pydream_it

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pydream_it is script to that reads/imports PySB models and generates a template script that is used for PyDREAM calibration of the model. pydream_it inspects the model and identifies the kinetic parameters and generates the SampledParam code lines. pydream_it currently has limited functionality for #PYDREAM_IT directives that can be added to the model code alter pydream_it behavior.

Install and basic usage

Warning: pydream_it is still under heavy development and may rapidly change.

pydream_it run dependencies

pydream_it does not have any special dependencies itself, but PySB is of course needed to run the PySB models:

pydream_it does not require any special installation to use, just clone or download the GitHub repo

git clone https://github.com/blakeaw/pydream_it.git

Then to use pydream_it, simply call the script with python and passing as input the model file

python pydream_it.py model.py

The file model.py should be a PySB model file. NOTE: pydream_it currently doesn't inspect for the location of model.py, so you need to be in the same directory as the model.py file when you call pydream_it. In this case pydream_it will generate a file run_pydream_model.py which will contain some basic code to calibrate the model using PyDREAM.

pydream_it directives

The #PYDREAM_IT directives will appear as comments in the model code and are parsed by pydream_it at runtime. pydream_it currently has the following directives that can be added to the model code file:

• #PYDREAM_IT prior [param_name, param_index] [norm, uniform] - tell pydream_it to use a specific prior (other than the default) for the specified parameter. The parameter can be specified by either it name (param_name) or its index (param_index). pydream_it currently supports using normal distribution (norm) of uniform priors.
• #PYDREAM_IT no-sample [param_name, param_index] - define a fixed parameter, i.e., pydream_it will not add it to the sample parameters list for the PyDREAM run.

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Contact

To report problems or bugs please open a GitHub Issue. Additionally, any comments, suggestions, or feature requests for pydream_it can also be submitted as a GitHub Issue.

For any other inquiries, including questions about pydream_it use or implementation, you can contact Blake directly via e-mail at either blake.a.wilson@vanderbilt.edu or blakeaw1102@gmail.com; please include "pydream_it inquiry" in the e-mail subject line.

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Contributing

If you would like to contribute directly to pydream_it's development please

1. Fork the repo (https://github.com/blakeaw/pydream_it/fork)
2. Create a new branch for your feature (git checkout -b feature/foo_bar)
3. Create test code for your feature
4. Once your feature passes its own test, run all the tests using pytest (python -m pytest)
5. Once your feature passes all the tests, commit your changes (git commit -am 'Add the foo_bar feature.')
6. Push to the branch (git push origin feature/foo_bar)
7. Create a new Pull Request

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License

This project is licensed under the MIT License - see the LICENSE file for details

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Acknowledgments

• This code and the template run scripts it generates are based on the examples given in the PyDREAM repo.

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