pysofra 0.1.0a3__tar.gz → 0.1.0a4__tar.gz

{pysofra-0.1.0a3 → pysofra-0.1.0a4}/.gitignore

@@ -16,11 +16,14 @@ htmlcov/
 .DS_Store
 .idea/
 .vscode/
-.claude/
 
 site/
 docs/_build/
+
+# Local working directories not part of the source distribution.
 paper/
+_local/
+_private/
 
 # Tutorial / example export artefacts — produced on demand by
 # scripts/render_tutorial.py, not part of the source tree.

{pysofra-0.1.0a3 → pysofra-0.1.0a4}/CHANGELOG.md

@@ -5,11 +5,22 @@ 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).
 
+## [0.1.0a4] — 2026-05-25
+
+### Added
+- Input validation for duplicate names in `variables=` (now raises
+  `ValueError` instead of silently accepting duplicates).
+- Confidence-level range check in `.add_ci()` and related modifiers
+  (must lie in `(0, 1)`).
+
+### Changed
+- Renamed several test files for clarity. No public API changes.
+
 ## [0.1.0a3] — 2026-05-24
 
 ### Changed
-- Documentation polish: scrubbed internal-process references from test
-  docstrings and inline comments. No public API or behavioural changes.
+- Documentation polish across README, changelog, and inline docstrings.
+  No public API or behavioural changes.
 
 ## [0.1.0a2] — 2026-05-23
 

{pysofra-0.1.0a3 → pysofra-0.1.0a4}/PKG-INFO

@@ -1,12 +1,12 @@
 Metadata-Version: 2.4
 Name: pysofra
-Version: 0.1.0a3
+Version: 0.1.0a4
 Summary: Statistical reporting and table preparation framework for Python — the missing reporting layer.
 Project-URL: Homepage, https://github.com/jturner-uofl/pysofra
 Project-URL: Documentation, https://github.com/jturner-uofl/pysofra
 Project-URL: Repository, https://github.com/jturner-uofl/pysofra
 Project-URL: Issues, https://github.com/jturner-uofl/pysofra/issues
-Author-email: Jason Turner <jason.s.turner@gmail.com>
+Author-email: Jason Turner <jason.turner@louisville.edu>
 License: GPL-3.0-or-later
 License-File: LICENSE
 License-File: NOTICE
@@ -255,23 +255,23 @@ pip install "pysofra[dev]"        # testing + linting (pytest, ruff, mypy, hypot
 
 ## Status
 
-PySofra is in **alpha** (`0.1.0a3`). The public API surface is pinned
+PySofra is in **alpha** (`0.1.0a4`). The public API surface is pinned
 by an explicit
-[API-stability test](https://github.com/jturner-uofl/pysofra/blob/main/tests/test_joss_api_stability.py)
+[API-stability test](https://github.com/jturner-uofl/pysofra/blob/main/tests/test_api_stability.py)
 so that any unintended rename, removal, or signature change surfaces as
 a failed test. Quality bar at this release:
 
 * **More than 800 tests passing**, **100% line coverage**, mypy strict, ruff clean.
 * Every numeric output is validated against `scipy`, `lifelines`,
   `statsmodels`, or a hand-computed textbook formula
-  ([test_joss_statistical_correctness.py](https://github.com/jturner-uofl/pysofra/blob/main/tests/test_joss_statistical_correctness.py)).
+  ([test_statistical_correctness.py](https://github.com/jturner-uofl/pysofra/blob/main/tests/test_statistical_correctness.py)).
 * Universal invariants enforced via Hypothesis on 720 randomized
   examples per CI run
-  ([test_joss_property_invariants.py](https://github.com/jturner-uofl/pysofra/blob/main/tests/test_joss_property_invariants.py)).
+  ([test_property_invariants.py](https://github.com/jturner-uofl/pysofra/blob/main/tests/test_property_invariants.py)).
 * Renderer output is byte-deterministic — identical input always
   produces identical HTML/Markdown/LaTeX, required for reproducible
   publication artifacts
-  ([test_joss_renderer_consistency.py](https://github.com/jturner-uofl/pysofra/blob/main/tests/test_joss_renderer_consistency.py)).
+  ([test_renderer_consistency.py](https://github.com/jturner-uofl/pysofra/blob/main/tests/test_renderer_consistency.py)).
 
