Changelog#

All notable changes to this project will be documented in this file.

The format is based on Keep a Changelog and this project adheres to Semantic Versioning.

Unreleased#

v0.10.1 - 2026-03-25#

Added#

lightmotif#

  • Lossy constructor for EncodedSequence replacing unknown characters with Alphabet::default_symbol.

  • block_size option to change the number of rows of the block used in a Scanner.

Fixed#

lightmotif#

  • ScoringMatrix::to_discrete failing conversion on cells with -inf scores (due to zero pseudocounts).

  • Panic in Scanner::next caused by empty scores buffer.

  • Non-saturating add being used in score_u8_neon causing Scanner to ignore some hits on Arm platforms.

Changed#

lightmotif#

  • Update rand dependency to v0.10.0.

lightmotif-py#

  • Update pyo3 dependency to v0.28.0..

v0.10.0 - 2025-05-19#

Added#

lightmotif#

  • Experimental Gibbs sampler implementation for motif detection in zoops and oops modes.

  • IndexMut<MatrixCoordinates> trait implementation for DenseMatrix type.

  • AsRef<Vec<T>> for Scores<T>.

  • information_content methods to WeightMatrix and ScoringMatrix.

  • consensus method to CountMatrix.

  • FrequencyMatrix::into_scoring to take ownership of a frequency matrix and converting it inplace into a ScoringMatrix.

  • Implement size_hint for StripedScores iterator.

  • Cumulative distribution approximation for ScoringMatrix.

  • Add ScoringMatrix::to_score_distribution method to compute a score distribution suitable for P-value estimation.

  • Trait to compute correlations for lightmotif::pwm matrices.

  • new_unchecked constructors to lightmotif::pwm types (undocumented).

  • Efficient look-up table implementation for Aarch64 NEON f32-scoring.

lightmotif-io#

  • Reader for MEME format files.

Changed#

lightmotif#

  • Implement DenseMatrix iterators without unsafe code.

  • Make lightmotif::scan::Hit fields read-only.

  • Inline short functions in lightmotif core moduels.

  • Make the ravel methods of DenseMatrix unsafe.

  • Allow accessing and configuring the row capacity of a DenseMatrix.

  • Always pre-allocate additional rows when creating a new StripedSequence to avoid reallocation for wrap rows.

  • Use pointers to avoid matrix indexing inside pipeline hot loops.

  • Skip use of NEON for Score<Protein> since generic code is faster.

lightmotif-io#

  • Update nom dependency to 8.0.

lightmotif-py#

  • Update pyo3 dependency to 0.23.

  • Use maturin instead of setuptools-rust to build Python bindings from source.

Fixed#

lightmotif#

  • Use all columns of the matrix in CountMatrix::entropy.

  • Fix missing _mm_sfence in score_f32_avx2_permute code.

  • Avoid multiple log calls in FrequencyMatrix::to_scoring.

Removed#

lightmotif#

  • Const method declaration for matrix traits not const in lightmotif::pwm.

v0.9.1 - 2024-09-03#

Added#

lightmotif-py#

  • Arch User Repository package python-lightmotif to distribute the Python package on ArchLinux.

Fixed#

lightmotif-py#

  • Fix issues with source distribution missing required files for compilation.

  • Remove unused test data to reduce size of source distribution.

v0.9.0 - 2024-09-02#

Added#

lightmotif#

  • DenseMatrix::ravel to get the array of a DenseMatrix as a single continuous slice.

lightmotif-py#

  • Support for protein alphabets (#5).

  • protein property to CountMatrix, WeightMatrix, ScoringMatrix, EncodedSequence and StripedSequence.

  • Scanner class to use the new DNA scanning algorithm.

  • Buffer protocol implmementation for ScoringMatrix objects.

  • lightmotif.load function to load one or more Motif from a file-like object (#6).

  • Motif.name property to store the optional name of a Motif.

  • Several Motif subclasses to store motif and metadata loaded from a file.

  • Type annotations for the lightmotif.lib package.

Fixed#

lightmotif-io#

  • Parsing of floating-point numbers in JASPAR parser.

  • Panic on error unwrapping in lightmotif-io.

Changed#

lightmotif#

  • Rewrite DenseMatrix with constant platform-specific alignment to reduce amount of unsafe code.

Removed#

lightmotif-py#

  • alphabet parameter of ScoringMatrix and EncodedSequence.

v0.8.0 - 2024-06-28#

Added#

lightmotif#

  • lightmotif::pwm::DiscreteMatrix to store a discretized ScoringMatrix.

  • MatrixElement marker trait for Default + Copy types that can be used as a DenseMatrix element.

  • lightmotif::scores::Scores wrapper of Vec<T> with shortcut max, threshold and argmax methods.

  • AVX2 and NEON implementations of Score<u8, Dna> pipeline operation.

Fixed#

lightmotif#

  • Remove requirement for T: Debug in Clone implementation of DenseMatrix<T>.

  • SSE2 and AVX2 implementations of Argmax not returning the last index in case of ties.

lightmotif-tfmpvalue#

  • Cache internal buffer for Q-values to avoid reallocation between iterations.

