update env creation

assets/dev/scripts/create_env.sh

@@ -8,23 +8,19 @@ function construct_env {
   arm_platform=$(uname -a | grep "Darwin")
   echo "Creating environment from ./environment.yml on $arm_platform..."
   source /Users/alexanderpatrie/miniconda3/etc/profile.d/conda.sh
-
-  # update base pip
   conda run pip3 install --upgrade pip
   conda run pip install --upgrade pip
-
-  # create and activate env
   conda env create -f ./environment.yml -y
-  conda activate bio-compose-server
-
-  # install pysces and poetry deps
-  conda install -n bio-compose-server -c conda-forge -c pysces pysces -y
-  poetry config virtualenvs.create false
-  sudo conda run -n bio-compose-server poetry env use 3.10
-  sudo conda run -n bio-compose-server poetry lock
-  sudo conda run -n bio-compose-server poetry install --only=dev
+  conda run -n bio-compose-server pip3 install --upgrade pip
+  conda run -n bio-compose-server pip install --upgrade pip
   ./assets/dev/scripts/install-smoldyn-mac-silicon.sh || poetry run pip3 install smoldyn
-  sudo conda run -n bio-compose-server poetry run pip3 install amici biosimulators-amici biosimulators-pysces
+  conda run -n bio-compose-server pip3 install amici biosimulators-amici  # biosimulators-pysces
+  # conda install -n bio-compose-server -c conda-forge -c pysces pysces -y
+  # poetry config virtualenvs.create false
+  # sudo conda run -n bio-compose-server poetry env use 3.10
+  # sudo conda run -n bio-compose-server poetry lock
+  # sudo conda run -n bio-compose-server poetry install --only=dev
+  .
   # poetry run pip install ./api ./worker
 
   echo "Environment created!"

environment.yml

@@ -8,27 +8,28 @@ dependencies:
   - python=3.10
   - poetry
   - pysces
-  # - pip:
-  #     - pip-autoremove
-  #     - requests-toolbelt
-  #     - python-dotenv
-  #     - google-cloud-storage
-  #     - python-multipart
-  #     - fastapi
-  #     - toml
-  #     - typing-extensions
-  #     - pymongo
-  #     - pydantic-settings
-  #     - pydantic
-  #     - uvicorn
-  #     - pyyaml
-  #     - simulariumio
-  #     - copasi-basico
-  #     - tellurium
-  #     - biosimulators-copasi
-  #     - biosimulators-tellurium
-  #     - seaborn
-  #     - jupyterlab
-  #     - process-bigraph
-  #     - bigraph-schema
-  #     - pytest
+  - pip:
+      - pip-autoremove
+      - requests-toolbelt
+      - python-dotenv
+      - google-cloud-storage
+      - python-multipart
+      - fastapi
+      - toml
+      - typing-extensions
+      - pymongo
+      - pydantic-settings
+      - pydantic
+      - uvicorn
+      - pyyaml
+      - simulariumio
+      - copasi-basico
+      - tellurium
+      - biosimulators-copasi
+      - biosimulators-tellurium
+      - biosimulators-pysces
+      - seaborn
+      - jupyterlab
+      - process-bigraph
+      - bigraph-schema
+      - pytest

pyproject.toml

@@ -13,7 +13,6 @@ classifiers=[
     ]
 keywords=['systems', 'biology', 'modeling', 'simulation']
 
-
 [tool.poetry.dependencies]
 python = "^3.10"
 

worker/service/__init__.py

@@ -1,42 +1,4 @@
-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)

worker/service/main.py

@@ -1,15 +1,51 @@
 import os
 import asyncio
 import logging
+from typing import List, Tuple
 
+from process_bigraph import ProcessTypes
 from dotenv import load_dotenv
 
-from service import APP_PROCESS_REGISTRY
 from service.shared_worker import MongoDbConnector
 from service.log_config import setup_logging
 from service.job import Supervisor
 
 
+def register_module(
+        items_to_register: List[Tuple[str, str]],
+        core: ProcessTypes,
+        verbose=False
+) -> None:
+    for process_name, path in items_to_register:
+        module_name, class_name = path.rsplit('.', 1)
+        try:
+            import_statement = f'worker.service.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
+            core.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
+
+
+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')
+]
+register_module(IMPLEMENTATIONS, APP_PROCESS_REGISTRY, verbose=True)
+
+
 load_dotenv('../../assets/dev/config/.env_dev')
 
 # logging TODO: implement this.

worker/service/shared_worker.py

@@ -17,6 +17,7 @@
 
 # -- globally-shared content-- #
 
+
 load_dotenv('../../assets/dev/config/.env_dev')
 
 DB_TYPE = "mongo"  # ie: postgres, etc