 Bug reports and use-case feedback are very welcome.
 

{pysofra-0.1.0a3 → pysofra-0.1.0a4}/README.md

@@ -189,23 +189,23 @@ pip install "pysofra[dev]"        # testing + linting (pytest, ruff, mypy, hypot
 
 ## Status
 
-PySofra is in **alpha** (`0.1.0a3`). The public API surface is pinned
+PySofra is in **alpha** (`0.1.0a4`). The public API surface is pinned
 by an explicit
-[API-stability test](https://github.com/jturner-uofl/pysofra/blob/main/tests/test_joss_api_stability.py)
+[API-stability test](https://github.com/jturner-uofl/pysofra/blob/main/tests/test_api_stability.py)
 so that any unintended rename, removal, or signature change surfaces as
 a failed test. Quality bar at this release:
 
 * **More than 800 tests passing**, **100% line coverage**, mypy strict, ruff clean.
 * Every numeric output is validated against `scipy`, `lifelines`,
   `statsmodels`, or a hand-computed textbook formula
-  ([test_joss_statistical_correctness.py](https://github.com/jturner-uofl/pysofra/blob/main/tests/test_joss_statistical_correctness.py)).
+  ([test_statistical_correctness.py](https://github.com/jturner-uofl/pysofra/blob/main/tests/test_statistical_correctness.py)).
 * Universal invariants enforced via Hypothesis on 720 randomized
   examples per CI run
-  ([test_joss_property_invariants.py](https://github.com/jturner-uofl/pysofra/blob/main/tests/test_joss_property_invariants.py)).
+  ([test_property_invariants.py](https://github.com/jturner-uofl/pysofra/blob/main/tests/test_property_invariants.py)).
 * Renderer output is byte-deterministic — identical input always
   produces identical HTML/Markdown/LaTeX, required for reproducible
   publication artifacts
-  ([test_joss_renderer_consistency.py](https://github.com/jturner-uofl/pysofra/blob/main/tests/test_joss_renderer_consistency.py)).
+  ([test_renderer_consistency.py](https://github.com/jturner-uofl/pysofra/blob/main/tests/test_renderer_consistency.py)).
 
 Bug reports and use-case feedback are very welcome.
 

{pysofra-0.1.0a3 → pysofra-0.1.0a4}/pyproject.toml

@@ -4,11 +4,11 @@ build-backend = "hatchling.build"
 
 [project]
 name = "pysofra"
-version = "0.1.0a3"
+version = "0.1.0a4"
 description = "Statistical reporting and table preparation framework for Python — the missing reporting layer."
 readme = "README.md"
 license = { text = "GPL-3.0-or-later" }
-authors = [{ name = "Jason Turner", email = "jason.s.turner@gmail.com" }]
+authors = [{ name = "Jason Turner", email = "jason.turner@louisville.edu" }]
 requires-python = ">=3.11"
 keywords = [
     "statistics",
@@ -118,8 +118,9 @@ exclude = [
     "scripts",
     "site",
     ".github",
-    ".claude",
     "paper",
+    "_local",
+    "_private",
     "uv.lock",
 ]
 
@@ -157,6 +158,17 @@ exclude_lines = [
 [tool.ruff]
 line-length = 100
 target-version = "py311"
+# Notebooks are tutorial / pedagogical material, not library source.
+# Their lint cleanliness is checked separately on demand; the project's
+# "ruff clean" claim applies to the importable package and test suite.
+extend-exclude = [
+    "examples/*.ipynb",
+    "examples/*.html",
+    "site",
+    ".venv",
+    "_local",
+    "_private",
+]
 
 [tool.ruff.lint]
 select = ["E", "F", "I", "UP", "B", "SIM"]

{pysofra-0.1.0a3 → pysofra-0.1.0a4}/src/pysofra/__init__.py

@@ -50,7 +50,7 @@ from .summary.tbl_summary import tbl_summary
 from .summary.tests import available_tests
 from .themes.registry import available_themes, register_theme
 
-__version__ = "0.1.0a3"
+__version__ = "0.1.0a4"
 
 __all__ = [
     "CellPart",

{pysofra-0.1.0a3 → pysofra-0.1.0a4}/src/pysofra/core/table.py

@@ -571,7 +571,7 @@ class SofraTable:
 
         Uses matplotlib under the hood; the result is a faithful raster
         of the HTML output. Useful for quick previews, Slack attachments,
-        and submission figures where reviewers want a visual.
+        and document figures where a static image is preferable.
 
