v0.2.7

[ktmeaton]

plague-phylogeography Pull Request

Thank you for contributing to plague-phylogeography! Please complete the following steps:

• I have read the Contributor's Guide.

1. Description

This PR is a jupyter notebook overhaul. Removing many old notebooks and consolidating most visualization to a single auspice notebook.

2. Submission Type

• Bug fix
• New feature
• Other

3. Continuous Integration

After submitting, Continuous integration (CI) will run via Github Actions. This includes:

• Install (nextflow and conda installation)
• Linting (lints markdown, yaml, and python)
• Docs (builds sphinx docs for ReadTheDocs)
• Pipeline Database (processes related to ncbimeta creation and update)
• Pipeline Local (phylogenetic analysis of local reads and assemblies)
• Pipeline SRA (phylogenetic analysis of remote sra data)
• Pipeline Assembly (phylogenetic analysis of remote assembly data)

If CI fails, additional troubleshooting may be required on your part to resolve errors.

3. Final

• All new and existing tests pass.
• Tests have been added to cover changes.
• This PR requires a change to the documentation.
• The documentation has been updated accordingly.
• Code lints locally prior to submission (pre-commit).