lint

dsehnal · dsehnal · commit 216bed1f3584 · 2022-08-16T18:58:33.000+02:00
diff --git a/README.md b/README.md
@@ -7,5 +7,5 @@ A library for reading and writing (Binary)CIF files in Python.
 ## Linting
 
 ```
-autoflake --remove-all-unused-imports --remove-unused-variables --ignore-init-module-imports -ir ciftools && isort . && black .
+autoflake --remove-all-unused-imports --remove-unused-variables --ignore-init-module-imports -ir . && isort . && black .
 ```
diff --git a/ciftools/binary/decoder.py b/ciftools/binary/decoder.py
@@ -115,7 +115,7 @@ def _decode_string_array(data: np.ndarray, encoding: StringArrayEncoding) -> lis
     strings = [""]
 
     for i in range(1, len(offsets)):
-        strings.append(string_data[offsets[i - 1]: offsets[i]])  # type: ignore
+        strings.append(string_data[offsets[i - 1] : offsets[i]])  # type: ignore
 
     return [strings[i + 1] for i in indices]  # type: ignore
 
diff --git a/ciftools/binary/encoding/base/binary_cif_encoder_base.py b/ciftools/binary/encoding/base/binary_cif_encoder_base.py
@@ -1,9 +1,9 @@
 import abc
+
 from ciftools.binary.encoding.types import EncodedCIFData
 
 
 class BinaryCIFEncoderBase(abc.ABC):
     @abc.abstractmethod
     def encode_cif_data(self, data: any) -> EncodedCIFData:
         pass
-
diff --git a/ciftools/binary/encoding/impl/binary_cif_encoder.py b/ciftools/binary/encoding/impl/binary_cif_encoder.py
@@ -26,4 +26,3 @@ def encode_cif_data(self, data: any) -> EncodedCIFData:
             )
 
         return {"encoding": encodings, "data": data}
-
diff --git a/ciftools/binary/encoding/impl/encoders/byte_array.py b/ciftools/binary/encoding/impl/encoders/byte_array.py
@@ -1,8 +1,8 @@
 import sys
 
 import numpy as np
-from ciftools.binary.encoding.data_types import DataType, DataTypeEnum
 from ciftools.binary.encoding.base.cif_encoder_base import CIFEncoderBase
+from ciftools.binary.encoding.data_types import DataType, DataTypeEnum
 from ciftools.binary.encoding.encodings import ByteArrayEncoding, EncodingEnun
 from ciftools.binary.encoding.types import EncodedCIFData
 
diff --git a/ciftools/binary/encoding/impl/encoders/delta.py b/ciftools/binary/encoding/impl/encoders/delta.py
@@ -1,6 +1,6 @@
 import numpy as np
-from ciftools.binary.encoding.data_types import DataType, DataTypeEnum
 from ciftools.binary.encoding.base.cif_encoder_base import CIFEncoderBase
+from ciftools.binary.encoding.data_types import DataType, DataTypeEnum
 from ciftools.binary.encoding.encodings import DeltaEncoding, EncodingEnun
 from ciftools.binary.encoding.types import EncodedCIFData
 
diff --git a/ciftools/binary/encoding/impl/encoders/fixed_point.py b/ciftools/binary/encoding/impl/encoders/fixed_point.py
@@ -1,6 +1,6 @@
 import numpy as np
-from ciftools.binary.encoding.data_types import DataTypeEnum
 from ciftools.binary.encoding.base.cif_encoder_base import CIFEncoderBase
+from ciftools.binary.encoding.data_types import DataTypeEnum
 from ciftools.binary.encoding.encodings import EncodingEnun, FixedPointEncoding
 from ciftools.binary.encoding.types import EncodedCIFData
 from numpy import float64
diff --git a/ciftools/binary/encoding/impl/encoders/interval_quantization.py b/ciftools/binary/encoding/impl/encoders/interval_quantization.py
@@ -1,6 +1,6 @@
 import numpy as np
-from ciftools.binary.encoding.data_types import DataType, DataTypeEnum
 from ciftools.binary.encoding.base.cif_encoder_base import CIFEncoderBase
+from ciftools.binary.encoding.data_types import DataType, DataTypeEnum
 from ciftools.binary.encoding.encodings import EncodingEnun, IntervalQuantizationEncoding
 from ciftools.binary.encoding.types import EncodedCIFData
 
