Commits · 8b41a59a7d451dbaf23124b3992477a2d7d244a7 · Martin Larralde / PyHMMER · GitLab

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Jun 06, 2024
- Make `HMMFile` and `HMMPressedFile` raise `AlphabetMismatch` on files with mixed alphabets · 8b41a59a
  Martin Larralde authored 9 months ago
  
  8b41a59a
- Update `AlphabetMismatch` error to allow for an unknown actual alphabet · c23e798c
  Martin Larralde authored 9 months ago
  
  c23e798c
Apr 25, 2024
- Release v0.10.12 · 735ec14a
  Martin Larralde authored 11 months ago
  
  v0.10.12
  
  735ec14a
- Update `test.yml` Actions workflow to use `macos-12` runner image · b5be2e41
  Martin Larralde authored 11 months ago
  
  b5be2e41
- Fix bug with model composition and cutoffs in `HMM.__setstate__` (#67) · 7b1ffb83
  Martin Larralde authored 11 months ago
  
  7b1ffb83
Apr 20, 2024
- Replace `t2pks.hmm` with `RREFam` in documentation [ci skip] · c5234e58
  Martin Larralde authored 11 months ago
  
  c5234e58
Mar 28, 2024
- Delete unused HMMER2-formatted HMMs in tests data · 8cf9a2eb
  Martin Larralde authored 1 year ago
  
  8cf9a2eb
- Add missing BibTex file with citations to documentation [ci skip] · a260b8cf
  Martin Larralde authored 1 year ago
  
  a260b8cf
- Add more rules to `.gitignore` files [ci skip] · 75b4b02f
  Martin Larralde authored 1 year ago
  
  75b4b02f
- Complete replacement of `t2pks.hmm` with `RREFam.hmm` in tests data · ba340839
  Martin Larralde authored 1 year ago
  
  ba340839
- Replace `t2pks.hmm` in remaining `Pipeline` and `HMMFile` tests · 52b54a9a
  Martin Larralde authored 1 year ago
  
  52b54a9a
- Start replacing `t2pks.hmm` with `RREFam.hmm` to reduce test data size · bab9851a
  Martin Larralde authored 1 year ago
  
  bab9851a
- Use smaller genome for `RF0001` test and remove full genome from test sequences · 511ed0e0
  Martin Larralde authored 1 year ago
  
  511ed0e0
- Use smaller genome file to test `nhmmer` with `bmyd.hmm` · c93ee7d6
  Martin Larralde authored 1 year ago
  
  c93ee7d6
- Use `-g1` instead of `--strip-all` to retain debug tracebacks in release mode · f2658eb0
  Martin Larralde authored 1 year ago
  
  f2658eb0
Mar 27, 2024
- Allow skipping tests using `t2pks.hmm` to reduce size of distribution · 8f9c9b3d
  Martin Larralde authored 1 year ago
  
  8f9c9b3d
- Strip built extensions to reduce wheels size · 3f7f0f57
  Martin Larralde authored 1 year ago
  
  3f7f0f57
- Release v0.10.11 · 018a6506
  Martin Larralde authored 1 year ago
  
  v0.10.11
  
  018a6506
- Add instructions to install package with BioArchLinux · b896f9fb
  Martin Larralde authored 1 year ago
  
  b896f9fb
- Fix HMMER being built without SSE4.1 support after b3d71d83 · 0e032298
  Martin Larralde authored 1 year ago
  
  0e032298
Mar 18, 2024
- Release v0.10.10 · 03b66255
  Martin Larralde authored 1 year ago
  
  v0.10.10
  
  03b66255
- Fix handling of NULL buffers in `fopencookie` functions · 8d28bca9
  Martin Larralde authored 1 year ago
  
  8d28bca9
- Fix handling of file objects in `Sequence.write` and `MSA.write` · ccdb403d
  Martin Larralde authored 1 year ago
  
  ccdb403d
Mar 17, 2024
- Use `off_t` instead of `off64_t` for `fopencookie` implementation · 295176ca
  Martin Larralde authored 1 year ago
  
  295176ca
Mar 13, 2024
- Fix typo in documentation [ci skip] · 31671a7d
  Martin Larralde authored 1 year ago
  
  31671a7d
Mar 12, 2024
- Release v0.10.9 · 343e71db
  Martin Larralde authored 1 year ago
  
  v0.10.9
  
  343e71db
- Fix array reallocation formula causing segfaults in `nhmmer` (#62) · d61316c5
  Martin Larralde authored 1 year ago
  
  d61316c5
Mar 05, 2024
- Release v0.10.8 · 824962da
  Martin Larralde authored 1 year ago
  
  v0.10.8
  
  824962da
- Add getter to access the strand of a `nhmmer` domain · 9862cc73
  Martin Larralde authored 1 year ago
  
  9862cc73
- Make sure `IsADirectory` is raised when passed path to folders in file classes · 330e536a
  Martin Larralde authored 1 year ago
  
  330e536a
- Remove `aarch64` tests from CI until GitHub supports native runners · 53d5d353
  Martin Larralde authored 1 year ago
  
  53d5d353
- Add more tests to improve coverage of `pyhmmer.plan7` · 060b0715
  Martin Larralde authored 1 year ago
  
  060b0715
- Add missing `RF00001` HMM for tests · ebd15e5c
  Martin Larralde authored 1 year ago
  
  ebd15e5c
- Check for E-values consistency in `nhmmer` across different window lengths · 15252021
  Martin Larralde authored 1 year ago
  
  15252021
- Update `nhmmer` to use `window_length` and `window_beta` parameters for `bUilder` · 0088ef46
  Martin Larralde authored 1 year ago
  
  0088ef46
- Fix `versionadded` directives in `OptimizedProfile` · 35ece5ef
  Martin Larralde authored 1 year ago
  
  35ece5ef
- Allow `LongTargetsPipeline` to be configured with window length and beta parameters · f510f0a1
  Martin Larralde authored 1 year ago
  
  f510f0a1
- Update `MissingCutoffs` exception to display model and cutoff names · 37237222
  Martin Larralde authored 1 year ago
  
  37237222
Mar 04, 2024
- Release v0.10.7 · 43aa46cf
  Martin Larralde authored 1 year ago
  
  v0.10.7
  
  43aa46cf
- Compile wheels for PyPy 3.10 in `package.yml` · d326100b
  Martin Larralde authored 1 year ago
  
  d326100b