Commits · 629c3f06851b68430ba2d3444abd500140e4cc4c · Martin Larralde / PyHMMER · GitLab

Snippets Groups Projects

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
- Fix logic error causing out-of-buffer access in `__getstate__` method of empty `TopHits` · 1451794e
  Martin Larralde authored 5 months ago
  
  1451794e
- Reorganize `pyhmmer.hmmer` into different submodules · 3aead9cc
  Martin Larralde authored 5 months ago
  
  3aead9cc
- Make `pyhmmer.hmmer` a Python submodule · ce2f8c66
  Martin Larralde authored 5 months ago
  
  ce2f8c66
- Update `CONTRIBUTING.md` with new build instructions using `pip` editable mode · 39487006
  Martin Larralde authored 4 months ago
  
  39487006
Oct 13, 2024
- Remove outdated GitLab-CI configuration files [ci skip] · b79f0168
  Martin Larralde authored 5 months ago
  
  b79f0168
- Update install instructions in documentation [ci skip] · df55ac2d
  Martin Larralde authored 5 months ago
  
  df55ac2d
- Add setters for residue-wise annotation properties in `HMM` · fbca9822
  Martin Larralde authored 5 months ago
  
  fbca9822
Oct 12, 2024
- Merge branch 'cmake-build' · 940a56f5
  Martin Larralde authored 5 months ago
  
  940a56f5
- Update `package.yml` Actions workflow to use `pyproject.toml` for AUR · df78a4d9
  Martin Larralde authored 5 months ago
  
  df78a4d9
- Remove outdated code from `CythonExtension.cmake` [ci skip] · 8c6ecd14
  Martin Larralde authored 5 months ago
  
  8c6ecd14
- Remove outdated `setuptools` configuration files · 200c1bb4
  Martin Larralde authored 5 months ago
  
  200c1bb4
- Remove Python 3.6 from the project classifiers in `pyproject.toml` · 601de3af
  Martin Larralde authored 5 months ago
  
  601de3af
- Fix detection of `PyInterpreterState_GetID` in CMake files · 2bb79a90
  Martin Larralde authored 5 months ago
  
  2bb79a90
- Attempt fixing detection of `PyInterpreterState_GetID` · 2146a98f
  Martin Larralde authored 5 months ago
  
  2146a98f
- Fix detection of Python implementation in `CythonExtension.cmake` script · 8f4f6abb
  Martin Larralde authored 5 months ago
  
  8f4f6abb
Oct 11, 2024
- Update CMake files to avoid rebuilding when not needed · d4ca7f3c
  Martin Larralde authored 5 months ago
  
  d4ca7f3c
- Make Cython generate depfiles to use with CMake · 340da4aa
  Martin Larralde authored 5 months ago
  
  340da4aa
- Show `esl_config_h` while building to debug CI · be087b37
  Martin Larralde authored 5 months ago
  
  be087b37
- Fix detection of `PyInterpreterState_GetID` · 921dfd54
  Martin Larralde authored 5 months ago
  
  921dfd54
Oct 10, 2024
- Add Ninja to the build dependencies in CI · e6a453bd
  Martin Larralde authored 5 months ago
  
  e6a453bd
- Fix issues with continuous integration setup · 8e62ef81
  Martin Larralde authored 5 months ago
  
  8e62ef81
- Add missing `CMakeLists.txt` for `pyhmmer` module · 55752e49
  Martin Larralde authored 5 months ago
  
  55752e49
- Fix new CMake build steps in CI · 405f3e3a
  Martin Larralde authored 5 months ago
  
  405f3e3a
Oct 09, 2024
- Fix detection of SIMD compile flags in CMake lists · f37361ee
  Martin Larralde authored 5 months ago
  
  f37361ee
- Fix redefinition of variables between `esl_config.h` and `Python.h` · 8fb98a54
  Martin Larralde authored 5 months ago
  
  8fb98a54
- Add `pyproject.toml` file to handle build `scikit-build-core` · dcbef082
  Martin Larralde authored 5 months ago
  
  dcbef082