@@ -42,5 +42,5 @@ def encode(self, data: np.ndarray, *args, **kwargs) -> EncodedCIFData:
         np.round(quantized, 0, out=quantized)
 
         encoded_data = np.array(quantized, dtype=dtype)
-       
+
         return EncodedCIFData(data=encoded_data, encoding=[encoding])
diff --git a/ciftools/binary/encoding/impl/encoders/run_length.py b/ciftools/binary/encoding/impl/encoders/run_length.py
@@ -1,6 +1,6 @@
 import numpy as np
-from ciftools.binary.encoding.data_types import DataType, DataTypeEnum
 from ciftools.binary.encoding.base.cif_encoder_base import CIFEncoderBase
+from ciftools.binary.encoding.data_types import DataType, DataTypeEnum
 from ciftools.binary.encoding.encodings import EncodingEnun, RunLengthEncoding
 from ciftools.binary.encoding.types import EncodedCIFData
 
diff --git a/ciftools/binary/encoding/impl/encoders/string_array.py b/ciftools/binary/encoding/impl/encoders/string_array.py
@@ -1,9 +1,9 @@
 from typing import Union
 
 import numpy as np
-from ciftools.binary.encoding.impl.binary_cif_encoder import BinaryCIFEncoder
 from ciftools.binary.encoding.base.cif_encoder_base import CIFEncoderBase
 from ciftools.binary.encoding.encodings import EncodingEnun, StringArrayEncoding
+from ciftools.binary.encoding.impl.binary_cif_encoder import BinaryCIFEncoder
 from ciftools.binary.encoding.impl.encoders.delta import DELTA_CIF_ENCODER
 from ciftools.binary.encoding.impl.encoders.integer_packing import INTEGER_PACKING_CIF_ENCODER
 from ciftools.binary.encoding.impl.encoders.run_length import RUN_LENGTH_CIF_ENCODER
diff --git a/setup.py b/setup.py
@@ -1,4 +1,4 @@
-from setuptools import find_packages, setup
+from setuptools import setup
 
 setup(
     name="CifTools",
diff --git a/tests/_decoding.py b/tests/_decoding.py
@@ -2,7 +2,6 @@
 import urllib.request
 
 import msgpack
-
 from ciftools.cif_format.binary.file import BinaryCIFFile
 from ciftools.cif_format.value_presence import ValuePresenceEnum
 
@@ -12,7 +11,7 @@ def test(self):
         # TODO: set assert expectations
 
         print("mmCIF test")
-        data =  urllib.request.urlopen("https://models.rcsb.org/1tqn.bcif").read()
+        data = urllib.request.urlopen("https://models.rcsb.org/1tqn.bcif").read()
         parsed = BinaryCIFFile.loads(data, lazy=False)
 
         atom_site = parsed["1TQN"].atom_site
diff --git a/tests/_encoding.py b/tests/_encoding.py
@@ -75,9 +75,9 @@ def __init__(self, length: int):
         self.length = length
 
     def category_writer(self, ctx: TestVolumeData) -> CategoryWriter:
-        lattice_encoding = BinaryCIFEncoder([
-            FixedPointCIFEncoder(1000), DELTA_CIF_ENCODER, INTEGER_PACKING_CIF_ENCODER
-        ])
+        lattice_encoding = BinaryCIFEncoder(
+            [FixedPointCIFEncoder(1000), DELTA_CIF_ENCODER, INTEGER_PACKING_CIF_ENCODER]
+        )
 
