Commits · 8bbcecb41cb617a60cd53904acca0ed590cc86dc · Martin Larralde / LightMotif · GitLab

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Aug 31, 2023
- Skip buffer protocol tests on PyPy · 8bbcecb4
  Martin Larralde authored 1 year ago
  
  8bbcecb4
- Improve `Threshold` for AVX2 using streaming stores · 5703379d
  Martin Larralde authored 1 year ago
  
  5703379d
- Keep buffer uninitialized when allocating output in `Threshold` implementations · a419d5a3
  Martin Larralde authored 1 year ago
  
  a419d5a3
- Add copy protocol to `EncodedSequence` and `StripedSequence` · 5d191584
  Martin Larralde authored 1 year ago
  
  5d191584
- Add buffer protocol for `EncodedSequence` and `StripedSequence` · a9727b9f
  Martin Larralde authored 1 year ago
  
  a9727b9f
- Add support for indexing an `EncodedSequence` · 26c650f5
  Martin Larralde authored 1 year ago
  
  26c650f5
- Implement the buffer protocol for Python `StripedSequence` · 6dc317ee
  Martin Larralde authored 1 year ago
  
  6dc317ee
- Update `Encode` trait to return an `EncodedSequence` · 453bdc99
  Martin Larralde authored 1 year ago
  
  453bdc99
- Add a `PartialEq` implementation for `EncodedSequence` · 5aab90ca
  Martin Larralde authored 1 year ago
  
  5aab90ca
- Require `Symbol` implementors to be `Eq` · 1858af0e
  Martin Larralde authored 1 year ago
  
  1858af0e
- Add some convenience methods and traits to `TfmPvalue` · a8b8afd3
  Martin Larralde authored 1 year ago
  
  a8b8afd3
- Make `TfmPvalue` generic over the reference to the `ScoringMatrix` · 9086f036
  Martin Larralde authored 1 year ago
  
  9086f036
- Avoid initialization when allocating new buffer in `EncodedSequence::encode` · 4d975710
  Martin Larralde authored 1 year ago
  
  4d975710
- Update Python wrapper to use the dynamic dispatch pipeline · 6830cdb6
  Martin Larralde authored 1 year ago
  
  6830cdb6
- Update example in `README.md` to use the dynamic dispatch pipeline · bb00dc69
  Martin Larralde authored 1 year ago
  
  bb00dc69
- Fix bug in `Encode` implementation for `Pipeline<_, Dispatch>` · 88b6ad22
  Martin Larralde authored 1 year ago
  
  88b6ad22
- Update tests and benchmarks to use the dispatched pipeline · 7eb22b0c
  Martin Larralde authored 1 year ago
  
  7eb22b0c
- Add a dynamic dispatched pipeline backend to `lightmotif` · 228979ec
  Martin Larralde authored 1 year ago
  
  228979ec
- Fix name of helper methods for `Stripe` trait · ed2bbb6e
  Martin Larralde authored 1 year ago
  
  ed2bbb6e
- Fix broken tests in `lightmotif::seq` module · cf3f397d
  Martin Larralde authored 1 year ago
  
  cf3f397d
Aug 30, 2023
- Add AVX2 implementation of the `Stripe` trait using 32x32 matrix transpose · 9f0c4162
  Martin Larralde authored 1 year ago
  
  9f0c4162
- Add tests for the `Transpose` trait implementations · c7bdb341
  Martin Larralde authored 1 year ago
  
  c7bdb341
- Make `StripedSequence::new` return an error when given an invalid length · 8d763605
  Martin Larralde authored 1 year ago
  
  8d763605
- Add new pipeline trait to stripe an encoded sequence · e26e11ef
  Martin Larralde authored 1 year ago
  
  e26e11ef
- Add convenience methods to `StripedSequence` · 001da6dd
  Martin Larralde authored 1 year ago
  
  001da6dd
- Fix `Debug` for `DenseMatrix` now to render the padding bytes · 4645a543
  Martin Larralde authored 1 year ago
  
  4645a543
- Add method to fill all a `DenseMatrix` with a given value · 49267733
  Martin Larralde authored 1 year ago
  
  49267733
- Improve performance of AVX2 and NEON `Encode` by removing non-const functions in loop · 51bc3fc8
  Martin Larralde authored 1 year ago
  
  51bc3fc8
- Add `Alphabet::as_str` method to get all symbols from an alphabet · 7e8bdf38
  Martin Larralde authored 1 year ago
  
  7e8bdf38
- Add multiplexed NEON implementation of `Encode` for NEON · 53da5b92
  Martin Larralde authored 1 year ago
  
  53da5b92
- Add NEON implementation of the `Threshold` operation · 935ac549
  Martin Larralde authored 1 year ago
  
  935ac549
- Add NEON benchmarks to `lightmotif` benches · 1aef6b77
  Martin Larralde authored 1 year ago
  
  1aef6b77
Aug 10, 2023
- Release v0.4.0 · 5cf94f5d
  Martin Larralde authored 1 year ago
  
  View commits for tag v0.4.0 v0.4.0
  
  5cf94f5d
- Update GitHub Actions CI (#3) · 2d0fa41f
  Dirk Stolle authored 1 year ago
  
  The following updates are performed: * update actions/cache to v3 * replace unmaintained actions-rs/toolchain by dtolnay/rust-toolchain * replace unmaintained actions-rs/cargo by direct invocation of cargo
  2d0fa41f
- Update code example in `README.md` · 71368843
  Martin Larralde authored 1 year ago
  
  71368843
- Add `max` and `argmax` methods to the Python `StripedScores` interface · 4fd9360b
  Martin Larralde authored 1 year ago
  
  4fd9360b
- Add `StripedScores.is_empty` method · 6d65a9fa
  Martin Larralde authored 1 year ago
  
  6d65a9fa
- Rename `BestPosition` trait to `Maximum` to prepare for fast maximum score extraction · 09c99260
  Martin Larralde authored 1 year ago
  
  09c99260
- Update `BestPosition` to return first position on equal maxima · 67829490
  Martin Larralde authored 1 year ago
  
  67829490
Aug 09, 2023
- Fix `Score` causing an overflow on sequences shorter than PSSM · 24f941e7
  Martin Larralde authored 1 year ago
  
  24f941e7