Expand support for creating new artifacts

[lazappi]

This PR:

• Adds a from_path() method to create artifacts from paths
• Adds a from_anndata() method to create artifacts from AnnData objects

Removed

• Adds a from_dir() method to create lists of artifacts from directories
• Adds a Instance$save() method which can save lists of records

Checklist:

• Add tests (partially)
• Pass CI checks
• Update man pages and regenerate
• Add new features to vignettes
• Update architecture vignette
• Update development vignette
• Update features in README
• Update CHANGELOG

[lazappi]

There are some differences from the Python interface here:

• from_file() doesn't exist in Python which instead uses ln.Artifact(). This kind of interface is only possible with some hacky workarounds.
  • Alternatively, we could have $create() or similar which replicates what Python does.
• The Python ln.save() is optimised for speed and doesn't create related records. Instead, the current Instance$save() just calls record$save() for each record in the list. Something similar to Python is probably possible but needs some more work.

[falexwolf]

Great! 🤩

One question: Rather than calling it from_file(), should it maybe be called from_path()? Otherwise we also need from_folder() and that'd be very confusing with from_dir().

If possible, to be honest, I'd hold off from adding from_dir() to the API -- we might even remove it from Python or rename it somehow because it's pretty confusing that it returns a list of artifacts rather than a single artifact or the whole directory.

[rcannood]

LGTM!