Migrate to Parcels v4

[j-atkins]

This PR migrates to using Parcels v4 for VirtualShip.

---

• Update instrument kernels
• Update fieldset ingestion workflows
• Update to Parquet output
• Implement new fieldset/performance handling strategy, i.e. new v4 docs
• Implement Refactor underway instruments #231
• Check expedition / workflow
  • including underway instruments
  • Argo float bug [in kernel(s)?], immediately goes out of bounds after first timestep... likely depth convention related
• Implement initial timestep sampling (i.e. Parcels #2622)
• Update to work with local data / --from-data
• Update tests
• Add new tests for v4 specific logic(?)
• Update docs / tutorials (e.g. notebooks using .zarr output) [new PR]
  • Plus new requirements for local data ingestion: depth dim has positive: down or positive: up
• ARGO_FLOATS: Enhance performance + no need to update cycle_age during ascent?

---

Closes #239, closes #232, closes #231, closes #323, closes #238

[j-atkins]

cc @erikvansebille

This PR is ready for re-review. Please note a couple of things, which have been added more recently, including tinkering around _via_tmp_ds in base.py (e.g. using Zarr stores to try and squeeze out a bit more performance), plus moving to execute instrument simulations with a context manager protocol for a better handling of the tmp directory writing. Also, changing the Argo Float DT (now matching the 5 min output dt) which speeds up the actual Parcels simulation considerably (unless there is a reason to keep it as DT = 10.0?).

Also, there are some changes that have been reviewed already, most notably the updates to the docs, and probably don’t need much time spent on them. Apologies this probably wasn’t the most efficient way of structuring the PRs.

[erikvansebille]

Impressive effort, @j-atkins! See below some small comments/questions

[j-atkins]

Thanks for the review, @erikvansebille! Comments now addressed, including moving to using boolean indexing across all (non-underway) instrument kernels.

@VeckoTheGecko I have updated/unpinned pixi in the pixi.toml so should be up to date. Do you just want to have a quick once over though?

[VeckoTheGecko]

I have updated/unpinned pixi in the pixi.toml so should be up to date. Do you just want to have a quick once over though?

Heya - just seeing this. Will take a look at the pixi.toml

[VeckoTheGecko]

The pixi.toml looks good! (only question is about sortedcontainers, which is a dependency but not used anywhere in the project - but that's not from this PR)

[erikvansebille]

Looks good - happy for you to merge!