Commits · 8da67d92869b1504ae7cf21c13f149b318a63731 · Martin Larralde / LightMotif · GitLab

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Jun 16, 2023
- Add `__eq__` method to matrices in `lightmotif-py` · 8da67d92
  Martin Larralde authored 1 year ago
  
  8da67d92
- Add `PartialEq` implementation to matrix types in `lightmotif` · 6868b68e
  Martin Larralde authored 1 year ago
  
  6868b68e
May 19, 2023
- Update instructions to use AVX2 in `README.md` [ci skip] · 2899bf15
  Martin Larralde authored 1 year ago
  
  2899bf15
May 17, 2023
- Update `README.md` with up-to-date benchmark results [ci skip] · cde4077c
  Martin Larralde authored 1 year ago
  
  cde4077c
- Rewrite the SSE2 maximum implementation using a generic number of columns · 4264ca28
  Martin Larralde authored 1 year ago
  
  4264ca28
- Release v0.2.0 · fc274e33
  Martin Larralde authored 1 year ago
  
  View commits for tag v0.2.0 v0.2.0
  
  fc274e33
- Re-export `typenum` crate in the `lightmotif::num` module · 6bb7ce31
  Martin Larralde authored 1 year ago
  
  6bb7ce31
- Add proper `Display` trait implementation for `EncodedSequence` · e7e76b1a
  Martin Larralde authored 1 year ago
  
  e7e76b1a
- Add tests to check the TRANSFAC parser works on TRANSFAC, JASPAR and PRODORIC matrices · 8e940621
  Martin Larralde authored 1 year ago
  
  8e940621
- Fix TRANSFAC parser to accept zero-decimal floats in the count matrix · 45e53759
  Martin Larralde authored 1 year ago
  
  45e53759
- Apply `clippy` suggestions · 2d131b9c
  Martin Larralde authored 1 year ago
  
  2d131b9c
- Disable warning about overflowing literals in AVX2 code · 068523db
  Martin Larralde authored 1 year ago
  
  068523db
- Use AVX2 broadcast instructions to load scores from the PSSM rows · 1464911a
  Martin Larralde authored 1 year ago
  
  1464911a
- Update Python wrapper to use NEON backend when supported · fee4ab59
  Martin Larralde authored 1 year ago
  
  fee4ab59
- Make NEON pipeline generic over the column count · c8f383dd
  Martin Larralde authored 1 year ago
  
  c8f383dd
May 16, 2023
- Add Arm NEON implementation of the scoring algorithm · 3ab0c763
  Martin Larralde authored 1 year ago
  
  3ab0c763
- Fix build of SSE2 tests · a1c02b8c
  Martin Larralde authored 1 year ago
  
  a1c02b8c
- Update `WeightMatrix.calculate` in Python version to use SSE2 as a fallback · a7970f44
  Martin Larralde authored 1 year ago
  
  a7970f44
- Fix build of `lightmotif-bench` and `lightmotif-transfac` tests · 87659cea
  Martin Larralde authored 1 year ago
  
  87659cea
- Use `typenum` to generate SSE2 functions accepting striped matrix with `16n` columns · c22a4a19
  Martin Larralde authored 1 year ago
  
  c22a4a19
- Update `lightmotif-py` and `lightmotif-transfac` with the new pipeline API · 12a2db0e
  Martin Larralde authored 1 year ago
  
  12a2db0e
- Add helper trait for strictly positive typenums · 6eb702e2
  Martin Larralde authored 1 year ago
  
  6eb702e2
- Reorganize code and add more documentation to individual modules · 271bd8d4
  Martin Larralde authored 1 year ago
  
  271bd8d4
- Refactor tests and benchmarks using generics · 2682fb6c
  Martin Larralde authored 1 year ago
  
  2682fb6c
- Remove unused imports from the `lightmotif` code · 1244dcfd
  Martin Larralde authored 1 year ago
  
  1244dcfd
- Reorganize pipeline code into several submodules · 0dee6009
  Martin Larralde authored 1 year ago
  
  0dee6009
- Move pipeline code to a new dedicated module · 0781efb0
  Martin Larralde authored 1 year ago
  
  0781efb0
- Rewrite swizzle of SSSE3 implementation to use SSE2 instructions · aae97369
  Martin Larralde authored 1 year ago
  
  aae97369
May 15, 2023
- Avoid initializing matrix before scoring in `Score` · 54c9e4dc
  Martin Larralde authored 1 year ago
  
  54c9e4dc
- Add an unsafe constructor to create an uninitialized `DenseMatrix` · b32502ea
  Martin Larralde authored 1 year ago
  
  b32502ea
- Fix benchmarks to work with new `typenum` API · 3929e16f
  Martin Larralde authored 1 year ago
  
  3929e16f
- Update `lightmotif-py` with the new `typenum` API · fd54401d
  Martin Larralde authored 1 year ago
  
  fd54401d
- Make `Score` trait generic over the striped sequence columns · 53b25d75
  Martin Larralde authored 1 year ago
  
  53b25d75
- Update `lightmotif-transfac` with new `typenum` API · 5776de5f
  Martin Larralde authored 1 year ago
  
  5776de5f
- Select a default vector type for `Pipeline` based on compile-time features · 684b4091
  Martin Larralde authored 1 year ago
  
  684b4091
- Fix broken SSSE3 maximum position implementation · f7c39a37
  Martin Larralde authored 1 year ago
  
  f7c39a37
- Use `typenum` and `generic-array` crates to handle constant alphabet sizes · 3f0c8c94
  Martin Larralde authored 1 year ago
  
  3f0c8c94
- Update SSSE3 implementation to support `Protein` alphabet · 738b7e28
  Martin Larralde authored 1 year ago
  
  738b7e28
- Add `Protein` alphabet to base crate · c1ac593d
  Martin Larralde authored 1 year ago
  
  c1ac593d
May 11, 2023
- Add links to both versions of the library in `README.md` [ci skip] · c2042d29
  Martin Larralde authored 1 year ago
  
  c2042d29