Parcels

<!-- Release notes generated using configuration in .github/release.yaml at main -->
This is a minor update from Parcels v3.1.1, made in preparation for development on Parcels v4.


What's Changed
* Rename test file by VeckoTheGecko in https://github.com/OceanParcels/Parcels/pull/1793
* remove duplicate cftime dependency by observingClouds in https://github.com/OceanParcels/Parcels/pull/1805
* Fixing a bug with default ParticleFile outputdt value by erikvansebille in https://github.com/OceanParcels/Parcels/pull/1808
* Check misaligned timestepping outputdt by erikvansebille in https://github.com/OceanParcels/Parcels/pull/1809
* Ignore bot PRs in release notes by VeckoTheGecko in https://github.com/OceanParcels/Parcels/pull/1794
* Deprecating curvilnear halo support by erikvansebille in https://github.com/OceanParcels/Parcels/pull/1811
* Harmonise Field dimensions order by erikvansebille in https://github.com/OceanParcels/Parcels/pull/1812
* Implement warning for particles initialised outside time domain by erikvansebille in https://github.com/OceanParcels/Parcels/pull/1810
* Remove git, and unused formatting deps by VeckoTheGecko in https://github.com/OceanParcels/Parcels/pull/1817
* Update default branch by VeckoTheGecko in https://github.com/OceanParcels/Parcels/pull/1818
* pin zarr<3 by VeckoTheGecko in https://github.com/OceanParcels/Parcels/pull/1820
* Move Field tests to separate file by VeckoTheGecko in https://github.com/OceanParcels/Parcels/pull/1821
* Refactor example dataset download tests by VeckoTheGecko in https://github.com/OceanParcels/Parcels/pull/1828
* DOC: update maintainer notes by VeckoTheGecko in https://github.com/OceanParcels/Parcels/pull/1830
* Fixing an inconsistency in vertical index search between JIT and Scipy by erikvansebille in https://github.com/OceanParcels/Parcels/pull/1834
* Remove `trajan` as core dependency by VeckoTheGecko in https://github.com/OceanParcels/Parcels/pull/1833
* Small refactors of VectorField and pragma comments by VeckoTheGecko in https://github.com/OceanParcels/Parcels/pull/1836
* Refactoring field interpolation and allow custom interpolation methods in Scipy mode by VeckoTheGecko in https://github.com/OceanParcels/Parcels/pull/1816
* Support for Fields in multiple files without a `time` dimension by erikvansebille in https://github.com/OceanParcels/Parcels/pull/1835
* Small refactors in `particlefile.py` by VeckoTheGecko in https://github.com/OceanParcels/Parcels/pull/1843
* Improve pset.execute time management by erikvansebille in https://github.com/OceanParcels/Parcels/pull/1627

New Contributors
* observingClouds made their first contribution in https://github.com/OceanParcels/Parcels/pull/1805

**Full Changelog**: https://github.com/OceanParcels/Parcels/compare/v3.1.1...v3.2.0

Important
* Implementing correct depth-to-sigma calculation by erikvansebille in https://github.com/OceanParcels/Parcels/pull/1772
* Adding new tutorial on the impact of grid and velocity interpolation scheme on trajectories by erikvansebille in https://github.com/OceanParcels/Parcels/pull/1769
* Adding support for grid.negate_depth() method by erikvansebille in https://github.com/OceanParcels/Parcels/pull/1778
* Add Python 3.13 support by VeckoTheGecko in https://github.com/OceanParcels/Parcels/pull/1785

Other
* Update doc dep versions by VeckoTheGecko in https://github.com/OceanParcels/Parcels/pull/1757
* Minor changes (3rd party license, repr) by VeckoTheGecko in https://github.com/OceanParcels/Parcels/pull/1759
* Update ParticleType repr by VeckoTheGecko in https://github.com/OceanParcels/Parcels/pull/1766
* DOC: particlefile metadata by VeckoTheGecko in https://github.com/OceanParcels/Parcels/pull/1765
* Fixing wrong calculation of C-grid velocities in Peninsula example Field by erikvansebille in https://github.com/OceanParcels/Parcels/pull/1768
* Fixture in `test_examples.py` to clean up generated data files by VeckoTheGecko in https://github.com/OceanParcels/Parcels/pull/1770
* CI: Add py310 to integration test matrix by VeckoTheGecko in https://github.com/OceanParcels/Parcels/pull/1771
* Patch Ruff config (isort in notebooks) by VeckoTheGecko in https://github.com/OceanParcels/Parcels/pull/1775
* Fixing a warn_outputdt_release_desync bug by erikvansebille in https://github.com/OceanParcels/Parcels/pull/1747
* Cleanup macOS debugging files by VeckoTheGecko in https://github.com/OceanParcels/Parcels/pull/1779
* Add `tmp_zarr` fixture by VeckoTheGecko in https://github.com/OceanParcels/Parcels/pull/1784
* Update default value of particlefile chunks to length of pset by erikvansebille in https://github.com/OceanParcels/Parcels/pull/1788


**Full Changelog**: https://github.com/OceanParcels/Parcels/compare/v3.1.0...v3.1.1

Parcels v3.1.0 implements support for CROCO sigma grids, adds reprs for key parcels classes (allowing you to easily introspect fieldsets etc), and makes changes to the API (complete with user warnings) to clearly distinguish what the user is expected to use.

