add VLenNDArray

fixture/vlen-ndarray/codec.00/config.json

@@ -0,0 +1,4 @@
+{
+    "dtype": "|i1",
+    "id": "vlen-ndarray"
+}

fixture/vlen-ndarray/codec.01/config.json

@@ -0,0 +1,4 @@
+{
+    "dtype": "<i2",
+    "id": "vlen-ndarray"
+}

fixture/vlen-ndarray/codec.02/config.json

@@ -0,0 +1,4 @@
+{
+    "dtype": "<i4",
+    "id": "vlen-ndarray"
+}

fixture/vlen-ndarray/codec.03/config.json

@@ -0,0 +1,4 @@
+{
+    "dtype": "<i8",
+    "id": "vlen-ndarray"
+}

fixture/vlen-ndarray/codec.04/config.json

@@ -0,0 +1,4 @@
+{
+    "dtype": "|u1",
+    "id": "vlen-ndarray"
+}

fixture/vlen-ndarray/codec.05/config.json

@@ -0,0 +1,4 @@
+{
+    "dtype": "<u2",
+    "id": "vlen-ndarray"
+}

fixture/vlen-ndarray/codec.06/config.json

@@ -0,0 +1,4 @@
+{
+    "dtype": "<u4",
+    "id": "vlen-ndarray"
+}

fixture/vlen-ndarray/codec.07/config.json

@@ -0,0 +1,4 @@
+{
+    "dtype": "<u8",
+    "id": "vlen-ndarray"
+}

numcodecs/__init__.py

@@ -114,3 +114,10 @@
     register_codec(VLenArray)
 except ImportError:  # pragma: no cover
     pass
+
+try:
+    from numcodecs import vlen_nd
+    from numcodecs.vlen_nd import VLenNDArray
+    register_codec(VLenNDArray)
+except ImportError:  # pragma: no cover
+    pass

numcodecs/tests/test_vlen_ndarray.py

@@ -0,0 +1,105 @@
+# -*- coding: utf-8 -*-
+from __future__ import absolute_import, print_function, division
+import unittest
+
+
+import numpy as np
+import pytest
+
+
+from numcodecs.compat import PY2
+try:
+    from numcodecs.vlen_nd import VLenNDArray
+except ImportError:  # pragma: no cover
+    raise unittest.SkipTest("vlen-ndarray not available")
+from numcodecs.tests.common import (check_config, check_repr,
+                                    check_encode_decode_array,
+                                    check_backwards_compatibility,
+                                    assert_array_items_equal)
+
+
+arrays = [
+    np.array([np.array([1, 2, 3]),
+              np.array([[4]]),
+              np.array([[5, 6], [7, 8]])] * 300, dtype=object),
+    np.array([np.array([1, 2, 3]),
+              np.array([[4]]),
+              np.array([[5, 6], [7, 8]])] * 300, dtype=object).reshape(90, 10),
+]
+
+
+codecs = [
+    VLenNDArray('<i1'),
+    VLenNDArray('<i2'),
+    VLenNDArray('<i4'),
+    VLenNDArray('<i8'),
+    VLenNDArray('<u1'),
+    VLenNDArray('<u2'),
+    VLenNDArray('<u4'),
+    VLenNDArray('<u8'),
+]
+
+
+def test_encode_decode():
+    for arr in arrays:
+        for codec in codecs:
+            check_encode_decode_array(arr, codec)
+
+
+def test_config():
+    codec = VLenNDArray('<i8')
+    check_config(codec)
+
+
+def test_repr():
+    check_repr("VLenNDArray(dtype='<i8')")
+
+
+def test_backwards_compatibility():
+    check_backwards_compatibility(VLenNDArray.codec_id, arrays, codecs)
+
+
+def test_encode_errors():
+    codec = VLenNDArray('<i8')
+    with pytest.raises(ValueError):
+        codec.encode('foo')
+    with pytest.raises(ValueError):
+        codec.encode(['foo', 'bar'])
+
+
+def test_decode_errors():
+    codec = VLenNDArray('<i8')
+    with pytest.raises(TypeError):
+        codec.decode(1234)
+    # these should look like corrupt data
+    with pytest.raises(ValueError):
+        codec.decode(b'foo')
+    with pytest.raises(ValueError):
+        codec.decode(np.arange(2, 3, dtype='i4'))
+    with pytest.raises(ValueError):
+        codec.decode(np.arange(10, 20, dtype='i4'))
+    with pytest.raises(ValueError if PY2 else TypeError):
+        # exports old-style buffer interface on PY2, hence ValueError
+        codec.decode(u'foo')
+
+    # test out parameter
+    enc = codec.encode(arrays[0])
+    with pytest.raises(TypeError):
+        codec.decode(enc, out=b'foo')
+    with pytest.raises(TypeError):
+        codec.decode(enc, out=u'foo')
+    with pytest.raises(TypeError):
+        codec.decode(enc, out=123)
+    with pytest.raises(ValueError):
+        codec.decode(enc, out=np.zeros(10, dtype='i4'))
+
+
+def test_encode_none():
+    a = np.array([[1, 3], None, [[4, 7]]], dtype=object)
+    codec = VLenNDArray(int)
+    enc = codec.encode(a)
+    dec = codec.decode(enc)
+    expect = np.array([np.array([1, 3]),
+                       np.array([]),
+                       np.array([[4, 7]])], dtype=object)
+    assert_array_items_equal(expect, dec)