Parcels

What's Changed

Most relevant for users
* Adding support for using Field.from_netcdf() with variable as a dict by erikvansebille in https://github.com/OceanParcels/parcels/pull/1446
* Expanding explanation of output chunks parameter by erikvansebille in https://github.com/OceanParcels/parcels/pull/1494
* Running parcels in a grid with a coordinate grid with missing values (nans) by dicaearchus in https://github.com/OceanParcels/parcels/pull/1495

Refactoring, cleaning etc
* Remove python from binder environment file by erikvansebille in https://github.com/OceanParcels/parcels/pull/1444
* Fixing links in documentation by erikvansebille in https://github.com/OceanParcels/parcels/pull/1445
* Field compatible with np.datetime64 entries by dicaearchus in https://github.com/OceanParcels/parcels/pull/1449
* Fixing that Fieldset.from_data() sets "time_origin" to 0 by default by dicaearchus in https://github.com/OceanParcels/parcels/pull/1451
* Update tutorial_kernelloop.ipynb by dicaearchus in https://github.com/OceanParcels/parcels/pull/1454
* Fixing the installation instructions for v3.0 by setting conda solver by erikvansebille in https://github.com/OceanParcels/parcels/pull/1455
* Clarify order of the start and end arguments in particleset.from_line() in documentation by erikvansebille in https://github.com/OceanParcels/parcels/pull/1458
* Pep8 compliancy for import statements by dicaearchus in https://github.com/OceanParcels/parcels/pull/1469
* Updating timestamps tutorial to remove time_periodic=True option by erikvansebille in https://github.com/OceanParcels/parcels/pull/1476
* Fixing a bug in Kernel definition in the preventing stuck particles documentation by erikvansebille in https://github.com/OceanParcels/parcels/pull/1479
* Fixing bug in zarr output when setting chunking and repeatdt by erikvansebille in https://github.com/OceanParcels/parcels/pull/1488
* Add prettier by VeckoTheGecko in https://github.com/OceanParcels/parcels/pull/1474

New Contributors
* dicaearchus made their first contribution in https://github.com/OceanParcels/parcels/pull/1449

**Full Changelog**: https://github.com/OceanParcels/parcels/compare/v3.0.0...v3.0.1

Parcels v3.0.0 is a major update to v2.4.2. The most important change is that the kernel loop has been changed, to support vectorial summing of particle displacements, in 1402. This change and its implications are explained in the new [Kernel Loop tutorial](https://docs.oceanparcels.org/en/latest/examples/tutorial_kernelloop.html).

This version also deprecates the in-built plotting methods `field.show()` and `pset.show()` in 1397. Furthermore, this version includes a major code clean-up, mostly by retiring support for Array-of-Structure (AoS) data architecture, in 1423.

What's Changed

New features
* Re-ordering of Kernel actions to vectorially sum particle displacements by erikvansebille in https://github.com/OceanParcels/parcels/pull/1402
* Create tutorial_kernelloop.ipynb by erikvansebille in https://github.com/OceanParcels/parcels/pull/1421
* Update collectionsoa.py to allow user defined MPI partitioning by JamiePringle in https://github.com/OceanParcels/parcels/pull/1414
* Repeatdt small chunksize warning by erikvansebille in https://github.com/OceanParcels/parcels/pull/1430
* Compilation info as metadata by erikvansebille in https://github.com/OceanParcels/parcels/pull/1433
* Adding support for OperationCode.StopAllExecution by erikvansebille in https://github.com/OceanParcels/parcels/pull/1115
* Storing particle.xi in output files by erikvansebille in https://github.com/OceanParcels/parcels/pull/1147

Deprecated features
* Removing inbuilt plotting methods by erikvansebille in https://github.com/OceanParcels/parcels/pull/1397
* Retiring AoS support by erikvansebille in https://github.com/OceanParcels/parcels/pull/1423

Code clean-ups
* Removing the header message from documentation notebooks by erikvansebille in https://github.com/OceanParcels/parcels/pull/1381
* Adding thumbnail for geospatial documentation by erikvansebille in https://github.com/OceanParcels/parcels/pull/1380
* Fixing typo in allow_time_extrapolation docstrings by erikvansebille in https://github.com/OceanParcels/parcels/pull/1383
* Printing cfile-name in compilation info by erikvansebille in https://github.com/OceanParcels/parcels/pull/1396
* Simplification of the MPI partition_function explanation by erikvansebille in https://github.com/OceanParcels/parcels/pull/1424
* Code cleanups by erikvansebille in https://github.com/OceanParcels/parcels/pull/1427
* Removing stray recovery kernel mentions by erikvansebille in https://github.com/OceanParcels/parcels/pull/1431
* Removing particleset.density by erikvansebille in https://github.com/OceanParcels/parcels/pull/1434
* Renumbering statuscodes so that they are increasing by erikvansebille in https://github.com/OceanParcels/parcels/pull/1439
* More small codecleanups in preparation for parcels v3 by erikvansebille in https://github.com/OceanParcels/parcels/pull/1438

