Merge pull request #270 from alimanfoo/upgrade_deps_20190614

Upgrade requirements 20190614

.travis.yml

@@ -9,7 +9,6 @@ sudo: true
 dist: xenial
 
 python:
-  - "3.5"
   - "3.6"
   - "3.7"
 

allel/model/dask.py

@@ -97,6 +97,40 @@ def da_subset(d, sel0, sel1):
     return out
 
 
+def da_compress(condition, a, axis=None):
+    """Temporary workaround for https://github.com/dask/dask/issues/4940"""
+    from dask.array.core import asarray
+    from dask.array.utils import validate_axis
+    from dask.utils import is_arraylike
+
+    if not is_arraylike(condition):
+        # Allow `condition` to be anything array-like, otherwise ensure `condition`
+        # is a dask array.
+        condition = asarray(condition)
+    condition = condition.astype(bool)
+    a = asarray(a)
+
+    if condition.ndim != 1:
+        raise ValueError("Condition must be one dimensional")
+
+    if axis is None:
+        a = a.ravel()
+        axis = 0
+    axis = validate_axis(axis, a.ndim)
+
+    # Treat `condition` as filled with `False` (if it is too short)
+    a = a[tuple(slice(None, len(condition))
+                if i == axis else slice(None)
+                for i in range(a.ndim))]
+
+    # Use `condition` to select along 1 dimension
+    a = a[tuple(condition
+                if i == axis else slice(None)
+                for i in range(a.ndim))]
+
+    return a
+
+
 class DaskArrayWrapper(ArrayWrapper):
 
     def __init__(self, data, chunks=None, name=None, lock=False):
@@ -287,7 +321,7 @@ def compress(self, condition, axis=0, out=None):
             # argument is only there for numpy API compatibility
             raise NotImplementedError('out argument is not supported')
         return compress_genotypes(self, condition, axis=axis, wrap_axes={0},
-                                  cls=type(self), compress=da.compress)
+                                  cls=type(self), compress=da_compress)
 
     def take(self, indices, axis=0, out=None, mode='raise'):
         if out is not None:
@@ -465,7 +499,7 @@ def compress(self, condition, axis=0, out=None):
             # argument is only there for numpy API compatibility
             raise NotImplementedError('out argument is not supported')
         return compress_genotypes(self, condition, axis=axis, wrap_axes={0, 1},
-                                  cls=type(self), compress=da.compress)
+                                  cls=type(self), compress=da_compress)
 
     def take(self, indices, axis=0, out=None, mode='raise'):
         if out is not None:
@@ -635,7 +669,7 @@ def compress(self, condition, axis=0, out=None):
             # argument is only there for numpy API compatibility
             raise NotImplementedError('out argument is not supported')
         return compress_haplotype_array(self, condition, axis=axis, cls=type(self),
-                                        compress=da.compress)
+                                        compress=da_compress)
 
     def take(self, indices, axis=0, out=None, mode='raise'):
         if out is not None:
@@ -794,7 +828,7 @@ def compress(self, condition, axis=0, out=None):
             # argument is only there for numpy API compatibility
             raise NotImplementedError('out argument is not supported')
         return compress_allele_counts_array(self, condition, axis=axis, cls=type(self),
-                                            compress=da.compress)
+                                            compress=da_compress)
 
     def take(self, indices, axis=0, out=None, mode='raise'):
         if out is not None:
@@ -906,7 +940,7 @@ def compress(self, condition, axis=0, out=None):
             # argument is only there for numpy API compatibility
             raise NotImplementedError('out argument is not supported')
         return compress_genotype_ac(self, condition, axis=axis, wrap_axes={0},
-                                    cls=type(self), compress=da.compress)
+                                    cls=type(self), compress=da_compress)
 
     def take(self, indices, axis=0, out=None, mode='raise'):
         if out is not None:
@@ -989,7 +1023,7 @@ def compress(self, condition, axis=0, out=None):
             # argument is only there for numpy API compatibility
             raise NotImplementedError('out argument is not supported')
         return compress_genotype_ac(self, condition=condition, axis=axis, wrap_axes={0, 1},
-                                    cls=type(self), compress=da.compress)
+                                    cls=type(self), compress=da_compress)
 
     def take(self, indices, axis=0, out=None, mode='raise'):
         if out is not None:

allel/model/ndarray.py

@@ -4463,7 +4463,7 @@ class VariantTable(NumpyRecArrayWrapper):
     Access multiple columns::
 
         >>> vt[['DP', 'QD']]
-        <VariantTable shape=(5,) dtype=(numpy.record, [('DP', '<i8'), ('QD', '<f8')])>
+        <VariantTable shape=(5,) dtype=(numpy.record, {'names':['DP','QD'], ...
         [(35, 4.5) (12, 6.7) (78, 1.2) (22, 4.4) (99, 2.8)]
 
     Access a row::