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Tools for simulation-based model checking and diagnostics.

Project description

checkrs

Tools for simulation-based model checking.

Description

The checkrs package contains functions for creating 7 model checking/diagnostic plots described in

Brathwaite, Timothy. "Check yourself before you wreck yourself: Assessing discrete choice models through predictive simulations" arXiv preprint arXiv:1806.02307 (2018). https://arxiv.org/abs/1806.02307.

Beyond the plots described in this paper, checkrs enables the creation of reliability and marginal model plots that use continuous scatterplot smooths based on Extremely Randomized Trees as kernel estimators, as opposed to only allowing discrete smooths based on binning.

As for the name, checkrs is a play on the word "checkers," i.e., those tools one uses to check, or one who checks. The name is also a play on the phrases "check the research of scientists" and "check research scientists."

Usage Installation

pip install checkrs

To-Do:

  • Add usage examples
  • Add tests
  • Set up tox
  • Set up pre-commit
  • Set up continuous integration
  • Refactor to remove pandas dependency
  • Architecture overhaul to go from prototype to v1.
  • Add package to conda and conda-forge

Development installation

To work on and edit checkrs, the following setup process may be useful.

  1. from the project root, create an environment checkrs with the help of conda,
    cd checkrs
    conda env create -f environment.yaml
    
  2. activate the new environment with
    conda activate checkrs
    
  3. install checkrs in an editable fashion using:
    pip install -e .
    

Optional and needed only once after git clone:

  1. install several pre-commit git hooks with:

    pre-commit install
    

    and checkout the configuration under .pre-commit-config.yaml. The -n, --no-verify flag of git commit can be used to deactivate pre-commit hooks temporarily.

  2. install [jupytext] git hooks to store notebooks as formatted python files:

    #!/bin/sh
    # For every ipynb file in the git index:
    # - apply black and flake8
    # - export the notebook to a Python script in folder 'python'
    # - and add it to the git index
    jupytext --from ipynb --pipe black --check flake8 --pre-commit
    jupytext --from ipynb --to py:light --pre-commit
    

    This is useful to avoid large diffs due to plots in your notebooks.

Then take a look into the scripts and notebooks folders.

Dependency Management & Reproducibility

  1. Always keep your abstract (unpinned) dependencies updated in environment.yaml, requirements.in, and eventually in setup.cfg and if you want to ship and install your package via pip later on.
  2. Create concrete dependencies as environment.lock.yaml and requirements.txt for the exact reproduction of your environment with:
    pip-compile requirements.in
    conda env export -n checkrs -f environment.lock.yaml
    
    For multi-OS development, consider using --no-builds during the export.
  3. Update your current environment with respect to a new environment.lock.yaml using:
    conda env update -f environment.lock.yaml --prune
    
    Or
    pip install -r requirements.txt
    

Project Organization

├── AUTHORS.rst             <- List of developers and maintainers.
├── CHANGELOG.rst           <- Changelog to keep track of new features and fixes.
├── LICENSE.txt             <- License as chosen on the command-line.
├── README.md               <- The top-level README for developers.
├── configs                 <- Directory for configurations of model & application.
├── data
│   ├── external            <- Data from third party sources.
│   ├── interim             <- Intermediate data that has been transformed.
│   ├── processed           <- The final, canonical data sets for modeling.
│   └── raw                 <- The original, immutable data dump.
├── docs                    <- Directory for Sphinx documentation in rst or md.
├── environment.yaml        <- The conda environment file for reproducibility.
├── models                  <- Trained and serialized models, model predictions,
│                              or model summaries.
├── notebooks               <- Jupyter notebooks. Naming convention is a number (for
│                              ordering), the creator's initials and a description,
│                              e.g. `1.0-fw-initial-data-exploration`.
├── references              <- Data dictionaries, manuals, and all other materials.
├── reports                 <- Generated analysis as HTML, PDF, LaTeX, etc.
│   └── figures             <- Generated plots and figures for reports.
├── scripts                 <- Analysis and production scripts which import the
│                              actual PYTHON_PKG, e.g. train_model.
├── setup.cfg               <- Declarative configuration of your project.
├── setup.py                <- Use `python setup.py develop` to install for development or
|                              or create a distribution with `python setup.py bdist_wheel`.
├── src
│   └── checkrs             <- Actual Python package where the main functionality goes.
├── tests                   <- Unit tests which can be run with `py.test`.
├── .coveragerc             <- Configuration for coverage reports of unit tests.
├── .isort.cfg              <- Configuration for git hook that sorts imports.
└── .pre-commit-config.yaml <- Configuration of pre-commit git hooks.

Note

This project has been set up using PyScaffold 3.3a1 and the dsproject extension 0.4. For details and usage information on PyScaffold see https://pyscaffold.org/.

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