updated changes schema string in process_types

biosimulator_processes/process_types.py

@@ -1,4 +1,4 @@
-"""The following types have been derived from both SEDML L1v4 and basico itself.
+CHANGES_SCHEMA = """The following types have been derived from both SEDML L1v4 and basico itself.
 
         BASICO_MODEL_CHANGES_TYPE = {
             'species_changes': {   # <-- this is done like set_species('B', kwarg=) where the inner most keys are the kwargs

notebooks/copasi_process_composer.ipynb

@@ -24,17 +24,33 @@
   },
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 1,
    "id": "c6c10dc5988e52d4",
    "metadata": {
-    "collapsed": false
+    "collapsed": false,
+    "ExecuteTime": {
+     "end_time": "2024-02-28T20:57:05.779779Z",
+     "start_time": "2024-02-28T20:57:03.764811Z"
+    }
    },
-   "outputs": [],
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "CobraProcess registered successfully.\n",
+      "CopasiProcess registered successfully.\n",
+      "SmoldynProcess registered successfully.\n",
+      "TelluriumProcess registered successfully.\n"
+     ]
+    }
+   ],
    "source": [
     "import os \n",
     "from basico import *\n",
     "from process_bigraph import Composite, pf \n",
-    "from biosimulator_processes.processes.copasi_process import CopasiProcess"
+    "from biosimulator_processes.processes.copasi_process import CopasiProcess\n",
+    "from biosimulator_processes.process_types import MODEL_TYPE, CHANGES_SCHEMA"
    ]
   },
   {
@@ -255,6 +271,31 @@
     "#### Example 2: Define a single-process composition from a given BioModels model id and make model changes. The options available for configuration of a `'model'` that can be run by the composite process are based on SEDML L1V4 specifications. Please note that not all parameters are required in this configuration."
    ]
   },
+  {
+   "cell_type": "code",
+   "outputs": [
+    {
+     "data": {
+      "text/plain": "'The following types have been derived from both SEDML L1v4 and basico itself.\\n\\n        BASICO_MODEL_CHANGES_TYPE = {\\n            \\'species_changes\\': {   # <-- this is done like set_species(\\'B\\', kwarg=) where the inner most keys are the kwargs\\n                \\'species_name\\': {\\n                    \\'unit\\': \\'maybe[string]\\',\\n                    \\'initial_concentration\\': \\'maybe[float]\\',\\n                    \\'initial_particle_number\\': \\'maybe[float]\\',\\n                    \\'initial_expression\\': \\'maybe[string]\\',\\n                    \\'expression\\': \\'maybe[string]\\'\\n                }\\n            },\\n            \\'global_parameter_changes\\': {   # <-- this is done with set_parameters(PARAM, kwarg=). where the inner most keys are the kwargs\\n                \\'global_parameter_name\\': {\\n                    \\'initial_value\\': \\'maybe[float]\\',\\n                    \\'initial_expression\\': \\'maybe[string]\\',\\n                    \\'expression\\': \\'maybe[string]\\',\\n                    \\'status\\': \\'maybe[string]\\',\\n                    \\'type\\': \\'maybe[string]\\'  # (ie: fixed, assignment, reactions)\\n                }\\n            },\\n            \\'reaction_changes\\': {\\n                \\'reaction_name\\': {\\n                    \\'parameters\\': {\\n                        \\'reaction_parameter_name\\': \\'maybe[int]\\'  # (new reaction_parameter_name value)  <-- this is done with set_reaction_parameters(name=\"(REACTION_NAME).REACTION_NAME_PARAM\", value=VALUE)\\n                    },\\n                    \\'reaction_scheme\\': \\'maybe[string]\\'   # <-- this is done like set_reaction(name = \\'R1\\', scheme = \\'S + E + F = ES\\')\\n                }\\n            }\\n        }\\n'"
+     },
+     "execution_count": 2,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "CHANGES_SCHEMA"
+   ],
+   "metadata": {
+    "collapsed": false,
+    "ExecuteTime": {
+     "end_time": "2024-02-28T20:57:27.860061Z",
+     "start_time": "2024-02-28T20:57:27.857520Z"
+    }
+   },
+   "id": "433d58bbe38402af",
+   "execution_count": 2
+  },
   {
    "cell_type": "code",
    "outputs": [],