The HIV Workflow (hiv_workflow) is a set of scripts and libraries utilizing idmtools, idmtools-calibra, and emodpy-hiv for calibration and running of EMOD.
Documentation is available at https://docs.idmod.org/projects/hiv_workflow/en/latest/index.html.
This guide assumes Python 3.7.X (3.7.7 or higher) (64-bit) is installed (https://www.python.org/downloads/release/python-377) in Windows or Linux and assumes it is custom-installed into C:Python37 in Windows or /c/Python37 in Linux. (Download the exe or tgz to install.)
This guide further assumes a Linux-like command terminal is being used for Windows (e.g. git bash in Windows), not the built-in Windows cmd.
Create and activate a clean virtual environment.
If you have Python installed to a different directory, please update the Python interpreter path below to match your installation of Python.
Create the virtual environment:
/c/Python37/python -m venv ~/environments/hiv_workflow
Activate the virtual environment:
Bash in Windows:
Ensure pip is up-to-date (the default version has major issues):
python -m pip install pip --upgrade
Obtain and install hiv_workflow:
git clone https://github.com/InstituteforDiseaseModeling/hiv_workflow.git cd hiv_workflow python -m pip install --upgrade pip pip install . -r requirements.txt
Verify the installation:
cd examples/rakai-optimtool python -m hiv_workflow.scripts.available_parameters -m baseline
The examples/rakai-optimtool/demo.md file contains example commands that highlight a simple but typical workflow linking the scripts contained in hiv_workflow. These commands are expected to be run with your working directory being examples/rakai-optimtool (the root of the example project).
If running pip install results on this error: ‘ERROR: THESE PACKAGES DO NOT MATCH THE HASHES FROM THE REQUIREMENTS FILE’
Try running adding
--no-cache-diras part of your pip install command. i.e.
pip install -e . -r requirements.txt --no-cache-dir
If running pip install results on dependencies issues:
Try updating pip:
python -m pip install --upgrade pip
If when running one of the demo samples you get a “hiv_workflow not found” or even “Python not found”:
Try activating your virtual environment as shown above