Add support for clearing and disabling the file cache

python/BioSimSpace/IO/__init__.py

@@ -28,6 +28,9 @@
 .. autosummary::
     :toctree: generated/
 
+    clearCache
+    disableCache
+    enableCache
     fileFormats
     formatInfo
     readMolecules
@@ -38,3 +41,4 @@
 """
 
 from ._io import *
+from ._file_cache import *

python/BioSimSpace/IO/_file_cache.py

@@ -24,7 +24,7 @@
 __author__ = "Lester Hedges"
 __email__ = "[email protected]"
 
-__all__ = ["check_cache", "update_cache"]
+__all__ = ["clearCache", "disableCache", "enableCache"]
 
 import collections as _collections
 import hashlib as _hashlib
@@ -80,8 +80,43 @@ def __delitem__(self, key):
 # to the same format, allowing us to re-use the existing file.
 _cache = _FixedSizeOrderedDict()
 
+# Whether to use the cache.
+_use_cache = True
 
-def check_cache(
+
+def clearCache():
+    """
+    Clear the file cache.
+    """
+    global _cache
+    _cache = _FixedSizeOrderedDict()
+
+
+def disableCache():
+    """
+    Disable the file cache.
+    """
+    global _use_cache
+    _use_cache = False
+
+
+def enableCache():
+    """
+    Enable the file cache.
+    """
+    global _use_cache
+    _use_cache = True
+
+
+def _cache_active():
+    """
+    Internal helper function to check whether the cache is active.
+    """
+    global _use_cache
+    return _use_cache
+
+
+def _check_cache(
     system,
     format,
     filebase,
@@ -157,6 +192,8 @@ def check_cache(
     if not isinstance(skip_water, bool):
         raise TypeError("'skip_water' must be of type 'bool'.")
 
+    global _cache
+
     # Create the key.
     key = (
         system._sire_object.uid().toString(),
@@ -221,7 +258,7 @@ def check_cache(
         return ext
 
 
-def update_cache(
+def _update_cache(
     system,
     format,
     path,
@@ -284,6 +321,8 @@ def update_cache(
     if not isinstance(skip_water, bool):
         raise TypeError("'skip_water' must be of type 'bool'.")
 
+    global _cache
+
     # Convert to an absolute path.
     path = _os.path.abspath(path)
 

python/BioSimSpace/IO/_io.py

@@ -66,8 +66,9 @@
 from .._SireWrappers import System as _System
 from .. import _Utils
 
-from ._file_cache import check_cache as _check_cache
-from ._file_cache import update_cache as _update_cache
+from ._file_cache import _check_cache
+from ._file_cache import _update_cache
+from ._file_cache import _cache_active
 
 
 # Context manager for capturing stdout.
@@ -741,14 +742,17 @@ def saveMolecules(
     # Save the system using each file format.
     for format in formats:
         # Copy an existing file if it exists in the cache.
-        ext = _check_cache(
-            system,
-            format,
-            filebase,
-            match_water=match_water,
-            property_map=property_map,
-            **kwargs,
-        )
+        if _cache_active():
+            ext = _check_cache(
+                system,
+                format,
+                filebase,
+                match_water=match_water,
+                property_map=property_map,
+                **kwargs,
+            )
+        else:
+            ext = None
         if ext:
             files.append(_os.path.abspath(filebase + ext))
             continue
@@ -835,7 +839,10 @@ def saveMolecules(
             files += file
 
             # If this is a new file, then add it to the cache.
-            _update_cache(system, format, file[0], match_water=match_water, **kwargs)
+            if _cache_active():
+                _update_cache(
+                    system, format, file[0], match_water=match_water, **kwargs
+                )
 
         except Exception as e:
             msg = "Failed to save system to format: '%s'" % format

python/BioSimSpace/Sandpit/Exscientia/IO/__init__.py

@@ -28,6 +28,9 @@
 .. autosummary::
     :toctree: generated/
 
+    clearCache
+    disableCache
+    enableCache
     fileFormats
     formatInfo
     readMolecules
@@ -37,6 +40,5 @@
     savePerturbableSystem
 """
 
-from glob import glob
-
 from ._io import *
+from ._file_cache import *

python/BioSimSpace/Sandpit/Exscientia/IO/_file_cache.py

@@ -24,7 +24,7 @@
 __author__ = "Lester Hedges"
 __email__ = "[email protected]"
 
-__all__ = ["check_cache", "update_cache"]
+__all__ = ["clearCache", "disableCache", "enableCache"]
 
 import collections as _collections
 import hashlib as _hashlib
@@ -80,8 +80,43 @@ def __delitem__(self, key):
 # to the same format, allowing us to re-use the existing file.
 _cache = _FixedSizeOrderedDict()
 
+# Whether to use the cache.
+_use_cache = True
 
-def check_cache(
+
+def clearCache():
+    """
+    Clear the file cache.
+    """
+    global _cache
+    _cache = _FixedSizeOrderedDict()
+
+
+def disableCache():
+    """
+    Disable the file cache.
+    """
+    global _use_cache
+    _use_cache = False
+
+
+def enableCache():
+    """
+    Enable the file cache.
+    """
+    global _use_cache
+    _use_cache = True
+
+
+def _cache_active():
+    """
+    Internal helper function to check whether the cache is active.
+    """
+    global _use_cache
+    return _use_cache
+
+
+def _check_cache(
     system,
     format,
     filebase,
@@ -157,6 +192,8 @@ def check_cache(
     if not isinstance(skip_water, bool):
         raise TypeError("'skip_water' must be of type 'bool'.")
 
