Commits · 2b2a5ff727c90930ff9f8b3790b13dd7b60cdb81 · Martin Larralde / PyFastANI · GitLab

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Aug 20, 2022
- Release v0.4.1 · 2b2a5ff7
  Martin Larralde authored 2 years ago
  
  v0.4.1
  
  2b2a5ff7
- Skip decoding of sequences too small to be processed in `Mapper.query_draft` · 9d1c177d
  Martin Larralde authored 2 years ago
  
  9d1c177d
- Sort hits by identity in descending order before returning them in `Mapper` · 5d52cc60
  Martin Larralde authored 2 years ago
  
  5d52cc60
Aug 12, 2022
- Add a lock to `Sketch` to avoid data races · b461c5f5
  Martin Larralde authored 2 years ago
  
  b461c5f5
- Reduce footprint of pickled `Mapper` objects by skipping index serialization · 2cb3f635
  Martin Larralde authored 2 years ago
  
  2cb3f635
Aug 05, 2022
- Use lists instead of arrays to store state of `Minimizers` · 125528c9
  Martin Larralde authored 2 years ago
  
  125528c9
Aug 04, 2022
- Add `multi-threading` feature to the documentation index [ci skip] · b7d37fbd
  Martin Larralde authored 2 years ago
  
  b7d37fbd
- Add instructions on how to run benchmarks to `CONTRIBUTING.md` [ci skip] · d1f18c60
  Martin Larralde authored 2 years ago
  
  d1f18c60
- Fix link to `v0.4.0` in `CHANGELOG.md` [ci skip] · 46dcfacb
  Martin Larralde authored 2 years ago
  
  46dcfacb
- Add benchmark results to `README.md` [ci skip] · eb918b1f
  Martin Larralde authored 2 years ago
  
  eb918b1f
Aug 03, 2022
- Release v0.4.0 · 090629be
  Martin Larralde authored 2 years ago
  
  v0.4.0
  
  090629be
- Fix missing include path in `setup.py` for building against `cpu_features` · f96e7051
  Martin Larralde authored 2 years ago
  
  f96e7051
- Setup `package.yml` workflow to compile wheels for Aarch64 Linux platforms · 0d06f6a8
  Martin Larralde authored 2 years ago
  
  0d06f6a8
- Avoid spawning a pool if `Mapper` methods are called with `threads=1` · b3c2a724
  Martin Larralde authored 2 years ago
  
  b3c2a724
- Add benchmarks for next `pyfastani` release · 37031d74
  Martin Larralde authored 2 years ago
  
  37031d74
- Fix path to data folder in `benches/mapping/bench.py` · d5b107ae
  Martin Larralde authored 2 years ago
  
  d5b107ae
- Add scripts to benchmark the effect of threads on the query mapping performance · f3038fb1
  Martin Larralde authored 2 years ago
  
  f3038fb1
- Add `versionadded` directive for new `thread` argument of `Mapper` methods · 574ea624
  Martin Larralde authored 2 years ago
  
  574ea624
- Allow configuring thread count when calling `Mapper` query methods · 16180c2c
  Martin Larralde authored 2 years ago
  
  16180c2c
- Make `_Map` deallocate the compute map when garbage collected · 0592817c
  Martin Larralde authored 2 years ago
  
  0592817c
- Reorganize `Mapper` code and remove unneeded arguments · d1e2636c
  Martin Larralde authored 2 years ago
  
  d1e2636c
- Rewrite `Mapper` methods so that `Mapper._query_fragment` can be parallelized · 4b3abeac
  Martin Larralde authored 2 years ago
  
  4b3abeac
- Add an `atomic_vector` wrapper for `vector` where `push_back` is thread-safe · c3ce403d
  Martin Larralde authored 2 years ago
  
  c3ce403d
Jul 23, 2022
- Fix Arm NEON compile flags in `setup.py` · 8558fda7
  Martin Larralde authored 2 years ago
  
  8558fda7
Jul 22, 2022
- Fix `check` step of `PKGBUILD` [ci skip] · ee34237b
  Martin Larralde authored 2 years ago
  
  ee34237b
- Fix include guards in `sequtils.cpp` to compile for Arm platforms · fb18bcfe
  Martin Larralde authored 2 years ago
  
  fb18bcfe
- Fix AUR package name in `package.yml` workflow [ci skip] · 62f72976
  Martin Larralde authored 2 years ago
  
  62f72976
- Fix references in some `Sketch` method docstrings [ci skip] · 1c5e04fa
  Martin Larralde authored 2 years ago
  
  1c5e04fa
- Release v0.3.1 · b58006bd
  Martin Larralde authored 2 years ago
  
  v0.3.1
  
  b58006bd
- Add links and documentation to install the package with `conda` · fab635f2
  Martin Larralde authored 2 years ago
  
  fab635f2
Jul 18, 2022
- Add Python 3.10 to the Python versions supported in `setup.cfg` · c3ec0bef
  Martin Larralde authored 2 years ago
  
  c3ec0bef
- Fix badges and text in Sphinx documentation [ci skip] · 0914f3ca
  Martin Larralde authored 2 years ago
  
  0914f3ca
- Configure `package.yml` Actions workflow to release an Arch User Repository `PKGBUILD` · 7bd2e9da
  Martin Larralde authored 2 years ago
  
  7bd2e9da
- Fix project short description in `setup.cfg` [ci skip] · 51212d57
  Martin Larralde authored 2 years ago
  
  51212d57
- Add Sphinx configuration files to build the project documentation · 0be30707
  Martin Larralde authored 2 years ago
  
  0be30707
- Improve some parts of the `pyfastani` class documentation · 507020f9
  Martin Larralde authored 2 years ago
  
  507020f9
- Fix name of headers included in `sequtils.h` · 32525ab4
  Martin Larralde authored 2 years ago
  
  32525ab4
- Import all public classes to the main `pyfastani` module · db264304
  Martin Larralde authored 2 years ago
  
  db264304
Jul 17, 2022
- Release v0.3.0 · 28036437
  Martin Larralde authored 2 years ago
  
  v0.3.0
  
  28036437
- Fix `package.yml` workflow not updating `setuptools` before testing wheels · fae4a843
  Martin Larralde authored 2 years ago
  
  fae4a843