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normanrznormanrz
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docs and renames all codecs
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‎docs/zarr3.rst‎

Lines changed: 21 additions & 21 deletions
Original file line numberDiff line numberDiff line change
@@ -5,95 +5,95 @@ Zarr 3 codecs
55

66
Bytes-to-bytes codecs
77
---------------------
8-
.. autoclass:: BloscCodec()
8+
.. autoclass:: Blosc()
99

1010
.. autoattribute:: codec_name
1111

12-
.. autoclass:: Lz4Codec()
12+
.. autoclass:: LZ4()
1313

1414
.. autoattribute:: codec_name
1515

16-
.. autoclass:: ZstdCodec()
16+
.. autoclass:: Zstd()
1717

1818
.. autoattribute:: codec_name
1919

20-
.. autoclass:: ZlibCodec()
20+
.. autoclass:: Zlib()
2121

2222
.. autoattribute:: codec_name
2323

24-
.. autoclass:: GzipCodec()
24+
.. autoclass:: GZip()
2525

2626
.. autoattribute:: codec_name
2727

28-
.. autoclass:: Bz2Codec()
28+
.. autoclass:: BZ2()
2929

3030
.. autoattribute:: codec_name
3131

32-
.. autoclass:: LzmaCodec()
32+
.. autoclass:: LZMA()
3333

3434
.. autoattribute:: codec_name
3535

36-
.. autoclass:: ShuffleCodec()
36+
.. autoclass:: Shuffle()
3737

3838
.. autoattribute:: codec_name
3939

4040

4141
Array-to-array codecs
4242
---------------------
43-
.. autoclass:: DeltaCodec()
43+
.. autoclass:: Delta()
4444

4545
.. autoattribute:: codec_name
4646

47-
.. autoclass:: BitroundCodec()
47+
.. autoclass:: BitRound()
4848

4949
.. autoattribute:: codec_name
5050

51-
.. autoclass:: FixedScaleOffsetCodec()
51+
.. autoclass:: FixedScaleOffset()
5252

5353
.. autoattribute:: codec_name
5454

55-
.. autoclass:: QuantizeCodec()
55+
.. autoclass:: Quantize()
5656

5757
.. autoattribute:: codec_name
5858

59-
.. autoclass:: PackbitsCodec()
59+
.. autoclass:: PackBits()
6060

6161
.. autoattribute:: codec_name
6262

63-
.. autoclass:: AsTypeCodec()
63+
.. autoclass:: AsType()
6464

6565
.. autoattribute:: codec_name
6666

6767

6868
Bytes-to-bytes checksum codecs
6969
------------------------------
70-
.. autoclass:: Crc32Codec()
70+
.. autoclass:: CRC32()
7171

7272
.. autoattribute:: codec_name
7373

74-
.. autoclass:: Crc32cCodec()
74+
.. autoclass:: CRC32C()
7575

7676
.. autoattribute:: codec_name
7777

78-
.. autoclass:: Adler32Codec()
78+
.. autoclass:: Adler32()
7979

8080
.. autoattribute:: codec_name
8181

82-
.. autoclass:: Fletcher32Codec()
82+
.. autoclass:: Fletcher32()
8383

8484
.. autoattribute:: codec_name
8585

86-
.. autoclass:: JenkinsLookup3Codec()
86+
.. autoclass:: JenkinsLookup3()
8787

8888
.. autoattribute:: codec_name
8989

9090

9191
Array-to-bytes codecs
9292
---------------------
93-
.. autoclass:: PCodecCodec()
93+
.. autoclass:: PCodec()
9494

9595
.. autoattribute:: codec_name
9696

97-
.. autoclass:: ZFPYCodec()
97+
.. autoclass:: ZFPY()
9898

9999
.. autoattribute:: codec_name

‎numcodecs/tests/test_zarr3.py‎

Lines changed: 69 additions & 82 deletions
Original file line numberDiff line numberDiff line change
@@ -3,18 +3,7 @@
33
import numpy as np
44
import pytest
55