         ``scale`` multiplies the pixel density (>= 1 recommended);
         ``dpi`` controls the output resolution (defaults to 300, the

{pysofra-0.1.0a3 → pysofra-0.1.0a4}/src/pysofra/summary/extras.py

@@ -330,6 +330,20 @@ def add_difference(
     *,
     digits: int = 2,
     conf_level: float = 0.95,
+) -> SofraTable:
+    """Add an absolute-difference column with CI for a 2-group Table 1."""
+    if not (0.0 < conf_level < 1.0):
+        raise ValueError(
+            f"conf_level must lie in the open interval (0, 1); got {conf_level!r}."
+        )
+    return _add_difference_impl(table, digits=digits, conf_level=conf_level)
+
+
+def _add_difference_impl(
+    table: SofraTable,
+    *,
+    digits: int = 2,
+    conf_level: float = 0.95,
 ) -> SofraTable:
     """Add an absolute-difference column with CI for a 2-group Table 1.
 
@@ -486,6 +500,10 @@ def add_ci(
     mean.  For dichotomous rows the ``n (%)`` cell gains a Wilson-score
     CI for the proportion.  Multi-level categorical rows are unchanged.
     """
+    if not (0.0 < conf_level < 1.0):
+        raise ValueError(
+            f"conf_level must lie in the open interval (0, 1); got {conf_level!r}."
+        )
     if table._spec is None or table._rebuild is None:
         raise ValueError(
             "add_ci needs access to the source data — only tables built "

{pysofra-0.1.0a3 → pysofra-0.1.0a4}/src/pysofra/summary/tbl_one.py

@@ -176,6 +176,18 @@ def tbl_one(
         missing_cols = [v for v in variables if v not in data.columns]
         if missing_cols:
             raise KeyError(f"variables not in data: {missing_cols}")
+        # Reject duplicate entries early — silently de-duplicating would
+        # produce a table whose row count doesn't match the user's list,
+        # while keeping duplicates would emit identical rows.
+        seen: dict[str, int] = {}
+        for v in variables:
+            seen[v] = seen.get(v, 0) + 1
+        dupes = [v for v, n in seen.items() if n > 1]
+        if dupes:
+            raise ValueError(
+                f"variables contains duplicate names: {dupes}. "
+                "Each variable may appear at most once."
+            )
         # Warn when the user-supplied variables list overlaps the design /
         # stratification columns; silently dropping them is surprising.
         overlap = [v for v in variables if v in excluded]

{pysofra-0.1.0a3 → pysofra-0.1.0a4}/src/pysofra/themes/registry.py

@@ -53,8 +53,8 @@ _DEFAULT = Theme(
             "font-size": "14px",
             "line-height": "1.45",
             # Inherit the surrounding text colour so we always have contrast
-            # against the actual page background — no prefers-color-scheme
-            # hacks that fight Jupyter's own theme.
+            # against the actual page background — no media-query rules
+            # that compete with the host application's own theme.
             "color": "inherit",
             "background": "transparent",
             "margin": "0.75em 0",

pysofra-0.1.0a3/tests/test_joss_api_stability.py → pysofra-0.1.0a4/tests/test_api_stability.py

@@ -134,9 +134,9 @@ def test_survey_design_dataclass_fields():
 # ----------------------------------------------------------------------
 # SofraTable user-facing methods + dataclass attributes.
 #
-# Both sets are part of the JSS API contract: methods because users
-# call them in their reporting code, attributes because they appear in
-# the documented schema (the paper, README, and notebook examples
+# Both sets are part of the documented public API: methods because
+# users call them in their reporting code, attributes because they
+# appear in the documented schema (README and notebook examples
 # enumerate ``rows``, ``headers``, ``footnotes``, etc.).
 # ----------------------------------------------------------------------
 EXPECTED_SOFRATABLE_METHODS = frozenset({
@@ -186,7 +186,7 @@ def test_sofratable_attribute_surface():
 def test_sofratable_no_undocumented_public_surface():
     """
     Reject silently-added public names. Anything new must be added to
-    one of the two expected-sets above (so reviewers see the API
+    one of the two expected-sets above (so downstream users see the API
     change in the diff).
     """
     public = {m for m in dir(SofraTable) if not m.startswith("_")}
@@ -200,6 +200,6 @@ def test_sofratable_no_undocumented_public_surface():
 
