Merge pull request #51 from quantifyearth/mwd-misc-fixes-again

Misc fixes again

Author: mdales

CHANGES.md

@@ -1,3 +1,13 @@
+## v2.1.1 (18/03/2026)
+
+### Changed
+
+* For model validation results return all species, not just the ones marked as outliers.
+
+### Fixed
+
+* Remove Yirgacheffe chunk size override that was being inherited globally rather than just for aohcalc.
+
 ## v2.1.0 (09/03/2026)
 
 ### Changed

aoh/_internal/aoh_fractional.py

@@ -11,8 +11,6 @@
 
 logger = logging.getLogger(__name__)
 
-yg.constants.YSTEP = 2048
-
 def aohcalc_fractional(
     habitats_directory_path: Path | str,
     elevation_path: Path | str | tuple[Path,Path] | tuple[str,str],

aoh/validation/validate_map_prevalence.py

@@ -133,7 +133,7 @@ def model_validation(aoh_df: pd.DataFrame) -> tuple[pd.DataFrame, pd.DataFrame,
         raise ValueError("No species classes were found")
 
     # Fit models for each class
-    per_class_outliers_df = []
+    per_class_results_df = []
     per_class_model_coefficients = []
     per_class_random_effects = []
 
@@ -159,7 +159,7 @@ def model_validation(aoh_df: pd.DataFrame) -> tuple[pd.DataFrame, pd.DataFrame,
         klass_df = add_diagnostic_columns(klass_df, upper_fence, lower_fence)
         klass_outliers = klass_df[klass_df.outlier == True]  # pylint: disable = C0121
         print(f"\toutliers: {len(klass_outliers)}")
-        per_class_outliers_df.append(klass_outliers)
+        per_class_results_df.append(klass_df)
 
         coef_df = extract_model_coefficients(model, klass)
         per_class_model_coefficients.append(coef_df)
@@ -168,7 +168,7 @@ def model_validation(aoh_df: pd.DataFrame) -> tuple[pd.DataFrame, pd.DataFrame,
         per_class_random_effects.append(ranef_df)
 
     # Concatenate results
-    outliers_df = pd.concat(per_class_outliers_df)  # type: ignore[arg-type]
+    outliers_df = pd.concat(per_class_results_df)  # type: ignore[arg-type]
     model_coefficients_df = pd.concat(per_class_model_coefficients)  # type: ignore[arg-type]
     random_effects_df = pd.concat(per_class_random_effects)  # type: ignore[arg-type]
 

pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "aoh"
-version = "2.1.0"
+version = "2.1.1"
 description = "A library for calculating Area of Habitat for species distribution mapping"
 authors = [
     {name = "Michael Dales", email = "mwd24@cam.ac.uk"}