diff --git a/.github/workflows/linting.yaml b/.github/workflows/linting.yaml index 59dc89013..c54199197 100644 --- a/.github/workflows/linting.yaml +++ b/.github/workflows/linting.yaml @@ -54,6 +54,8 @@ jobs: - name: Run yaml-lint run: yamllint $(find ${GITHUB_WORKSPACE} -type f -name "*.yaml") + # TO DO: Python linting for scripts/ dir + # Disable RST linting for now, rethink for sphinx #rst_lint: # runs-on: ubuntu-latest diff --git a/CHANGELOG.md b/CHANGELOG.md index 97f8c42d8..13e42acef 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -8,7 +8,8 @@ and this project "attempts" to adhere to [Semantic Versioning](http://semver.org ## [Development] - Rewrite shell scripts in python? -- Overabundance of files in database update and snippy_filtering +- Then add python linting +- Overabundance of files in database update - Deal with the fail to publish issue with NCBImeta db - Add exact-repeats and tandem repeats detection - Add GeoPy to phylo-env environment @@ -25,6 +26,7 @@ and this project "attempts" to adhere to [Semantic Versioning](http://semver.org - scripts/sqlite_EAGER_tsv.py scripts/sqlite_NextStrain_tsv.py scripts/geocode_NextStrain.py - pre-commit and linting - gh-actions workflow +- Automate SNPEff db creation ### Changed