Commits · 069d11cfd233c0b90e977ccc6471865544dbf50e · Martin Larralde / pyrodigal · GitLab

05 Apr, 2022 3 commits
- Add `Gene.score` property to get a gene score as reported in the score data · 069d11cf
  Martin Larralde authored Apr 06, 2022
  
  069d11cf
- Fix `OrfFinder.find_genes` not rebuilding node scores of the maximum phase in meta mode · 1f1528ee
  Martin Larralde authored Apr 06, 2022
  
  1f1528ee
- Fix random behaviour caused by occasional out-of-bound access while in meta mode · c883d994
  Martin Larralde authored Apr 06, 2022
  
  c883d994
15 Mar, 2022 19 commits
- Release v0.7.2 · e08f5014
  Martin Larralde authored Mar 15, 2022
  
  e08f5014
- Add bench plot for next patch release · c693dcea
  Martin Larralde authored Mar 15, 2022
  
  c693dcea
- Return double precision numbers from `Node._intergenic_mod` functions · 252f5db0
  Martin Larralde authored Mar 15, 2022
  
  252f5db0
- Disable coverage measurement since it takes too long · d6654d1c
  Martin Larralde authored Mar 15, 2022
  
  d6654d1c
- Use original Prodigal code instead of the generic filter when SIMD is unavailable · 1327832f
  Martin Larralde authored Mar 15, 2022
  
  1327832f
- Update plot script in `connection_scoring` benchmark · 172297d4
  Martin Larralde authored Mar 15, 2022
  
  172297d4
- Replace `add_nodes` with `Nodes.extract` in `connection_scoring` benchmark code · 9666df6e
  Martin Larralde authored Mar 15, 2022
  
  9666df6e
- Make `ConnectionScorer._index` a no-op when using Prodigal backend · 7cec8f63
  Martin Larralde authored Mar 15, 2022
  
  7cec8f63
- Update `neon` SIMD code to use generic filter on edges · 5b1c6b75
  Martin Larralde authored Mar 15, 2022
  
  5b1c6b75
- Update `connection_scoring` benchmark to test the generic filter · cd5d3ef4
  Martin Larralde authored Mar 15, 2022
  
  cd5d3ef4
- Test that the generic connection filter produces the same score as the Prodigal code · f9640791
  Martin Larralde authored Mar 15, 2022
  
  f9640791
- Add option to use original Prodigal code in `ConnectionScoring` for testing · f3f6e717
  Martin Larralde authored Mar 15, 2022
  
  f3f6e717
- Rewrite `dprog.score_connection` as a `ConnectionScorer` static method · d6af8598
  Martin Larralde authored Mar 15, 2022
  
  d6af8598
- Add `const` qualifier where possible for C function arguments · 33ed2a05
  Martin Larralde authored Mar 15, 2022
  
  33ed2a05
- Fix `_sequence.h` not being inlined as expected · 1d87ee6d
  Martin Larralde authored Mar 15, 2022
  
  1d87ee6d
- Fix some repeated calls to `_mer_ndx` in `TrainingInfo._update_motif_counts` · 34044ae5
  Martin Larralde authored Mar 15, 2022
  
  34044ae5
- Add functions to compute the intergenic node modifier as `Node` static methods · 9c177488
  Martin Larralde authored Mar 15, 2022
  
  9c177488
- Use a generic implementation of the connection scoring filter for unsupported CPUs · 1c2f9b89
  Martin Larralde authored Mar 15, 2022
  
  1c2f9b89
- Reword `Memory` subsection of `README.md` [ci skip] · 4ba781f4
  Martin Larralde authored Mar 15, 2022
  
  4ba781f4
14 Mar, 2022 18 commits
- Remove the `embedsignature` Cython directive from `_pyrodigal.pyx` · b54cfb82
  Martin Larralde authored Mar 14, 2022
  
  b54cfb82
- Update `PKGBUILD.in` to run all tests during `check` phase [ci skip] · 4c4b9c31
  Martin Larralde authored Mar 14, 2022
  
  4c4b9c31
- Release v0.7.1 · 1f78e006
  Martin Larralde authored Mar 14, 2022
  
  1f78e006
- Fix older compilers failing to use `inline` functions in `_sequence.h` · 14e87a34
  Martin Larralde authored Mar 14, 2022
  
  14e87a34
- Fix memory leak caused by memory not being freed in `calc_most_gc_frame` · a284c96b
  Martin Larralde authored Mar 14, 2022
  
  a284c96b
- Build extension in release mode on Windows Actions runner · d72b130f
  Martin Larralde authored Mar 14, 2022
  
  d72b130f
- Make Cython compile with additional warnings when in debug mode · 8e1f29cc
  Martin Larralde authored Mar 14, 2022
  
  8e1f29cc
- Fix `Gene.translate` ignoring the `unknown_residue` argument value · b068dd94
  Martin Larralde authored Mar 14, 2022
  
  b068dd94
- Only run coverage measurement on the `main` branch · 845d9fe0
  Martin Larralde authored Mar 14, 2022
  
  845d9fe0
- Skip measuring coverage for PyPy · de16af2f
  Martin Larralde authored Mar 14, 2022
  
  de16af2f
- Use `nucleotide` enum values defined in `_sequence.h` · 36d98238
  Martin Larralde authored Mar 14, 2022
  
  36d98238
- Use bit-twiddling instead of LUT to complement nucleotides when possible in `_sequence.h` · d81ce87c
  Martin Larralde authored Mar 14, 2022
  
  d81ce87c
- Implement `_mer_ndx` in `_sequence.h` so that it can be inlined · 1287df62
  Martin Larralde authored Mar 14, 2022
  
  1287df62
- Fix coverage not being properly collected in GitHub Actions · 1f9b509c
  Martin Larralde authored Mar 14, 2022
  
  1f9b509c
- Fix debug flags used to build extension with `--debug` argument · 236263c2
  Martin Larralde authored Mar 14, 2022
  
  236263c2
- Inline functions used for nucleotide matching using an additional C header · ad36a0cd
  Martin Larralde authored Mar 14, 2022
  
  ad36a0cd
- Fix bug causing `Nodes.copy` to fail when copying an empty collection · 59010c3c
  Martin Larralde authored Mar 14, 2022
  
  59010c3c
- Fix `TestGenes.test_write_scores` to skip comparing formatted float values · 1906f10b
  Martin Larralde authored Mar 14, 2022
  
  1906f10b