syncoder 0.0.6a0__tar.gz → 0.1.0a0__tar.gz

{syncoder-0.0.6a0 → syncoder-0.1.0a0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.5
 Name: syncoder
-Version: 0.0.6a0
+Version: 0.1.0a0
 Summary: A codec for DNA data storage
 Project-URL: Homepage, https://example.com/TBD
 Project-URL: Issues, https://example.com/TBD/issues

syncoder-0.1.0a0/src/syncoder/CodecHelpers.py

@@ -0,0 +1,115 @@
+import inspect
+import warnings
+from functools import wraps
+import typing
+from typing import Callable
+import numpy as np
+
+__all__ = ["reverse_complement", "_int_to_baseN", "_baseN_to_int", \
+           "_check_deprecated", "_is_pow_two", "eeleopard_available"]
+
+
+def _is_pow_two(n: int):
+    """Returns if a number is a power of two."""
+    return (n > 0) and ((n & ( ~(n-1) )) == n)
+ 
+def reverse_complement(dna_sequence: str) -> str:
+    """Returns the reverse complement of a DNA sequence."""
+    complement = {'A': 'T', 'T': 'A', 'C': 'G', 'G': 'C', 'a': 't', 't': 'a', 'c': 'g', 'g': 'c'}
+    reversed_sequence = dna_sequence[::-1]
+    reverse_complement_sequence = ''.join(complement[nucleotide] for nucleotide in reversed_sequence)
+    return reverse_complement_sequence
+
+def _int_to_baseN(n:int,base:int,length:int=-1)->list[int]:
+    """Converts an integer to a base N number in little endian order.
+
+    Args:
+        n (int): The integer to be converted.
+        base (int): The base of the number system.
+        length (int, optional): If specified, the number will be zero padded to this length.
+
+    Returns:
+        list[int]: The list of digits representing the base N number.
+
+    """ 
+
+    digits = []
+    while n>0:
+        n,r = divmod(n,base)
+        digits.append(r)
+        
+    #do zero padding
+    while len(digits)<length: 
+        digits.append(0)
+    return digits
+
+def _baseN_to_int(digits: list[int], base: int) -> int:
+    """
+    Converts a base N number to an integer using little endian order.
+
+    Args:
+        digits (list[int]): The list of digits representing the base N number.
+        base (int): The base of the number.
+
+    Returns:
+        int: The converted integer value.
+
+    """
+
+    n = 0
+    for d in reversed(digits):
+        n = n*base + d
+    return n
+
+
+def _check_deprecated(func: Callable[..., typing.Any]) -> Callable[..., typing.Any]:
+    """Translate deprecated keyword arguments before calling ``func``."""
+    signature = inspect.signature(func)
+
+    @wraps(func)
+    def wrapper(*args: typing.Any, **kwargs: typing.Any) -> typing.Any:
+        positional_arguments = signature.bind_partial(*args).arguments
+        replacements = (("words", "alphabet"),
+                        ("alternate_words", "alternate_alphabet"))
+        for deprecated_name, current_name in replacements:
+            if deprecated_name not in kwargs:
+                continue
+            if current_name in kwargs or current_name in positional_arguments:
+                raise TypeError(
+                    f"Cannot specify both '{current_name}' and '{deprecated_name}'"
+                )
+            kwargs[current_name] = kwargs.pop(deprecated_name)
+            warnings.warn(
+                f"The '{deprecated_name}' parameter is deprecated. Please use "
+                f"'{current_name}' instead.",
+                DeprecationWarning,
+                stacklevel=2,
+            )
+        return func(*args, **kwargs)
+
+    return wrapper
+
+
+eeleopard_available = False
+try:
+    import eeleopard
+    eeleopard_available = True
+except ImportError: 
+    pass
+
+if eeleopard_available:
+    class WrappedLeopard(eeleopard.ReedSolomon): # pyright: ignore[reportPossiblyUnboundVariable] .. this is bound >:( 
+        def encode(self, message: list[int]):
+            temp = super().encode(message)
+            ecc = temp[:-self.k]
+            data = temp[-self.k:]
+            return np.concatenate((data, ecc))
+
+        def decode(self, received, erasures = None,**kwargs): # pyright: ignore[reportIncompatibleMethodOverride]  That's the point
+            data = received[:self.k ]
+            ecc = received[self.k:]
+            orig_codeword = np.concatenate((ecc,data))
+            dec_result = super().decode(orig_codeword, erasures,**kwargs)
+            return (dec_result.message, dec_result.num_errors,dec_result.error_positions)
+
+    __all__.append( "WrappedLeopard" )

{syncoder-0.0.6a0 → syncoder-0.1.0a0}/src/syncoder/__init__.py

@@ -3,4 +3,4 @@ from .codec import _default_b32_alphabet, _default_b32_alphabet_alt
 default_b32_alphabet = _default_b32_alphabet
 default_b32_alphabet_alt = _default_b32_alphabet_alt
 
-__version__ = "0.0.6a0"
+__version__ = "0.1.0a0"