file organization for package creation (#243)

* directory reorganization and renaming to src dir

* moving config.py into src and abstract_azure_runner.py into mechanistic_azure

* some comment changes

* removing old experiments

* changing path of sero initializer

* packaging resp_ode draft

* removing unneccessary packagewithin resp_ode

* updating azure related scripts to new packaged resp-ode

* fixing import in shiny apps

* moving azure code into src

* removing config dir out of the package

.gitignore

@@ -56,7 +56,6 @@ testing.py
 !config/*.json
 !tests/*.json
 !exp/*/*.json
-!docker_template_configs/*.json
 !data/serological-data/*.csv
 !data/hospitalization-data/*.csv
 !data/vaccination-data/state-spline-fits/*.csv

Dockerfile

@@ -18,10 +18,10 @@ RUN pip install 'poetry==1.8.3'
 ENV PATH="/root/.local/bin:/app/:${PATH}"
 # set workdir to /app for installing packages
 WORKDIR /app
+# now copy in the mechanistic model code and config code
+COPY ./src/ /app/src
 # turn off interaction since we cant type `yes` on the prompts in docker build
 RUN poetry install --no-interaction --no-ansi
-# now copy in the mechanistic model code and config code
 # we will upload the experiment itself into the cloud and refer to from /input
-COPY ./mechanistic_model/ /app/mechanistic_model
-COPY ./config/config.py /app/config/config.py
-COPY ./model_odes/seip_model.py /app/model_odes/seip_model.py
+COPY ./mechanistic_azure/abstract_azure_runner.py /app/mechanistic_azure/abstract_azure_runner.py
+COPY ./mechanistic_azure/azure_utilities.py /app/mechanistic_azure/azure_utilities.py

config/config_initializer_covid.json

@@ -1,7 +1,50 @@
 {
     "INITALIZER_NAME": "base initializer covid",
-    "SEROLOGICAL_DATA_PATH": "data/serological-data/",
-    "SIM_DATA_PATH": "data/abm-data/abm_population.csv",
+    "SEROLOGICAL_DATA_PATH": "data/serological-data/sero-initializer-csvs",
+    "CONTACT_MATRIX_PATH": "data/demographic-data/contact_matrices",
     "POP_SIZE": 1000000,
-    "INITIAL_INFECTIONS": 32000
+    "INITIAL_INFECTIONS": 32000,
+    "WANING_PROTECTIONS": [
+        1.0,
+        0.942,
+        0.942,
+        0.942,
+        0.0
+    ],
+    "INFECTIOUS_PERIOD": 7.0,
+    "EXPOSED_TO_INFECTIOUS": 3.6,
+    "STRAIN_INTERACTIONS": [
+        [
+            1.0,
+            0.7,
+            0.49
+        ],
+        [
+            0.7,
+            1.0,
+            0.7
+        ],
+        [
+            0.49,
+            0.7,
+            1.0
+        ]
+    ],
+    "VACCINE_EFF_MATRIX": [
+        [
+            0,
+            0.34,
+            0.68
+        ],
+        [
+            0,
+            0.24,
+            0.48
+        ],
+        [
+            0,
+            0.14,
+            0.28
+        ]
+    ]
 }

example_end_to_end_run.py → examples/example_end_to_end_run.py

@@ -16,12 +16,14 @@
 
 # the different segments of code responsible for runing the model
 # each will be explained as they are used below
-from mechanistic_model.covid_initializer import CovidInitializer
-from mechanistic_model.mechanistic_inferer import MechanisticInferer
-from mechanistic_model.mechanistic_runner import MechanisticRunner
-from mechanistic_model.solution_iterpreter import SolutionInterpreter
-from mechanistic_model.static_value_parameters import StaticValueParameters
-from model_odes.seip_model import seip_ode
+from resp_ode import (
+    CovidSeroInitializer,
+    MechanisticInferer,
+    MechanisticRunner,
+    SolutionInterpreter,
+    StaticValueParameters,
+)
+from resp_ode.model_odes import seip_ode
 
 parser = argparse.ArgumentParser()
 parser.add_argument(
@@ -51,7 +53,9 @@
 
     # step 2: Set up your initializer
     # sets up the initial conditions, initializer.get_initial_state() passed to runner
-    initializer = CovidInitializer(INITIALIZER_CONFIG_PATH, GLOBAL_CONFIG_PATH)
+    initializer = CovidSeroInitializer(
+        INITIALIZER_CONFIG_PATH, GLOBAL_CONFIG_PATH
+    )
 
     # step 3: set up your parameters object
     # reads and interprets values from config, sets up downstream parameters

exp/example_azure_experiment/run_task.py

@@ -12,12 +12,14 @@
 
 sys.path.append("/app/")
 
-from mechanistic_model.abstract_azure_runner import AbstractAzureRunner
-from mechanistic_model.covid_sero_initializer import CovidSeroInitializer
-from mechanistic_model.mechanistic_inferer import MechanisticInferer
-from mechanistic_model.mechanistic_runner import MechanisticRunner
-from mechanistic_model.static_value_parameters import StaticValueParameters
-from model_odes.seip_model import seip_ode
+from mechanistic_azure.abstract_azure_runner import AbstractAzureRunner
+from resp_ode import (
+    CovidSeroInitializer,
+    MechanisticInferer,
+    MechanisticRunner,
+    StaticValueParameters,
+)
+from resp_ode.model_odes import seip_ode
 
 
 class ExampleRunner(AbstractAzureRunner):