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Example run changes directory to repository root #289

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Example run changes directory to repository root #289

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21 changes: 13 additions & 8 deletions examples/example_end_to_end_run.py
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Original file line number Diff line number Diff line change
@@ -1,4 +1,4 @@
#!/usr/bin/env python
#!/usr/bin/env python3
"""
A basic local covid example meant to show off the flow of running the mechanistic model

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import matplotlib.pyplot as plt
import numpy as np

# the different segments of code responsible for runing the model
SCRIPT_PATH = os.path.abspath(os.path.dirname(__file__))
ROOT_PATH = os.path.join(SCRIPT_PATH, "..")

os.chdir(ROOT_PATH)

# the different segments of code responsible for running the model
# each will be explained as they are used below
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This causes the file to fail pre-commit checks: E402 Module level import not at top of file. You have two solutions, either add the following command: # ruff: noqa: E402 to disable the particular pre-commit check. Or move the lines below the import. I suggest the latter unless you have a good reason to keep the current ordering

from resp_ode import (
CovidSeroInitializer,
Expand Down Expand Up @@ -44,18 +49,18 @@
os.mkdir("output")

# step 1: define your paths
config_path = "config/"
config_path = os.path.join(ROOT_PATH, "config")
# global_config include definitions such as age bin bounds and strain definitions
# Any value or data structure that needs context to be interpretted is here.
GLOBAL_CONFIG_PATH = config_path + "config_global.json"
GLOBAL_CONFIG_PATH = os.path.join(config_path, "config_global.json")
# defines the init conditions of the scenario: pop size, initial infections etc.
INITIALIZER_CONFIG_PATH = config_path + "config_initializer_covid.json"
INITIALIZER_CONFIG_PATH = os.path.join(config_path, "config_initializer_covid.json")
# defines the running variables, strain R0s, external strain introductions etc.
RUNNER_CONFIG_PATH = config_path + "config_runner_covid.json"
RUNNER_CONFIG_PATH = os.path.join(config_path, "config_runner_covid.json")
# defines prior distributions for inferring variables.
INFERER_CONFIG_PATH = config_path + "config_inferer_covid.json"
INFERER_CONFIG_PATH = os.path.join(config_path, "config_inferer_covid.json")
# defines how the solution should be viewed, what slices examined, how to save.
INTERPRETER_CONFIG_PATH = config_path + "config_interpreter_covid.json"
INTERPRETER_CONFIG_PATH = os.path.join(config_path, "config_interpreter_covid.json")

# step 2: Set up your initializer
# sets up the initial conditions, initializer.get_initial_state() passed to runner
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