feat: implemented builder adjusted scripts for new smoldyn and updated l

biosimulators · Feb 29, 2024 · c57e576 · c57e576
1 parent 32a0192
commit c57e576
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Showing 6 changed files with 91 additions and 130 deletions.
diff --git a/Dockerfile b/Dockerfile
@@ -48,6 +48,8 @@ RUN apt-get update && apt-get install -y --no-install-recommends \
     && rm -rf /var/lib/apt/lists/* \
     && pip install --upgrade pip && pip install poetry \
     && poetry config virtualenvs.in-project true \
+    # && poetry run pip install psutil \
+    && poetry update \
     && poetry install \
     && chmod +x ./trust-notebooks.sh \
     && ./trust-notebooks.sh \

diff --git a/biosimulator_processes/processes/__init__.py b/biosimulator_processes/processes/__init__.py
@@ -1,15 +1,18 @@
-from process_bigraph import process_registry
+from builder import ProcessTypes, Builder
 
 
 # Define a list of processes to attempt to import and register
-processes_to_register = [
+PROCESSES_TO_REGISTER = [
     ('cobra', 'cobra_process.CobraProcess'),
     ('copasi', 'copasi_process.CopasiProcess'),
     ('smoldyn', 'smoldyn_process.SmoldynProcess'),
     ('tellurium', 'tellurium_process.TelluriumProcess'),
 ]
 
-for process_name, process_path in processes_to_register:
+CORE = ProcessTypes()
+BIOSIMULATOR_PROCESS_BUILDER = Builder(core=CORE)
+
+for process_name, process_path in PROCESSES_TO_REGISTER:
     module_name, class_name = process_path.rsplit('.', 1)
     try:
         # Dynamically import the module
@@ -19,7 +22,7 @@
         process_class = getattr(process_module, class_name)
 