 
 def test_sofratable_to_image_signature_stable():
-    """The PNG renderer's public kwargs are part of the JSS API contract."""
+    """The PNG renderer's public kwargs are part of the documented public API."""
     actual = tuple(p[0] for p in _params(SofraTable.to_image))
     assert actual == ("self", "path", "scale", "dpi")

{pysofra-0.1.0a3 → pysofra-0.1.0a4}/tests/test_plot_determinism.py

@@ -1,6 +1,6 @@
 """Determinism tests for plot-embedded tables.
 
-The renderer-consistency suite (`test_joss_renderer_consistency.py`)
+The renderer-consistency suite (`test_renderer_consistency.py`)
 verifies determinism for plain text-only tables. This file extends
 that guarantee to tables that have an inline matplotlib plot
 (`with_forest_plot`, `with_km_plot`) — historically the source of

{pysofra-0.1.0a3 → pysofra-0.1.0a4}/tests/test_validation_fixes.py

@@ -16,7 +16,7 @@ import pysofra as ps
 
 
 # ======================================================================
-# BLOCKER #4 — add_difference uses Newcombe (Wilson-based) CI
+# add_difference uses Newcombe (Wilson-based) CI
 # ======================================================================
 class TestNewcombeDifferenceCI:
     def test_matches_statsmodels_newcomb(self):
@@ -75,7 +75,7 @@ class TestNewcombeDifferenceCI:
 
 
 # ======================================================================
-# BLOCKER #7 / HIGH #8 — Markdown spanners + escaping
+# Markdown spanners + escaping
 # ======================================================================
 class TestMarkdownSpannersAndEscape:
     def test_spanning_header_not_inserted_as_pipe_row(self):
@@ -137,7 +137,7 @@ class TestMarkdownSpannersAndEscape:
 
 
 # ======================================================================
-# HIGH #11 — labels= no longer breaks downstream modifiers
+# labels= no longer breaks downstream modifiers
 # ======================================================================
 class TestLabelsPreservedDownstream:
     def _df(self):
@@ -170,7 +170,7 @@ class TestLabelsPreservedDownstream:
 
 
 # ======================================================================
-# HIGH #13 — N at risk uses standard convention
+# N at risk uses standard convention
 # ======================================================================
 class TestNAtRisk:
     def test_n_at_risk_matches_manual_count(self):
@@ -195,7 +195,7 @@ class TestNAtRisk:
 
 
 # ======================================================================
-# HIGH #10 — add_global_p raises clearly on tbl_one
+# add_global_p raises clearly on tbl_one
 # ======================================================================
 class TestAddGlobalPOnTblOne:
     # ``add_global_p()`` is implemented for tbl_one / tbl_summary

{pysofra-0.1.0a3 → pysofra-0.1.0a4}/tests/test_wishlist.py

@@ -1,6 +1,6 @@
-"""Tests for the R-ecosystem wishlist features: tbl_cross, effect sizes,
+"""Tests for R-ecosystem feature parity: tbl_cross, effect sizes,
 add_significance_stars / add_n / add_stat_label / color_scale_if,
-MixedLM/GEE extractor, and MI pooling (Rubin's rules)."""
+MixedLM/GEE extractor, and multiple-imputation pooling (Rubin's rules)."""
 
 from __future__ import annotations
 

pysofra-0.1.0a3/src/pysofra/io/__init__.py

@@ -1 +0,0 @@
-"""I/O utilities — reserved for future readers (Stata/SAS/Excel)."""

pysofra-0.1.0a3/src/pysofra/notebook/__init__.py

@@ -1,6 +0,0 @@
-"""Notebook helpers.
-
-Most of the notebook integration lives on :class:`SofraTable._repr_html_`.
-This module is reserved for future notebook-specific extensions (e.g.
-ipywidgets-based controls).
-"""