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30 changes: 9 additions & 21 deletions README.md
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# emod-api
Python library/utilities/tools for interacting with DTK input and output files
Python library/utilities/tools for interacting with EMOD input and output files

Developer note: Any .py file in emod_api will be included in the package.

![](https://github.com/institutefordiseasemodeling/emod-api/workflows/Package%20and%20test%20on%20Ubuntu/badge.svg)
![](https://github.com/institutefordiseasemodeling/emod-api/workflows/Package%20and%20test%20on%20Windows/badge.svg)
[![Package and test on Ubuntu](https://github.com/EMOD-Hub/emod-api/actions/workflows/build_test_ubuntu.yaml/badge.svg)](https://github.com/EMOD-Hub/emod-api/actions/workflows/build_test_ubuntu.yaml)
[![Package and test on windows](https://github.com/EMOD-Hub/emod-api/actions/workflows/build_test_windows.yaml/badge.svg)](https://github.com/EMOD-Hub/emod-api/actions/workflows/build_test_windows.yaml)

## Documentation

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### Linux

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.
emod-api can use Snappy [de]compression (python-snappy) as necessary if it is installed which requires libdev-snappy (Debian/Ubuntu) or snappy-devel (RedHat/CentOS) on Linux.
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Is this still true? Hmm. This is serialization related. I wonder if it belongs here or in emodpy-malaria.

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Yes, kind of. There's a place in serialization that checks if snappy is available:
https://github.com/EMOD-Hub/emod-api/blob/main/emod_api/serialization/dtkFileSupport.py#L6

It's not currently a dependency, so not installed by default.

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I'm going to create a ticket in emodpy-malaria to make sure that snappy is installed by default. In EMOD, if the chunk to be serialized is greater than 0x7E000000, we use snappy for compression. Maybe there is an issue with snappy installation that I don't understand, but we should make sure it is handled well.


Ubuntu: ```[sudo] apt install libdev-snappy```

CentOS: ```[sudo] yum install snappy-devel``` (not yet tested)

### Windows

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

## user stories
## User Stories

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.
Expand Down Expand Up @@ -83,24 +76,19 @@ Output

### Running tests

`python3 tests/channel_reports.py`
`python3 tests/serialization.py`
`python3 tests/spatial_reports.py`
`python3 tests/weather_files.py`
Please see the documentation for [testing](/tests/README.md).


# Community

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:
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


# Disclaimer

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.
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.
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