TODO:

• Sync pixi.toml across all modules.
• Remove mkdocs / documentation pixi environment.
• run snakemake --lint --snakefile tests/integration/Snakefile (Post module sprint cleaning #28 (comment))
• use --cores 1 for the integration test, to avoid file system locking issues on Windows (Post module sprint cleaning #28 (comment))
• tell mypy to exclude .pixi/ and .snakemake/ folders to avoid explosive checks.
• consider forcing jsonschema >v4.0 to avoid this issue snakemake cannot validate JSON schema 2020-12 snakemake/snakemake#3299 (comment)
• improve log-artifacts to allow for folder setups (already happening)

@sjpfenninger done with the general updates.

Most important bits are the removal of mkdocs (faster pixi builds) and running --cores 1 (no more windows failures, hopefully).

More fixes:

• add .pixi/ to gitignore
• Add References file