pydream_it
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 given in the model code to tell pydream_it what prior distribution to use (norm or uniform).
pydream_it is script to that reads/importsInstall 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.
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.
Contributing
If you would like to contribute directly to pydream_it's development please
- Fork the repo (https://github.com/blakeaw/pydream_it/fork)
- Create a new branch for your feature (git checkout -b feature/foo_bar)
- Create test code for your feature
- Once your feature passes its own test, run all the tests using pytest (python -m pytest)
- Once your feature passes all the tests, commit your changes (git commit -am 'Add the foo_bar feature.')
- Push to the branch (git push origin feature/foo_bar)
- Create a new Pull Request
License
This project is licensed under the MIT License - see the LICENSE file for details
Acknowledgments
- This code and the template run scripts it generates are based on the examples given in the PyDREAM repo.