Adding run simulation flow

.env

@@ -9,7 +9,6 @@ DB_PASSWORD=password
 
 # MLFlow
 MLFLOW_BACKEND_STORE_URI=postgresql://${DB_USER}:${DB_PASSWORD}@postgres:5432/${DB_NAME}
-MLFLOW_TRACKING_URI=http://mlflow:5000
 
 # Prefect
 PREFECT_API_DATABASE_CONNECTION_URL=postgresql+asyncpg://${DB_USER}:${DB_PASSWORD}@postgres:5432/prefect

app/app.py

@@ -4,6 +4,8 @@
 # Imports
 ######################################
 
+import os
+
 import dash_bootstrap_components as dbc
 import pandas as pd
 import plotly.express as px
@@ -12,6 +14,13 @@
 from hydra import compose, initialize
 from hydra.utils import instantiate
 
+######################################
+# Environment
+######################################
+
+if os.environ.get("PREFECT_API_URL") is None:
+    os.environ["PREFECT_API_URL"] = "http://127.0.0.1:4200/api"
+
 ######################################
 # Functions
 ######################################

app/conf/form/common.yaml

@@ -310,11 +310,6 @@ components:
           children: Run model
           color: primary
           className: me-1
-      - id: download-sim-data-input
-        label: Download
-        help: Download the simulation output data
-        class_name: dash_daq.BooleanSwitch.BooleanSwitch 
-        kwargs: {}
       - id: save-param-button
         label: Save
         help: Save current parameter configuration to file

app/flows/prefect.yaml

@@ -19,15 +19,37 @@ pull:
 
 # the deployments section allows you to provide configuration for deploying flows
 deployments:
-- name: Hello Flow
-  description: Hello description.
-  entrypoint: /app/flows/hello_flow.py:hello_flow
+- name: run_simulation_flow
+  description: Run a single simulation for the root model.
+  entrypoint: /app/flows/run_simulation.py:run_simulation_flow
   parameters: {}
   work_pool:
     name: default
-- name: Bye Flow
-  description: Bye description.
-  entrypoint: /app/flows/bye_flow.py:bye_flow
+
+- name: run_optimisation_flow
+  description: Run an optimisation procedure for the root model.
+  entrypoint: /app/flows/run_optimisation.py:run_optimisation_flow
+  parameters: {}
+  work_pool:
+    name: default
+
+- name: run_sensitivity_analysis_flow
+  description: Run a sensitivity analysis for the root model.
+  entrypoint: /app/flows/run_sensitivity_analysis.py:run_sensitivity_analysis_flow
+  parameters: {}
+  work_pool:
+    name: default
+
+- name: run_abc_flow
+  description: Perform Bayesian parameter estimation for the root model using Approximate Bayesian Computation.
+  entrypoint: /app/flows/run_abc.py:run_abc_flow
+  parameters: {}
+  work_pool:
+    name: default
+
+- name: run_snpe_flow
+  description: Perform Bayesian parameter estimation for the root model using Sequential Neural Posterior Estimation.
+  entrypoint: /app/flows/run_snpe.py:run_snpe_flow
   parameters: {}
   work_pool:
     name: default

app/flows/run_abc.py

@@ -0,0 +1,38 @@
+#!/usr/bin/env python
+
+######################################
+# Imports
+######################################
+
+import mlflow
+from prefect import context, flow, task
+from prefect.task_runners import ConcurrentTaskRunner
+
+from deeprootgen.data_model import RootSimulationModel
+from deeprootgen.model import RootSystemSimulation
+from deeprootgen.pipeline import (
+    begin_experiment,
+    log_config,
+    log_experiment_details,
+    log_simulation,
+)
+
+######################################
+# Main
+######################################
+
+
+@task
+def run_abc() -> None:
+    print("hello")
+
+
+@flow(
+    name="abc",
+    description="Perform Bayesian parameter estimation for the root model using Approximate Bayesian Computation.",
+    task_runner=ConcurrentTaskRunner(),
+)
+def run_abc_flow(
+    # input_params: RootSimulationModel
+) -> None:
+    run_abc.submit()

app/flows/run_optimisation.py

@@ -0,0 +1,38 @@
+#!/usr/bin/env python
+
+######################################
+# Imports
+######################################
+
+import mlflow
+from prefect import context, flow, task
+from prefect.task_runners import ConcurrentTaskRunner
+
+from deeprootgen.data_model import RootSimulationModel
+from deeprootgen.model import RootSystemSimulation
+from deeprootgen.pipeline import (
+    begin_experiment,
+    log_config,
+    log_experiment_details,
+    log_simulation,
+)
+
+######################################
+# Main
+######################################
+
+
+@task
+def run_optimisation() -> None:
+    print("hello")
+
+
+@flow(
+    name="optimisation",
+    description="Run an optimisation procedure for the root model.",
+    task_runner=ConcurrentTaskRunner(),
+)
+def run_optimisation_flow(
+    # input_params: RootSimulationModel
+) -> None:
+    run_optimisation.submit()

app/flows/run_sensitivity_analysis.py

@@ -0,0 +1,38 @@
+#!/usr/bin/env python
+
+######################################
+# Imports
+######################################
+
+import mlflow
+from prefect import context, flow, task
+from prefect.task_runners import ConcurrentTaskRunner
+
+from deeprootgen.data_model import RootSimulationModel
+from deeprootgen.model import RootSystemSimulation
+from deeprootgen.pipeline import (
+    begin_experiment,
+    log_config,
+    log_experiment_details,
+    log_simulation,
+)
+
+######################################
+# Main
+######################################
+
+
+@task
+def run_sensitivity_analysis() -> None:
+    print("hello")
+
+
+@flow(
+    name="sensitivity_analysis",
+    description="Run a sensitivity analysis for the root model.",
+    task_runner=ConcurrentTaskRunner(),
+)
+def run_sensitivity_analysis_flow(
+    # input_params: RootSimulationModel
+) -> None:
+    run_sensitivity_analysis.submit()