From cf288824188a8d3c735095162da4d8e29845c677 Mon Sep 17 00:00:00 2001
From: Sebastian Kloth <sebastian.kloth@pkm.tu-darmstadt.de>
Date: Sun, 5 Nov 2023 19:39:02 +0100
Subject: [PATCH] Removed CachedReader

---
 src/mdevaluate/reader.py | 54 +++-------------------------------------
 1 file changed, 4 insertions(+), 50 deletions(-)

diff --git a/src/mdevaluate/reader.py b/src/mdevaluate/reader.py
index c97ec3d..7152fc1 100755
--- a/src/mdevaluate/reader.py
+++ b/src/mdevaluate/reader.py
@@ -32,18 +32,11 @@ class WrongTopologyError(Exception):
 
 
 def open_with_mdanalysis(
-    topology, trajectory, cached=False, index_file=None, charges=None, masses=None
+    topology, trajectory, index_file=None, charges=None, masses=None
 ):
     """Open the topology and trajectory with mdanalysis."""
     uni = mdanalysis.Universe(topology, trajectory, convert_units=False)
-    if cached is not False:
-        if cached is True:
-            maxsize = 128
-        else:
-            maxsize = cached
-        reader = CachedReader(uni.trajectory, maxsize)
-    else:
-        reader = BaseReader(uni.trajectory)
+    reader = BaseReader(uni.trajectory)
     reader.universe = uni
     if topology.endswith(".tpr"):
         charges = uni.atoms.charges
@@ -274,11 +267,6 @@ class BaseReader:
         self._nojump_matrixes = mats
 
     def __init__(self, rd):
-        """
-        Args:
-            filename: Trajectory file to open.
-            reindex (bool, opt.): If True, regenerate the index file if necessary.
-        """
         self.rd = rd
         self._nojump_matrixes = None
         if path.exists(nojump_load_filename(self)):
@@ -291,39 +279,5 @@ class BaseReader:
         return len(self.rd)
 
     def __checksum__(self):
-        if hasattr(self.rd, "cache"):
-            # Has an pygmx reader
-            return checksum(self.filename, str(self.rd.cache))
-        elif hasattr(self.rd, "_xdr"):
-            # Has an mdanalysis reader
-            cache = array("L", self.rd._xdr.offsets.tobytes())
-            return checksum(self.filename, str(cache))
-
-
-class CachedReader(BaseReader):
-    """A reader that has a least-recently-used cache for frames."""
-
-    @property
-    def cache_info(self):
-        """Get Information about the lru cache."""
-        return self._get_item.cache_info()
-
-    def clear_cache(self):
-        """Clear the cache of the frames."""
-        self._get_item.cache_clear()
-
-    def __init__(self, rd, maxsize):
-        """
-        Args:
-            filename (str): Trajectory file that will be opened.
-            maxsize: Maximum size of the lru_cache or None for infinite cache.
-        """
-        super().__init__(rd)
-        self._get_item = lru_cache(maxsize=maxsize)(self._get_item)
-
-    def _get_item(self, item):
-        """Buffer function for lru_cache, since __getitem__ can not be cached."""
-        return super().__getitem__(item)
-
-    def __getitem__(self, item):
-        return self._get_item(item)
+        cache = array("L", self.rd._xdr.offsets.tobytes())
+        return checksum(self.filename, str(cache))