Impr/fix refactor sfcf read (#164)

* refactor read_sfcf

* adding tests for find_corr and read_compact_file

* add necessary broken data for tests

* fixed appended mode reading

* factored out sort_names and find_files

* now also using sort_files in sfcf.py

* edited tests to fit with new structure

* added find_files function

* shifted helpfunctions to bottom of file

* removed some debug lines

* linting

* Fixed requested changes, added silent mode

* added Exception if correlator is not found by read_append_rep

* use tmp_path fixture

* linting silent keyword

* try to fix testing for a_bb

* tests: Exception testing in test_find_corr made more explicit.

---------

Co-authored-by: Fabian Joswig <fabian.joswig@ed.ac.uk>

pyerrors/input/utils.py

@@ -1,6 +1,51 @@
+import re
 """Utilities for the input"""
 
 
+def sort_names(ll):
+    """Sorts a list of names of replika with searches for `r` and `id` in the replikum string.
+    If this search fails, a fallback method is used,
+    where the strings are simply compared and the first diffeing numeral is used for differentiation.
+
+    Parameters
+    ----------
+    ll: list
+        list to sort
+
+    Returns
+    -------
+    ll: list
+        sorted list
+    """
+    if len(ll) > 1:
+        r_pattern = r'r(\d+)'
+        id_pattern = r'id(\d+)'
+
+        # sort list by id first
+        if all([re.search(id_pattern, entry) for entry in ll]):
+            ll.sort(key=lambda x: int(re.findall(id_pattern, x)[0]))
+        # then by replikum
+        if all([re.search(r_pattern, entry) for entry in ll]):
+            ll.sort(key=lambda x: int(re.findall(r_pattern, x)[0]))
+        # as the rearrangements by one key let the other key untouched, the list is sorted now
+
+        else:
+            # fallback
+            sames = ''
+            if len(ll) > 1:
+                for i in range(len(ll[0])):
+                    checking = ll[0][i]
+                    for rn in ll[1:]:
+                        is_same = (rn[i] == checking)
+                    if is_same:
+                        sames += checking
+                    else:
+                        break
+                print("Using prefix:", ll[0][len(sames):])
+            ll.sort(key=lambda x: int(re.findall(r'\d+', x[len(sames):])[0]))
+    return ll
+
+
 def check_idl(idl, che):
     """Checks if list of configurations is contained in an idl