Merge pull request #189 from cggh/zarr-upgrade-20180409

Zarr upgrade 2.2

allel/chunked/__init__.py

@@ -28,20 +28,17 @@
     >>> import numpy as np
     >>> a = np.arange(10000000)
     >>> chunked.copy(a)
-    Array((10000000,), int64, chunks=(39063,), order=C)
-      ...
+    <zarr.core.Array (10000000,) int64>
     >>> chunked.copy(a, storage='bcolzmem')
     carray((10000000,), int64)
       ...
     >>> chunked.copy(a, storage='bcolztmp')
     carray((10000000,), int64)
       ...
     >>> chunked.copy(a, storage='zarrmem')
-    Array((10000000,), int64, chunks=(39063,), order=C)
-      ...
+    <zarr.core.Array (10000000,) int64>
     >>> chunked.copy(a, storage='zarrtmp')
-    Array((10000000,), int64, chunks=(39063,), order=C)
-      ...
+    <zarr.core.Array (10000000,) int64>
     >>> chunked.copy(a, storage=chunked.BcolzStorage(cparams=bcolz.cparams(cname='lz4')))
     carray((10000000,), int64)
       ...

allel/chunked/core.py

@@ -27,11 +27,11 @@ def store(data, arr, start=0, stop=None, offset=0, blen=None):
         raise ValueError('invalid stop/start')
 
     # copy block-wise
-    for i in range(start, stop, blen):
-        j = min(i+blen, stop)
-        l = j-i
-        arr[offset:offset+l] = data[i:j]
-        offset += l
+    for bi in range(start, stop, blen):
+        bj = min(bi+blen, stop)
+        bl = bj - bi
+        arr[offset:offset+bl] = data[bi:bj]
+        offset += bl
 
 
 def copy(data, start=0, stop=None, blen=None, storage=None, create='array',
@@ -900,13 +900,13 @@ def ndim(self):
 
     @property
     def dtype(self):
-        l = []
+        items = []
         for n, c in zip(self._names, self._columns):
             # need to account for multidimensional columns
             t = (n, c.dtype) if len(c.shape) == 1 else \
                 (n, c.dtype, c.shape[1:])
-            l.append(t)
-        return np.dtype(l)
+            items.append(t)
+        return np.dtype(items)
 
     @property
     def nbytes(self):

allel/io/util.py

@@ -86,9 +86,9 @@ def recarray_from_hdf5_group(*args, **kwargs):
         h5f = h5py.File(file_path, mode='r')
         try:
             group = h5f[node_path]
-        except:
+        except Exception as e:
             h5f.close()
-            raise
+            raise e
 
     else:
         raise ValueError('bad arguments; expected group or (file_path, '

allel/model/chunked.py

@@ -792,15 +792,15 @@ class VariantChunkedTable(ChunkedTableWrapper):
 
         >>> vt.copy()  # doctest: +ELLIPSIS
         <VariantChunkedTable shape=(5,) dtype=[('CHROM', 'S4'), ('POS', '<i8'), ('AC', ...
-           nbytes=220 cbytes=1.7K cratio=0.1
+           nbytes=220 cbytes=... cratio=...
            values=allel.chunked.storage_zarr.ZarrTable>
         >>> vt.copy(storage='bcolzmem')  # doctest: +ELLIPSIS
         <VariantChunkedTable shape=(5,) dtype=[('CHROM', 'S4'), ('POS', '<i8'), ('AC', ...
-           nbytes=220 cbytes=80.0K cratio=0.0
+           nbytes=220 cbytes=... cratio=...
            values=bcolz.ctable.ctable>
         >>> vt.copy(storage='hdf5mem_zlib1')  # doctest: +ELLIPSIS
         <VariantChunkedTable shape=(5,) dtype=[('CHROM', 'S4'), ('POS', '<i8'), ('AC', ...
-           nbytes=220 cbytes=131 cratio=1.7
+           nbytes=220 cbytes=... cratio=...
            values=h5py._hl.files.File>
 
     """

allel/model/generic.py

@@ -163,10 +163,11 @@ def _check_condition_length(a, condition, axis):
     # because numpy allows condition to be shorter than the axis under selection,
     # however we've found this allows mistakes to creep through and so we'll be stricter here
     if axis is not None:
-        l = a.shape[axis]
+        expected_length = a.shape[axis]
         k = condition.shape[0]
-        if k != l:
-            raise ValueError('bad length of condition; expected %s, found %s' % (l, k))
+        if k != expected_length:
+            raise ValueError('bad length of condition; expected %s, found %s' %
+                             (expected_length, k))
 
 
 def compress_genotypes(g, condition, axis, wrap_axes, cls, compress, **kwargs):