https://github.com/althonos/pyopal - v0.7.3

Fixed

• Memory missalocation in opal (#8).

- Cython
Published by github-actions[bot] 10 months ago

https://github.com/althonos/pyopal - v0.7.2

Fixed

• Memory leak in Aligner.align when running in buckets overflow mode.

- Cython
Published by github-actions[bot] 12 months ago

https://github.com/althonos/pyopal - v0.7.1

Fixed

• Extra key in pyproject.toml causing build issues with version 0.11.0 of scikit-build-core.
• Broken detection of default SSE2 support for x86-64 CPUs on Windows.
• Missing opal.h file in Python site install to allow Cython imports.

- Cython
Published by github-actions[bot] about 1 year ago

https://github.com/althonos/pyopal - v0.7.0

Added

• Support for Python 3.13.

Changed

• Bump required scoring-matrices dependency to v0.3.0.
• Reorganize project to build with CMake and scikit-build-core.
• Update documentation to use the PyData theme.

Fixed

• Signature of Cython classes constructors not displaying in documentation.

Removed

• Support for Python 3.6.

- Cython
Published by althonos over 1 year ago

https://github.com/althonos/pyopal - v0.6.1

Fixed

• Import of pyopal on non-AVX2-enabled CPUs causing a crash (#7).
• Type hints for Database.__init__ not accepting alphabet as a Python string.

- Cython
Published by github-actions[bot] almost 2 years ago

https://github.com/althonos/pyopal - v0.6.0

Changed

• Use scoring-matrices package to handle scoring matrices.
• Import Cython classes from pyopal.lib in the main pyopal namespace.

Fixed

• Patching of architecture flags of MacOS compilers.

Removed

• The ScoreMatrix class from pyopal.lib.

- Cython
Published by github-actions[bot] about 2 years ago

https://github.com/althonos/pyopal - v0.5.2

Fixed

• Segmentation fault when attempting to align to an empty Database (#6).

- Cython
Published by github-actions[bot] over 2 years ago

https://github.com/althonos/pyopal - v0.5.1

Fixed

• Broken behaviour of the ordered keyword in pyopal.align.

- Cython
Published by github-actions[bot] over 2 years ago

https://github.com/althonos/pyopal - v0.5.0

Added

• Support for compiling and running package on Windows.
• Support for Python 3.12.
• pyopal.Alphabet class for handling sequence encoding outside of ScoreMatrix.
• Additional score matrices using the data files from Opal.
• encode_into and decode_into sans-io methods of Alphabet.
• Aligner class to handle alignment of a query to a database.
• ScoreMatrix.__eq__ implementation.
• Database.lengths property to get the lengths of all the sequences in a database without decoding them.
• pyopal.align top-level function to handle multithreaded alignments.
• Alphabet.__eq__ implementation comparing letters.
• pool argument to pyopal.align to support reusing a ThreadPool.

Changed

• Store Database sequences using shared_ptr for fast slicing and extraction of a database subset.
• Use templates to generate platform-specific Cython files.
• Make internal extension public as pyopal.lib submodule.
• Avoid temporary data copy in Database._encode.
• Move Cython and Opal headers inside package to allow Cython import in other extensions.
• Make Database use mostly the pointer array to make the algorithms more generic over the storage class.
• Make MAX_ALPHABET_SIZE a constant of pyopal.lib rather than a user-defined macro for compatibility in other extensions.
• Update Aligner.align to use the BaseDatabase Cython API.

Fixed

• SSE2 not being detected on x86-64, where it is mandatory.
• Mark Opal search functions as noexcept in Cython to avoid exception checks.
• ScoreMatrix buffer-protocol not returning a read-only buffer.
• Database.mask accessing out-of-bound elements when building pointer array.
• Broken detection of PyInterpreterState_GetID in setup.py.
• FullResult.cigar crashing on alignments starting with X.
• Memory leak in Aligner.align caused by faulty allocation of pointer array.
• __repr__ implementations of Alphabet and FullResult.
• Alphabet.__getitem__ reading past the letters buffer.

Removed

• Database.search method.

- Cython
Published by github-actions[bot] over 2 years ago

https://github.com/althonos/pyopal - v0.5.0-a5

Added

• Alphabet.__eq__ implementation comparing letters.
• pool argument to pyopal.align to support reusing a ThreadPool.

Changed

• Update Aligner.align to use the BaseDatabase Cython API.

