7 +254,6 @@ class ParameterScan(Step):
         'timestep': 'float',
         'runtime': 'float'}
 
-
     def __init__(self, config, core):
         super().__init__(config, core)
 
@@ -338,18 +326,15 @@ def __init__(self, config, core):
 
         self.results_schema = results_schema
 
-
     def first_process(self):
         for key, value in self.scan.state.items():
             if key.startswith('process_'):
                 return value['instance'].composite.state['process']['instance']
 
-
     def outputs(self):
         return {
             'results': self.results_schema}
 
-
     def update(self, inputs):
         results = self.scan.update({}, 0.0)
 

setup.py

@@ -2,7 +2,7 @@
 from setuptools import setup, find_packages
 
 
-VERSION = '0.0.20'
+VERSION = '0.0.21'
 
 
 with open("README.md", "r") as readme:
@@ -29,6 +29,7 @@
     # packages=find_packages(),
     packages=[
         'process_bigraph',
+        'process_bigraph.processes',
     ],
     classifiers=[
         "Development Status :: 3 - Alpha",