Commits · 84d210d9cb4a8b4d6ea88d60d171685f8edcfade · Martin Larralde / PyHMMER · GitLab

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Jan 20, 2025
- Fix MathJax in `LongTargetsPipeline` docstring [ci skip] · 84d210d9
  Martin Larralde authored 1 month ago
  
  84d210d9
Jan 10, 2025
- Add link to PiWheels in `pyproject.toml` [ci skip] · 97808f1e
  Martin Larralde authored 2 months ago
  
  97808f1e
- Fix issue on existing virtualenv in `PKGBUILD` [ci skip] · e9a401ec
  Martin Larralde authored 2 months ago
  
  e9a401ec
- Fix use of `query_name` in example of `README.md` [ci skip] · fb3f4a08
  Martin Larralde authored 2 months ago
  
  fb3f4a08
- Fix link to exmaple data in documentation notebooks [ci skip] · 2f62cd56
  Martin Larralde authored 2 months ago
  
  2f62cd56
- Fix tests on MacOS failing in `test.yml` Actions workflow · a161f399
  Martin Larralde authored 2 months ago
  
  a161f399
- Fix AUR deployment step in `package.yml` Actions workflow · 4ab2fdae
  Martin Larralde authored 2 months ago
  
  4ab2fdae
- Remove 'experimental' disclaimer from `README.md` [ci skip] · 6cb7afb9
  Martin Larralde authored 2 months ago
  
  6cb7afb9
- Update `test.yml` Actions workflow to run tests with Python 3.13 · a97a444f
  Martin Larralde authored 2 months ago
  
  a97a444f
- Release v0.11.0 · 04b929b1
  Martin Larralde authored 2 months ago
  
  v0.11.0
  
  04b929b1
- Fix outdated runners in GitHub Actions [ci skip] · 2a95d121
  Martin Larralde authored 2 months ago
  
  2a95d121
- Remove deprecated query properties of `TopHits` · 36f1dda8
  Martin Larralde authored 2 months ago
  
  36f1dda8
Nov 05, 2024
- Use `test-extras` to install test requirements in `cibuildwheel` [ci skip] · 57fdadea
  Martin Larralde authored 4 months ago
  
  57fdadea
Oct 27, 2024
- Setup compilation of HMMER impl for NEON and VMX platforms · 67894e0b
  Martin Larralde authored 4 months ago
  
  67894e0b
- Fix path to test data in docs and update Biopython inventory URL [ci skip] · aef87413
  Martin Larralde authored 4 months ago
  
  aef87413
- Update documentation to use `related.rst` from GitHub Gists [ci skip] · 83699634
  Martin Larralde authored 4 months ago
  
  83699634
- Fix documentation build using outdated metadata [ci skip] · 50fd6809
  Martin Larralde authored 4 months ago
  
  50fd6809
Oct 25, 2024
- Add tests for `__getbuffer__` implementation of `TextSequence` and `DigitalSequence` · f4cf040c
  Martin Larralde authored 4 months ago
  
  f4cf040c
- Silence `BrokenPipeError` exceptions of `pyhmmer.hmmer` workers · 6d2b28a6
  Martin Larralde authored 4 months ago
  
  6d2b28a6
- Fix issue with buffer export in `TextSequence` and `DigitalSequence` · 003379bd
  Martin Larralde authored 4 months ago
  
  003379bd
- Add `mypy` type hints to buffer-protocol classes in `pyhmmer.easel` · fdfbbfb7
  Martin Larralde authored 4 months ago
  
  fdfbbfb7
- Implement read-only buffer protocol for `TextSequence` and `DigitalSequence` · fec78d0c
  Martin Larralde authored 4 months ago
  
  fec78d0c
- Disable `cibuildwheel` builds for free-threaded Python · 16045f52
  Martin Larralde authored 4 months ago
  
  16045f52
- Update `cibuildwheel` configuration in `package.yml` Actions workflow · 4eaaa507
  Martin Larralde authored 4 months ago
  
  4eaaa507
Oct 24, 2024
- Add `cibuildwheel` configuration to avoid rebuilding HMMER between Python versions · 7f5ca71c
  Martin Larralde authored 4 months ago
  
  7f5ca71c
Oct 21, 2024
- Fix extraction of package version in `package.yml` [ci skip] · 4333c80b
  Martin Larralde authored 4 months ago
  
  4333c80b
Oct 18, 2024
- Fix some Cython extension definitions and defines in `CythonExtension.cmake` · 629c3f06
  Martin Larralde authored 4 months ago
  
  629c3f06
Oct 16, 2024
- Update `PKGBUILD` to use new `scikit-build-core` build [ci skip] · be2eabf2
  Martin Larralde authored 4 months ago
  
  be2eabf2
Oct 15, 2024
- Document the `backend` parameter to `pyhmmer.hmmer` functions · 33e976e2
  Martin Larralde authored 5 months ago
  
  33e976e2
- Add support for multiprocessing parallelism in `jackhmmer` · cb43e596
  Martin Larralde authored 5 months ago
  
  cb43e596
- Fix detection of `easel` test files in `pyhmmer.tests.utils` · 464f4782
  Martin Larralde authored 5 months ago
  
  464f4782
- Remove configurable pipeline class from `pyhmmer.hmmer` classes · cb2c44f8
  Martin Larralde authored 5 months ago
  
  cb2c44f8
- Use a `Literal` to mark allowed types for `backend` argument of `pyhmmer.hmmer` methods · 75b18bf3
  Martin Larralde authored 5 months ago
  
  75b18bf3
- Make documentation of worker abstract about processes or threads · 136b1fd8
  Martin Larralde authored 5 months ago
  
  136b1fd8
- Fix type annotation issues in `pyhmmer.hmmer` module · ae2ce706
  Martin Larralde authored 5 months ago
  
  ae2ce706
- Ignore `pyhmmer.tests` module when running `mypy` typechecking · 5fdc573d
  Martin Larralde authored 5 months ago
  
  5fdc573d
- Update `_BaseWorker` to avoid creating a new `Pipeline` in the main thread · 6bd85b2a
  Martin Larralde authored 5 months ago
  
  6bd85b2a
- Add tests for `multiprocessing`-driven `hmmsearch` and fix some exit conditions · da0d0f78
  Martin Larralde authored 5 months ago
  
  da0d0f78
- Implement process-based workers for `hmmscan`, `hmmsearch`, `phmmer` and `nhmmer` · 26ec8b2e
  Martin Larralde authored 5 months ago
  
  26ec8b2e
- Refactor the `pyhmmer.hmmer` worker/dispatcher model to support `Process` workers · 60683a96
  Martin Larralde authored 5 months ago
  
  60683a96