+    global _cache
+
     # Create the key.
     key = (
         system._sire_object.uid().toString(),
@@ -221,7 +258,7 @@ def check_cache(
         return ext
 
 
-def update_cache(
+def _update_cache(
     system,
     format,
     path,
@@ -284,6 +321,8 @@ def update_cache(
     if not isinstance(skip_water, bool):
         raise TypeError("'skip_water' must be of type 'bool'.")
 
+    global _cache
+
     # Convert to an absolute path.
     path = _os.path.abspath(path)
 

python/BioSimSpace/Sandpit/Exscientia/IO/_io.py

@@ -66,8 +66,9 @@
 from .._SireWrappers import System as _System
 from .. import _Utils
 
-from ._file_cache import check_cache as _check_cache
-from ._file_cache import update_cache as _update_cache
+from ._file_cache import _check_cache
+from ._file_cache import _update_cache
+from ._file_cache import _cache_active
 
 
 # Context manager for capturing stdout.
@@ -741,14 +742,17 @@ def saveMolecules(
     # Save the system using each file format.
     for format in formats:
         # Copy an existing file if it exists in the cache.
-        ext = _check_cache(
-            system,
-            format,
-            filebase,
-            match_water=match_water,
-            property_map=property_map,
-            **kwargs,
-        )
+        if _cache_active():
+            ext = _check_cache(
+                system,
+                format,
+                filebase,
+                match_water=match_water,
+                property_map=property_map,
+                **kwargs,
+            )
+        else:
+            ext = None
         if ext:
             files.append(_os.path.abspath(filebase + ext))
             continue
@@ -835,7 +839,10 @@ def saveMolecules(
             files += file
 
             # If this is a new file, then add it to the cache.
-            _update_cache(system, format, file[0], match_water=match_water, **kwargs)
+            if _cache_active():
+                _update_cache(
+                    system, format, file[0], match_water=match_water, **kwargs
+                )
 
         except Exception as e:
             msg = "Failed to save system to format: '%s'" % format
@@ -1162,7 +1169,7 @@ def readPerturbableSystem(top0, coords0, top1, coords1, property_map={}):
         prop = property_map.get("time", "time")
         time = system0._sire_object.property(prop)
         system0._sire_object.removeSharedProperty(prop)
-        system0._sire_object.setPropery(prop, time)
+        system0._sire_object.setProperty(prop, time)
     except:
         pass
 

tests/IO/test_file_cache.py

@@ -15,7 +15,7 @@ def test_file_cache():
     """
 
     # Clear the file cache.
-    BSS.IO._file_cache._cache = BSS.IO._file_cache._FixedSizeOrderedDict()
+    BSS.IO.clearCache()
 
     # Load the molecular system.
     s = BSS.IO.readMolecules(["tests/input/ala.crd", "tests/input/ala.top"])
@@ -82,6 +82,21 @@ def test_file_cache():
     # Make sure the number of atoms in the cache was decremented.
     assert BSS.IO._file_cache._cache._num_atoms == total_atoms - num_atoms
 
+    # Clear the file cache.
+    BSS.IO.clearCache()
+
+    # The cache should now be empty.
+    assert len(BSS.IO._file_cache._cache) == 0
+
+    # Disable the cache.
+    BSS.IO.disableCache()
+
+    # Write to PDB and GroTop format. The PDB from the cache should not be reused.
+    BSS.IO.saveMolecules(f"{tmp_path}/tmp5", s, ["pdb", "grotop"])
+
+    # The cache should still be empty.
+    assert len(BSS.IO._file_cache._cache) == 0
+
 
 @pytest.mark.skipif(
     has_amber is False or has_openff is False,
@@ -93,8 +108,11 @@ def test_file_cache_mol_nums():
     contain different MolNUms.
     """
 
+    # Enable the cache.
+    BSS.IO.enableCache()
+
     # Clear the file cache.
-    BSS.IO._file_cache._cache = BSS.IO._file_cache._FixedSizeOrderedDict()
+    BSS.IO.clearCache()
 
     # Create an initial system.
     system = BSS.Parameters.openff_unconstrained_2_0_0("CO").getMolecule().toSystem()

tests/Sandpit/Exscientia/IO/test_file_cache.py

@@ -16,7 +16,7 @@ def test_file_cache():
     """
 
     # Clear the file cache.
-    BSS.IO._file_cache._cache = BSS.IO._file_cache._FixedSizeOrderedDict()
+    BSS.IO.clearCache()
 
     # Load the molecular system.
     s = BSS.IO.readMolecules([f"{root_fp}/input/ala.crd", f"{root_fp}/input/ala.top"])
@@ -83,6 +83,21 @@ def test_file_cache():
     # Make sure the number of atoms in the cache was decremented.
     assert BSS.IO._file_cache._cache._num_atoms == total_atoms - num_atoms
 
+    # Clear the file cache.
+    BSS.IO.clearCache()
+
+    # The cache should now be empty.
+    assert len(BSS.IO._file_cache._cache) == 0
+
+    # Disable the cache.
+    BSS.IO.disableCache()
+
+    # Write to PDB and GroTop format. The PDB from the cache should not be reused.
+    BSS.IO.saveMolecules(f"{tmp_path}/tmp5", s, ["pdb", "grotop"])
+
+    # The cache should still be empty.
+    assert len(BSS.IO._file_cache._cache) == 0
+
 
 @pytest.mark.skipif(
     has_amber is False or has_openff is False,
@@ -94,8 +109,11 @@ def test_file_cache_mol_nums():
     contain different MolNUms.
     """
 
+    # Enable the cache.
+    BSS.IO.enableCache()
+
     # Clear the file cache.
-    BSS.IO._file_cache._cache = BSS.IO._file_cache._FixedSizeOrderedDict()
+    BSS.IO.clearCache()
 
     # Create an initial system.
     system = BSS.Parameters.openff_unconstrained_2_0_0("CO").getMolecule().toSystem()