Merge pull request #5 from biosimulators/main

updated poetry lock and configs for version

.gitignore

@@ -21,3 +21,4 @@ submit-biosimulators-container.sh
 ._vagrant
 .THIS-IS-FOR-CONTAINER-DEV-ONLY
 buildDockerImage.yml
+.env

Dockerfile

@@ -13,16 +13,19 @@ ENV DEBIAN_FRONTEND=noninteractive \
 WORKDIR /app
 
 # copy and make dirs
-COPY ./biosimulator_processes/processes /app/biosimulator_processes
+COPY ./biosimulator_processes /app/biosimulator_processes
 COPY ./notebooks /app/notebooks
 
 # copy files
 COPY ./pyproject.toml ./poetry.lock ./data ./scripts/trust-notebooks.sh /app/
 COPY ./scripts/xvfb-startup.sh /xvfb-startup.sh
 
+VOLUME /app/data
+
 RUN apt-get update && apt-get install -y --no-install-recommends \
     python3.10  \
     python3-pip  \
+    python3-dev \
     build-essential  \
     libncurses5  \
     cmake  \
@@ -46,18 +49,18 @@ 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 \
     && rm ./trust-notebooks.sh
 
-VOLUME /app/data
-
 CMD ["poetry", "run", "jupyter", "lab", "--ip=0.0.0.0", "--port=8888", "--no-browser", "--allow-root"]
 
 
 # PLEASE NOTE: We do not need to add a USER in the Dockerfile as Singularity will handle
- # such logic in conversion on the HPC.
+# such logic in conversion on the HPC.
 
 # type imports
 # dist

biosimulator_processes/__init__.py

@@ -1,30 +1,27 @@
-from process_bigraph import process_registry
+from builder import ProcessTypes
 
 
 # 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()
+
+for process_name, process_path in PROCESSES_TO_REGISTER:
     module_name, class_name = process_path.rsplit('.', 1)
     try:
         # Dynamically import the module
-        process_module = __import__(f'biosimulator_processes.{module_name}', fromlist=[class_name])
+        process_module = __import__(
+            f'biosimulator_processes.processes.{module_name}', fromlist=[class_name])
         # Get the class from the module
         process_class = getattr(process_module, class_name)
 
         # Register the process
-        process_registry.register(process_name, process_class)
+        CORE.process_registry.register(class_name, process_class)
         print(f"{class_name} registered successfully.")
     except ImportError as e:
         print(f"{class_name} not available. Error: {e}")
-
-
-from biosimulator_processes.copasi_process import CopasiProcess
-from biosimulator_processes.smoldyn_process import SmoldynProcess
-from biosimulator_processes.cobra_process import CobraProcess
-from biosimulator_processes.tellurium_process import TelluriumProcess

biosimulator_processes/biosimulator_builder.py

@@ -0,0 +1,9 @@
+from typing import *
+from builder import Builder
+from biosimulator_processes import CORE
+
+
+class BiosimulatorBuilder(Builder):
+    def __init__(self, schema: Dict, tree: Dict, filepath: str):
+        super().__init__(schema=schema, tree=tree, file_path=filepath, core=CORE)
+