What's changed
- Fix for #570
- Updated packaging metadata and build configuration (new pyproject.toml, adjusted setup, and environment changes), including adding the package data module for bundled assets.
- Modernized Snakemake integration, allowing update of dependency. This removes the direct call to the snakemake API, which is deprecated in recent versions and instead handles Snakemake calls in a new function in misc (imaginatively named dir).
- This removed the legacy custom logger utility, as it is no longer compatible with the updated api calls, consequences of this will be more verbose output to screen from snakemake as snakemake is running within pangolin, but this is a small change and allows us to update a lot of the pins so worth it.
- Refactored utilities around I/O and initialization to support the new Snakemake call path.
- Adjusted dependency checks and data validation logic to align with the updated packaging approach.
- Minor metadata update in pyproject (author info changed to cov-lineages team).