tablassert 7.4.13__tar.gz → 7.4.14__tar.gz

{tablassert-7.4.13 → tablassert-7.4.14}/CHANGELOG.md

@@ -2,6 +2,12 @@
 
 All notable changes to this project are documented in this file.
 
+## 7.4.14 - 2026-06-30
+
+### Changes
+- Extended `sig()` in `lib.py` to select a p-value column by fuzzy matching rather than requiring an exact `"p value"` name. All schema columns whose names contain the substring `"p value"` are now considered candidates; `fuzz.ratio` (rapidfuzz) scores each against the literal `"p value"` and the highest-scoring column is used to compute the `"significant"` output. An exact `"p value"` column scores 100 and is always preferred; columns like `"adjusted p value"` or `"log p value"` are used only when no exact match is present. If no column contains the substring the function continues to emit `"UNSURE"` for all rows.
+- Added five regression tests in `test_lib.py` covering: exact-match preference, non-exact fallback, closest-match selection among multiple non-exact candidates, no-p-value column (UNSURE), and null value handling.
+
 ## 7.4.13 - 2026-06-30
 
 ### Changes

{tablassert-7.4.13 → tablassert-7.4.14}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: tablassert
-Version: 7.4.13
+Version: 7.4.14
 Summary: Extract knowledge assertions from tabular data into NCATS Translator-compliant KGX NDJSON — declaratively, with entity resolution and quality control built in.
 Project-URL: Homepage, https://github.com/SkyeAv/Tablassert
 Project-URL: Source, https://github.com/SkyeAv/Tablassert

{tablassert-7.4.13 → tablassert-7.4.14}/docs/changelog.md

@@ -4,6 +4,13 @@ The canonical release history lives in the repository root at [`CHANGELOG.md`](h
 
 ## Current Release Notes
 
+## 7.4.14 - 2026-06-30
+
+### Changes
+
+- Extended `sig()` in `lib.py` to select a p-value column by fuzzy matching rather than requiring an exact `"p value"` name. All schema columns whose names contain the substring `"p value"` are now considered candidates; `fuzz.ratio` (rapidfuzz) scores each against the literal `"p value"` and the highest-scoring column is used to compute the `"significant"` output. An exact `"p value"` column scores 100 and is always preferred; columns like `"adjusted p value"` or `"log p value"` are used only when no exact match is present. If no column contains the substring the function continues to emit `"UNSURE"` for all rows.
+- Added five regression tests in `test_lib.py` covering: exact-match preference, non-exact fallback, closest-match selection among multiple non-exact candidates, no-p-value column (UNSURE), and null value handling.
+
 ## 7.4.13 - 2026-06-30
 
 ### Changes

{tablassert-7.4.13 → tablassert-7.4.14}/pyproject.toml

@@ -1,6 +1,6 @@
 [project]
 name = "tablassert"
-version = "7.4.13"
+version = "7.4.14"
 description = "Extract knowledge assertions from tabular data into NCATS Translator-compliant KGX NDJSON — declaratively, with entity resolution and quality control built in."
 authors = [
     { name = "Skye Lane Goetz", email = "sgoetz@isbscience.org" }
@@ -90,11 +90,11 @@ qc-cuda = [
 
 [dependency-groups]
 dev = [
-    "grayskull>=3.1.0",
     "mkdocs>=1.6.1",
     "pre-commit>=4.5.1",
     "pyright>=1.1.408",
     "pytest>=9.0.2",
+    "pytest-cov>=7.1.0",
     "ruff>=0.15.6",
 ]
 

{tablassert-7.4.13 → tablassert-7.4.14}/src/tablassert/lib.py

@@ -101,14 +101,18 @@ def sig(
     out: str = "significant",
 ) -> pl.LazyFrame:
     # ? Creates The "significant" Column
-    if col in lf.collect_schema().names():
-        expr: pl.Expr = pl.col(col).cast(pl.Float64, strict=False)
+    from rapidfuzz import fuzz
+
+    names: list[str] = lf.collect_schema().names()
+    candidates: list[str] = [c for c in names if col in c]
+    chosen: Optional[str] = max(candidates, key=lambda c: fuzz.ratio(c, col)) if candidates else None
+    if chosen is not None:
+        expr: pl.Expr = pl.col(chosen).cast(pl.Float64, strict=False)
         cond: pl.Expr = le(expr, cutoff)
         cutoff: pl.Expr = (
             pl.when(expr.is_null()).then(pl.lit("UNSURE")).when(cond).then(pl.lit("YES")).otherwise(pl.lit("NO"))
         )
         return lf.with_columns(cutoff.alias(out))
-
     else:
         return lf.with_columns(pl.lit("UNSURE").alias(out))
 

{tablassert-7.4.13 → tablassert-7.4.14}/tests/test_lib.py

@@ -267,3 +267,39 @@ def test_resolve_many_runs_qc(monkeypatch: Any, tmp_path: Path) -> None:
 
     assert result == [{"subject": "brca1", "original subject": "BRCA1", "subject two": "brca1", "passed": "YES"}]
     assert ("qc", "subject", "", "", "passed", True, None) in calls
+
+
+# ? sig Uses Exact "p value" Column When Present Alongside Other P-Value Columns
+def test_sig_prefers_exact_p_value_column() -> None:
+    lf: pl.LazyFrame = pl.DataFrame({"p value": [0.01, 0.1], "adjusted p value": [0.5, 0.5]}).lazy()
+    result: pl.DataFrame = lib.sig(lf).collect()
+    assert list(result["significant"]) == ["YES", "NO"]
+
+
+# ? sig Falls Back To Non-Exact P-Value Column When No Exact Match
+def test_sig_uses_non_exact_p_value_column() -> None:
+    lf: pl.LazyFrame = pl.DataFrame({"adjusted p value": [0.01, 0.1]}).lazy()
+    result: pl.DataFrame = lib.sig(lf).collect()
+    assert list(result["significant"]) == ["YES", "NO"]
+
+
+# ? sig Picks Closest Match When Multiple Non-Exact Columns Present
+def test_sig_picks_closest_non_exact_match() -> None:
+    lf: pl.LazyFrame = pl.DataFrame({"log p value": [0.01], "adjusted p value corrected": [0.5]}).lazy()
+    result: pl.DataFrame = lib.sig(lf).collect()
+    # "log p value" has higher fuzz.ratio to "p value" than "adjusted p value corrected"
+    assert list(result["significant"]) == ["YES"]
+
+
+# ? sig Returns UNSURE When No P-Value Column Exists
+def test_sig_returns_unsure_with_no_p_value_column() -> None:
+    lf: pl.LazyFrame = pl.DataFrame({"gene": ["BRCA1"]}).lazy()
+    result: pl.DataFrame = lib.sig(lf).collect()
+    assert list(result["significant"]) == ["UNSURE"]
+
+
+# ? sig Marks Null P-Values As UNSURE
+def test_sig_marks_null_as_unsure() -> None:
+    lf: pl.LazyFrame = pl.DataFrame({"p value": [None, 0.01, 0.1]}).lazy()
+    result: pl.DataFrame = lib.sig(lf).collect()
+    assert list(result["significant"]) == ["UNSURE", "YES", "NO"]

{tablassert-7.4.13 → tablassert-7.4.14}/uv.lock

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