         def lattice_value_getter(lid: int):
             return lambda data, i: data.lattices[lid][i]
@@ -96,10 +96,8 @@ def lattice_value_getter(lid: int):
                 name=f"volume",
                 dtype="f4",
                 # TODO: use interval quantization
-                encoder=lambda _: BinaryCIFEncoder([
-                    FixedPointCIFEncoder(1000),
-                    DELTA_CIF_ENCODER,
-                    INTEGER_PACKING_CIF_ENCODER]
+                encoder=lambda _: BinaryCIFEncoder(
+                    [FixedPointCIFEncoder(1000), DELTA_CIF_ENCODER, INTEGER_PACKING_CIF_ENCODER]
                 ),
                 value=lambda data, i: data.volume[i],
             )
diff --git a/tests/byte_array.py b/tests/byte_array.py
@@ -3,8 +3,8 @@
 import msgpack
 import numpy as np
 from ciftools.binary.decoder import decode_cif_data
-from ciftools.binary.encoding.impl.binary_cif_encoder import BinaryCIFEncoder
 from ciftools.binary.encoding.data_types import DataTypeEnum
+from ciftools.binary.encoding.impl.binary_cif_encoder import BinaryCIFEncoder
 from ciftools.binary.encoding.impl.encoders.byte_array import BYTE_ARRAY_CIF_ENCODER
 
 
diff --git a/tests/fixed_point.py b/tests/fixed_point.py
@@ -20,7 +20,7 @@ def test(self):
         ]
 
         for test_arr, e in test_suite:
-            encoder = BinaryCIFEncoder([FixedPointCIFEncoder(10 ** e), BYTE_ARRAY_CIF_ENCODER])
+            encoder = BinaryCIFEncoder([FixedPointCIFEncoder(10**e), BYTE_ARRAY_CIF_ENCODER])
             encoded = encoder.encode_cif_data(test_arr)
             decoded = decode_cif_data(encoded)
 
@@ -39,9 +39,7 @@ def test(self):
         ]
 
         for test_arr, e in test_suite:
-            encoder = BinaryCIFEncoder([
-                FixedPointCIFEncoder(10 ** e), DELTA_CIF_ENCODER, BYTE_ARRAY_CIF_ENCODER
-            ])
+            encoder = BinaryCIFEncoder([FixedPointCIFEncoder(10**e), DELTA_CIF_ENCODER, BYTE_ARRAY_CIF_ENCODER])
             encoded = encoder.encode_cif_data(test_arr)
             msgpack.loads(msgpack.dumps(encoded))
             decoded = decode_cif_data(encoded)
diff --git a/tests/interval_quantization.py b/tests/interval_quantization.py
@@ -3,8 +3,8 @@
 import msgpack
 import numpy as np
 from ciftools.binary.decoder import decode_cif_data
-from ciftools.binary.encoding.impl.binary_cif_encoder import BinaryCIFEncoder
 from ciftools.binary.encoding.data_types import DataTypeEnum
+from ciftools.binary.encoding.impl.binary_cif_encoder import BinaryCIFEncoder
 from ciftools.binary.encoding.impl.encoders.byte_array import BYTE_ARRAY_CIF_ENCODER
 from ciftools.binary.encoding.impl.encoders.interval_quantization import IntervalQuantizationCIFEncoder
 
@@ -15,16 +15,16 @@ def test(self):
         test_suite = [
             (np.random.rand(100) * 100, 100, DataTypeEnum.Uint8),
             (np.random.rand(100) * 100, 2**8, DataTypeEnum.Uint8),
-            (np.array([0, 255], dtype='f4'), 2**8, DataTypeEnum.Uint8),
+            (np.array([0, 255], dtype="f4"), 2**8, DataTypeEnum.Uint8),
             (np.random.rand(100) * 100, 2**16, DataTypeEnum.Uint16),
             (np.random.rand(100) * 100, 2**24, DataTypeEnum.Uint32),
         ]
 
         for test_arr, steps, dtype in test_suite:
             low, high = np.min(test_arr), np.max(test_arr)
-            encoder = BinaryCIFEncoder([
-                IntervalQuantizationCIFEncoder(low, high, steps, dtype), BYTE_ARRAY_CIF_ENCODER
-            ])
+            encoder = BinaryCIFEncoder(
+                [IntervalQuantizationCIFEncoder(low, high, steps, dtype), BYTE_ARRAY_CIF_ENCODER]
+            )
             encoded = encoder.encode_cif_data(test_arr)
             msgpack.loads(msgpack.dumps(encoded))
             decoded = decode_cif_data(encoded)

Original file line number	Diff line number	Diff line change
`@@ -26,4 +26,3 @@ def encode_cif_data(self, data: any) -> EncodedCIFData:`
`26`	`26`	`)`
`27`	`27`
`28`	`28`	`return {"encoding": encodings, "data": data}`
`29`		`-`