Commits · main · Martin Larralde / pyrodigal · GitLab

27 Jan, 2023 1 commit
- Bump vendored Prodigal to `v2.6.3+c1e2d36` · 14ab4caa
  Martin Larralde authored Jan 27, 2023
  
  14ab4caa
09 Jan, 2023 6 commits
- Override Python target detection when building on MacOS for Python 3.11 · 989c2a26
  Martin Larralde authored Jan 09, 2023
  
  989c2a26
- Show platform name when building `libprodigal` in `setup.py` · e16a4adf
  Martin Larralde authored Jan 09, 2023
  
  e16a4adf
- Fix AUR package generation in `package.yml` Actions workflow [ci skip] · 7deb7e97
  Martin Larralde authored Jan 09, 2023
  
  7deb7e97
- Release v2.0.4 · 523a4fa1
  Martin Larralde authored Jan 09, 2023
  
  523a4fa1
- Fix `Node._rbs_score` to allow computing RBS at contig edges · 96c40e65
  Martin Larralde authored Jan 09, 2023
  
  96c40e65
- Fix computation of GC% missing edge codon on reverse-strand genes · f6ce949e
  Martin Larralde authored Jan 09, 2023
  
  f6ce949e
20 Dec, 2022 10 commits
- Disable coverage measurement in `test.yml` workflow · c98f3948
  Martin Larralde authored Dec 20, 2022
  
  c98f3948
- Fix `package.yml` workflow not releasing a source distribution · 01fad1e8
  Martin Larralde authored Dec 20, 2022
  
  01fad1e8
- Make sure to run MacOS tests on x86-64 in `test.yml` workflow · 7d4b8b6f
  Martin Larralde authored Dec 20, 2022
  
  7d4b8b6f
- Release v2.0.3 · 74d68862
  Martin Larralde authored Dec 20, 2022
  
  74d68862
- Reorganize platform detection in `setup.py` to support cross-compilation with... · 0e57d7e6
  Martin Larralde authored Dec 20, 2022
```
Reorganize platform detection in `setup.py` to support cross-compilation with the `--plat-name` flag
```
  0e57d7e6
- Only install `coverage` package when testing for CPython · 3d705c55
  Martin Larralde authored Dec 20, 2022
  
  3d705c55
- Switch to `cibuildwheel` to package the program in `package.yml` · 53c9ed4f
  Martin Larralde authored Dec 20, 2022
  
  53c9ed4f
- Pin Ubuntu runner in `test.yml` Actions workflow to keep testing on older Python versions · 134789af
  Martin Larralde authored Dec 20, 2022
  
  134789af
- Fix off-by-one error in sequence mask generation code · 38fe94d0
  Martin Larralde authored Dec 20, 2022
  
  38fe94d0
- Fix sequence masking not using a minimum size of 50 nucleotides like Prodigal · 74570b19
  Martin Larralde authored Dec 20, 2022
  
  74570b19
19 Dec, 2022 1 commit
- Update GitHub Actions badge in `README.md` [ci skip] · 7928d4a2
  Martin Larralde authored Dec 18, 2022
  
  7928d4a2
01 Nov, 2022 9 commits
- Release v2.0.2 · 9214b334
  Martin Larralde authored Nov 01, 2022
  
  9214b334
- Fix declaration of `TrainingInfo._on_modification` [ci skip] · 87ec9c23
  Martin Larralde authored Nov 01, 2022
  
  87ec9c23
- Release v2.0.1 · 24084725
  Martin Larralde authored Nov 01, 2022
  
  24084725
- Attempt fixing compilation issue in Bioconda builder · 2caccca6
  Martin Larralde authored Nov 01, 2022
  
  2caccca6
- Release v2.0.0 · dfa48f5d
  Martin Larralde authored Nov 01, 2022
  
  dfa48f5d
- Add packaging jobs for Python 3.11 in `package.yml` Actions workflow · 6d519a7b
  Martin Larralde authored Nov 01, 2022
  
  6d519a7b
- Improve API documentation and add a dedicated page for `pyrodigal.Masks` · e34bfc76
  Martin Larralde authored Nov 01, 2022
  
  e34bfc76
- Expose several constants to the main `pyrodigal` namespace · f74c5856
  Martin Larralde authored Nov 01, 2022
  
  f74c5856
- Mention the Prodigal comparison in `README.md` and documentation index [ci skip] · 670db7f3
  Martin Larralde authored Nov 01, 2022
  
  670db7f3
31 Oct, 2022 13 commits
- Release v2.0.0-rc.4 · 7c75e0d9
  Martin Larralde authored Oct 31, 2022
  
  7c75e0d9
- Update benchmark section of the documentation [ci skip] · dd5af295
  Martin Larralde authored Oct 31, 2022
  
  dd5af295
- Add benchmarks of single mode for `v2.0.0` [ci skip] · 34f129d6
  Martin Larralde authored Oct 31, 2022
  
  34f129d6
- Fix `OrfFinder` ignoring the `backend` argument · e3e16696
  Martin Larralde authored Oct 31, 2022
  
  e3e16696
- Add `versionadded` and `versionchanged` directives to interface changes in `2.0.0` · 598a0630
  Martin Larralde authored Oct 31, 2022
  
  598a0630
- Fix `run_single` benchmark script only using the best SIMD backend · 95e9a6a4
  Martin Larralde authored Oct 31, 2022
  
  95e9a6a4
- Add tests for Python 3.11 in `test.yml` Actions workflow · 4bc74614
  Martin Larralde authored Oct 31, 2022
  
  4bc74614
- Document how to use the comparison repository in `CONTRIBUTING.md` [ci skip] · 05e03fdd
  Martin Larralde authored Oct 31, 2022
  
  05e03fdd
- Add script to benchmark Pyrodigal against Prodigal in single mode [ci skip] · 239ef965
  Martin Larralde authored Oct 31, 2022
  
  239ef965
- Allow selecting the SIMD backend when creating a new `OrfFinder` · 90853594
  Martin Larralde authored Oct 31, 2022
  
  90853594
- Move benchmark data to the main `benches` folder · ff963abf
  Martin Larralde authored Oct 31, 2022
  
  ff963abf
- Mock `Bio.SeqIO.parse` in doctests so they can run without Biopython · da31b8b2
  Martin Larralde authored Oct 31, 2022
  
  da31b8b2
- Make `Sequence.__init__` the main constructor and remove associated classmethods · d7ee7adb
  Martin Larralde authored Oct 31, 2022
  
  d7ee7adb