Commits · b40420585e037c858affd4488b026ba8be410ba9 · Martin Larralde / PyHMMER · GitLab

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Jul 09, 2024
- Implement detection of SSE flush modes in `setup.py` · 915ac0c5
  Martin Larralde authored 8 months ago
  
  915ac0c5
Mar 28, 2024
- Use `-g1` instead of `--strip-all` to retain debug tracebacks in release mode · f2658eb0
  Martin Larralde authored 1 year ago
  
  f2658eb0
Mar 27, 2024
- Strip built extensions to reduce wheels size · 3f7f0f57
  Martin Larralde authored 1 year ago
  
  3f7f0f57
- Fix HMMER being built without SSE4.1 support after b3d71d83 · 0e032298
  Martin Larralde authored 1 year ago
  
  0e032298
Feb 21, 2024
- Fix rendering of Cython function signatures · c3446c53
  Martin Larralde authored 1 year ago
  
  c3446c53
Aug 31, 2023
- Use `nonecheck` Cython directive when compiling in debug mode · 24ff032c
  Martin Larralde authored 1 year ago
  
  24ff032c
Aug 17, 2023
- Fix platform name detection in `setup.py` · d1aca346
  Martin Larralde authored 1 year ago
  
  d1aca346
Aug 16, 2023
- Fix flags used for detecting NEON on Arm platforms · f782ee49
  Martin Larralde authored 1 year ago
  
  f782ee49
- Fix handling of target platform between commands in `setup.py` · d0249ff6
  Martin Larralde authored 1 year ago
  
  d0249ff6
- Attempt fixing platform detection for MacOS in `setup.py` · b18c721b
  Martin Larralde authored 1 year ago
  
  b18c721b
- Rewrite the `setup.py` platform detection code to facilitate MacOS cross-compilation · b3d71d83
  Martin Larralde authored 1 year ago
  
  b3d71d83
- Add patch for missing `PyInterpreterState_GetID` on PyPy · 1e34754b
  Martin Larralde authored 1 year ago
  
  1e34754b
Aug 04, 2023
- Add Cython headers for NEON port of the HMMER implementation · c145e69f
  Martin Larralde authored 2 years ago
  
  c145e69f
- Update `test.yml` Actions workflow to build wheels for Aarch64 Linux · e4105ef7
  Martin Larralde authored 2 years ago
  
  e4105ef7
- Update platform detection code in `setup.py` to compile NEON code on Arm platforms · b354ec5f
  Martin Larralde authored 2 years ago
  
  b354ec5f
Aug 03, 2023
- Port `fileobj` implementation to C to enable conditional compilation · 40bc99f7
  Martin Larralde authored 1 year ago
  
  40bc99f7
Aug 02, 2023
- Update `setup.py` to ignore `-Wunused-variable` errors when building Cython code · f98f4284
  Martin Larralde authored 1 year ago
  
  f98f4284
Apr 13, 2023
- Use parallel build to speed-up CI in `test.yml` workflow · b47b5dd9
  Martin Larralde authored 1 year ago
  
  b47b5dd9
Dec 14, 2022
- Use proper function arguments when detecting available C functions in `setup.py` · 71913302
  Martin Larralde authored 2 years ago
  
  71913302
- Remove silent compiler spawning in `configure` command of `setup.py` · 8454c0db
  Martin Larralde authored 2 years ago
  
  8454c0db
Jun 28, 2022
- Fix unsound decoding of `Matrix` and `Vector` from bytes without checking endianness · c54273dc
  Martin Larralde authored 2 years ago
  
  c54273dc
Jun 21, 2022
- Remove `arm64` compilation flags from OSX in `setup.py` · 011305c6
  Martin Larralde authored 2 years ago
  
  011305c6
Jun 20, 2022
- Setup parallel compilation of vendored C libraries · 666967bc
  Martin Larralde authored 2 years ago
  
  666967bc
Apr 19, 2022
- Rename `hmmpgmd` module to more intuitive `daemon` module · e8dfd296
  Martin Larralde authored 2 years ago
  
  e8dfd296
- Add the `hmmpgmd` module implementing the `hmmc2` client · 4d0de49f
  Martin Larralde authored 2 years ago
  
  4d0de49f
Oct 18, 2021
- Update `plan7.Cutoffs` to allow setting the cutoffs of an `HMM` or a `Profile` · 34a1d097
  Martin Larralde authored 3 years ago
  
  34a1d097
Oct 08, 2021
- Allow opening a `SequenceFile` directly from a file-like object · fbe00e61
  Martin Larralde authored 3 years ago
  
  fbe00e61
Aug 23, 2021
- Expose the Python version for which the extensions are compiled in `setup.py` · 22c92e4f
  Martin Larralde authored 3 years ago
  
  22c92e4f
Jul 18, 2021
- Enable Cython debugging symbols when compiling extensions with `--debug` flag · 9bf9fc97
  Martin Larralde authored 3 years ago
  
  9bf9fc97
Jul 01, 2021
- Make `python setup.py configure` actually check compiler supports SSE or VMX · 508d149c
  Martin Larralde authored 3 years ago
  
  508d149c
Jun 12, 2021
- Manually pass static libraries as extra link objects in `build_ext` command of `setup.py` · 1cb1d195
  Martin Larralde authored 3 years ago
  
  1cb1d195
Mar 09, 2021
- Fix typo in `setup.py` preventing compilation on OSX platforms · d018844e
  Martin Larralde authored 4 years ago
  
  d018844e
- Use `-Og` instead of `-O0` when compiling libraries and extensions in debug mode · 7583990a
  Martin Larralde authored 4 years ago
  
  7583990a
Mar 08, 2021
- Make extensions in `setup.py` use the include dirs of their library dependencies · 378e5165
  Martin Larralde authored 4 years ago
  
  378e5165
Mar 03, 2021
- Add GitHub Actions workflow to build on Linux and OSX · db7ccc90
  Martin Larralde authored 4 years ago
  
  db7ccc90
Dec 02, 2020
- Expose `sys.implementation` as a Cython compile-time variable · e6615db8
  Martin Larralde authored 4 years ago
  
  e6615db8
Nov 28, 2020
- Fix `setup.py` to avoid copying all vendored sources · 1f86f098
  Martin Larralde authored 4 years ago
  
  1f86f098
Nov 26, 2020
- Make `p7_hmmfile` patch in `setup.py` work with cached files · c31d2876
  Martin Larralde authored 4 years ago
  
  c31d2876
- Fix patching of `p7_hmmfile.c` in `setup.py` · d26ea76f
  Martin Larralde authored 4 years ago
  
  d26ea76f
- Allow opening a `HMMFile` from a Python file-handle instead of a path · ca5be952
  Martin Larralde authored 4 years ago
  
  ca5be952