Parcels

Parcels v2.4.0 implements a completely new way of outputting trajectory data (1199). It writes directly to a `.zarr` directory, which can seamlessly be loaded with the `xarray.open_zarr()` method. For more info, see the [Reading the output file tutorial](https://nbviewer.org/github/OceanParcels/parcels/blob/master/parcels/examples/tutorial_output.ipynb#Reading-the-output-file).

Output is now smaller in size and faster to write. There is no need for temporary dumps and hence also not to convert these at the end of a simulation. This makes working with Parcels output during a simulation much easier.

What's Changed
* Saving Parcels output directly in zarr format (https://github.com/OceanParcels/parcels/pull/1199)
* Updating documentation notebooks (https://github.com/OceanParcels/parcels/pull/1237)
* Fixing 'fatal: not a git repository' warning (https://github.com/OceanParcels/parcels/pull/1251)

**Full Changelog**: https://github.com/OceanParcels/parcels/compare/v2.3.2...v2.4.0

This is a minor update to Parcels with mostly bugfixes; in preparation for a new v2.4.0 in a few weeks with support for writing directly to zarr.

What's Changed
Most relevant for users:
* Adding option to silence xarray decodewarnings (https://github.com/OceanParcels/parcels/pull/1208)
* Updating the structure and particle-particle interaction tutorial (by pdnooteboom, https://github.com/OceanParcels/parcels/pull/1197)
* Clarification on the `show_time` parameter (by VeckoTheGecko, https://github.com/OceanParcels/parcels/pull/1215)
* Adding section to delaystart tutorial on adding particles during execution (https://github.com/OceanParcels/parcels/pull/1223)
* Implementing fieldset.UV.eval for SummedVectorFields too (https://github.com/OceanParcels/parcels/pull/1200)

Other fixes
* Bugfix for ParticleSet.add() in mpi mode (https://github.com/OceanParcels/parcels/pull/1194)
* Fixing the `sh: None: command not found warning` (https://github.com/OceanParcels/parcels/pull/1201)
* Fixing pipy upload script (https://github.com/OceanParcels/parcels/pull/1202)
* Adding hint for export CC=gcc in compilation error message (https://github.com/OceanParcels/parcels/pull/1203)
* Fixing new flake8 requirements (https://github.com/OceanParcels/parcels/pull/1206)
* Fixing numpy DeprecationWarning in timeslices concatenation (https://github.com/OceanParcels/parcels/pull/1207)
* Fixing DeprecationWarning on elementwise comparison in converters (in https://github.com/OceanParcels/parcels/pull/1125)
* Fix broken ipynb link (by VeckoTheGecko, https://github.com/OceanParcels/parcels/pull/1219)
* Using f-string in logger info for plotting (https://github.com/OceanParcels/parcels/pull/1222)
* Throwing explicit error in codegenerator when using random() in JIT Kernel (https://github.com/OceanParcels/parcels/pull/1230)

New Contributors
* VeckoTheGecko made their first contribution in https://github.com/OceanParcels/parcels/pull/1215

**Full Changelog**: https://github.com/OceanParcels/parcels/compare/v2.3.1...v2.3.2

- Support to save Parcels output in `zarr` format (1165)
- Automatically compress temporary *.npy files with gzip (1171 by JamiePringle)
- Support for curvilinear MITgcm-like indexing (1166 by daanreijnders)
- Switching to `tqdm` for the progressbar (1111)
- Support for installation of Parcels via a pypi package (1163 by gmaze)
- Extended netcdf export format dictionary to unsigned ints (1152 by nvogtvincent)
- Support for periodic boundaries in `InteractionKernels` (1096 by pdnooteboom)

Furthermore, it fixes a number of bugs; most notably 1072, 1089 (fix by daanreijnders), 1105 (fix by cpierard), 1113 (fix by nvogtvincent), 1175, 1182 (fix by ocefpaf)

- Prototype implementation of [Particle-Particle interaction](https://nbviewer.jupyter.org/github/OceanParcels/parcels/blob/master/parcels/examples/tutorial_interaction.ipynb?flush_cache=true) in Scipy mode (#1031, thanks to qubixes and RoelBrouwer ).
- Implementation of [Particle-Field interaction](https://nbviewer.jupyter.org/github/OceanParcels/parcels/blob/master/parcels/examples/tutorial_particle_field_interaction.ipynb?flush_cache=true) in Scipy mode (#1045, thanks to fedeguerr)
- Implementation of a second type of ParticleSet (Array-of-Structures, `ParticleSetAOS`) as addition to the default Structure-of-Arrays (`ParticleSetSOA`) (999)
- [Partial- and free-slip boundary interpolation methods](https://nbviewer.jupyter.org/github/OceanParcels/parcels/blob/master/parcels/examples/documentation_unstuck_Agrid.ipynb#3.-Slip-boundary-conditions) for velocity fields on A-grids (1052, thanks to reint-fischer )

Furthermore, it includes a few minor bug fixes and removes some of the non-relevant logger Info/warning messages (such as when casting `lon` and `lat` to `np.float32`) (1022)

- Reduced the memory required by Parcels in `deferred_load=True` mode, especially when using large FieldSets, by storing only two snapshots in memory, instead of three (978)
- Better and more efficient implementation of dask auto-chunking (note that signature has changed, see updates in the [MPI tutorial](https://nbviewer.jupyter.org/github/OceanParcels/parcels/blob/master/parcels/examples/documentation_MPI.ipynb)) (#976)
- Much faster interpolation in Scipy mode for Curvilinear Grids (940)
- A new method to more efficiently initiate particles on Curvilinear Grids by using a kdtree (954 by angus-g )
- Improvements to 2D diffusion kernels (976 by daanreijnders )
- Added a new high-level tutorial on how to start using Parcels on oceanparcels.org (944 by reint-fischer )

Plus a large number of minor bug fixes

- Renaming `parcels.random` to `parcels.ParcelsRandom` (912). *Note that this change is not backward-compatible, so update your code*
- Support for **MITgcm** output on C-grids where the U and V are on the west and north of the f-points (897)
- Support for **MOM5** output on B-grids, where the W-fields are given _below_ the U and V-fields (923)
- Support larger `ParticleSets` by changing Particle-ID type to int64 (934)
- Added a `depth_units` keyword for `FieldSet.from_pop()` to support depth units in both 'm' and 'cm' (857)
- New tutorials on [how to sample Fields](http://nbviewer.jupyter.org/github/OceanParcels/parcels/blob/master/parcels/examples/tutorial_sampling.ipynb) and [how to postprocess Parcels output](https://nbviewer.jupyter.org/github/OceanParcels/parcels/blob/master/parcels/examples/tutorial_output.ipynb) (#915 and 929)
- Control over Cartopy feature options (coastline, land colour etc) in `plotTrajectoriesFile()` (939, thanks to axnsantana)
- Support for `math.nan` and `!=` operators in JIT Kernels (908)
- Support for `applyConversion=False` in Field Interpolation (898)
- Support to set the write status of a `Variable` after it's been created via `ParticleFile.set_variable_write_status()` (892)

Plus a large number of minor bug fixes