pysofra 0.1.0a1__tar.gz

pysofra-0.1.0a1/.gitignore

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+__pycache__/
+*.py[cod]
+*.egg-info/
+dist/
+build/
+.venv/
+venv/
+.env
+
+.pytest_cache/
+.mypy_cache/
+.ruff_cache/
+.coverage
+htmlcov/
+
+.DS_Store
+.idea/
+.vscode/
+.claude/
+
+site/
+docs/_build/
+
+# Tutorial / example export artefacts — produced on demand by
+# scripts/render_tutorial.py, not part of the source tree.
+*.docx
+*.pptx
+*.xlsx
+examples/tutorial_*.docx
+examples/tutorial_*.pptx
+examples/tutorial_*.xlsx
+examples/tutorial_*.png
+!tests/fixtures/**/*.docx
+!tests/fixtures/**/*.pptx
+!tests/fixtures/**/*.xlsx
+
+# Hypothesis example database (auto-managed)
+.hypothesis/
+
+# uv writes a lockfile when ``uv add`` / ``uv pip install`` is used
+# locally; the project pins its runtime versions explicitly in
+# pyproject.toml + paper/replication/requirements.txt, so the uv
+# lockfile is a local convenience that should not ship.
+uv.lock
+
+# JSS paper bundle — paper/ contains the manuscript, bibliography,
+# embedded figures, and replication archive. The .tex / .bib / .py /
+# .R sources are ALWAYS tracked. Replication outputs are tracked in
+# the text formats reviewers diff (json / tex / md / html / png /
+# pdf / svg) so the archive ships with a working baseline; only the
+# heavy regenerable Office binaries (docx / pptx / xlsx) and the
+# fontconfig / mpl cache directories are ignored.
+paper/replication/trial.csv
+paper/replication/table*.docx
+paper/replication/table*.pptx
+paper/replication/table*.xlsx
+paper/replication/.mplconfig/
+
+# Submission-required text outputs and figures: explicit re-include.
+# The blanket repo-wide ``*.docx`` rule at the top of this file would
+# otherwise eat ``paper/replication/table*.html`` etc. — these
+# negations keep them tracked.
+!paper/replication/paper_outputs*.json
+!paper/replication/table*.html
+!paper/replication/table*.tex
+!paper/replication/table*.md
+!paper/replication/figures/
+!paper/replication/figures/*
+
+# The `paper/figures/` directory IS tracked because paper.tex embeds
+# its PDFs/PNGs via \includegraphics. To regenerate, run
+# paper/replication/example_trial.py then copy the desired files in.
+!paper/figures/
+!paper/figures/*
+
+# LaTeX build artefacts (in case anyone compiles paper.tex locally).
+paper/*.aux
+paper/*.log
+paper/*.out
+paper/*.toc
+paper/*.bbl
+paper/*.blg
+paper/*.synctex.gz
+paper/paper.pdf
+
+
+# paper/ is excluded from the public repo until JSS submission lands.
+# It stays in the local working tree for editing; the replication
+# archive moves into the repo at submission time.
+paper/

pysofra-0.1.0a1/CHANGELOG.md

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+# Changelog
+
+All notable changes to PySofra will be documented in this file.
+
+The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.1.0/),
+and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
+
+## [0.1.0a1] — 2026-05-20
+
+### Added
+
+- Initial alpha release.
+- Core `SofraTable` object with immutable method chaining.
+- `tbl_one()` — baseline characteristic tables (Table 1) with continuous /
+  categorical summaries, stratification, missing data summaries, overall
+  column, p-values, and standardized mean differences (SMDs).
+- `tbl_summary()` — general descriptive summary tables with grouping and
+  configurable statistics.
+- `tbl_regression()` — regression tables for `statsmodels` linear / logistic
+  / Poisson models, with confidence intervals, exponentiation, and p-values.
+- `tbl_merge()` / `tbl_stack()` — table composition.
+- HTML renderer with rich notebook `_repr_html_` output (dark-mode aware,
+  responsive, sticky headers).
+- Markdown renderer.
+- DOCX renderer via `python-docx` (publication-quality Word tables with
+  captions, footnotes, merged spanning headers).
+- Themes: `clinical`, `compact`, `jama`, `nejm`, `minimal`.
+- Automatic statistical test selection with override hooks.
+- Snapshot tests for HTML output.