New Jupyter Notebook for Visualization and Validation

[MarkEwert03]

Description

Please include a summary of the changes and the related issue. Please also include relevant motivation and context. List any dependencies that are required for this change.

The main purpose of this PR is to create a Jupyter notebook to allow for easier user accessibility running leap and performing analysis with the results. Along the way, a couple of bugs were fixed and additional features were added including:

• ignore_pollution_flag added to leap cmd arguments. Currently, air pollution is just a framework in the model and has no actual effect on it. This conditional flag is passed through simulation.py and agent.py so that errors are not generated by check_year() by utils.py (This stems from issue Issue with Incidence Module #8 and this is a temporary workaround until air pollution functionality is added)
• additional error checking in severity.py/compute_distribution() to avoid leap from crashing due to non-stochastic values being passed to np.multinomial
• np.clip() added in utils.py/sigmoid() to avoid np overflow warnings
• additional features for users running leap:
  • If directory doesn't exist with -o flag, users are prompted to create one
  • If directory does exist with -o flag, users are warned that they will overwrite existing files
  • Log file created after each successful run with relevant metadata and simulation parameters

Type of Change

• Bug fix (non-breaking change which fixes an issue)
• New feature (non-breaking change which adds functionality)
• Breaking change (fix or feature that would cause existing functionality to not work as expected)
• Documentation (updated docstrings or README files)
• Tests (added new tests or modified current test suite)
• Refactoring (changes in the design of the code that don't change the functionality)

Tests

Please describe the tests that you ran to verify your changes. Provide instructions so we can reproduce. Please also list any relevant details for your test configuration.

• Ran leap with various parameters to obtain data files used for jupyter notebook

Linked PRs / Issues

List here any related pull requests (from this repo or other repos) and/or the issue this PR is addressing.

This addresses GitHub Issue #14. We will confirm with Kate what additional plots are desired.

Checklist:

• I have performed a self-review of my code
• I have documented my code with appropriate docstrings
• I have made corresponding changes to the documentation / README files
• I have added tests that prove my fix is effective or that my feature works
• New and existing unit tests pass locally with my changes

[ahill187]

Looks good! I've added a few comments, a few things to change, but overall looks good to go.