Updated from_items() function due to pandas deprecation (#228)

* updated io/vcf_read.py and stats/misc.py for pandas deprecation. changed all occurences of pandas.DataFrame.from_items(items) to pandas.DataFrame.from_dict(OrderedDict(items))

* add missing import

* release notes [ci skip]

allel/io/vcf_read.py

@@ -15,6 +15,7 @@
 import time
 import subprocess
 import textwrap
+from collections import OrderedDict
 
 
 import numpy as np
@@ -1771,7 +1772,7 @@ def _chunk_to_dataframe(fields, chunk):
                 items.append(('%s_%s' % (name, i + 1), a[:, i]))
         else:
             warnings.warn('cannot handle array %r with >2 dimensions, skipping' % name)
-    df = pandas.DataFrame.from_items(items)
+    df = pandas.DataFrame.from_dict(OrderedDict(items))
     # treat empty string as missing
     df.replace('', np.nan, inplace=True)
     return df

allel/stats/misc.py

@@ -1,5 +1,6 @@
 # -*- coding: utf-8 -*-
 from __future__ import absolute_import, print_function, division
+from collections import OrderedDict
 
 
 import numpy as np
@@ -244,8 +245,7 @@ def tabulate_state_transitions(x, states, pos=None):
                   ('rpos', switch_positions[:, 1])]
 
     import pandas
-    return pandas.DataFrame.from_items(items)
-
+    return pandas.DataFrame.from_dict(OrderedDict(items))
 
 def tabulate_state_blocks(x, states, pos=None):
     """Construct a dataframe where each row provides information about continuous state blocks.
@@ -345,4 +345,4 @@ def tabulate_state_blocks(x, states, pos=None):
         ]
 
     import pandas
-    return pandas.DataFrame.from_items(items)
+    return pandas.DataFrame.from_dict(OrderedDict(items))

docs/release.rst

@@ -12,6 +12,9 @@ v1.2.0 (work in progress)
 * Added a convenience function :func:`allel.read_vcf_headers`, to obtain just
   header information from a VCF file.
 
+* Fixed pandas deprecation warning (`Summer Rae <https://github.com/summerela>`_,
+  `#228 <https://github.com/cggh/scikit-allel/pull/228>`_).
+
 * Various documentation improvements (`Peter Ralph
   <https://github.com/petrelharp>`_ and `CJ Battey
   <https://github.com/cjbattey>`_, `#229