update scripts

assets/dev/scripts/install-smoldyn-mac-silicon.sh

@@ -9,7 +9,7 @@ tarball_name=smoldyn-2.73-mac.tgz
 dist_dir=${tarball_name%.tgz}
 
 # uninstall existing version
-poetry run pip uninstall smoldyn || return
+conda run pip uninstall smoldyn || return
 
 # download the appropriate distribution from smoldyn
 wget $dist_url
@@ -23,7 +23,7 @@ rm $tarball_name
 # install smoldyn from the source
 cd $dist_dir || return
 
-if poetry run sudo -H ./install.sh; then
+if conda run sudo -H ./install.sh; then
   cd ..
   # remove the smoldyn dist
   rm -r $dist_dir

worker/service/__init__.py

@@ -0,0 +1,44 @@
+from typing import List, Tuple
+
+from process_bigraph import ProcessTypes
+
+
+APP_PROCESS_REGISTRY = ProcessTypes()
+IMPLEMENTATIONS = [
+    ('output-generator', 'steps.OutputGenerator'),
+    ('time-course-output-generator', 'steps.TimeCourseOutputGenerator'),
+    ('smoldyn_step', 'steps.SmoldynStep'),
+    ('simularium_smoldyn_step', 'steps.SimulariumSmoldynStep'),
+    ('mongo-emitter', 'steps.MongoDatabaseEmitter')
+]
+
+
+def register_module(
+        items_to_register: List[Tuple[str, str]],
+        verbose=False
+) -> None:
+    for process_name, path in items_to_register:
+        module_name, class_name = path.rsplit('.', 1)
+        try:
+            import_statement = f'worker.bigraph.{module_name}'
+
+            module = __import__(
+                 import_statement, fromlist=[class_name])
+
+            # Get the class from the module
+            bigraph_class = getattr(module, class_name)
+
+            # Register the process
+            APP_PROCESS_REGISTRY.process_registry.register(process_name, bigraph_class)
+            print(f'Registered {process_name}') if verbose else None
+        except Exception as e:
+            print(f"Cannot register {class_name}. Error:\n**\n{e}\n**") if verbose else None
+            continue
+
+
+register_module(IMPLEMENTATIONS)
+
+
+# APP_PROCESS_REGISTRY.process_registry.register('time-course-output-generator', TimeCourseOutputGenerator)
+# APP_PROCESS_REGISTRY.process_registry.register('output-generator', OutputGenerator)
+

worker/service/bigraph/steps.py

@@ -13,9 +13,6 @@
 from simulariumio import InputFileData, UnitData, DisplayData, DISPLAY_TYPE
 from simulariumio.smoldyn import SmoldynData
 
-from worker.service.io_worker import get_sbml_species_mapping
-from worker.service.verification import SBML_EXECUTORS
-
 try:
     import smoldyn as sm
     from smoldyn._smoldyn import MolecState
@@ -26,8 +23,10 @@
         'on installing Smoldyn.'
     )
 
-from worker.service.simularium_utils import calculate_agent_radius, translate_data_object, write_simularium_file
-from worker import APP_PROCESS_REGISTRY
+from service.io_worker import get_sbml_species_mapping
+from service.verification import SBML_EXECUTORS
+from service.simularium_utils import calculate_agent_radius, translate_data_object, write_simularium_file
+from service import APP_PROCESS_REGISTRY
 
 process_registry = APP_PROCESS_REGISTRY.process_registry
 

worker/service/main.py

@@ -4,9 +4,10 @@
 
 from dotenv import load_dotenv
 
-from worker.service.shared_worker import MongoDbConnector
-from worker.service.log_config import setup_logging
-from worker.service.job import Supervisor
+from service import APP_PROCESS_REGISTRY
+from service.shared_worker import MongoDbConnector
+from service.log_config import setup_logging
+from service.job import Supervisor
 
 
 load_dotenv('../../assets/dev/config/.env_dev')