Skip to content

CONTRIBUTING.md

Latest commit

 

History

History
48 lines (38 loc) · 1.84 KB

CONTRIBUTING.md

File metadata and controls

48 lines (38 loc) · 1.84 KB
Raw

Contributing to traceCB

Please open an issue before making a substantial change to the statistical method, input schema, or paper analysis workflow. Keep scientific behavior changes separate from formatting-only changes so that reviewers can audit the effect on results.

Development setup

python -m pip install -e ".[ci,docs]"

Before submitting a pull request, run:

python -m build
python -m twine check --strict dist/*
mkdocs build --strict
jupyter nbconvert --to notebook --execute \
  docs/tutorial/run_traceCB.ipynb \
  --output run_traceCB_checked.ipynb \
  --output-dir /tmp \
  --ExecutePreprocessor.timeout=600

Do not commit controlled-access data, credentials, local absolute-path configuration, generated result directories, or notebook execution caches. When an analysis result changes, record the command, parameters, random seed, software revision, and affected manuscript figure or table in the pull request.

Release artifacts

Build from a clean checkout of the intended release commit. The wheel contains only the installable traceCB library and its metadata. The source archive also contains workflows, documentation, and the public toy inputs. Local tests/ files are excluded from Git and release archives. Install the wheel, verify the public toy-input checksums from the extracted source archive, and execute both tutorial notebooks against the installed package. CI checks package installation on Python 3.10 and 3.12; notebook execution uses Python 3.12.

Before publishing, ensure that the release tag points to the reviewed commit and that pyproject.toml, traceCB.__version__, and CITATION.cff agree. Record the commit and environment used for manuscript results. Passing the toy example and package checks does not replace reproducing the full analyses with their external datasets and R/PLINK/LDSC dependencies.