Other minor fixes to code, installation and Continuous Integration
* Update linkcheck_ignore by VeckoTheGecko in https://github.com/OceanParcels/parcels/pull/1374
* Patch test_mpi_run failing test by VeckoTheGecko in https://github.com/OceanParcels/parcels/pull/1375
* Update umamba gha by ocefpaf in https://github.com/OceanParcels/parcels/pull/1373
* Updated Binder by VeckoTheGecko in https://github.com/OceanParcels/parcels/pull/1368
* Fix Binder filepath typo by VeckoTheGecko in https://github.com/OceanParcels/parcels/pull/1378
* Updating citation to latest version by erikvansebille in https://github.com/OceanParcels/parcels/pull/1385
* Jupyter QA tooling (black, isort, ast) by VeckoTheGecko in https://github.com/OceanParcels/parcels/pull/1389
* Migrate to `pyproject.toml` (project metadata, tool config cleanup) by VeckoTheGecko in https://github.com/OceanParcels/parcels/pull/1392
* Fix casting warnings by erikvansebille in https://github.com/OceanParcels/parcels/pull/1400
* Fix flake8 E721 in `baseparticlefile.py` by VeckoTheGecko in https://github.com/OceanParcels/parcels/pull/1405
* Adding installation instructions to documentation by erikvansebille in https://github.com/OceanParcels/parcels/pull/1403
* Add UVsample code and improve consistency by ammedd in https://github.com/OceanParcels/parcels/pull/1415
* Fixing the link to instructions for parallel installation by erikvansebille in https://github.com/OceanParcels/parcels/pull/1419
* From lon towrite to lon nextloop by erikvansebille in https://github.com/OceanParcels/parcels/pull/1422
* Adding explicit message on how to deal with interpolated output by erikvansebille in https://github.com/OceanParcels/parcels/pull/1437
* Towards a noarch environment file for developer installation by erikvansebille in https://github.com/OceanParcels/parcels/pull/1416
* Fix dask chunking error by erikvansebille in https://github.com/OceanParcels/parcels/pull/1436
* Simplifying binder environment file by erikvansebille in https://github.com/OceanParcels/parcels/pull/1441
* [pre-commit.ci] pre-commit autoupdate by pre-commit-ci in https://github.com/OceanParcels/parcels/pull/1442
* Updating all tutorials with latest conda environment and parcels v3 code by erikvansebille in https://github.com/OceanParcels/parcels/pull/1443
* Towards parcels v3.0 by erikvansebille in https://github.com/OceanParcels/parcels/pull/1426

New Contributors
* ammedd made their first contribution in https://github.com/OceanParcels/parcels/pull/1415

**Full Changelog**: https://github.com/OceanParcels/parcels/compare/v2.4.2...v3.0.0

What's Changed

Documentation changes
* Cleaning the documentation and moving to ReadTheDocs in https://github.com/OceanParcels/parcels/pull/1321, https://github.com/OceanParcels/parcels/pull/1341, https://github.com/OceanParcels/parcels/pull/1342, https://github.com/OceanParcels/parcels/pull/1346, https://github.com/OceanParcels/parcels/pull/1355 and https://github.com/OceanParcels/parcels/pull/1371 (by VeckoTheGecko)
* A new tutorial on how to use Parcels output in geospatial datatypes and software https://github.com/OceanParcels/parcels/pull/1359 (by VeckoTheGecko)

Code changes
* Create combined kernel from kernel function list in https://github.com/OceanParcels/parcels/pull/1351 (by VeckoTheGecko)
* Speedup C-contiguous arrays in https://github.com/OceanParcels/parcels/pull/1074
* `isort` support in https://github.com/OceanParcels/parcels/pull/1323 (by VeckoTheGecko)
* Upgrade syntax to Python 3.8 in https://github.com/OceanParcels/parcels/pull/1328 (by VeckoTheGecko)

GitHub Continuous Integration changes
* Add `black` as dev dependency and intialise .git-blame-ignore-revs in https://github.com/OceanParcels/parcels/pull/1327 (by VeckoTheGecko)
* Configure pre-commit and pre-commit CI in https://github.com/OceanParcels/parcels/pull/1286 (by VeckoTheGecko)
* Update to use mamba in https://github.com/OceanParcels/parcels/pull/1337 (by VeckoTheGecko)
* Issue templates in https://github.com/OceanParcels/parcels/pull/1361 (by VeckoTheGecko)

**Full Changelog**: https://github.com/OceanParcels/parcels/compare/v2.4.1...v2.4.2

What's Changed
* Fixing a bug in 2D scipy linear_invdist_land interpolation in https://github.com/OceanParcels/parcels/pull/1306
* Implementing time_periodic also for FieldSet.from_xarray_dataset in https://github.com/OceanParcels/parcels/pull/1253
* Adding info on periodic boundaries in global models to tutorial in https://github.com/OceanParcels/parcels/pull/1255
* Support for running on systems with MPI but without sklearn in https://github.com/OceanParcels/parcels/pull/1262
* Fixing the vonmises distribution tests in test_diffusion in https://github.com/OceanParcels/parcels/pull/1279
* Clean up CI/CD workflows in https://github.com/OceanParcels/parcels/pull/1278 (by VeckoTheGecko)
* Fix Readthedocs in https://github.com/OceanParcels/parcels/pull/1290 (by VeckoTheGecko)
* Running MPI test without writing Stommel hydrodynamic fields in https://github.com/OceanParcels/parcels/pull/1291
* Updating fieldfilebuffer to not not unravel lonlat-indices when not provided in https://github.com/OceanParcels/parcels/pull/1258
* Allow for Zarr stores being passed to ParticleFile in https://github.com/OceanParcels/parcels/pull/1303 (by willirath)
* Cleaning up deprecated methods and increasing codecoverage for Parcels in https://github.com/OceanParcels/parcels/pull/1287 (by VeckoTheGecko) and in https://github.com/OceanParcels/parcels/pull/1295, https://github.com/OceanParcels/parcels/pull/1296, https://github.com/OceanParcels/parcels/pull/1309


**Full Changelog**: https://github.com/OceanParcels/parcels/compare/v2.4.0...v2.4.1

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