         # Register the process
-        process_registry.register(process_name, process_class)
+        BIOSIMULATOR_PROCESS_BUILDER.register_process(process_name, process_class)
         print(f"{class_name} registered successfully.")
     except ImportError as e:
         print(f"{class_name} not available. Error: {e}")
diff --git a/notebooks/copasi_process_composer.ipynb b/notebooks/copasi_process_composer.ipynb
@@ -12,9 +12,14 @@
   },
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 1,
    "id": "initial_id",
-   "metadata": {},
+   "metadata": {
+    "ExecuteTime": {
+     "end_time": "2024-02-29T19:54:21.729902Z",
+     "start_time": "2024-02-29T19:54:21.723041Z"
+    }
+   },
    "outputs": [],
    "source": [
     "import sys \n",
@@ -24,16 +29,34 @@
   },
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 2,
    "id": "c6c10dc5988e52d4",
    "metadata": {
-    "collapsed": false
+    "collapsed": false,
+    "ExecuteTime": {
+     "end_time": "2024-02-29T19:54:23.693482Z",
+     "start_time": "2024-02-29T19:54:22.908092Z"
+    }
    },
-   "outputs": [],
+   "outputs": [
+    {
+     "ename": "ImportError",
+     "evalue": "cannot import name 'process_registry' from 'process_bigraph' (/Users/alex/Library/Caches/pypoetry/virtualenvs/biosimulator-processes-KVuYbFzt-py3.10/lib/python3.10/site-packages/process_bigraph/__init__.py)",
+     "output_type": "error",
+     "traceback": [
+      "\u001B[0;31m---------------------------------------------------------------------------\u001B[0m",
+      "\u001B[0;31mImportError\u001B[0m                               Traceback (most recent call last)",
+      "Cell \u001B[0;32mIn[2], line 5\u001B[0m\n\u001B[1;32m      3\u001B[0m \u001B[38;5;28;01mfrom\u001B[39;00m \u001B[38;5;21;01mprocess_bigraph\u001B[39;00m \u001B[38;5;28;01mimport\u001B[39;00m Composite, pf \n\u001B[1;32m      4\u001B[0m \u001B[38;5;28;01mfrom\u001B[39;00m \u001B[38;5;21;01mbuilder\u001B[39;00m \u001B[38;5;28;01mimport\u001B[39;00m Builder, Process \u001B[38;5;28;01mas\u001B[39;00m builderProcess, ProcessTypes\n\u001B[0;32m----> 5\u001B[0m \u001B[38;5;28;01mfrom\u001B[39;00m \u001B[38;5;21;01mbiosimulator_processes\u001B[39;00m\u001B[38;5;21;01m.\u001B[39;00m\u001B[38;5;21;01mprocesses\u001B[39;00m\u001B[38;5;21;01m.\u001B[39;00m\u001B[38;5;21;01mcopasi_process\u001B[39;00m \u001B[38;5;28;01mimport\u001B[39;00m CopasiProcess\n\u001B[1;32m      6\u001B[0m \u001B[38;5;28;01mfrom\u001B[39;00m \u001B[38;5;21;01mbiosimulator_processes\u001B[39;00m\u001B[38;5;21;01m.\u001B[39;00m\u001B[38;5;21;01mprocess_types\u001B[39;00m \u001B[38;5;28;01mimport\u001B[39;00m MODEL_TYPE, CHANGES_SCHEMA\n\u001B[1;32m      7\u001B[0m \u001B[38;5;28;01mfrom\u001B[39;00m \u001B[38;5;21;01mbiosimulator_processes\u001B[39;00m\u001B[38;5;21;01m.\u001B[39;00m\u001B[38;5;21;01mutils\u001B[39;00m \u001B[38;5;28;01mimport\u001B[39;00m play_composition\n",
+      "File \u001B[0;32m~/Desktop/uchc_work/biosimulator-processes/notebooks/../biosimulator_processes/processes/__init__.py:1\u001B[0m\n\u001B[0;32m----> 1\u001B[0m \u001B[38;5;28;01mfrom\u001B[39;00m \u001B[38;5;21;01mprocess_bigraph\u001B[39;00m \u001B[38;5;28;01mimport\u001B[39;00m process_registry\n\u001B[1;32m      4\u001B[0m \u001B[38;5;66;03m# Define a list of processes to attempt to import and register\u001B[39;00m\n\u001B[1;32m      5\u001B[0m processes_to_register \u001B[38;5;241m=\u001B[39m [\n\u001B[1;32m      6\u001B[0m     (\u001B[38;5;124m'\u001B[39m\u001B[38;5;124mcobra\u001B[39m\u001B[38;5;124m'\u001B[39m, \u001B[38;5;124m'\u001B[39m\u001B[38;5;124mcobra_process.CobraProcess\u001B[39m\u001B[38;5;124m'\u001B[39m),\n\u001B[1;32m      7\u001B[0m     (\u001B[38;5;124m'\u001B[39m\u001B[38;5;124mcopasi\u001B[39m\u001B[38;5;124m'\u001B[39m, \u001B[38;5;124m'\u001B[39m\u001B[38;5;124mcopasi_process.CopasiProcess\u001B[39m\u001B[38;5;124m'\u001B[39m),\n\u001B[1;32m      8\u001B[0m     (\u001B[38;5;124m'\u001B[39m\u001B[38;5;124msmoldyn\u001B[39m\u001B[38;5;124m'\u001B[39m, \u001B[38;5;124m'\u001B[39m\u001B[38;5;124msmoldyn_process.SmoldynProcess\u001B[39m\u001B[38;5;124m'\u001B[39m),\n\u001B[1;32m      9\u001B[0m     (\u001B[38;5;124m'\u001B[39m\u001B[38;5;124mtellurium\u001B[39m\u001B[38;5;124m'\u001B[39m, \u001B[38;5;124m'\u001B[39m\u001B[38;5;124mtellurium_process.TelluriumProcess\u001B[39m\u001B[38;5;124m'\u001B[39m),\n\u001B[1;32m     10\u001B[0m ]\n",
+      "\u001B[0;31mImportError\u001B[0m: cannot import name 'process_registry' from 'process_bigraph' (/Users/alex/Library/Caches/pypoetry/virtualenvs/biosimulator-processes-KVuYbFzt-py3.10/lib/python3.10/site-packages/process_bigraph/__init__.py)"
+     ]
+    }
+   ],
    "source": [
     "import os \n",
     "from basico import *\n",
     "from process_bigraph import Composite, pf \n",
+    "from builder import Builder, Process as builderProcess, ProcessTypes\n",
     "from biosimulator_processes.processes.copasi_process import CopasiProcess\n",
     "from biosimulator_processes.process_types import MODEL_TYPE, CHANGES_SCHEMA\n",
     "from biosimulator_processes.utils import play_composition"
@@ -269,67 +292,6 @@
    "id": "433d58bbe38402af",
    "execution_count": null
   },
-  {
-   "cell_type": "code",
-   "outputs": [],
-   "source": [
-    "instance2 = {\n",
-    "    'copasi': {\n",
-    "        '_type': 'process',\n",
-    "        'address': 'local:copasi',\n",
-    "        'config': {\n",
-    "            'model': {\n",
-    "                'model_changes': {\n",
-    "                    'reaction_changes': {\n",
-    "                        'R1': 'A -> B'\n",
-    "                    }\n",
-    "                }\n",
-    "            }\n",
-    "        },\n",
-    "        'inputs': {\n",
-    "            'floating_species': ['floating_species_store'],\n",
-    "            'model_parameters': ['model_parameters_store'],\n",
-    "            'time': ['time_store'],\n",
-    "            'reactions': ['reactions_store']\n",
-    "        },\n",
-    "        'outputs': {\n",
-    "            'floating_species': ['floating_species_store'],\n",
-    "            'time': ['time_store'],\n",
-    "        }\n",
-    "    },\n",
-    "    'emitter': {\n",
-    "        '_type': 'step',\n",
-    "        'address': 'local:ram-emitter',\n",
-    "        'config': {\n",
-    "            'emit': {\n",
-    "                'floating_species': 'tree[float]',\n",
-    "                'time': 'float',\n",
-    "            },\n",
-    "        },\n",
-    "        'inputs': {\n",
-    "            'floating_species': ['floating_species_store'],\n",
-    "            'time': ['time_store'],\n",
-    "        }\n",
-    "    }\n",
-    "}\n",
-    "\n",
-    "\n",
-    "results = play_composition(instance2, 10)"
-   ],
-   "metadata": {
-    "collapsed": false
-   },
-   "id": "8178d3c295764eb6",
-   "execution_count": null
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "id": "1a51b92b-35af-4d94-b9d5-97da90cfa5bd",
-   "metadata": {},
-   "outputs": [],
-   "source": []
-  },
   {
    "cell_type": "markdown",
    "source": [
@@ -364,28 +326,6 @@
    "id": "1ecc10e496abe9cb",
    "execution_count": null
   },
-  {
-   "cell_type": "code",
-   "outputs": [],
-   "source": [],
-   "metadata": {
-    "collapsed": false
-   },
-   "id": "35ea2649d0f98801",
-   "execution_count": null
-  },
-  {
-   "cell_type": "code",
-   "outputs": [],
-   "source": [
-    "results = play_composition(instance=parameter_scan_instance, duration=10)"
-   ],
-   "metadata": {
-    "collapsed": false
-   },
-   "id": "87cced9f87885d4e",
-   "execution_count": null
-  },
   {
    "cell_type": "code",
    "outputs": [],