6-
from numcodecs.registry import get_codec
7-
from numcodecs.zarr3 import (
8-
BloscCodec,
9-
BZ2Codec,
10-
GZipCodec,
11-
LZ4Codec,
12-
LZMACodec,
13-
NumcodecsCodec,
14-
ShuffleCodec,
15-
ZlibCodec,
16-
ZstdCodec,
17-
)
6+
import numcodecs.zarr3
187

198
zarr = pytest.importorskip("zarr")
209

@@ -40,42 +29,50 @@ def store() -> Store:
4029

4130

4231
@pytest.mark.parametrize(
43-
"codec_name", ["blosc", "lz4", "zstd", "zlib", "gzip", "bz2", "lzma", "shuffle"]
32+
("codec_name", "codec_class"),
33+
[
34+
("numcodecs.blosc", numcodecs.zarr3.Blosc),
35+
("numcodecs.lz4", numcodecs.zarr3.LZ4),
36+
("numcodecs.zstd", numcodecs.zarr3.Zstd),
37+
("numcodecs.zlib", numcodecs.zarr3.Zlib),
38+
("numcodecs.gzip", numcodecs.zarr3.GZip),
39+
("numcodecs.bz2", numcodecs.zarr3.BZ2),
40+
("numcodecs.lzma", numcodecs.zarr3.LZMA),
41+
("numcodecs.shuffle", numcodecs.zarr3.Shuffle),
42+
("numcodecs.delta", numcodecs.zarr3.Delta),
43+
("numcodecs.bitround", numcodecs.zarr3.BitRound),
44+
("numcodecs.fixedscaleoffset", numcodecs.zarr3.FixedScaleOffset),
45+
("numcodecs.quantize", numcodecs.zarr3.Quantize),
46+
("numcodecs.packbits", numcodecs.zarr3.PackBits),
47+
("numcodecs.astype", numcodecs.zarr3.AsType),
48+
("numcodecs.crc32", numcodecs.zarr3.CRC32),
49+
("numcodecs.crc32c", numcodecs.zarr3.CRC32C),
50+
("numcodecs.adler32", numcodecs.zarr3.Adler32),
51+
("numcodecs.fletcher32", numcodecs.zarr3.Fletcher32),
52+
("numcodecs.jenkins_lookup3", numcodecs.zarr3.JenkinsLookup3),
53+
("numcodecs.pcodec", numcodecs.zarr3.PCodec),
54+
("numcodecs.zfpy", numcodecs.zarr3.ZFPY),
55+
],
4456
)
45-
def test_generic_codec(store: Store, codec_name: str):
46-
data = np.arange(0, 256, dtype="uint16").reshape((16, 16))
47-
48-
with pytest.warns(UserWarning, match=EXPECTED_WARNING_STR):
49-
a = Array.create(
50-
store / "generic",
51-
shape=data.shape,
52-
chunk_shape=(16, 16),
53-
dtype=data.dtype,
54-
fill_value=0,
55-
codecs=[
56-
BytesCodec(),
57-
get_codec_class(f"numcodecs.{codec_name}")({"id": codec_name}),
58-
],
59-
)
60-
61-
a[:, :] = data.copy()
62-
np.testing.assert_array_equal(data, a[:, :])
57+
def test_entry_points(codec_name: str, codec_class: type[numcodecs.zarr3._NumcodecsCodec]):
58+
assert codec_class.codec_name == codec_name
59+
assert get_codec_class(codec_name) == codec_class
6360

