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 0.1.2 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 292 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 0.1.2 is a quality-completion and robustness maintenance release. It preserves the frozen 81-function scientific API and R 0.3.0 parity contracts while raising the Python validation suite to 292 tests, 100% statement and branch coverage, and a 3/3 mutation-smoke gate. It also expands the documentation and hardens PyArrow/pandas preparation and grouped plotting edge cases.

Installation

For development installs from the repository:

uv sync --extra time

From PyPI:

pip install gp3sequencespy==0.1.2

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.