Contributing

Development setup

git clone https://github.com/hadesllm/morie.git
cd morie
python -m venv .venv && source .venv/bin/activate
pip install -e ".[test,interactive]"

Python tests

pytest -q

R tests

Rscript -e "library(morie); testthat::test_dir('r-package/morie/tests/testthat')"

Build docs

python -m sphinx -b html docs/source docs/build/html
open docs/build/html/index.html

Documentation conventions

• Python docstrings use NumPy style (Napoleon parses them).

• Include :math: inline and .. math:: display blocks for all estimators.

• R documentation uses roxygen2 markdown.

• New modules must be registered in morie.modules.MODULE_SPECS with a ModuleSpec entry listing all output file names.

• Every non-trivial Python function needs a pytest test; every R export needs a testthat test.

Code quality

• Type annotations on all Python function signatures.

• No hardcoded file paths; use DatasetRegistry.

• Row-level data from non-public sources must never be committed.

Adding a new module

1. Add a ModuleSpec entry to MODULE_SPECS in src/morie/modules.py.

2. Add a branch in run_module() that calls an implementation function.

3. Implement the analysis function in the appropriate module file (causal.py, investigation.py, etc.).

4. Add the module name to the R list_morie_modules() table in r-package/morie/R/modules.R.

5. Add a page to docs/source/methods/ if the module has significant logic.

6. Write tests in tests/ (Python) and r-package/morie/tests/testthat/ (R).

License

Contributions are accepted under GPL-2.0-only. By submitting a pull request you agree to license your contribution under that licence.