6461

6562
@pytest.mark.parametrize(
6663
"codec_class",
6764
[
68-
BloscCodec,
69-
LZ4Codec,
70-
ZstdCodec,
71-
ZlibCodec,
72-
GZipCodec,
73-
BZ2Codec,
74-
LZMACodec,
75-
ShuffleCodec,
65+
numcodecs.zarr3.Blosc,
66+
numcodecs.zarr3.LZ4,
67+
numcodecs.zarr3.Zstd,
68+
numcodecs.zarr3.Zlib,
69+
numcodecs.zarr3.GZip,
70+
numcodecs.zarr3.BZ2,
71+
numcodecs.zarr3.LZMA,
72+
numcodecs.zarr3.Shuffle,
7673
],
7774
)
78-
def test_generic_codec_class(store: Store, codec_class: type[NumcodecsCodec]):
75+
def test_generic_codec_class(store: Store, codec_class: type[numcodecs.zarr3._NumcodecsCodec]):
7976
data = np.arange(0, 256, dtype="uint16").reshape((16, 16))
8077

8178
with pytest.warns(UserWarning, match=EXPECTED_WARNING_STR):
@@ -85,23 +82,20 @@ def test_generic_codec_class(store: Store, codec_class: type[NumcodecsCodec]):
8582
chunk_shape=(16, 16),
8683
dtype=data.dtype,
8784
fill_value=0,
88-
codecs=[
89-
BytesCodec(),
90-
codec_class(),
91-
],
85+
codecs=[BytesCodec(), codec_class()],
9286
)
9387

9488
a[:, :] = data.copy()
9589
np.testing.assert_array_equal(data, a[:, :])
9690

9791

9892
@pytest.mark.parametrize(
99-
"codec_config",
93+
("codec_class", "codec_config"),
10094
[
101-
{"id": "delta", "dtype": "float32"},
102-
{"id": "fixedscaleoffset", "offset": 0, "scale": 25.5},
103-
{"id": "fixedscaleoffset", "offset": 0, "scale": 51, "astype": "uint16"},
104-
{"id": "astype", "encode_dtype": "float32", "decode_dtype": "float64"},
95+
(numcodecs.zarr3.Delta, {"dtype": "float32"}),
96+
(numcodecs.zarr3.FixedScaleOffset, {"offset": 0, "scale": 25.5}),
97+
(numcodecs.zarr3.FixedScaleOffset, {"offset": 0, "scale": 51, "astype": "uint16"}),
98+
(numcodecs.zarr3.AsType, {"encode_dtype": "float32", "decode_dtype": "float64"}),
10599
],
106100
ids=[
107101
"delta",
@@ -110,12 +104,11 @@ def test_generic_codec_class(store: Store, codec_class: type[NumcodecsCodec]):
110104
"astype",
111105
],
112106
)
113-
def test_generic_filter(store: Store, codec_config: dict[str, JSON]):
107+
def test_generic_filter(
108+
store: Store, codec_class: type[numcodecs.zarr3._NumcodecsCodec], codec_config: dict[str, JSON]
109+
):
114110
data = np.linspace(0, 10, 256, dtype="float32").reshape((16, 16))
115111

116-
codec_name = codec_config["id"]
117-
del codec_config["id"]
118-
119112
with pytest.warns(UserWarning, match=EXPECTED_WARNING_STR):
120113
a = Array.create(
121114
store / "generic",
@@ -124,7 +117,7 @@ def test_generic_filter(store: Store, codec_config: dict[str, JSON]):
124117
dtype=data.dtype,
125118
fill_value=0,
126119
codecs=[
127-
get_codec_class(f"numcodecs.{codec_name}")(codec_config),
120+
codec_class(**codec_config),
128121
BytesCodec(),
129122
],
130123
)
@@ -144,10 +137,7 @@ def test_generic_filter_bitround(store: Store):
144137
chunk_shape=(16, 16),
145138
dtype=data.dtype,
146139
fill_value=0,
147-
codecs=[
148-
get_codec_class("numcodecs.bitround")({"keepbits": 3}),
149-
BytesCodec(),
150-
],
140+
codecs=[numcodecs.zarr3.BitRound(keepbits=3), BytesCodec()],
151141
)
152142

153143
a[:, :] = data.copy()
@@ -165,10 +155,7 @@ def test_generic_filter_quantize(store: Store):
165155
chunk_shape=(16, 16),
166156
dtype=data.dtype,
167157
fill_value=0,
168-
codecs=[
169-
get_codec_class("numcodecs.quantize")({"digits": 3}),
170-
BytesCodec(),
171-
],
158+
codecs=[numcodecs.zarr3.Quantize(digits=3), BytesCodec()],
172159
)
173160

