major refactor of library structure for unused content

Dockerfile

@@ -14,7 +14,7 @@ WORKDIR /app
 
 # copy and make dirs
 COPY ./biosimulator_processes /app/biosimulator_processes
-COPY notebooks /app/notebooks
+COPY composer-notebooks /app/notebooks
 
 # copy files
 COPY ./pyproject.toml ./poetry.lock ./data ./scripts/trust-notebooks.sh /app/
@@ -51,10 +51,10 @@ RUN apt-get update && apt-get install -y --no-install-recommends \
     && poetry config virtualenvs.in-project true \
     && poetry update \
     && poetry install \
-    && chmod +x ./trust-notebooks.sh \
+    && chmod +x ./trust-composer-notebooks.sh \
     && chmod +x /usr/local/bin/enter-lab.sh \
-    && ./trust-notebooks.sh \
-    && rm ./trust-notebooks.sh \
+    && ./trust-composer-notebooks.sh \
+    && rm ./trust-composer-notebooks.sh \
     && apt-get clean \
     && apt-get autoclean
 

biosimulator_processes/data_model/compare_data_model.py

@@ -1,6 +1,9 @@
 from typing import *
 
 
+__all__ = ['ComparisonDocument']
+
+
 class ComparisonDocument:
     """To be called 'behind-the-scenes' by the Comparison REST API"""
     def __init__(self,

biosimulator_processes/data_model/sed_data_model.py

@@ -7,6 +7,8 @@
 from biosimulator_processes.data_model import _BaseClass
 
 
+__all__ = ['SedDataModel']
+
 @dataclass
 class SimulationModelParameter(_BaseClass):
     """
@@ -135,7 +137,7 @@ class SedModel(_BaseClass):
     model_source: Union[BiomodelID, ModelFilepath, str]
     model_id: str = None
     model_name: str = None
-    model_language: str = 'sbml'
+    model_language: str = Field(default='sbml')
     model_changes: ModelChanges = None
     model_units: ModelUnits = None
 
@@ -198,11 +200,11 @@ class TimeCourseModel(SedModel):
         Attributes:
             model_id: `str`
             model_source: `Union[biosimulator_processes.data_model.ModelFilepath, biosimulator_processes.data_model.BiomodelId]`
-            model_language: `str`
+            model_language: `str` defaults to sbml
             model_name: `str`
             model_changes: `biosimulator_processes.data_model.TimeCourseModelChanges`
     """
-    model_language: str = None,
+    model_language: str = 'sbml',
     model_changes: TimeCourseModelChanges = None,
     model_units: ModelUnits = None
 
@@ -256,6 +258,7 @@ class TimeCourseProcess(_BaseClass):
     """Used as config for BioBuilder API"""
     model: SedModel
     method: str = 'lsoda'
+    model_language: str = 'sbml'
 
 
 @dataclass

biosimulator_processes/processes/copasi_process.py

@@ -82,12 +82,15 @@ def __init__(self,
         # Option C:
         else:
             if not self.model_changes:
-                raise AttributeError("You must pass a source of model changes specifying params, reactions, species or all three if starting from an empty model.")
+                raise AttributeError(
+                    """You must pass a source of model changes specifying params, reactions, 
+                        species or all three if starting from an empty model.""")
             model_units = self.config['model'].get('model_units', {})
             self.copasi_model_object = new_model(
                 name='CopasiProcess TimeCourseModel',
                 **model_units)
 
+        # handle context of species output
         context_type = self.config['species_context']
         self.species_context_key = f'floating_species_{context_type}'
         self.use_counts = 'concentrations' in context_type
@@ -131,8 +134,8 @@ def __init__(self,
         # Get the species (floating only)  TODO: add boundary species
         species_data = get_species(model=self.copasi_model_object)
         self.floating_species_list = species_data.index.tolist()
-        self.floating_species_initial = species_data.concentration.tolist() \
-            if 'concentrations' in self.config['species_context'] else species_data.particle_number.tolist()
+        self.floating_species_initial = species_data.particle_number.tolist() \
+            if self.use_counts else species_data.concentration.tolist()
 
