From f56151ccdca3dbb96a6c84b1e0a2b8976b0983d2 Mon Sep 17 00:00:00 2001
From: Fabian Joswig <fabian.joswig@ed.ac.uk>
Date: Mon, 1 Nov 2021 17:27:48 +0000
Subject: [PATCH] adjusted input routines for sfcf and openQCD

---
 pyerrors/input/openQCD.py | 10 +++++++++-
 pyerrors/input/sfcf.py    | 22 +++++++++++++++++++---
 2 files changed, 28 insertions(+), 4 deletions(-)

diff --git a/pyerrors/input/openQCD.py b/pyerrors/input/openQCD.py
index 39135510..9aaf30be 100644
--- a/pyerrors/input/openQCD.py
+++ b/pyerrors/input/openQCD.py
@@ -65,6 +65,14 @@ def read_rwms(path, prefix, version='2.0', names=None, **kwargs):
 
     print('Read reweighting factors from', prefix[:-1], ',', replica, 'replica', end='')
 
+    # Adjust replica names to new bookmarking system
+    if names is None:
+        rep_names = []
+        for entry in ls:
+            truncated_entry = entry.split('.')[0]
+            idx = truncated_entry.index('r')
+            rep_names.append(truncated_entry[:idx] + '|' + truncated_entry[idx:])
+
     print_err = 0
     if 'print_err' in kwargs:
         print_err = 1
@@ -149,7 +157,7 @@ def read_rwms(path, prefix, version='2.0', names=None, **kwargs):
     result = []
     for t in range(nrw):
         if names is None:
-            result.append(Obs(deltas[t], [w.split(".")[0] for w in ls]))
+            result.append(Obs(deltas[t], rep_names))
         else:
             print(names)
             result.append(Obs(deltas[t], names))
diff --git a/pyerrors/input/sfcf.py b/pyerrors/input/sfcf.py
index 7dd3544e..2513b7f7 100644
--- a/pyerrors/input/sfcf.py
+++ b/pyerrors/input/sfcf.py
@@ -56,7 +56,12 @@ def read_sfcf(path, prefix, name, **kwargs):
         if len(new_names) != replica:
             raise Exception('Names does not have the required length', replica)
     else:
-        new_names = ls
+        # Adjust replica names to new bookmarking system
+        new_names = []
+        for entry in ls:
+            idx = entry.index('r')
+            new_names.append(entry[:idx] + '|' + entry[idx:])
+
     print(replica, 'replica')
     for i, item in enumerate(ls):
         print(item)
@@ -153,7 +158,12 @@ def read_sfcf_c(path, prefix, name, quarks='.*', noffset=0, wf=0, wf2=0, **kwarg
         if len(new_names) != replica:
             raise Exception('Names does not have the required length', replica)
     else:
-        new_names = ls
+        # Adjust replica names to new bookmarking system
+        new_names = []
+        for entry in ls:
+            idx = entry.index('r')
+            new_names.append(entry[:idx] + '|' + entry[idx:])
+
     print('Read', part, 'part of', name, 'from', prefix[:-1], ',', replica, 'replica')
     for i, item in enumerate(ls):
         sub_ls = []
@@ -271,6 +281,12 @@ def read_qtop(path, prefix, **kwargs):
 
         deltas.append(np.array(tmp))
 
-    result = Obs(deltas, [(w.split('.'))[0] for w in ls])
+    rep_names = []
+    for entry in ls:
+        truncated_entry = entry.split('.')[0]
+        idx = truncated_entry.index('r')
+        rep_names.append(truncated_entry[:idx] + '|' + truncated_entry[idx:])
+
+    result = Obs(deltas, rep_names)
 
     return result