174161
a[:, :] = data.copy()
@@ -187,10 +174,7 @@ def test_generic_filter_packbits(store: Store):
187174
chunk_shape=(16, 16),
188175
dtype=data.dtype,
189176
fill_value=0,
190-
codecs=[
191-
get_codec_class("numcodecs.packbits")(),
192-
BytesCodec(),
193-
],
177+
codecs=[numcodecs.zarr3.PackBits(), BytesCodec()],
194178
)
195179

196180
a[:, :] = data.copy()
@@ -204,15 +188,21 @@ def test_generic_filter_packbits(store: Store):
204188
chunk_shape=(16, 16),
205189
dtype="uint32",
206190
fill_value=0,
207-
codecs=[
208-
get_codec_class("numcodecs.packbits")(),
209-
BytesCodec(),
210-
],
191+
codecs=[numcodecs.zarr3.PackBits(), BytesCodec()],
211192
)
212193

213194

214-
@pytest.mark.parametrize("codec_name", ["crc32", "adler32", "fletcher32", "jenkins_lookup3"])
215-
def test_generic_checksum(store: Store, codec_name: str):
195+
@pytest.mark.parametrize(
196+
"codec_class",
197+
[
198+
numcodecs.zarr3.CRC32,
199+
numcodecs.zarr3.CRC32C,
200+
numcodecs.zarr3.Adler32,
201+
numcodecs.zarr3.Fletcher32,
202+
numcodecs.zarr3.JenkinsLookup3,
203+
],
204+
)
205+
def test_generic_checksum(store: Store, codec_class: type[numcodecs.zarr3._NumcodecsCodec]):
216206
data = np.linspace(0, 10, 256, dtype="float32").reshape((16, 16))
217207

218208
with pytest.warns(UserWarning, match=EXPECTED_WARNING_STR):
@@ -222,28 +212,25 @@ def test_generic_checksum(store: Store, codec_name: str):
222212
chunk_shape=(16, 16),
223213
dtype=data.dtype,
224214
fill_value=0,
225-
codecs=[
226-
BytesCodec(),
227-
get_codec_class(f"numcodecs.{codec_name}")(),
228-
],
215+
codecs=[BytesCodec(), codec_class()],
229216
)
230217

231218
a[:, :] = data.copy()
232219
a = Array.open(store / "generic_checksum")
233220
np.testing.assert_array_equal(data, a[:, :])
234221

235222

236-
@pytest.mark.parametrize("codec_name", ["pcodec", "zfpy"])
237-
def test_generic_bytes_codec(store: Store, codec_name: str):
223+
@pytest.mark.parametrize("codec_class", [numcodecs.zarr3.PCodec, numcodecs.zarr3.ZFPY])
224+
def test_generic_bytes_codec(store: Store, codec_class: type[numcodecs.zarr3._NumcodecsCodec]):
238225
try:
239-
get_codec({"id": codec_name})
226+
codec_class()
240227
except ValueError as e:
241228
if "codec not available" in str(e):
242-
pytest.xfail(f"{codec_name} is not available: {e}")
229+
pytest.xfail(f"{codec_class.codec_name} is not available: {e}")
243230
else:
244231
raise # pragma: no cover
245232
except ImportError as e:
246-
pytest.xfail(f"{codec_name} is not available: {e}")
233+
pytest.xfail(f"{codec_class.codec_name} is not available: {e}")
247234

248235
data = np.arange(0, 256, dtype="float32").reshape((16, 16))
249236

@@ -255,7 +242,7 @@ def test_generic_bytes_codec(store: Store, codec_name: str):
255242
dtype=data.dtype,
256243
fill_value=0,
257244
codecs=[
258-
get_codec_class(f"numcodecs.{codec_name}")({"id": codec_name}),
245+
codec_class(),
259246
],
260247
)
261248

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