Python library/utilities/tools for interacting with DTK input and output files
Developer note: Any .py file in emod_api will be included in the package.
Documentation available at https://docs.idmod.org/projects/emod-api/en/latest/.
To build the documentation locally, do the following:
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Create and activate a venv.
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Navigate to the root directory of the repo and enter the following
pip install -r requirements.txt cd docs pip install -r requirements.txt cd .. pip install -e .
emod-api can use Snappy [de]compression (python-snappy, actually) as necessary if it is installed which requires libdev-snappy (Debian/Ubuntu) or snappy-devel (RedHat/CentOS) on Linux.
Ubuntu: [sudo] apt install libdev-snappy
CentOS: [sudo] yum install snappy-devel (not yet tested)
If Snappy compression support is desired or needed, consider downloading and installing the latest python-snappy package for Windows from Christoph Gohlke's python package website: https://www.lfd.uci.edu/~gohlke/pythonlibs/#python-snappy
Input
- User wants to be able to create a minimal working config.json for any sim type guaranteed to work with a given Eradication binary.
- User wants to be able to create config.json from large static 'defaults' file and small variable parameters-of-interest file.
- User wants to be able to create guaranteed to work campaigns without having to interact with campaign.json files.
- User wants to create a migration file without having to grok our custom binary migration format.
- User wants to be able to create large multi-node demographics files programatically.
Output
- User wants to be able to get post-processed (cleaned up) schema.
- User wants to be able to get data from InsetChart.json without worrying about exact file format of the files.
- User wants to be able to extract data of interest from spatial binary files.
- User wants to be able to work easily with serialization files.
- User wants to be able to work easily with (pending) events.sql file.
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To build package:
python setup.py build -
To build wheel (.whl):
python setup.py bdist_wheel -
To import package, you can either:
- Set symlink to built module in build subdirectory
- do python setup.py install
- do python setup.py develop
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To install package (fill in actual version number in filename):
pip install dist/emod_api...whl -
To update the installed package (fill in actual version number in filename):
pip install --upgrade dist/emod_api...whl
- Migration files: users should never have to edit migration binary or header files.
- Serialization: Population manipulation, such as adding IPs or adding risk factors.
- Demographics: HINT matrices should not be created directly in demographics.
- Demographics: Population demographic initalization should be easier and reliable.
- Config: param_overrides & w5ml & custom events.
python3 tests/channel_reports.py
python3 tests/serialization.py
python3 tests/spatial_reports.py
python3 tests/weather_files.py
The EMOD Community is made up of researchers and software developers, primarily focused on malaria and HIV research. We value mutual respect, openness, and a collaborative spirit. If these values resonate with you, we invite you to join our EMOD Slack Community by completing this form:
https://forms.office.com/r/sjncGvBjvZ
The code in this repository was developed by IDM and other collaborators to support our joint research on flexible agent-based modeling. We've made it publicly available under the MIT License to provide others with a better understanding of our research and an opportunity to build upon it for their own work. We make no representations that the code works as intended or that we will provide support, address issues that are found, or accept pull requests. You are welcome to create your own fork and modify the code to suit your own modeling needs as permitted under the MIT License.