Commits · main · Martin Larralde / pyrodigal · GitLab

13 May, 2022 2 commits
- Release v1.0.2 · d0d48f70
  Martin Larralde authored May 13, 2022
  
  d0d48f70
- Fix detection of Arm64 platform in `setup.py` · 5fee93d8
  Martin Larralde authored May 13, 2022
  
  5fee93d8
28 Apr, 2022 2 commits
- Release v1.0.1 · c0f76965
  Martin Larralde authored Apr 28, 2022
  
  c0f76965
- Update `pyrodigal.cli` to concatenate training sequences when in single mode · 0ec36465
  Martin Larralde authored Apr 28, 2022
  
  0ec36465
26 Apr, 2022 6 commits
- Fix rendering of main `pyrodigal` docstring in terminal · 16b04cd5
  Martin Larralde authored Apr 26, 2022
  
  16b04cd5
- Change color of JOSS badge in documentation [ci skip] · e6ad2466
  Martin Larralde authored Apr 26, 2022
  
  e6ad2466
- Update documentation and project metadata with JOSS paper references · 81b5bbf5
  Martin Larralde authored Apr 26, 2022
  
  81b5bbf5
- Add `extlinks` Sphinx extension to render DOI and PMID links in the documentation · 8a5c8e05
  Martin Larralde authored Apr 26, 2022
  
  8a5c8e05
- Merge branch 'paper' after paper acceptance in openjournals/joss-papers#3171 · 94647e9c
  Martin Larralde authored Apr 26, 2022
  
  94647e9c
- Add published paper from JOSS to the repository as PDF [ci skip] · d0629237
  Martin Larralde authored Apr 26, 2022
  
  d0629237
25 Apr, 2022 1 commit
- Fix title and grammatical error in `paper.md` · 96dfc50d
  Martin Larralde authored Apr 25, 2022
  
  96dfc50d
20 Apr, 2022 21 commits
- Update paper figure 2 with benchmarks from `v1.0.0` · 85228597
  Martin Larralde authored Apr 20, 2022
  
  85228597
- Update `figure2.svg` to use latest benchmark results · 9a2eef93
  Martin Larralde authored Mar 13, 2022
  
  9a2eef93
- Add connection scoring benches for release `v0.7.0` · 63fa930e
  Martin Larralde authored Mar 13, 2022
  
  63fa930e
- Fix affiliation in paper metadata (#9) · 60aa0c27
  Arfon Smith authored Feb 27, 2022 and Martin Larralde committed Apr 20, 2022
  
  60aa0c27
- Reword some sentences in the `Statement of need` section · 4ab8b55d
  Martin Larralde authored Feb 26, 2022
  
  4ab8b55d
- Address remaining comments from @lmc297 · 1d376d86
  Martin Larralde authored Feb 26, 2022
  
  1d376d86
- Update connection scoring benchmark plot to show R² instead of R · de904759
  Martin Larralde authored Feb 25, 2022
  
  de904759
- Improve packing of last step in Figure 1 · 5862e803
  Martin Larralde authored Feb 25, 2022
  
  5862e803
- Reword some sentences in `paper.md` · fd822bce
  Martin Larralde authored Feb 25, 2022
  
  fd822bce
- Update Figure 1 to make node boundaries more obvious · e7028196
  Martin Larralde authored Feb 25, 2022
  
  e7028196
- Update `Method` section and add documentation and repository references · dde3ed0c
  Martin Larralde authored Feb 25, 2022
  
  dde3ed0c
- Fix rendering of text in Figure 1 · d4dbb0af
  Martin Larralde authored Feb 25, 2022
  
  d4dbb0af
- Add a figure draft showing how Prodigal identifies genes · 2d97c02e
  Martin Larralde authored Feb 25, 2022
  
  2d97c02e
- Reword some parts of the paper and fix display of equations · 16d1b573
  Martin Larralde authored Feb 25, 2022
  
  16d1b573
- 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