Throwaway utility scripts for one-off maintenance tasks.

A simple script to check for updates to conda packages in environment.yml files, since dependabot doesn't support conda dependencies.

Usage:

python3 maintenance-scripts/check_conda_versions.py

Queries conda-forge and bioconda for the latest versions and reports which packages can be updated.

Update process:

1. Check for updates: Run the script to see which packages have newer versions available
2. Update the versions: Edit the environment.yml files with the new versions:
   • preprocessing/nextclade/environment.yml
   • ingest/environment.yml
   • ena-submission/environment.yml
3. Keep ruff in sync: If updating ruff in ena-submission/environment.yml, also update it in .pre-commit-config.yaml to match
4. Pin all dependencies: All dependencies should use exact version pinning (e.g., =1.2.3) rather than minimum version constraints (e.g., >=1.2.3) to ensure reproducible builds
5. Run pre-commit: After updating ruff or other linting tools, run pre-commit on all files to catch any new linting issues:

   pre-commit run --all-files