Releases | Open Source Science

https://github.com/althonos/pytrimal - v0.8.2

Fixed

RepresentativeTrimmer not working as intended (#5) because of trimAl code issues (inab/trimal#117, inab/trimal#118).

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

https://github.com/althonos/pytrimal - v0.8.0

Changed

Update vendored trimAl to d89ffc3 (2.0_RC).
Use scoring-matrices package to get a base for the SimilarityMatrix class.
Rename backend to platform for all trimmer classes.
Use trimAl platform-specific code to accelerate computations.
Migrate documentation to pydata-sphinx-theme.

Fixed

Missing trimmer classes in API documentation.
Pin supported versions of scoring-matrices package to ~=0.2.0.

Removed

Outdated platform-specific code.
archspec dependency (replaced by cpu_features used internally in trimAl).

- Cython
Published by althonos almost 2 years ago

https://github.com/althonos/pytrimal - v0.8.0-alpha1

Changed

Update vendored trimAl to d89ffc3 (2.0_RC).
Use scoring-matrices package to get a base for the SimilarityMatrix class.
Rename backend to platform for all trimmer classes.
Use trimAl platform-specific code to accelerate computations.

Fixed

Missing trimmer classes in API documentation.

Removed

Outdated platform-specific code.
archspec dependency (replaced by cpu_features used internally in trimAl).

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

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

Changed

Bumped Cython dependency to v3.0.

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

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

Fixed

Overflow in calculateSpuriousVector for certain sequence block sizes.
MMX backend never being used unless explicitly required even when being the best supported backend. ### Changed
Use archspec Python package instead of cpu-features library for CPU feature detection at runtime.
Use importlib.resources.files to load package data in pytrimal.tests.

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

https://github.com/althonos/pytrimal - v0.5.5

Fixed

calculateSpuriousVector method of SIMD implementations not being declared override. ### Changed
Replaced aligned_alloc with posix_memalign for compatibility with MacOS.

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

https://github.com/althonos/pytrimal - v0.5.4

Added

AVX2 and MMX implementations of the SIMD statistics computation.
Tests for all SIMD implementations supported on the local machine. ### Changed
Refactor SIMD code using C++ templates and generic implementation. ### Fixed
Broken rendering of function signatures in Sphinx documentation.
residues_mask and sequences_mask attributes of TrimmedAlignment not being documented (#1).

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

https://github.com/althonos/pytrimal - v0.5.3

Fixed

SimilarityMatrix.nt inverting the degenerated argument value.

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

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

Changed

Replace NEON horizontal sums with implementations using vaddvq on Aarch64 and vpaddl on Armv7.
Remove one layer of table lookup in all Similarity::CalculateVectors implementations.
Make all SIMD code use local buffers and deallocate early.

Fixed

Invalid operator being used in Cython code to deallocate C++ arrays.

Added

SSE2 and NEON implementations for the Gaps statistic.

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

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

Fixed

Build of cpu_features for platforms without hardware detection support.

- Cython
Published by github-actions[bot] almost 4 years ago

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

Added

pytrimal.RepresentativeTrimmer class to trim by maximum identity or fixed number of cluster representatives.
pickle protocol support for all trimmer classes.
Conversion methods to convert an Alignment from and to Biopython or PyHMMER objects.
Arm NEON implementation of the statistics computation algorithm, with speed-up similar to that of the SSE implementation.

Fixed

std::streambuf implementation based on the readinto Python method not working on Arm because of char being used to read ASCII.

Removed

Support for Python 3.5, due to Cython compatibility issues.

- Cython
Published by github-actions[bot] almost 4 years ago

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

Added

BaseTrimmer.backend property to get the backend used by a trimmer object.
Zero-copy slicing for AlignmentSequences and AlignmentResidues objects.
noduplicateseqs method for AutomaticTrimmer objects.
OverlapTrimmer class to perform overlap trimming with SSE-accelerated implementation.
AutomaticTrimmer.METHODS attribute to expose all supported automatic trimming methods.
__repr__ implementation to all trimmer classes.

Fixed

Missing deallocation code for standalone AlignmentResidues objects.
Alignment.load not working properly in PyPy environments.
Alignment constructor sometimes crashing when not given any sequence.

Changed

Use aligned memory for some temporary buffers used in SIMD code.
Enable loop unrolling when supported by the compiler.
Skip letter validation when creating an Alignment object with sequences from an AlignmentSequences object.

Removed

consistency_threshold and consistency_window arguments of ManualTrimmer.

- Cython
Published by github-actions[bot] almost 4 years ago

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

Added

Support for loading an Alignment from a file-like object for certain formats.
Generic optimized backend using caching optimizations from inab/trimal#66.

Fixed

Compilation of code for OSX platforms in Python 3.10.
File not being closed on error when loading a FASTA alignment.

Changed

Add tests for loading an Alignment without requiring importlib.resources.

- Cython
Published by github-actions[bot] almost 4 years ago

https://github.com/althonos/pytrimal - v0.2.2