build(deps): bump lightmotif-io from 0.6.0 to 0.7.2

[dependabot[bot]]

Bumps lightmotif-io from 0.6.0 to 0.7.2.

Release notes

Sourced from lightmotif-io's releases.

v0.7.2

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.

v0.7.0

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

... (truncated)

Changelog

Sourced from lightmotif-io's changelog.

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.

... (truncated)

Commits

• 4606588 Release v0.7.2
• d44e7b0 Implement __getitem__ for row access for matrices of lightmotif-py
• f7e791d Allow changing log base in WeightMatrix.log_odds method
• 7b58f7e Add __len__ implementation for all matrix classes of lightmotif-py
• d3cce92 Release v0.7.1
• 200d85c Fix resizing of striped scores in NEON score implementation
• d8e791d Release v0.7.0
• 2fb9aad Fix compilation of NEON code [ci skip]
• 4584268 Remove lightmotif-transfac from workspace [ci skip]
• ce89359 Remove the deprecated lightmotif-transfac crate
• Additional commits viewable in compare view

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