Commits · 340da4aad0af16f5eeb77e65385ab1c8cfe63289 · Martin Larralde / PyHMMER · GitLab

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Oct 11, 2024
- 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
- Add files for building Easel and HMMER with CMake · 80bd3e71
  Martin Larralde authored 5 months ago
  
  80bd3e71
- Fix build error when attempting to build on an unsupported platform · dcb6b464
  Martin Larralde authored 5 months ago
  
  dcb6b464
- Setup detection of AltiVec extensions for PowerPC platforms · f029b54a
  Martin Larralde authored 5 months ago
  
  f029b54a
- Fix handling of required SIMD flags in CMake · 66556abd
  Martin Larralde authored 5 months ago
  
  66556abd
- Fix setup of target system when compiling Cython code · 0af106b7
  Martin Larralde authored 5 months ago
  
  0af106b7
- Fix issue in `CythonExtension` script on missing `.pxd` file · 499d059c
  Martin Larralde authored 5 months ago
  
  499d059c
- Add `CMakeLists.txt` files to compile Easel and HMMER · dff7b8c6
  Martin Larralde authored 5 months ago
  
  dff7b8c6
- Move `pyhmmer` into a dedicated `src` directory · 156ab49e
  Martin Larralde authored 5 months ago
  
  156ab49e
- Remove `pyproject.toml` from `.gitignore` to support up-to-date build · 4e114835
  Martin Larralde authored 5 months ago
  
  4e114835
- Implement `__len__` for `HMMPressedFile` using the SSI index · c7cc98b9
  Martin Larralde authored 5 months ago
  
  c7cc98b9
Oct 08, 2024
- Make `MSAFile` generic over the `MSA` type based on `digital` flag · 480b7fb8
  Martin Larralde authored 5 months ago
  
  480b7fb8
- Overload `SequenceFile.read_block` with concrete `SequenceBlock` types · f7a37a3b
  Martin Larralde authored 5 months ago
  
  f7a37a3b
- Make `SequenceFile` generic on the sequence type · c59025e0
  Martin Larralde authored 5 months ago
  
  c59025e0
- Use faster `PyUnicode` functions to decode fixed-sized strings of `HMM` and `Profile` · 5433c1a8
  Martin Larralde authored 5 months ago
  
  5433c1a8
- Fix type annotations for Python 3.8 to 3.10 · c2fb99e4
  Martin Larralde authored 5 months ago
  
  c2fb99e4
- Add `SequenceFile` as an accepted type for most `hmmer` functions · 21600453
  Martin Larralde authored 5 months ago
  
  21600453
- Fix detection of alphabet from arbitrary queries in `phmmer` and `hmmscan` · f4f81a18
  Martin Larralde authored 5 months ago
  
  f4f81a18
- Reorganize detection and handling of alphabets in `pyhmmer.hmmer` · 950e7238
  Martin Larralde authored 5 months ago
  
  950e7238
- Fix type annotations for `LongTargetsPipeline` specific options and properties · f8e443de
  Martin Larralde authored 5 months ago
  
  f8e443de
- Use new `TypedDict` API to a typing information to `pyhmmer.hmmer` functions · 5ec54584
  Martin Larralde authored 5 months ago
  
  5ec54584
- Release v0.10.15 · 274cee30
  Martin Larralde authored 5 months ago
  
  v0.10.15
  
  274cee30
- Fix rendering of `TopHits.query` doctest · 127d95ab
  Martin Larralde authored 5 months ago
  
  127d95ab
- Disable detection of CPU float behaviour in `setup.py` · 88a66e28
  Martin Larralde authored 5 months ago
  
  88a66e28
- Merge pull request #78 from althonos/top-hits-query · b2627eb0
  Martin Larralde authored 5 months ago
  
  Record query object in every `TopHits` object.
  b2627eb0
- Fix handling of `TopHits` in `pyhmmer.daemon.Client` · 41c377e6
  Martin Larralde authored 5 months ago
  
  41c377e6
- Fix use of deprecated `TopHits` properties in documentation · a13e32aa
  Martin Larralde authored 5 months ago
  
  a13e32aa
- Fix use of deprecated `TopHits` properties in pyhmmer.tests · 85c532e4
  Martin Larralde authored 5 months ago
  
  85c532e4
- Add deprecation warnings to old `TopHits` query properties · 5ad28e24
  Martin Larralde authored 5 months ago
  
  5ad28e24
- Fix type annotations in `pyhmmer.hmmer` to pass the query type transparently · 54259b60
  Martin Larralde authored 5 months ago
  
  54259b60
- Fix type hints in `pyhmmer.hmmer` · e64bb172
  Martin Larralde authored 5 months ago
  
  e64bb172