Add Hypothesis property-based tests (#1038)

.gitignore

@@ -15,6 +15,7 @@
 coverage.xml
 htmlcov/
 .pytest_cache/
+.hypothesis/
 *.bai
 
 # Backup files from some Unix editors

cnvlib/descriptives.py

@@ -156,11 +156,11 @@ def weighted_median(a: ndarray, weights: ndarray) -> float64:
     cumulative_weight = weights.cumsum()
     midpoint_idx = cumulative_weight.searchsorted(midpoint)
     if (
-        midpoint_idx > 0
-        and cumulative_weight[midpoint_idx - 1] - midpoint < sys.float_info.epsilon
+        midpoint_idx < len(a) - 1
+        and abs(cumulative_weight[midpoint_idx] - midpoint) < sys.float_info.epsilon
     ):
-        # Midpoint of 2 array values
-        return a[midpoint_idx - 1 : midpoint_idx + 1].mean()  # type: ignore[no-any-return]
+        # Cumulative weight exactly at midpoint: average two adjacent values
+        return a[midpoint_idx : midpoint_idx + 2].mean()  # type: ignore[no-any-return]
     return a[midpoint_idx]  # type: ignore[no-any-return]
 
 

environment-dev.yml

@@ -24,6 +24,7 @@ dependencies:
   - pytest-cov
   - pytest-xdist
   - coverage
+  - hypothesis
   - ruff
   - safety
   - bandit

pyproject.toml

@@ -65,12 +65,15 @@ optional-dependencies = {test = {file = "requirements/tests.txt"}}
 testpaths = ["test"]
 markers = [
     "slow: tests that take >5 seconds (skip with -m 'not slow')",
+    "hypothesis: property-based tests using Hypothesis (skip with -m 'not hypothesis')",
 ]
 filterwarnings = [
     "error",
     # bioframe <=0.8.0 uses df.groupby(['col']).groups with a single-element
     # list, which pandas 3.0 deprecates via Pandas4Warning.
     "ignore:In a future version, the keys of:Warning",
+    # Hypothesis internal warnings that would otherwise be promoted to errors
+    "ignore::hypothesis.errors.NonInteractiveExampleWarning",
 ]
 
 [tool.coverage.run]

requirements/tests.txt

@@ -2,6 +2,7 @@ pytest
 pytest-cov
 pytest-xdist
 coverage[all]
+hypothesis[numpy]
 mypy
 ruff
 safety