diff --git a/poetry.lock b/poetry.lock
diff --git a/pyproject.toml b/pyproject.toml
@@ -17,12 +17,14 @@ numpy = "*" # "^1.26.4"
 copasi-basico = "*"
 cobra = "*"
 tellurium = "*"
-smoldyn = "*"
-bigraph-viz = "^0.0.31"
+smoldyn = ">=2.72"
+bigraph-viz = ">=0.0.31"
+bigraph-builder = ">=0.0.4"
 python-libsbml = "^5.20.2"
 docker = ">=7.0"
 python-libnuml = "^1.1.6" # ">=1.0.0"
 notebook = "^7.1.1"
+# psutil = "^5.9.8"
 
 [tool.poetry.group.dev.dependencies]
 pytest = "*"

diff --git a/scripts/install-smoldyn-mac-silicon.sh b/scripts/install-smoldyn-mac-silicon.sh
@@ -4,8 +4,8 @@
 # The following script serves as a utility for installing this repository with the Smoldyn requirement on a Silicon Mac
 
 # set installation parameters
-dist_url=https://www.smoldyn.org/smoldyn-2.72-mac.tgz
-tarball_name=smoldyn-2.72-mac.tgz
+dist_url=https://www.smoldyn.org/smoldyn-2.73-mac.tgz
+tarball_name=smoldyn-2.73-mac.tgz
 dist_dir=${tarball_name%.tgz}
 
 # uninstall existing version