         # ----GLOBAL PARAMS: set global parameter changes
         global_parameter_changes = self.model_changes.get('global_parameter_changes', [])
@@ -154,9 +157,10 @@ def __init__(self,
 
         # Get the list of parameters and their values (it is possible to run a model without any parameters)
         model_parameters = get_parameters(model=self.copasi_model_object)
-
-        self.model_parameters_list = model_parameters.index.tolist() if isinstance(model_parameters, DataFrame) else []
-        self.model_parameters_values = model_parameters.initial_value.tolist() if isinstance(model_parameters, DataFrame) else []
+        self.model_parameters_list = model_parameters.index.tolist() \
+            if isinstance(model_parameters, DataFrame) else []
+        self.model_parameters_values = model_parameters.initial_value.tolist() \
+            if isinstance(model_parameters, DataFrame) else []
 
         # Get a list of compartments
         self.compartments_list = get_compartments(model=self.copasi_model_object).index.tolist()
@@ -236,14 +240,31 @@ def update(self, inputs, interval):
 
         # extract end values of concentrations from the model and set them in results
         results = {'time': interval}
-        measurement_type = 'particle_number' if self.use_counts else 'concentration'
-        results[self.species_context_key] = {
-            mol_id: float(get_species(
+        for mol_id in self.floating_species_list:
+            raw_mol_data = get_species(
                 name=mol_id,
                 exact=True,
-                model=self.copasi_model_object
-            )[measurement_type][0])
-            for mol_id in self.floating_species_list
-        }
+                model=self.copasi_model_object)
+
+            mol_data = raw_mol_data.particle_number[0] if self.use_counts else raw_mol_data.concentration[0]
+            results[self.species_context_key] = {
+                mol_id: float(mol_data)
+            }
+        """if self.use_counts:
+            results[self.species_context_key] = {
+                mol_id: float(get_species(
+                    name=mol_id,
+                    exact=True,
+                    model=self.copasi_model_object
+                ).particle_number[0])
+                for mol_id in self.floating_species_list}
+        else:
+            results[self.species_context_key] = {
+                mol_id: float(get_species(
+                    name=mol_id,
+                    exact=True,
+                    model=self.copasi_model_object
+                ).concentration[0])
+                for mol_id in self.floating_species_list}"""
 
         return results

biosimulator_processes/steps/viz.py

@@ -24,7 +24,7 @@ def parse_composition_results(composition: Composite) -> Dict[float, Dict[str, U
         float(n)
         for n in range(int(composition.state['global_time']) + 1) # python ranges are not as they appear ;)
     ]
-    assert len(timescale) == len(result_vals)  # internal check: is there a better way to perform the check?
+    assert len(timescale) == len(result_vals)  # src check: is there a better way to perform the check?
     return dict(zip(timescale, result_vals))
 
 

biosimulator_processes/tests/test_copasi_process.py

@@ -54,7 +54,7 @@ def test_process():
 
 def test_process_from_document():
     # read the document from local file:
-    five_process_fp = 'notebooks/out/five_process_composite.json'
+    five_process_fp = 'composer-notebooks/out/five_process_composite.json'
     with open(five_process_fp, 'r') as fp:
         instance = json.load(fp)
 

biosimulator_processes/utils.py

@@ -330,7 +330,7 @@ def fix_execution_count(notebook_path):
 
 
 def fix_notebooks_execution_count():
-    for root, _, files in os.walk('../notebooks'):
+    for root, _, files in os.walk('../composer-notebooks'):
         for _file in files:
             notebook_path = os.path.join(root, _file)
             fix_execution_count(notebook_path)

compare_api/main.py

@@ -6,7 +6,7 @@
 from fastapi import FastAPI, HTTPException, Query, File, UploadFile
 from fastapi.middleware.cors import CORSMiddleware
 from compare_api.datamodel import SimulatorComparisonResult, CompositeRunError
-from compare_api.internal.composite_doc import create_comparison_document, generate_workflow, run_workflow
+from compare_api.src.composite_doc import create_comparison_document, generate_workflow, run_workflow
 
 # logger for this module
 logger = logging.getLogger(__name__)