Fixed

• Memory leak in Aligner.align caused by faulty allocation of pointer array.
• __repr__ implementations of Alphabet and FullResult.
• Alphabet.__getitem__ reading past the letters buffer.

- Cython
Published by github-actions[bot] over 2 years ago

https://github.com/althonos/pyopal - v0.5.0-a4

Added

• encode_into and decode_into sans-io methods of Alphabet.
• Aligner class to handle alignment of a query to a database.
• ScoreMatrix.__eq__ implementation.
• Database.lengths property to get the lengths of all the sequences in a database without decoding them.
• pyopal.align top-level function to handle multithreaded alignments.

Fixed

• FullResult.cigar crashing on alignments starting with X.

- Cython
Published by github-actions[bot] over 2 years ago

https://github.com/althonos/pyopal - v0.5.0-a3

Added

• Additional score matrices using the data files from Opal.

Changed

• Avoid temporary data copy in Database._encode.
• Move Cython and Opal headers inside package to allow Cython import in other extensions.
• Make Database use mostly the pointer array to make the algorithms more generic over the storage class.
• Make MAX_ALPHABET_SIZE a constant of pyopal.lib rather than a user-defined macro for compatibility in other extensions.

Fixed

• ScoreMatrix buffer-protocol not returning a read-only buffer.
• Database.mask accessing out-of-bound elements when building pointer array.
• Broken detection of PyInterpreterState_GetID in setup.py.

- Cython
Published by github-actions[bot] over 2 years ago

https://github.com/althonos/pyopal - v0.5.0-a2

Added

• pyopal.Alphabet class for handling sequence encoding outside of ScoreMatrix.

Changed

• Make internal extension public as pyopal.lib submodule.

- Cython
Published by github-actions[bot] over 2 years ago

https://github.com/althonos/pyopal - v0.5.0-a1

Changed

• Store Database sequences using shared_ptr for fast slicing and extraction of a database subset.
• Use templates to generate platform-specific Cython files.

Fixed

• SSE2 not being detected on x86-64, where it is mandatory.
• Mark Opal search functions as noexcept in Cython to avoid exception checks.

Added

• Support for compiling and running package on Windows.
• Support for Python 3.12.

- Cython
Published by github-actions[bot] over 2 years ago

https://github.com/althonos/pyopal - v0.4.1

Fixed

• FullResult.__repr__ not returning a roundtripping string (#4, by @valentynbez).
• Database.search overflowing for long sequences with non-sw algorithms (#3).

Changed

• Make Database.search raise an OverflowError instead of a RuntimeError on score overflow.

- Cython
Published by github-actions[bot] almost 3 years ago

https://github.com/althonos/pyopal - v0.4.0

Changed

• Bumped Cython dependency to v3.0.

Fixed

• PyPy 3.9 builds failing on missing PyInterpreterState_GetID.

- Cython
Published by github-actions[bot] almost 3 years ago

https://github.com/althonos/pyopal - v0.3.0

Added

• Database.extract method to subset a database given a sequence of indices.
• Database.mask method to subset a database given a boolean mask.

Changed

• Replaced cpu-features library with archspec Python package for runtime detection of CPU features.

Fixed

• Segmentation fault in alignment reconstruction code for Needleman-Wunsch algorithm (#1).
• Erroneous error message in Database.search on invalid overflow value (#2).

- Cython
Published by github-actions[bot] about 3 years ago

https://github.com/althonos/pyopal - v0.2.0

Added

• query_length and target_length properties to FullResult to the lenghts of the complete query and target sequences.
• FullResult.coverage method to compute the coverage of the alignment using either the query or the target as the reference.

Changed

• Compile Cython extension with binding=False to fix rendering of documentation.

Fixed

• Insertion & deletion symbols being inverted in FullResult.cigar strings.

- Cython
Published by github-actions[bot] over 3 years ago

https://github.com/althonos/pyopal - v0.1.1

Added

• Buffer protocol implementation to pyopal.ScoreMatrix.
• Sphinx documentation hosted on ReadTheDocs.

Fixed

• Docstring now showing in the main pyopal module.
• Database.insert potentially crashing when given negative indexes.
• Database.search not listing the right return type.

- Cython
Published by github-actions[bot] over 3 years ago

https://github.com/althonos/pyopal - v0.1.0

Initial release.

- Cython
Published by github-actions[bot] over 3 years ago