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Main code for Parcels (Probably A Really Computationally Efficient Lagrangian Simulator)

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I'm working on removing `xfail` from some tests so that we can use `pytest.raises` instead so that we're more specific. The following test https://github.com/OceanParcels/Parcels/blob/aa716e44128b5eaaaac503dfb924a0539102f2ae/docs/examples/example_globcurrent.py#L222-L238 errors with ``` @pytest.mark.parametrize("mode", ["scipy", "jit"])...

Establishing and documenting a standard benchmark suite for Parcels would bring an active focus to performance within the Parcels project. This benchmarking suite could include whole simulation tests, as well...

discussion

> Cognitive Complexity is a measure of how difficult a unit of code is to intuitively understand. Unlike Cyclomatic Complexity, which determines how difficult your code will be to test,...

help wanted
refactor

Currently the `ParticleSet.populate_indices` only populates the `xi` and `yi` indices. For 3D simulations, a nice-to-have addition to the `ParticleSet.populate_indices` method is to include the `zi` index, and not just `xi`,...

enhancement

The writing of the `zarr` file in `particlefile.py` doesn't look to set a compressor. Setting a compressor can significantly help trading off compute for storage or vice versa [[1]](https://youtu.be/qyJXBlrdzBs?feature=shared&t=1565). The...

discussion

This PR implements a C version of the `AnalyticalAdvection` kernel for use with `JITParticles`, and thereby implements #1617 - [x] make unit tests work - [x] confirm AnalyticalAdvection also works...

Currently the test suite takes 15+ minutes to run (windows is much more, closer to 30 mins). It would be good to reduce this, as well as bring other improvements...

enhancement
discussion
coding/Python

### Parcels version v3.0.5 ### Description Field.from_netcdf() doesn't work for filenames provided as Path object. It would be good to ensure the whole codebase is Path object compatible. ### Code...

enhancement
help wanted
good first issue

The metadata for the simulation is stored in a dictionary (`ParticleFile.metadata`) which is passed to xarray during writing. https://github.com/OceanParcels/Parcels/blob/b007dcf0ee189ca85735d78c97f0fabf0ad485de/parcels/particlefile.py#L78-L84 Currently users can modify and add items to this dictionary, however...

help wanted
documentation
good first issue

I don't think the `GridSet` object really needs to be called by users at all, as they are not manually defining gridsets. All the grid information is available to the...

discussion
coding/Python
cleanup