Merge tag 'v0.20.2'

v0.20.2

allel/__init__.py

@@ -28,4 +28,4 @@
 except ImportError:
     pass
 
-__version__ = '0.20.1'
+__version__ = '0.20.2'

allel/util.py

@@ -1,7 +1,5 @@
 # -*- coding: utf-8 -*-
 from __future__ import absolute_import, print_function, division
-
-
 from contextlib import contextmanager
 from functools import update_wrapper
 import atexit
@@ -12,6 +10,9 @@
 from scipy.spatial.distance import squareform
 
 
+from allel.compat import string_types
+
+
 @contextmanager
 def ignore_invalid():
     err = np.seterr(invalid='ignore')
@@ -187,7 +188,7 @@ def _hdf5_cache_act(filepath, parent, container, key, names, no_cache,
                 # determine dataset name
                 if names is None:
                     n = 'data'
-                elif isinstance(names, str):
+                elif isinstance(names, string_types):
                     n = names
                 elif len(names) > 0:
                     n = names[0]
@@ -209,7 +210,13 @@ def _hdf5_cache_act(filepath, parent, container, key, names, no_cache,
         # load from cache
         else:
 
-            names = sorted(h5g.keys())
+            # determine dataset names
+            if names is None:
+                names = sorted(h5g.keys())
+            elif isinstance(names, string_types):
+                names = (names,)
+
+            # load result from cache
             if len(names) == 1:
                 result = h5g[names[0]]
                 result = result[:] if len(result.shape) > 0 else result[()]
@@ -222,7 +229,7 @@ def _hdf5_cache_act(filepath, parent, container, key, names, no_cache,
 
 
 def hdf5_cache(filepath=None, parent=None, group=None, names=None, typed=False,
-               hashed_key=True, **h5dcreate_kwargs):
+               hashed_key=False, **h5dcreate_kwargs):
     """HDF5 cache decorator.
 
     Parameters
@@ -244,8 +251,11 @@ def hdf5_cache(filepath=None, parent=None, group=None, names=None, typed=False,
         For example, f(3.0) and f(3) will be treated as distinct calls with
         distinct results.
     hashed_key : bool, optional
-        If False, the key will not be hashed, which makes for readable cache
-        group names, but may cause problems if key contains '/' characters.
+        If False (default) the key will not be hashed, which makes for
+        readable cache group names. If True the key will be hashed, however
+        note that on Python >= 3.3 the hash value will not be the same between
+        sessions unless the environment variable PYTHONHASHSEED has been set
+        to the same value.
 
     Returns
     -------
@@ -284,6 +294,20 @@ def hdf5_cache(filepath=None, parent=None, group=None, names=None, typed=False,
         >>> bar(3)
         (array([0, 1, 2]), array([0, 1, 4]), 9)
 
+    Names can also be specified for the datasets, e.g.::
+
+        >>> @allel.util.hdf5_cache(names=['z', 'x', 'y'])
+        ... def baz(n):
+        ...     print('executing baz')
+        ...     a = np.arange(n)
+        ...     return a, a**2, n**2
+        ...
+        >>> baz(3)
+        executing baz
+        (array([0, 1, 2]), array([0, 1, 4]), 9)
+        >>> baz(3)
+        (array([0, 1, 2]), array([0, 1, 4]), 9)
+
     """
 
     # initialise HDF5 file path
@@ -313,7 +337,7 @@ def wrapper(*args, **kwargs):
             if hashed_key:
                 key = str(hash(key))
             else:
-                key = str(key)
+                key = str(key).replace('/', '__slash__')
 
             return _hdf5_cache_act(filepath, parent, container, key, names,
                                    no_cache, user_function, args, kwargs,

docs/release.rst

@@ -1,6 +1,14 @@
 Release notes
 =============
 
+v0.20.2
+-------
+
+* Changed :func:`allel.util.hdf5_cache` to resolve issues with hashing and
+  argument order
+  (`#51 <https://github.com/cggh/scikit-allel/issues/51>`_,
+  `#52 <https://github.com/cggh/scikit-allel/issues/52>`_).
+
 v0.20.1
 -------