Commits · 07d1be919d8378e9d64ea2c324d420f5391a7dc1 · Martin Larralde / LightMotif · GitLab

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Sep 02, 2024
- Add missing `ipykernel` dependency to Sphinx documentation [ci skip] · 07d1be91
  Martin Larralde authored 6 months ago
  
  07d1be91
- Add Jupyter notebook with library usage in `lightmotif-py` docs [ci skip] · 6e1dd442
  Martin Larralde authored 6 months ago
  
  6e1dd442
- Display link to stable documentation in Python `README.md` [ci skip] · 5068087c
  Martin Larralde authored 6 months ago
  
  5068087c
- Remove `alphabet` parameter from `ScoringMatrix` Python class · 9ede4ee1
  Martin Larralde authored 6 months ago
  
  9ede4ee1
- Improve documentation of `lightmotif` Python module · d264b724
  Martin Larralde authored 6 months ago
  
  d264b724
- Fix logo and styling in Python documentation [ci skip] · 62107b07
  Martin Larralde authored 6 months ago
  
  62107b07
- 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
- 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
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
- 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
- Add support for protein alphabets in `lightmotif-py` module · f1744c1f
  Martin Larralde authored 6 months ago
  
  f1744c1f
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 20, 2024
- Make `StripedScores` generic over the score type · d14173a9
  Martin Larralde authored 9 months ago
  
  d14173a9
Jun 17, 2024
- Release v0.7.3 · 725f3bab
  Martin Larralde authored 9 months ago
  
  View commits for tag v0.7.3 v0.7.3
  
  725f3bab
Jun 14, 2024
- Release v0.7.2 · 46065881
  Martin Larralde authored 9 months ago
  
  View commits for tag v0.7.2 v0.7.2
  
  46065881
- Implement `__getitem__` for row access for matrices of `lightmotif-py` · d44e7b0e
  Martin Larralde authored 9 months ago
  
  d44e7b0e
- Allow changing log base in `WeightMatrix.log_odds` method · f7e791de
  Martin Larralde authored 9 months ago
  
  f7e791de
- Add `__len__` implementation for all matrix classes of `lightmotif-py` · 7b58f7e9
  Martin Larralde authored 9 months ago
  
  7b58f7e9
- Release v0.7.1 · d3cce922
  Martin Larralde authored 9 months ago
  
  View commits for tag v0.7.1 v0.7.1
  
  d3cce922
- Release v0.7.0 · d8e791db
  Martin Larralde authored 9 months ago
  
  View commits for tag v0.7.0 v0.7.0
  
  d8e791db
- Replace direct attribute access with getters in `StripedSequence` · 85263f04
  Martin Larralde authored 9 months ago
  
  85263f04
Jun 13, 2024
- Reorganize code for striped scores · 32508c48
  Martin Larralde authored 9 months ago
  
  32508c48
- Use a dedicated type for `ScoringMatrix.score` and refactor code · 840959f7
  Martin Larralde authored 9 months ago
  
  840959f7
- Revert book-keeping attributes used in `StripedScores` · 4d3145ff
  Martin Larralde authored 9 months ago
  
  4d3145ff
- Add method to build the reverse-complement of a PSSM · 87b63939
  Martin Larralde authored 9 months ago
  
  87b63939
- Implement back `StripedScores.__len__` and `StripedScores.__getitem__` · 984b5ea4
  Martin Larralde authored 9 months ago
  
  984b5ea4
Mar 11, 2024
- Make `StripedScores::sequence_index` take a `MatrixCoordinates` argument · 2f1eaa5d
  Martin Larralde authored 1 year ago
  
  2f1eaa5d
- Fix tests and benchmarks to use the new `Maximum` API · 4cd84026
  Martin Larralde authored 1 year ago
  
  4cd84026
Mar 10, 2024
- Remove platform-specific code for thresholding scores · 28adbffe
  Martin Larralde authored 1 year ago
  
  28adbffe