Commits · 5b3c2c8666b841a981114602ddcb39b05e2f0e2e · Martin Larralde / LightMotif · GitLab

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Sep 02, 2024
- Avoid use of unsafe `OsStr::from_encoded_bytes_unchecked` in `lightmotif-py` · 5b3c2c86
  Martin Larralde authored 6 months ago
  
  5b3c2c86
- Update documentation to use PyData theme [ci skip] · 02f682b0
  Martin Larralde authored 6 months ago
  
  02f682b0
- Add `protein` property to check whether `lightmotif` objects are for protein alphabets · b1dc337d
  Martin Larralde authored 6 months ago
  
  b1dc337d
- Implement `Scanner.__init__` and fix type annotations in Python package · f6950e9b
  Martin Larralde authored 6 months ago
  
  f6950e9b
- Add `DenseMatrix::ravel` function to get the full buffer of a matrix · 6d5eb3a8
  Martin Larralde authored 6 months ago
  
  6d5eb3a8
- Rewrite `DenseMatrix` with constant alignment and less unsafe code · 7e62d302
  Martin Larralde authored 6 months ago
  
  7e62d302
- Ensure `lightmotif.load` Python function supports `os.PathLike` arguments · 591923d1
  Martin Larralde authored 6 months ago
  
  591923d1
- Add type annotations for `lightmotif.lib` Python module · a6f23936
  Martin Larralde authored 6 months ago
  
  a6f23936
Sep 01, 2024
- Add `Motif` subclasss to store metadata from JASPAR or TRANSFAC records · ffe6ac09
  Martin Larralde authored 6 months ago
  
  ffe6ac09
Aug 31, 2024
- Fix `Scanner` in `lightmotif-py` to avoid copying data · cbc2ca63
  Martin Larralde authored 6 months ago
  
  cbc2ca63
- Update Rust version used to build documentation [ci skip] · 04ea4c8c
  Martin Larralde authored 6 months ago
  
  04ea4c8c
Aug 30, 2024
- Make `lightmotif.load` support file-like objects and add unit tests for various formats · f218b080
  Martin Larralde authored 6 months ago
  
  f218b080
- Fix TRANSFAC parser unwrapping potential error in `lightmotif-io` · a3cfd3f4
  Martin Larralde authored 6 months ago
  
  a3cfd3f4
- Add `Motif.name` property to store the name of a motif in `lightmotif-py` · cd460572
  Martin Larralde authored 6 months ago
  
  cd460572
- Add `load` function to `lightmotif-py` to support loading several `Motif` from a file · 1e43a171
  Martin Larralde authored 6 months ago
  
  1e43a171
- Implement buffer protocol for `ScoringMatrix` · 6b551229
  Martin Larralde authored 6 months ago
  
  6b551229
- Wrap the new DNA scanning algorithm in the `lightmotif-py` library · 5c36d18f
  Martin Larralde authored 6 months ago
  
  5c36d18f
Aug 29, 2024
- Fix issue with parsing of floating-point numbers in JASPAR parser · 76d0eda1
  Martin Larralde authored 6 months ago
  
  76d0eda1
- Add support for protein alphabets in `lightmotif-py` module · f1744c1f
  Martin Larralde authored 6 months ago
  
  f1744c1f
Aug 28, 2024
- Fix outdated key type in `package.yml` Actions workflow [ci skip] · 52009fb3
  Martin Larralde authored 6 months ago
  
  52009fb3
Jun 28, 2024
- Release v0.8.0 · b11557fa
  Martin Larralde authored 8 months ago
  
  View commits for tag v0.8.0 v0.8.0
  
  b11557fa
- Bump `pyo3` dependency to `v0.22` · e0f3530d
  Martin Larralde authored 8 months ago
  
  e0f3530d
Jun 25, 2024
- Compile `lightmotif` without `rand` by default · 972259e2
  Martin Larralde authored 8 months ago
  
  972259e2
- Cache Q-values buffer in `TfmPvalue` structure · 81301e87
  Martin Larralde authored 8 months ago
  
  81301e87
Jun 24, 2024
- Add benchmark for the `Maximum::max` pipeline operation · 59738a0e
  Martin Larralde authored 9 months ago
  
  59738a0e
- Update `Avx2::argmax_u8` to use a single comparison · 579d9527
  Martin Larralde authored 9 months ago
  
  579d9527
- Add dedicated `Maximum::<f32, _>::max` implementation for AVX2 · dae72f3f
  Martin Larralde authored 9 months ago
  
  dae72f3f
- Add naive baseline implementation to `dna.rs` benchmark in `lightmotif-bench` · 0a587d21
  Martin Larralde authored 9 months ago
  
  0a587d21
- Fix `u8` benches speed in `threshold.rs` benchmark · 81ece013
  Martin Larralde authored 9 months ago
  
  81ece013
- Add dedicated `Maximum::<u8, _>::max` implementation for AVX2 · 4132b956
  Martin Larralde authored 9 months ago
  
  4132b956
- Reorganize all benchmarks in `lightmotif` crate · cf46a38b
  Martin Larralde authored 9 months ago
  
  cf46a38b
- First check if block maximum is high enough before running `Pipeline::threshold` in `Scanner` · 5c258648
  Martin Larralde authored 9 months ago
  
  5c258648
- Refactor `dna.rs` code in `lightmotif-bench` · 45099ad0
  Martin Larralde authored 9 months ago
  
  45099ad0
Jun 21, 2024
- Add tests to ensure `Maximum::argmax` works as expected for all implementations · 41a6d1f7
  Martin Larralde authored 9 months ago
  
  41a6d1f7
- Fix SSE2 and AVX2 implementations of `argmax` not returning the last index · 641f89a5
  Martin Larralde authored 9 months ago
  
  641f89a5
- Clean code in NEON platform implementation · dacd23a8
  Martin Larralde authored 9 months ago
  
  dacd23a8
- Add tests for NEON implementation of `Score<u8>` · 9f3fe1a5
  Martin Larralde authored 9 months ago
  
  9f3fe1a5
- Rename unit tests in `lightmotif` for consistency · b617ed4e
  Martin Larralde authored 9 months ago
  
  b617ed4e
- Fix unused imports in `lightmotif::pli` and reorganize unit tests · 696bbbe7
  Martin Larralde authored 9 months ago
  
  696bbbe7
- Add SSE2 implementation of the `Encode` pipeline operation · b167120d
  Martin Larralde authored 9 months ago
  
  b167120d