Commits · main · Martin Larralde / pyrodigal · GitLab

03 Oct, 2022 1 commit
- Fix broken `v1.1.2` release link in `CHANGELOG.md` [ci skip] · a1c92970
  Martin Larralde authored Oct 03, 2022
  
  a1c92970
31 Aug, 2022 7 commits
- Release v1.1.2 · 05225c6b
  Martin Larralde authored Aug 31, 2022
  
  05225c6b
- Add benchmarks for `v1.1.2` [ci skip] · 6ff2b941
  Martin Larralde authored Aug 31, 2022
  
  6ff2b941
- Add connection scoring benchmark results to the documentation [ci skip] · a50a4e5c
  Martin Larralde authored Aug 31, 2022
  
  a50a4e5c
- Regenerate bench graphs with new color palette [ci skip] · 8a9e0d41
  Martin Larralde authored Aug 31, 2022
  
  8a9e0d41
- Add benches for `v1.1.2` using the NEON backend · 0cb77c68
  Martin Larralde authored Aug 31, 2022
  
  0cb77c68
- Update benchmark scripts to allow benchmarking the NEON backend · dfbdca42
  Martin Larralde authored Aug 31, 2022
  
  dfbdca42
- Fix detection of SIMD in `setup.py` not setting the right flags when linking · 4245c35f
  Martin Larralde authored Aug 30, 2022
  
  4245c35f
30 Aug, 2022 1 commit
- Use the `vbic` instruction in NEON instead of combining bitwise AND and NOT instructions · 762b14b5
  Martin Larralde authored Aug 30, 2022
  
  762b14b5
12 Aug, 2022 1 commit
- Link to the JOSS paper for optimization documentation in `README.md` [ci skip] · 0553eaae
  Martin Larralde authored Aug 12, 2022
  
  0553eaae
30 Jul, 2022 1 commit
- Prevent direct instantiation of `Node` and `Gene` objects · 828927a2
  Martin Larralde authored Jul 31, 2022
  
  828927a2
22 Jul, 2022 2 commits
- Add `CITATION.cff` file with JOSS paper reference [ci skip] · 14a5b2b1
  Martin Larralde authored Jul 22, 2022
  
  14a5b2b1
- Fix date of `v1.1.1` in `CHANGELOG.md` [ci skip] · f8aac91b
  Martin Larralde authored Jul 22, 2022
  
  f8aac91b
08 Jul, 2022 3 commits
- Release v1.1.1 · c33bce35
  Martin Larralde authored Jul 08, 2022
  
  c33bce35
- Add missing `cpu_features` sources to `MANIFEST.in` · 4a5f81d5
  Martin Larralde authored Jul 08, 2022
  
  4a5f81d5
- Test source distribution in `package.yml` Actions before deploying to PyPI · 29661209
  Martin Larralde authored Jul 08, 2022
  
  29661209
21 Jun, 2022 1 commit
- Remove `arm64` compilation flags from OSX in `setup.py` · d768b406
  Martin Larralde authored Jun 21, 2022
  
  d768b406
20 Jun, 2022 1 commit
- Setup parallel compilation of vendored C libraries · 2aded196
  Martin Larralde authored Jun 20, 2022
  
  2aded196
09 Jun, 2022 6 commits
- Release v1.1.0 · 08b3cc2c
  Martin Larralde authored Jun 09, 2022
  
  08b3cc2c
- Revert back to hardcoded NEON support on Aarch64 · 78431a8e
  Martin Larralde authored Jun 09, 2022
  
  78431a8e
- Fix compilation on Linux Aarch64 platform · 11659369
  Martin Larralde authored Jun 09, 2022
  
  11659369
- Update MyPy configuration in `setup.cfg` to only check type hints of the Cython extensions · 1d263783
  Martin Larralde authored Jun 09, 2022
  
  1d263783
- Update `pyrodigal.cli` to use `OrfFinder.train` with multiple sequences · 19bca75c
  Martin Larralde authored Jun 09, 2022
  
  19bca75c
- Allow calling `OrfFinder.train` with more than one sequence for training on unclosed genomes · aca751d2
  Martin Larralde authored Jun 09, 2022
  
  aca751d2
06 Jun, 2022 1 commit
- Remove path to vendored licenses in Sphinx documentation index [ci skip] · cf642c9a
  Martin Larralde authored Jun 06, 2022
  
  cf642c9a
05 Jun, 2022 1 commit
- Bump `cpu_features` to `v0.7.0` and properly detect NEON on Linux Aarch64 platforms · 7a7f9465
  Martin Larralde authored Jun 06, 2022
  
  7a7f9465
29 May, 2022 1 commit
- Add Macrel to the list of Pyrodigal users in docs [ci skip] · df3f8cde
  Martin Larralde authored May 29, 2022
  
  df3f8cde
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 2 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