Fix per stage ABFE BAR_Error by using correct loop var

AUTHORS

@@ -62,3 +62,6 @@ Chronological list of authors
 
 2025
   - Yuxuan Zhuang (@yuxuanzhuang)
+
+2026
+  - Jonathan Berg (@jberg5)

CHANGES

@@ -13,11 +13,12 @@ The rules for this file:
   * release numbers follow "Semantic Versioning" https://semver.org
 
 
-??/??/2026 jaclark5, jhenin, xiki-tempula
+??/??/2026 jaclark5, jhenin, xiki-tempula, jberg5
 
   * 2.6.0
 
 Fixes
+  - Correct BAR per-stage uncertainty in ABFE.generate_result (Issue #455)
   - Fix pandas warning (Issue #428, PR #429)
 
 Enhancements

CITATION.cff

@@ -110,6 +110,9 @@ authors:
     family-names: Clark
     orcid: https://orcid.org/0000-0003-4897-5651
     affiliation: National Institute of Standards and Technology
+  - given-names: Jonathan
+    family-names: Berg
+    orcid: 'https://orcid.org/0009-0007-4451-2824'
 identifiers:
   - type: swh
     value: 'swh:1:dir:4cd266754be413312ee7ef3f1f7fbe05b38192cf'

src/alchemlyb/tests/test_workflow_ABFE.py

@@ -231,6 +231,17 @@ def test_summary(self, workflow):
         assert np.isclose(summary["TI"]["Stages"]["TOTAL"], 21.8, 0.1)
         assert np.isclose(summary["BAR"]["Stages"]["TOTAL"], 21.8, 0.1)
 
+    def test_summary_bar_stage_errors_quadrature_sum_to_total_error(self, workflow):
+        """
+        For this ABFE fixture the stages (coul, vdw, bonded) partition all
+        adjacent-state transitions, so the quadrature sum of stage errors
+        must equal the TOTAL error.
+        """
+        summary = workflow.generate_result()
+        stage_errors = summary["BAR_Error"]["Stages"].drop("TOTAL").to_numpy()
+        total_error = summary["BAR_Error"]["Stages"]["TOTAL"]
+        assert np.isclose(np.sqrt((stage_errors**2).sum()), total_error)
+
     def test_no_name_estimate(self, workflow):
         with pytest.raises(ValueError):
             workflow.estimate("aaa")

src/alchemlyb/workflows/abfe.py

@@ -547,9 +547,9 @@ def generate_result(self) -> pd.DataFrame:
                        26 -- 27   1.243745    0.011239   1.245873   0.015711   1.248959  0.015762
                        27 -- 28   1.128429    0.012859   1.124554   0.016999   1.121892  0.016962
                        28 -- 29   1.010313    0.016442   1.005444   0.017692   1.019747  0.017257
-                Stages coul      10.215658    0.033903  10.017838   0.041839  10.017854  0.048744
-                       vdw       22.547489    0.098699  22.501150   0.060092  22.542936  0.106723
-                       bonded     2.374144    0.014995   2.341631   0.005507   2.363828  0.021078
+                Stages coul      10.215658    0.033903  10.017838   0.037086  10.017854  0.048744
+                       vdw       22.547489    0.098699  22.501150   0.077284  22.542936  0.106723
+                       bonded     2.374144    0.014995   2.341631   0.014988   2.363828  0.021078
                        TOTAL     35.137291    0.103580  34.860619   0.087022  34.924618  0.119206
 
         Attributes
@@ -632,8 +632,8 @@ def generate_result(self) -> pd.DataFrame:
                     error = np.sqrt(
                         sum(
                             [
-                                d_delta_f_.iloc[start, start + 1] ** 2  # type: ignore[operator,union-attr,misc]
-                                for i in range(start, end + 1)
+                                d_delta_f_.iloc[i, i + 1] ** 2  # type: ignore[operator,union-attr,misc]
+                                for i in range(start, end)
                             ]
                         )
                     )