Commits · v0.8.7 · Zeller Group / GECCO · GitLab

18 Feb, 2022 2 commits
- Release v0.8.7 · 12e34705
  Martin Larralde authored Feb 18, 2022
  
  12e34705
- Fix InterPro metadata file not being included in distributions · 0bf1d024
  Martin Larralde authored Feb 18, 2022
  
  0bf1d024
17 Feb, 2022 13 commits
- Fix missing docstring in `gecco.model.Protein.with_domains` · d4af0dc9
  Martin Larralde authored Feb 17, 2022
  
  d4af0dc9
- Bumped `scikit-learn` to `1.0` for Python 3.7+ · 6162c159
  Martin Larralde authored Feb 17, 2022
  
  6162c159
- Release v0.8.6 · bf666d2d
  Martin Larralde authored Feb 17, 2022
  
  bf666d2d
- Merge the `package.yml` and `release.yml` workflows · 1fd266fd
  Martin Larralde authored Feb 17, 2022
  
  1fd266fd
- Store InterPro metadata in sorted uncompressed JSON for versioning · b61d9610
  Martin Larralde authored Feb 17, 2022
  
  b61d9610
- Update CLI progress messages for consistency · e919f294
  Martin Larralde authored Feb 17, 2022
  
  e919f294
- Allow controlling the refinder edge distance from the CLI with the `-E` flag · 6fab7faa
  Martin Larralde authored Feb 17, 2022
  
  6fab7faa
- Add support for filtering BGCs based on distance to edge in `gecco.refine` · 316958c7
  Martin Larralde authored Feb 17, 2022
  
  316958c7
- Mark `BGC0000930` as a `Terpene` in `gecco/types/types.tsv` · fa55fb05
  Martin Larralde authored Feb 17, 2022
  
  fa55fb05
- Fix tests to work with the immutable data model · 78639c77
  Martin Larralde authored Feb 17, 2022
  
  78639c77
- Fix `Cluster.to_seq_record` not writing a type for `Unknown` type clusters · e567e671
  Martin Larralde authored Feb 17, 2022
  
  e567e671
- Add support for enabling Prodigal region masking from the CLI · 4e8396c5
  Martin Larralde authored Feb 17, 2022
  
  4e8396c5
- Update `pyrodigal` to `v0.6.4` to support region masking · c3133009
  Martin Larralde authored Feb 17, 2022
  
  c3133009
21 Jan, 2022 2 commits
- Fix `train` command to work with immutable data types · 03f59d0a
  Martin Larralde authored Jan 21, 2022
  
  03f59d0a
- Make `Gene` and `Protein` classes of `gecco.model` immutable · ecf73a2f
  Martin Larralde authored Jan 21, 2022
  
  ecf73a2f
12 Dec, 2021 3 commits
- Rewrite the `Training GECCO` guide in the documentation · 1f5b1e87
  Martin Larralde authored Dec 12, 2021
  
  1f5b1e87
- Update the `Installation` page of the docs with links to Galaxy · a9c7f807
  Martin Larralde authored Dec 12, 2021
  
  a9c7f807
- Update `README.md` with more information about the output files · d4fa20d4
  Martin Larralde authored Dec 12, 2021
  
  d4fa20d4
11 Dec, 2021 1 commit
- Fix number of allowed different lines in `galaxy/gecco.xml` tests · cc2518c2
  Martin Larralde authored Dec 11, 2021
  
  cc2518c2
21 Nov, 2021 13 commits
- Update Galaxy tool wrapper to follow the IUC best practices · 510d8e39
  Martin Larralde authored Nov 21, 2021
  
  510d8e39
- Add missing test file to `tests.test_cli` required for Galaxy tests · 1ef50ba0
  Martin Larralde authored Nov 21, 2021
  
  1ef50ba0
- Make the `galaxy.yml` Actions workflow always push the tool repository · d66ab63d
  Martin Larralde authored Nov 21, 2021
  
  d66ab63d
- Release v0.8.5 · 7c510d1d
  Martin Larralde authored Nov 21, 2021
  
  7c510d1d
- Add Galaxy tool badge to `README.md` [ci skip] · 0e262461
  Martin Larralde authored Nov 21, 2021
  
  0e262461
- Update Galaxy tool file to force GECCO to output a `clusters.tsv` file · 93ab7129
  Martin Larralde authored Nov 21, 2021
  
  93ab7129
- Add a flag to force writing `clusters.tsv` file even when no BGCs were found · 35e9d9de
  Martin Larralde authored Nov 21, 2021
  
  35e9d9de
- Fix link to contribution guide in `README.md` [ci skip] · 84e75c83
  Martin Larralde authored Nov 21, 2021
  
  84e75c83
- Fix broken syntax in `README.rst` file for Galaxy Tool Shed [ci skip] · 6c1bbcab
  Martin Larralde authored Nov 21, 2021
  
  6c1bbcab
- Setup deployment to the Tool Shed from GitHub Actions `galaxy.yml` workflow · 8f6be816
  Martin Larralde authored Nov 21, 2021
  
  8f6be816
- Add Actions workflow to test Galaxy tool wrapper and deployment · c54eb9ef
  Martin Larralde authored Nov 21, 2021
  
  c54eb9ef
- Add Galaxy tool configuration, test files, and Toolshed deployment files to `galaxy` · c3e58a61
  Martin Larralde authored Nov 21, 2021
  
  c3e58a61
- Update output files for BGC0001866 in `tests.test_cli` · 73b81129
  Martin Larralde authored Nov 21, 2021
  
  73b81129
13 Oct, 2021 1 commit
- Make sure to use all detected genes in `gecco annotate` · 707084f1
  Martin Larralde authored Oct 14, 2021
  
  707084f1
25 Sep, 2021 5 commits
- Replace notice of `multiprocessing.cpu_count` in `README.md` [ci skip] · 177b34a6
  Martin Larralde authored Sep 26, 2021
  
  177b34a6
- Release v0.8.4 · bae29fdc
  Martin Larralde authored Sep 26, 2021
  
  bae29fdc
- Bump minimum required `pyrodigal` version to `v0.6.2` · b6a01730
  Martin Larralde authored Sep 26, 2021
  
  b6a01730
- Add basic unit tests for the `gecco convert` subcommand · 50e9d758
  Martin Larralde authored Sep 26, 2021
  
  50e9d758
- Fix various bugs with `gecco convert gbk --format=bigslice` · b044999b
  Martin Larralde authored Sep 26, 2021
  
  b044999b