ALFAsim Score

What is alfasim-score?

Python package to convert the SCORE input JSON to Alfacase (ALFAsim input file).

Features

• Converter from Score input JSON to Alfacase
• Parser for the ALFAsim results and generate a JSON compatible with SCORE

How to use it

1. First, the user needs to create an instance of the converter:

   from pathlib import Path
   from alfasim_score.converter.alfacase.alfasim_score_converter import AlfasimScoreConverter
   # path indicating where the SCORE input file is
   score_input_filepath = Path("path/to/score_input.json")
   # path indicating where the output file (converted from ALFAsim results) should be created
   score_output_filepath = Path("path/to/score_output_result.json")
   # then create a converter instance
   converter = AlfasimScoreConverter(score_input_filepath, score_output_filepath)
   

2. To convert the SCORE input into an alfacase file, the user can do the following:

   alfacase_filepath = Path("path/where/save/converted_score.alfacase")
   converter.generate_alfasim_input_file(alfacase_filepath)
   

3. Run the ALFAsim with the generated file (and the pvt tables in the same folder)

4. Once the result file of ALFAsim is generated, one can call the converter for the output file:

   alfasim_results_directory = Path("path/to/alfasim_results_folder")
   converter.generate_score_output_file(alfasim_results_directory)
   

Development

For complete description of what type of contributions are possible, see the full CONTRIBUTING guide.

Here is a quick summary of the steps necessary to setup your environment to contribute to alfasim-score.

1. Create a virtual environment and activate it:

   $ python -m virtualenv .env
   $ .env\Scripts\activate  # windows
   $ source .env/bin/activate  # linux
   

   Note

   If you use conda, you can install virtualenv in the root environment:

   $ conda install -n root virtualenv
   

   Don't worry as this is safe to do.

2. Update pip:

   $ python -m pip install -U pip
   

3. Install development dependencies:

   $ pip install -e .[testing]
   

4. Install pre-commit:

   $ pre-commit install
   

5. Run tests:

   $ pytest --pyargs alfasim_score
   

6. Generate docs locally:

   $ tox -e docs
   

   The documentation files will be generated in docs/_build.

Release

A reminder for the maintainers on how to make a new release.

Note that the VERSION should folow the semantic versioning as X.Y.Z Ex.: v1.0.5

1. Create a release-VERSION branch from upstream/master.
2. Update CHANGELOG.rst.
3. Push a branch with the changes.
4. Once all builds pass, push a VERSION tag to upstream. Ex: git tag v1.0.5; git push origin --tags
5. Merge the PR.