Merge pull request #31 from BranniganLab/decorr

Add back decorrelation

safep/processing.py

@@ -133,19 +133,17 @@ def read_and_process(fepoutFiles, temperature, decorrelate, detectEQ):
     """
     Read NAMD fepout files for a single calculation and carry out any decorrelation or equilibrium detection
     Arguments: files to parse, temperature, decorrelate (boolean, whether or not to use alchemlyb's decorrelation functions), detectEQ (boolean, whether or not to use alchemlyb's equilibrium detection)
-    Returns: u_nk, affix (a string that describes the data processing)
+    Returns: u_nk
     """
     fepoutFiles = natsorted(fepoutFiles)
     u_nk = namd.extract_u_nk(fepoutFiles, temperature)
 
-    affix = ""
-
     if detectEQ:
-        print("Detecting Equilibrium")
-        affix = f"{affix}_AutoEquilibrium"
+        print("Detecting Equilibrium (includes decorrelating)")
         u_nk = detect_equilibrium_u_nk(u_nk)
-    else:
-        affix = f"{affix}_HardEquilibrium"
+    elif decorrelate:
+        print(f"Decorrelating samples")
+        u_nk = decorrelate_u_nk(u_nk)
 
     return u_nk