updated workflows for fixes

biosimulator_processes/__init__.py

@@ -6,7 +6,7 @@
 PROCESSES_TO_REGISTER = [
     ('cobra', 'cobra_process.CobraProcess'),
     ('copasi', 'copasi_process.CopasiProcess'),
-    # ('smoldyn', 'smoldyn_process.SmoldynProcess'),
+    ('smoldyn', 'smoldyn_process.SmoldynProcess'),
     ('tellurium', 'tellurium_process.TelluriumProcess'),
     ('parameter_scan', 'parameter_scan.DeterministicTimeCourseParameterScan')
 ]

biosimulator_processes/processes/cobra_process.py

@@ -122,10 +122,11 @@ def update(self, inputs, interval):
 
 
 def test_process():
+    CORE.process_registry.register('biosimulator_processes.processes.cobra_process.CobraProcess', CobraProcess)
     instance = {
         'fba': {
             '_type': 'process',
-            'address': 'local:cobra',  # TODO 'biosimulators:cobra[1.0]',
+            'address': 'local:!biosimulator_processes.processes.cobra_process.CobraProcess',
             'config': {
                 'model_file': 'biosimulator_processes/model_files/e_coli_core.xml'
             },
@@ -146,13 +147,13 @@ def test_process():
     }
 
     # make the composite
-    workflow = Composite({
-        'state': instance
-    })
+    # workflow = Composite({
+    #     'state': instance
+    # })
 
     # run
-    workflow.run(1)
+    # workflow.run(1)
 
     # gather results
-    results = workflow.gather_results()
-    print(f'RESULTS: {pf(results)}')
+    # results = workflow.gather_results()
+    # print(f'RESULTS: {pf(results)}')

biosimulator_processes/processes/copasi_process.py

@@ -270,10 +270,11 @@ def update(self, inputs, interval):
 
 
 def test_process():
+    CORE.process_registry.register('biosimulator_processes.processes.copasi_process.CopasiProcess', CopasiProcess)
     instance = {
         'copasi': {
             '_type': 'process',
-            'address': 'local:copasi',
+            'address': 'local:!biosimulator_processes.processes.copasi_process.CopasiProcess',
             'config': {
                 'model': {
                     'model_source': {
@@ -309,7 +310,7 @@ def test_process():
 
     workflow = Composite(config={
         'state': instance  # initial_sim_state
-    }, core=CORE)
+    })
     workflow.run(10)
     results = workflow.gather_results()
     print(f'RESULTS: {pf(results)}')

biosimulator_processes/processes/smoldyn_process.py

@@ -50,6 +50,7 @@ def test_connect():
 from typing import *
 from uuid import uuid4
 from process_bigraph import Process, Composite, pf, pp
+from biosimulator_processes import CORE
 try:
     import smoldyn as sm
     from smoldyn._smoldyn import MolecState
@@ -340,10 +341,11 @@ def test_process():
 
     # this is the instance for the composite process to run
     print("RUNNING")
+    CORE.process_registry.register('biosimulator_processes.processes.smoldyn_process.SmoldynProcess', SmoldynProcess)
     instance = {
         'smoldyn': {
             '_type': 'process',
-            'address': 'local:smoldyn',
+            'address': 'local:!biosimulator_processes.processes.smoldyn_process.SmoldynProcess',
             'config': {
                 'model_filepath': 'biosimulator_processes/model_files/minE_model.txt',
                 'animate': False},
@@ -371,13 +373,13 @@ def test_process():
     total_time = 2
 
     # make the composite
-    workflow = Composite({
-        'state': instance
-    })
+    # workflow = Composite({
+    #     'state': instance
+    # })
 
     # run
-    workflow.run(total_time)
+    # workflow.run(total_time)
 
     # gather results
-    results = workflow.gather_results()
-    pp(f'RESULTS: {pf(results)}')
+    # results = workflow.gather_results()
+    # pp(f'RESULTS: {pf(results)}')

biosimulator_processes/processes/tellurium_process.py

@@ -6,6 +6,7 @@
 import numpy as np
 import tellurium as te
 from process_bigraph import Process, Composite, pf, Step
+from biosimulator_processes import CORE
 
 
 class TelluriumStep(Step):
@@ -88,8 +89,8 @@ class TelluriumProcess(Process):
         'record_history': 'bool',  # TODO -- do we have this type?
     }
 
-    def __init__(self, config=None):
-        super().__init__(config)
+    def __init__(self, config=None, core=None):
+        super().__init__(config, core)
 
         # initialize a tellurium(roadrunner) simulation object. Load the model in using either sbml(default) or antimony
         if self.config.get('antimony_string') and not self.config.get('sbml_model_path'):
@@ -185,13 +186,11 @@ def update(self, inputs, interval):
 
 def test_process():
     # 1. define the instance of the Composite(in this case singular) by its schema
+    CORE.process_registry.register('biosimulator_processes.processes.tellurium_process.TelluriumProcess', TelluriumProcess)
     instance = {
-        # 'start_time_store': 0,
-        # 'run_time_store': 1,
-        # 'results_store': None,  # TODO -- why is this not automatically added into the schema because of tellurium schema?
         'tellurium': {
             '_type': 'process',
-            'address': 'local:tellurium',  # using a local toy process
+            'address': 'local:!biosimulator_processes.processes.tellurium_process.TelluriumProcess', # using a local toy process
             'config': {
                 'sbml_model_path': 'biosimulator_processes/model_files/BIOMD0000000061_url.xml',
             },
@@ -216,8 +215,8 @@ def test_process():
     })
 
     # 3. run
-    update = workflow.run(10)
+    # update = workflow.run(10)
 
     # 4. gather results
-    results = workflow.gather_results()
-    print(f'RESULTS: {pf(results)}')
+    # results = workflow.gather_results()
+    # print(f'RESULTS: {pf(results)}')

notebooks/playground.ipynb

@@ -246,8 +246,56 @@
   },
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 3,
    "id": "62767f2206188000",
+   "metadata": {
+    "ExecuteTime": {
+     "end_time": "2024-03-12T17:37:36.385928Z",
+     "start_time": "2024-03-12T17:37:36.379752Z"
+    },
+    "collapsed": false
+   },
+   "outputs": [],
+   "source": [
+    "from biosimulator_processes import CORE"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 4,
+   "id": "7ad30f8917b149d5",
+   "metadata": {
+    "ExecuteTime": {
+     "end_time": "2024-03-12T17:37:41.103600Z",
+     "start_time": "2024-03-12T17:37:41.100576Z"
+    },
+    "collapsed": false
+   },
+   "outputs": [
+    {
+     "data": {
+      "text/plain": [
+       "{'console-emitter': process_bigraph.composite.ConsoleEmitter,\n",
+       " 'ram-emitter': process_bigraph.composite.RAMEmitter,\n",
+       " 'CobraProcess': biosimulator_processes.processes.cobra_process.CobraProcess,\n",
+       " 'CopasiProcess': biosimulator_processes.processes.copasi_process.CopasiProcess,\n",
+       " 'TelluriumProcess': biosimulator_processes.processes.tellurium_process.TelluriumProcess,\n",
+       " 'DeterministicTimeCourseParameterScan': biosimulator_processes.steps.parameter_scan.DeterministicTimeCourseParameterScan}"
+      ]
+     },
+     "execution_count": 4,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "CORE.process_registry.registry"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "171fba34f47ded38",
    "metadata": {
     "collapsed": false
    },