Tools for simulation-based model checking and diagnostics.
Tools for simulation-based model checking.
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."
pip install checkrs
- 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
To work on and edit checkrs, the following setup process may be useful.
- from the project root, create an environment
checkrswith the help of conda,
cd checkrs conda env create -f environment.yaml
- activate the new environment with
conda activate checkrs
checkrsin an editable fashion using:
pip install -e .
Optional and needed only once after
install several pre-commit git hooks with:
and checkout the configuration under
-n, --no-verifyflag of
git commitcan be used to deactivate pre-commit hooks temporarily.
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
Dependency Management & Reproducibility
- Always keep your abstract (unpinned) dependencies updated in
requirements.in, and eventually in
setup.cfgand if you want to ship and install your package via
- Create concrete dependencies as
requirements.txtfor the exact reproduction of your environment with:
For multi-OS development, consider using
pip-compile requirements.in conda env export -n checkrs -f environment.lock.yaml
--no-buildsduring the export.
- Update your current environment with respect to a new
conda env update -f environment.lock.yaml --prune
pip install -r requirements.txt
├── 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.
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