gp3sequencespy

Zenodo archive DOI: 10.5281/zenodo.22166449

gp3sequencespy is the Python implementation of gp3sequences 0.3.0, providing transparent, reproducible, and auditable analysis of ordered categorical sequences and scanpaths.

The frozen R 0.3.0 tarball is the behavioral reference. Development is parity-first: preserve the frozen scientific contracts, validate them explicitly, and only then add Python-native extensions.

Version 0.1.1 status

• 81 / 81 frozen R public function counterparts are present and exported.
• 81 / 81 frozen R public signatures have been audited; every difference is either structurally matched or explicitly classified as an R→Python semantic/plotting translation.
• 130 / 130 frozen R test_that() blocks have dedicated Python translation tests recorded in PARITY_TEST_MATRIX.md.
• The current Python suite contains 182 tests, including documentation, release-contract, and R-hclust oracle-regression tests.
• GitHub Actions covers Linux, macOS, and Windows with Python 3.11–3.14, a dedicated Ruff/mypy/frozen-contract quality job, and a fresh-wheel smoke build.
• Fifteen Python-native articles port the full frozen R vignette set, with MkDocs documentation under docs/.
• The deterministic core, hierarchical/PAM, and time-varying-model cross-language oracle tranches have been executed against frozen R 0.3.0; remaining deliberate boundaries are documented in PARITY_EXCEPTIONS.md.

Documentation: https://stefanosbalaskas.github.io/gp3sequencespy/

Version 0.1.1 is a metadata and release-infrastructure maintenance release over the frozen 0.1.0 scientific implementation. It does not change the 81-function public scientific API or the frozen R 0.3.0 parity contracts. It corrects the PyPI-facing release wording, records the Zenodo archive DOI, and uses token-free PyPI Trusted Publishing.

Installation

For development installs from the repository:

uv sync --extra time

From PyPI:

pip install gp3sequencespy==0.1.1

The original v0.1.0 scientific release remains immutable. Stable releases from 0.1.1 onward publish the exact GitHub Release wheel and source distribution to PyPI through the registered Trusted Publisher described in PYPI_PUBLISHING.md.

Reproducibility and release governance

• Frozen-reference details: REPRODUCIBILITY.md
• Known parity boundaries: PARITY_EXCEPTIONS.md
• Release gates: RELEASE_CHECKLIST.md
• Changelog: CHANGELOG.md
• Citation metadata: CITATION.cff
• Contribution guidance: CONTRIBUTING.md
• PyPI publishing and Trusted Publishing: PYPI_PUBLISHING.md

Scientific interpretation guardrail

Sequence structure does not independently establish emotion, cognition, comprehension, personality, intention, deception, diagnosis, or causality. Observational group contrasts are associational unless a valid randomized design supports a causal interpretation.