Changed#

lightmotif#

  • Cache the Pipeline used in lightmotif::scan::Scanner.

  • Make lightmotif::scores::StripedScores generic over the score type.

  • Make Maximum and Threshold generic over the score type.

  • Use a discrete matrix in Scanner to quickly eliminate blocks without candidate position above given threshold.

  • Compile crate without the rand and rand-distr features by default.

lightmotif-py#

  • Update pyo3 dependency to v0.22.0.

v0.7.3 - 2024-06-17#

Added#

lightmotif-io#

  • lightmotif_io::jaspar to read matrices in raw JASPAR format.

  • Implementation of Clone and Error for the lightmotif_io::error::Error type.

Changed#

lightmotif#

  • Use logarithmic subtraction in FrequencyMatrix::to_scoring.

  • Use _mm256_permutevara8x32_ps instead of _mm256_permutevar_ps in AVX2 implementation to avoid special handling of unknown matric character N.

Fixed#

lightmotif#

  • Striping of empty sequences panicking on AVX2 implementation.

  • Scoring of empty range of rows panicking.

  • Invalid alignment of data in AVX2 code.

  • Clone implementation of DenseMatrix not preserving memory alignment.

v0.7.2 - 2024-06-14#

Added#

lightmotif-py#

  • Add __len__ implementation for all matrix clases.

  • Allow changing the logarithm base in WeightMatrix.log_odds method.

  • Implement __getitem__ for row access for all matrix classes.

v0.7.1 - 2024-06-14#

Fixed#

lightmotif#

  • Resizing of StripedScores output in NEON implementation of Score.

v0.7.0 - 2024-06-14#

Added#

lightmotif#

  • Implement indexing of StripedSequence by sequence index.

  • matrix accessor to all matrix types in lightmotif::pwm and lightmotif::seq.

  • entropy and information_content methods to CountMatrix.

  • SymbolCount trait for counting the number of occurrences of a symbol in an iterable.

  • Several Background constructors for counting occurences in one or more sequences.

  • FromIterator<A::Symbol> constructor for EncodedSequence<A>.

  • MultipleOf<N> trait to simplify typenums in platform code signatures.

  • Sampling of random sequences using the rand dependency under a feature flag.

  • ScoringMatrix.score_into method to re-use a StripedScores buffer.

  • ScoringMatrix.score_position method to score a single sequence position.

  • Indexing by MatrixCoordinates in DenseMatrix.

  • Support for chanding logarithm base when building a ScoringMatrix from a WeightMatrix.

  • Scanning algorithm for finding hits in a sequence with an iterator without allocating StripedScores for each sequence position.

lightmotif-py#

  • Support for optional TFMPvalue interface in Python bindings under GPLv3+ code.

  • Constructor for ScoringMatrix class.

  • ScoringMatrix.reverse_complement to compute the reverse-complement of a scoring matrix.

Changed#

lightmotif#

  • Make EncodedSequence.stripe use a dispatching Pipeline internally.

  • Require power-of-two alignment in DenseMatrix implementations.

  • Update generic-array dependency to v1.0.

  • Change order of parameters in ScoringMatrix.score.

  • Reorganize scoring trait and implement row-slice scoring for AVX2 and SSE2.

  • Rewrite Pipeline::threshold to return matrix coordinates instead of a sequence index.

  • Rewrite Pipeline::argmax to return matrix coordinates instead of a sequence index.

lightmotif-py#

  • Streamline the use of pipelined functions in Python bindings.

Fixed#

lightmotif#

  • Handling of unknown residues in permute implementation of Score on AVX2.

  • PartialEq for DenseMatrix to ignore alignment padding in each row.

Removed#

lightmotif#

  • Platform-specific code for thresholding a StripedScores matrix.

  • Direct attribute access in StripedSequence.

lightmotif-transfac#

  • Remove crate from repository, superseded by the lightmotif-io crate.

v0.6.0 - 2023-12-13#

Added#

lightmotif#

  • Validating constructor ::pwm::FrequencyMatrix::new testing for frequencies on each ranks.

  • Getter to the raw data matrix of a ::pwm::FrequencyMatrix.

lightmotif-io#

New crate with JASPAR, TRANSFAC and UNIPROBE format parsers.

Changed#

lightmotif#

  • Make max_score and min_score columns of ::pwm::ScoringMatrix ignore the wildcard symbol column.

lightmotif-tfmpvalue#

  • Invert decay in TfmPvalue to reduce rounding errors when computing granularity.

  • Use a fast integer hashing algorithm for i64 keys in maps used for recording Q-values.

  • Compute the optimal column permutation to accelerate the computation of score distributions.

Removed#

lightmotif-transfac#

Deprecate crate in favour of lightmotif-io.

v0.5.1 - 2023-08-31#

Fixed#

lightmotif#

  • Compilation for Arm NEON platforms.

v0.5.0 - 2023-08-31#

Added#

lightmotif#

  • Arm NEON implementation of Threshold and Encode.

  • Alphabet::as_str method to get the symbols of an alphabet as a string.

