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alchemistry · Jun 6, 2023 · 9cf90c7 · 9cf90c7
1 parent 89f855f
commit 9cf90c7
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Showing 3 changed files with 10 additions and 2 deletions.
diff --git a/CHANGES b/CHANGES
@@ -27,7 +27,11 @@ Enhancements
 
 Fixes
   - Fix the case where visualisation.plot_convergence would fail when the final
-   error is NaN (issue #318, PR#319).
+    error is NaN (issue #318, PR#319).
+
+DeprecationWarning
+  - The default MBAR error estimator will change from analytic to bootstrap
+    (issue #320, PR#322).
 
 
 06/04/2023 xiki-tempula

diff --git a/src/alchemlyb/tests/test_workflow_ABFE.py b/src/alchemlyb/tests/test_workflow_ABFE.py
@@ -242,7 +242,7 @@ def test_single_estimator_mbar(self, workflow, monkeypatch):
 
     def test_mbar_n_bootstraps(self, workflow, monkeypatch):
         monkeypatch.setattr(workflow, "estimator", dict())
-        workflow.estimate(estimators="MBAR", n_bootstraps=50)
+        workflow.estimate(estimators="MBAR", n_bootstraps=2)
         summary = workflow.generate_result()
         bootstrap_error = summary["MBAR_Error"]["Stages"]["TOTAL"]
         monkeypatch.setattr(workflow, "estimator", dict())

diff --git a/src/alchemlyb/workflows/abfe.py b/src/alchemlyb/workflows/abfe.py
@@ -439,6 +439,10 @@ def estimate(self, estimators=("MBAR", "BAR", "TI"), **kwargs):
         for estimator in estimators:
             if estimator == "MBAR":
                 logger.info("Run MBAR estimator.")
+                warnings.warn(
+                    "From 2.2.0, n_bootstraps=50 will be the default for estimating MBAR error.",
+                    DeprecationWarning,
+                )
                 self.estimator[estimator] = MBAR(**kwargs).fit(u_nk)
             elif estimator == "BAR":
                 logger.info("Run BAR estimator.")