Commits · a5b005a7088985bc1516b7608912bdfea941a0d4 · Martin Larralde / LightMotif · GitLab

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Mar 07, 2025
- Fix pointer variable confusion in `score_f32_neon` · a5b005a7
  Martin Larralde authored 1 week ago
  
  a5b005a7
- Fix `dense::test::stride` always expecting 32 bytes alignment · c666fbc8
  Martin Larralde authored 1 week ago
  
  c666fbc8
- Remove `check` stage from `rust.yml` Actions workflow · 1fc271f0
  Martin Larralde authored 1 week ago
  
  1fc271f0
- Run tests on Aarch64 in GitHub Actions to test NEON code · 4dc8ff6a
  Martin Larralde authored 1 week ago
  
  4dc8ff6a
- Pin MacOS runner version used in GitHub Actions to `macos-13` · fc21fb33
  Martin Larralde authored 1 week ago
  
  fc21fb33
- Replace `Py_NewRef` with manual `Py_INCREF` calls in `__getbuffer__` code · cd31649b
  Martin Larralde authored 1 week ago
  
  cd31649b
Mar 06, 2025
- Fix deprecated API use in `lightmotif/tests/unittest.rs` · be2bb697
  Martin Larralde authored 1 week ago
  
  be2bb697
- Add constant and skip `memoryview`-based tests when compiling Python with Limited API · 9fac8162
  Martin Larralde authored 1 week ago
  
  9fac8162
- Add support for building Python bindings in Limited API mode · bb8107fc
  Martin Larralde authored 1 week ago
  
  bb8107fc
- Bump `pyo3` dependency to `v0.23` · 445fbd13
  Martin Larralde authored 1 week ago
  
  445fbd13
Feb 25, 2025
- Use constant pointers to avoid matrix indexing inside pipeline hot loops · 6920a734
  Martin Larralde authored 2 weeks ago
  
  6920a734
- Add blanket implementation for `&T` where `T` is `SymbolCount` · 7dd2d459
  Martin Larralde authored 2 weeks ago
  
  7dd2d459
- Apply `clippy` suggested fixes to `lightmotif` modules · 050725a0
  Martin Larralde authored 2 weeks ago
  
  050725a0
- Remove `const fn` declaration where it makes no sense · e1672555
  Martin Larralde authored 2 weeks ago
  
  e1672555
- Use `_mm256_broadcast_ps` in `score_f32_avx2_permute` to reduce data latency · ce99f385
  Martin Larralde authored 2 weeks ago
  
  ce99f385
Feb 11, 2025
- Bump MacOS runner version used in GitHub Actions · a72094d2
  Martin Larralde authored 1 month ago
  
  a72094d2
- Update `cover` step of `rust.yml` Actions workflow to run with up-to-date `cargo-tarpaulin` · c1232f6f
  Martin Larralde authored 1 month ago
  
  c1232f6f
- Use native GitHub Actions runners to build `aarch64` wheels · daf5b93a
  Martin Larralde authored 1 month ago
  
  daf5b93a
Jan 27, 2025
- Bump `nom` dependency of `lightmotif-io` to `v8.0` · a764a3f9
  Martin Larralde authored 1 month ago
  
  a764a3f9
- Update `dna.rs` benchmark to reference the PSSM matrix in a constant variable · c1561794
  Martin Larralde authored 1 month ago
  
  c1561794
Jan 19, 2025
- Add SVG figure with method detail to `docs/_static` · 31d7976c
  Martin Larralde authored 1 month ago
  
  31d7976c
Dec 06, 2024
- Always pre-allocate additional rows when creating a new `StripedSequence` for wrap rows · bec87d81
  Martin Larralde authored 3 months ago
  
  bec87d81
- Allow accessing and configuring the row capacity of a `DenseMatrix` · 6927895a
  Martin Larralde authored 3 months ago
  
  6927895a
Nov 13, 2024
- Make the `ravel` methods of `DenseMatrix` unsafe as they may expose uninitialized elements · db96b24a
  Martin Larralde authored 4 months ago
  
  db96b24a
- Add a trait to compute correlations for `lightmotif::pwm` matrices · 992b92b1
  Martin Larralde authored 4 months ago
  
  992b92b1
- Use macros to refactor common code in `lightmotif-py` · d88807aa
  Martin Larralde authored 4 months ago
  
  d88807aa
Nov 12, 2024
- Fix slow implementation of `SymbolCount::count_symbols` fo r `StripedSequence` · 83ea36ed
  Martin Larralde authored 4 months ago
  
  83ea36ed
- Inline some short functions in `lightmotif` core modules · b85be7e8
  Martin Larralde authored 4 months ago
  
  b85be7e8
- Use default column type based on current platform in most `lightmotif` types · 015ef4ad
  Martin Larralde authored 4 months ago
  
  015ef4ad
- Add dedicated trait for positive column dimensions in `lightmotif` · 58c4dc67
  Martin Larralde authored 4 months ago
  
  58c4dc67
- Add tests for `SymbolCount` for `EncodedSequence` and `StripedSequence` · dca3f923
  Martin Larralde authored 4 months ago
  
  dca3f923
- Use macros in `lightmotif-py` to reduce duplicated code between alphabets · c125bcc9
  Martin Larralde authored 4 months ago
  
  c125bcc9
Nov 08, 2024
- Allow accessing the sampled survival function distribution for a PSSM in `lightmotif-py` · 033bd157
  Martin Larralde authored 4 months ago
  
  033bd157
- Use the `Dispatch` columns for matrices in `lightmotif-py` · 43065afc
  Martin Larralde authored 4 months ago
  
  43065afc
- Add new `ScoreDistribution` Python type to help with p-value computation · 7f2251fe
  Martin Larralde authored 4 months ago
  
  7f2251fe
- Update type hints to show different p-value methods · 5ccfcbf6
  Martin Larralde authored 4 months ago
  
  5ccfcbf6
- Update `lightmotif-py` to use the MEME implementation of p-value computation · 9bb0a98b
  Martin Larralde authored 4 months ago
  
  9bb0a98b
- Mark most `ScoreDistribution` methods as `inline` · 69185a8a
  Martin Larralde authored 4 months ago
  
  69185a8a
- Add small example to `lightmotif::pwm::dist` documentation · bb8aab65
  Martin Larralde authored 4 months ago
  
  bb8aab65
- Add `ScoringMatrix::to_score_distribution` method and document `ScoreDistribution` methods · 07c0ef8c
  Martin Larralde authored 4 months ago
  
  07c0ef8c