emod-generic-scripts's Introduction

EMOD-Generic-Scripts

See documentation at https://docs.idmod.org/projects/emod-generic-scripts/en/latest/ for additional information about how to use these scripts.

To get started:

Setup a virtual environment (e.g., conda)

Install requirements:

pip install -r requirements.txt --index-url=https://packages.idmod.org/api/pypi/pypi-production/simple

Run an experiment (requires COMPS credentials):

cd EMOD-Generic-Scripts/model_covariance01/experiment_covariance01
 python make01_param_dict.py
 python make02_lauch_sims.py
 python make03_pool_brick.py

Make figures:

cd EMOD-Generic-Scripts/model_covariance01/figure_attackfrac01
python make_fig_attackrate.py

To build the documentation locally, do the following:

Create and activate a venv.
Navigate to the root directory of the repo and enter the following
```
pip install -r docs/requirements.txt
```

Directory	Description
env_Alma9 env_Debian12 env_Fedora40 env_Rocky9 env_Ubuntu24	Contains the definition scripts for singularity containers. Produces the the EMOD executable, schema, and custom reporters; creates an environment for running EMOD on COMPS and contains the python packages available to the embedded python interpreter. All files remain on COMPS and are provided to the various workflows as Asset Collection IDs.
local_python	Contains additional python scripts that provide helper functions common to all of the workflows.
model_covariance01	Demonstration of the covariance feature.
model_covid01	Baseline simulations for SARS-CoV-2 in EMOD. Collab with MvG.
model_demographics01	Example demographics for UK measles simulations.
model_demographics02	Example demographics using UN WPP data as inputs.
model_measles_cod01	Documentation.
model_measles_gha01	Examination of RDT use and responsive campaigns for measles using Ghana as an example context.
model_measles_nga01	Documentation.
model_measles_nga02	Documentation.
model_measles01	Documentation.
model_network01	Demonstration of the network infectivity feature.
model_polio_nga01	Example outbreak simulations for cVDPV2 in Nigeria. Collab with JG and HL.
model_rubella01	Projections of rubella infections and CRS burden following RCV introduction.
model_transtree01	Demonstration of the infector labeling feature and generation of explicit transmission networks.
refdat_mcv1	IHME MCV1 coverage estimates used to construct input files for EMOD simulations.
refdat_namesets	Namesets used for region identification.
refdat_poppyr	UN WPP age structured population estimates used to construct input files for EMOD simulations.
refdat_sias	Documentation.

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emod-generic-scripts's Issues

Workitem fails to launch occasionally.

When launching calibration (ID: 5b4b1e1b-8b97-ee11-9eff-b88303912b51) I got an error while launching the workitem:

Error message:
Errors encountered during file download, directory creation, and/or symlink processing. The most common cause of this error is the use of long file paths and/or names. See logs for more details.
CorrelationId: 671015fe-77ad-4009-819e-f729b4c2f8e1

I was doing something very similar to:
https://github.com/InstituteforDiseaseModeling/EMOD-Generic-Scripts/blob/main/model_demographics01/experiment_demog_UK01_calib/make05_start_calib.py

I re-ran the make05_start_calib.py script and the workflow launched.

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