Commits · 2460bc1ac0172260c53fe9fd175c5eb7f1a1bb83 · Martin Larralde / pyrodigal · GitLab

20 Apr, 2022 7 commits
- Render text as curves in SVG figures · 2460bc1a
  Martin Larralde authored Feb 25, 2022
  
  2460bc1a
- Add reference to users in `paper.bib` and `paper.md` · 9dff0c75
  Martin Larralde authored Feb 25, 2022
  
  9dff0c75
- Start writing about the SIMD heuristic filter · 6a7be93a
  Martin Larralde authored Feb 25, 2022
  
  6a7be93a
- Add GitHub Actions workflow to build the JOSS paper · 71df8f8c
  Martin Larralde authored Feb 24, 2022
  
  71df8f8c
- Add an initial JOSS paper draft in the `paper` directory · 95b0fdf6
  Martin Larralde authored Feb 24, 2022
  
  95b0fdf6
- Release v1.0.0 · be141692
  Martin Larralde authored Apr 20, 2022
  
  be141692
- Fix remaining small issues with documentation · 04f23d48
  Martin Larralde authored Apr 20, 2022
  
  04f23d48
19 Apr, 2022 1 commit
- Improve examples and Prodigal comparison in `README.md` [ci skip] · 33348bc9
  Martin Larralde authored Apr 19, 2022
  
  33348bc9
18 Apr, 2022 2 commits
- Run `black` on the Python source files · 5fa7942d
  Martin Larralde authored Apr 18, 2022
  
  5fa7942d
- Add a doc section on how to install from the Arch User Repository [ci skip] · d9e938ad
  Martin Larralde authored Apr 18, 2022
  
  d9e938ad
15 Apr, 2022 1 commit
- Reorganize allocation code and use a smaller growth factor for dynamic arrays · 79dacd3f
  Martin Larralde authored Apr 15, 2022
  
  79dacd3f
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 4 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