Commits · 6c4efa66db91e8e6bb5731eb001195b12601a163 · Martin Larralde / pyrodigal · GitLab

14 Apr, 2022 4 commits
- Fix rendering of some docstrings in `pyrodigal.Gene` [ci skip] · 6c4efa66
  Martin Larralde authored Apr 14, 2022
  
  6c4efa66
- Document methods of `ConnectionScorer` and add `__sizeof__` method · 90b51ea1
  Martin Larralde authored Apr 14, 2022
  
  90b51ea1
- Move `_score_connections` into a C header and use function pointers where applicable · da417ab6
  Martin Larralde authored Apr 14, 2022
  
  da417ab6
- Rewrite connection scoring into different functions depending on the target node · fbe7a811
  Martin Larralde authored Apr 14, 2022
  
  fbe7a811
13 Apr, 2022 4 commits
- Refactor Shine-Dalgarno methods to force Cython to generate C switches · 243a540e
  Martin Larralde authored Apr 13, 2022
  
  243a540e
- Reorganize code in `Sequence._shine_dalgarno_exact` and `Sequence._shine_dalgarno_mm` · a3905479
  Martin Larralde authored Apr 13, 2022
  
  a3905479
- Refactor common code between `Sequence.from_string` and `Sequence.from_bytes` · 7ef79734
  Martin Larralde authored Apr 13, 2022
  
  7ef79734
- Implement buffer protocol for `Sequence` and refactor allocation in `Nodes` and `Genes` · 9033027e
  Martin Larralde authored Apr 13, 2022
  
  9033027e
11 Apr, 2022 5 commits
- Add missing `pyrodigal.tests.test_mask` file · 5e5e9d52
  Martin Larralde authored Apr 11, 2022
  
  5e5e9d52
- Wrap exceptions in `pyrodigal.cli.main` to display a better error message · 56693895
  Martin Larralde authored Apr 11, 2022
  
  56693895
- Expose `TRANSLATION_TABLES` and `METAGENOMIC_BINS` constants in `pyrodigal` module · 918e5588
  Martin Larralde authored Apr 11, 2022
  
  918e5588
- Add some magic methods to `Mask` · 96b6e2ce
  Martin Larralde authored Apr 11, 2022
  
  96b6e2ce
- Avoid naive search for mask on every position when region-masking is enabled · e6836a83
  Martin Larralde authored Apr 11, 2022
  
  e6836a83
08 Apr, 2022 4 commits
- Implement pickle protocol for `pyrodigal.Genes` · 9dfebbd2
  Martin Larralde authored Apr 08, 2022
  
  9dfebbd2
- Implement `TrainingInfo.__sizeof__` as a `cpdef` function · a3befd28
  Martin Larralde authored Apr 08, 2022
  
  a3befd28
- Implement pickle protocol for `pyrodigal.Sequence` · 01f1b84f
  Martin Larralde authored Apr 08, 2022
  
  01f1b84f
- Implement pickle protocol for `pyrodigal.OrfFinder` · 069d959a
  Martin Larralde authored Apr 08, 2022
  
  069d959a
07 Apr, 2022 2 commits
- Implement pickle protocol for `pyrodigal.TrainingInfo` · 382787a9
  Martin Larralde authored Apr 07, 2022
  
  382787a9
- Implement pickle protocol for `pyrodigal.Nodes` · 6013273e
  Martin Larralde authored Apr 07, 2022
  
  6013273e
06 Apr, 2022 3 commits
- Add regression test using data from #13 · cab5bb41
  Martin Larralde authored Apr 06, 2022
  
  cab5bb41
- Release v0.7.3 · d5293f70
  Martin Larralde authored Apr 06, 2022
  
  d5293f70
- Fix rescoring of best nodes in `OrfFinder._find_genes_meta` · b05826b6
  Martin Larralde authored Apr 06, 2022
  
  b05826b6
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 15 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