  • DenseMatrix::fill method to fill a dense matrix with a constant value.

  • Convenience getters and conversion traits to StripedSequence.

  • Stripe trait to implement striping of an encoded sequence with SIMD.

  • Dynamic dispatched pipeline selecting the best implementation as runtime.

  • PartialEq implementation for EncodedSequence.

lightmotif-py#

  • Buffer and copy protocols for StripedSequence and EncodedSequence.

  • Indexing support to EncodedSequence.

lightmotif-tfmpvalue#

  • Convenience methods to access the wrapped ScoringMatrix reference in TfmPvalue.

Changed#

lightmotif#

  • Encode::encode now returns an EncodedSequence instead of a raw Vec.

  • Performance improvements for Encode for AVX2 and NEON by removing non-const function calls in loop.

  • Performance improvements for Threshold by skipping the index buffer initialization.

  • Avoid buffer initialization when allocating a new buffer in EncodedSequence::encode.

  • Require Symbol implementors to implement Eq.

lightmotif-py#

  • Use the dynamic dispatch pipeline to run vectorized operations.

lightmotif-tfmpvalue#

  • Make TfmPvalue generic over the type of reference to the wrapped ScoringMatrix.

Fixed#

lightmotif#

  • Debug implementation of DenseMatrix crashing when attempting to render the padding bytes.

v0.4.0 - 2023-08-10#

Changed#

lightmotif#

  • Improve DenseMatrix::resize performance when downsizing.

  • Explicitly panic when sequence is too long to be processed with u32 indices in AVX2 and SSE2.

  • Reorganize DenseMatrix column alignment and index storage.

  • Improve Score performance by using pointers instead of slices in SIMD loops.

  • Rename DenseMatrix::columns_effective to DenseMatrix::stride.

  • Use streaming intrinsics to store data in AVX2 and SSE2 implementations.

  • Rename BestPosition trait to Maximum.

lightmotif-py#

  • Avoid error on missing symbols in CountMatrix.__init__

Added#

lightmotif#

  • Threshold trait to find all position above a certain score in a StripedScores matrix.

  • Encode trait to encode an ASCII sequence into a Vec<Symbol>.

  • AVX2 implementation of Score using gather instead of permute for protein alphabets.

  • From<Vec<_>> and Default trait implementations to EncodedSequence.

  • Alphabet methods to operate on ASCII strings.

  • StripedScores.is_empty method to check if a StripedScores contains any score.

lightmotif-py#

  • StripedScores.threshold method wrapping the Threshold pipeline operation.

  • StripedScores.max and StripedScores.argmax methods to get the best score and best position.

Fixed#

lightmotif#

  • Score causing an overflow when given a sequence shorter than the PSSM.

  • Maximum trait returns the smallest position on equal maxima.

v0.3.0 - 2023-06-25#

Changed#

  • Rewrite the SSE2 maximum search implementation using a generic number of columns.

  • Refactor lightmotif::pwm to avoid infinite odds-ratio for columns with zero background frequencies.

Added#

  • lightmotif-tfmpvalue crate implementing the TFMPvalue for computing p-values for a ScoringMatrix.

  • DenseMatrix::from_rows method to create a dense matrix from an iterable of rows.

  • PartialEq implementation for matrices in lightmotif.

  • Methods to compute the minimum and maximum scores of a ScoringMatrix.

v0.2.0 - 2023-05-15#

Changed#

  • Crate structure to avoid cluttering the main lightmotif module namespace.

  • Swizzling used in the SSSE3 implementation to make it require SSE2 only.

  • TRANSFAC parser to support parsing sections in arbitrary order and accept additional metadata.

  • Use memchr to parse lines faster in TRANSFAC parser.

  • Use typenum and generic-array to handle constant matrix dimensions.

  • Make Score trait generic over the number of columns in the striped sequence.

Added#

  • Accessors for some of the attributes of lightmotif_transfac::Matrix.

  • Pipeline method to extract the best position from a StripedScore matrix.

  • Child trait for alphabet complementation.

  • Methods for reverse-complementing all matrices from lightmotif::pwm.

  • Alphabet::symbols method to get all the symbols of an alphabet.

  • StripedSequence::encode constructor to encode and stripe a text sequence without allocating an extra EncodedSequence.

  • Iterator methods and helper struct for StripedScores.

  • Protein alphabet to lightmotif::abc.

  • DenseMatrix::uninitialized constructor to allocate a dense matrix without filling its contents.

  • lightmotif::num module with typenum re-exports and additional StrictlyPositive marker trait.

  • Arm NEON implementation of the position scoring algorithm.

  • Display implementation for EncodedSequence instead of an arbitrary ToString implementation.

v0.1.1 - 2023-05-04#

Added#

  • Helper crate to detect CPU features support at runtime.

Fixed#

  • AVX2 code being imported on x86-64 platforms without checking for OS support.

  • AVX2-enabled extension always being compiled even on platforms with no AVX2 support.

Removed#

  • built and pyo3-built build dependencies (causing issues with workspaces).

v0.1.0 - 2023-05-04#

Initial release.