bionumpy - npm Package Compare versions

Comparing version 1.0.4 to 1.0.5

bionumpy.egg-info/PKG-INFO

 Metadata-Version: 2.1
 Name: bionumpy
-Version: 1.0.4
+Version: 1.0.5
 Summary: Library for working with biological sequence data as numpy arrays.
@@ -5,0 +5,0 @@ Home-page: https://github.com/bionumpy/bionumpy

bionumpy/__init__.py

@@ -5,3 +5,3 @@ """Top-level package for bionumpy."""
 __email__ = "[e-mail]"
-__version__ = '1.0.4'
+__version__ = '1.0.5'
 
@@ -8,0 +8,0 @@ import npstructures as nps

bionumpy/encoded_array.py

@@ -161,5 +161,5 @@ """
 
-    def __init__(self, data: 'EncodedArray', shape):
+    def __init__(self, data: 'EncodedArray', shape, *args, **kwargs):
         assert isinstance(data, EncodedArray), data
-        super().__init__(data.raw(), shape)
+        super().__init__(data.raw(), shape, *args, **kwargs)
         self._encoding = data.encoding
@@ -166,0 +166,0 @@

bionumpy/encodings/vcf_encoding.py

@@ -98,3 +98,3 @@ import itertools
     _lookup = np.zeros(256, dtype=np.uint8)
-    _lookup[[ord(c) for c in ('0', '1', '.')]] = np.array([0, 1, np.nan])
+    _lookup[[ord(c) for c in ('0', '1', '.')]] = np.array([0, 1, 0]) # Changed nan to 0 here since that's the uint8 version of nan
 
@@ -101,0 +101,0 @@ def __init__(self, data, field_starts):

bionumpy/io/delimited_buffers.py

@@ -312,3 +312,3 @@ import io
                 mask = int_strings.lengths != 0
-                return RaggedArray(function(int_strings[mask]), (text == sep).sum(axis=-1))
+                return RaggedArray(function(int_strings[mask]), (text == sep).sum(axis=-1), safe_mode=False) # TODO: is it necessary with unsafe mode here
             return RaggedArray(function(int_strings), (text == sep).sum(axis=-1))
@@ -315,0 +315,0 @@ else:

bionumpy/sequence/kmers.py

@@ -96,3 +96,3 @@ import numpy as np
         else:
-            out = EncodedRaggedArray(convoluted, shape)
+            out = EncodedRaggedArray(convoluted, shape, safe_mode=False) # FIXME: Should not use unsafe here
 
@@ -99,0 +99,0 @@ return out[..., : (-window_size + 1)]

bionumpy/sequence/rollable.py

@@ -58,5 +58,5 @@ from abc import abstractmethod
             if isinstance(convoluted, EncodedArray):
-                out = EncodedRaggedArray(convoluted, shape)
+                out = EncodedRaggedArray(convoluted, shape, safe_mode=False) #FIXME: Should avoid use of unsafe
             else:
-                out = RaggedArray(convoluted, shape)
+                out = RaggedArray(convoluted, shape, safe_mode=False)
         elif isinstance(_sequence, (np.ndarray, EncodedArray)):
@@ -63,0 +63,0 @@ out = as_strided(convoluted, shape)

PKG-INFO

 Metadata-Version: 2.1
 Name: bionumpy
-Version: 1.0.4
+Version: 1.0.5
 Summary: Library for working with biological sequence data as numpy arrays.
@@ -5,0 +5,0 @@ Home-page: https://github.com/bionumpy/bionumpy

setup.py

@@ -49,3 +49,3 @@ #!/usr/bin/env python
     url='https://github.com/bionumpy/bionumpy',
-    version='1.0.4',
+    version='1.0.5',
     zip_safe=False,
@@ -52,0 +52,0 @@ extras_require={'full': ['isal']}

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