fix prepare message for RFE

news/fix-setup-messages.rst

@@ -0,0 +1,25 @@
+**Added:**
+
+* <news item>
+
+**Changed:**
+
+* <news item>
+
+**Deprecated:**
+
+* <news item>
+
+**Removed:**
+
+* <news item>
+
+**Fixed:**
+
+* Fix erroneous logging information message which would mention
+  setting up the alchemical system when running simulation or
+  analysis units with the hybrid topology, AHFE or ABFE Protocols (PR #1915).
+
+**Security:**
+
+* <news item>

src/openfe/protocols/openmm_afe/base_afe_units.py

@@ -111,9 +111,6 @@ def _prepare(
         """
         self.verbose = verbose
 
-        if self.verbose:
-            self.logger.info("setting up alchemical system")  # type: ignore[attr-defined]
-
         # set basepaths
         def _set_optional_path(basepath):
             if basepath is None:
@@ -691,6 +688,9 @@ def run(
         # General preparation tasks
         self._prepare(verbose, scratch_basepath, shared_basepath)
 
+        if self.verbose:
+            self.logger.info("Starting system setup unit")
+
         # Get components
         alchem_comps, solv_comp, prot_comp, small_mols = self._get_components()
 
@@ -1396,6 +1396,9 @@ def run(
         # Prepare paths & verbosity
         self._prepare(verbose, scratch_basepath, shared_basepath)
 
+        if self.verbose:
+            self.logger.info("Starting simulation unit")
+
         # Get the settings
         settings = self._get_settings()
 
@@ -1635,6 +1638,9 @@ def run(
         # Prepare paths & verbosity
         self._prepare(verbose, scratch_basepath, shared_basepath)
 
+        if self.verbose:
+            self.logger.info("Starting simulation analysis unit")
+
         # Get the settings
         settings = self._get_settings()
 

src/openfe/protocols/openmm_rfe/hybridtop_units.py

@@ -102,9 +102,6 @@ def _prepare(
         """
         self.verbose = verbose
 
-        if self.verbose:
-            self.logger.info("Setting up the hybrid topology simulation")  # type: ignore[attr-defined]
-
         # set basepaths
         def _set_optional_path(basepath):
             if basepath is None:
@@ -736,6 +733,9 @@ def run(
         # Prepare paths & verbosity
         self._prepare(verbose, scratch_basepath, shared_basepath)
 
+        if self.verbose:
+            self.logger.info("Starting system setup unit")
+
         # Get settings
         settings = self._get_settings(self._inputs["protocol"].settings)
 
@@ -1303,6 +1303,9 @@ def run(
         # Prepare paths & verbosity
         self._prepare(verbose, scratch_basepath, shared_basepath)
 
+        if self.verbose:
+            self.logger.info("Starting simulation unit")
+
         # Get the settings
         settings = self._get_settings(self._inputs["protocol"].settings)
 
@@ -1604,6 +1607,9 @@ def run(
         # Prepare paths & verbosity
         self._prepare(verbose, scratch_basepath, shared_basepath)
 
+        if self.verbose:
+            self.logger.info("Starting simulation analysis unit")
+
         # Get the settings
         settings = self._get_settings(self._inputs["protocol"].settings)