Patch werkzeug vuln and make minor cladetime API improvements #54
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The CLI portion of cladetime is not expected to work until we revamp it to use the NextClade-based methods for assigning clades. Furthermore, we need to add a service to the GitHub workflow that will allow Docker commands to run within the Docker-based CI process.
This changeset incorporates some of the API design principles discussed here: https://benhoyt.com/writings/python-api-design/ Specifically, we can stop importing individual functions from sequence.py AND streamline the function names by moving from this pattern: from cladetime.sequence import filter_sequence_metadata, etc. metdata = filter_sequence_metadata() to this one: from cladetime import sequence metadata = sequence.filter_metadata()
Another tweak to make the API more friendly.
Closes #46 This changeset bumps package dependencies (the prompt was addressing a werkzeug vuln, but let's take the opportunity to update everything).
The prior commit updated all of our packages, including ruff. The ruff update has different styling preferences for import formatting, causing a mismatch between what the pre-commit hook will accept and what "ruff check" flags as a problem.
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Closes #46
This PR combines a few minor cladetime updates to smooth the way for #53 and also addresses a werkzeug vuln reported by Dependabot: https://github.com/reichlab/cladetime/security/dependabot
Probably best to review commit by commit, as the various updates aren't really related to one another.