What's Changed

Important

* Add Parcels versioning/deprecation policies and maintainer docs by VeckoTheGecko in https://github.com/OceanParcels/Parcels/pull/1696
* Support for CROCO 3D velocities by erikvansebille in https://github.com/OceanParcels/Parcels/pull/1641
* API changes: `Field` and `FieldSet` by VeckoTheGecko in https://github.com/OceanParcels/Parcels/pull/1709
* API changes: `particlefile.py` and other touchups by VeckoTheGecko in https://github.com/OceanParcels/Parcels/pull/1727
* API changes: `particleset.py` and `grid.py` by VeckoTheGecko in https://github.com/OceanParcels/Parcels/pull/1713
* New and updated reprs for Variable, ParticleFile, Field, VectorField, and ParticleSet by VeckoTheGecko in https://github.com/OceanParcels/Parcels/pull/1743

Other

* Patch pypi release python version by VeckoTheGecko in https://github.com/OceanParcels/Parcels/pull/1692
* [pre-commit.ci] pre-commit autoupdate by pre-commit-ci in https://github.com/OceanParcels/Parcels/pull/1654
* Enable pyupgrade, add Grid repr, and other changes by VeckoTheGecko in https://github.com/OceanParcels/Parcels/pull/1680
* Update the Analytical Advection tutorial by michaeldenes in https://github.com/OceanParcels/Parcels/pull/1703
* [pre-commit.ci] pre-commit autoupdate by pre-commit-ci in https://github.com/OceanParcels/Parcels/pull/1707
* Test suite tooling by VeckoTheGecko in https://github.com/OceanParcels/Parcels/pull/1704
* Adding explicit explanation how to add tracers in FieldSet.from_nemo() by erikvansebille in https://github.com/OceanParcels/Parcels/pull/1702
* Bump pypa/gh-action-pypi-publish from 1.10.0 to 1.10.2 by dependabot in https://github.com/OceanParcels/Parcels/pull/1718
* [pre-commit.ci] pre-commit autoupdate by pre-commit-ci in https://github.com/OceanParcels/Parcels/pull/1714
* Fixing bug in backward-in-time-writing by erikvansebille in https://github.com/OceanParcels/Parcels/pull/1723
* DOC: Separate out linkcheck by VeckoTheGecko in https://github.com/OceanParcels/Parcels/pull/1725
* Update Git archive config by VeckoTheGecko in https://github.com/OceanParcels/Parcels/pull/1717
* [pre-commit.ci] pre-commit autoupdate by pre-commit-ci in https://github.com/OceanParcels/Parcels/pull/1726
* FieldSet.from_croco vertical velocities warning by erikvansebille in https://github.com/OceanParcels/Parcels/pull/1732
* [pre-commit.ci] pre-commit autoupdate by pre-commit-ci in https://github.com/OceanParcels/Parcels/pull/1735
* Fixing loaded_time_indices to support more advanced compute() functions by erikvansebille in https://github.com/OceanParcels/Parcels/pull/1733
* Documenting use of interp_method freeslip for B-grids by erikvansebille in https://github.com/OceanParcels/Parcels/pull/1740
* Adding warning particlestartime outputdt multiple by erikvansebille in https://github.com/OceanParcels/Parcels/pull/1739
* Refactors and bugfixes by VeckoTheGecko in https://github.com/OceanParcels/Parcels/pull/1736
* Bugfix warn_outputdt_release_desync for NaN release times by erikvansebille in https://github.com/OceanParcels/Parcels/pull/1744


**Full Changelog**: https://github.com/OceanParcels/Parcels/compare/v3.0.5...v3.1.0

Parcels v3.0.6 is a minor update to v3.0.5 that fixes a bug flagged in 1722 regarding time-stepping in the output file.

**Full Changelog**: https://github.com/OceanParcels/Parcels/compare/v3.0.5...v3.0.6

Parcels v3.0.5 is a minor update to [v3.0.4](https://github.com/OceanParcels/Parcels/releases/tag/v3.0.4) that fixes a few minor bugs, cleans up code and adds contribution guidelines.

Most important changes
* Implement warnings in Parcels by andrew-s28 in https://github.com/OceanParcels/Parcels/pull/1672
* Type annotations by VeckoTheGecko in https://github.com/OceanParcels/Parcels/pull/1660
* added: FieldSet.from_a_grid_dataset by KOMPALALOKESH in https://github.com/OceanParcels/Parcels/pull/1650
* Drop Python 3.8, 3.9 support by VeckoTheGecko in https://github.com/OceanParcels/Parcels/pull/1658
* Support use of parcels.rng in Kernels by erikvansebille in https://github.com/OceanParcels/Parcels/pull/1618 and update import statements https://github.com/OceanParcels/Parcels/pull/1610
* Fix bug in JIT when interpolation overrides error of previous interpolation by erikvansebille in https://github.com/OceanParcels/Parcels/pull/1645

Other minor changes
* Add deprecation decorators by VeckoTheGecko in https://github.com/OceanParcels/Parcels/pull/1683
* Updates properties for xarray API change by andrew-s28 in https://github.com/OceanParcels/Parcels/pull/1596
* Fixing customed_Cfunc_header_test to use particle_dlon by erikvansebille in https://github.com/OceanParcels/Parcels/pull/1606
* Documentation updates and numpy randint bugfix by VeckoTheGecko in https://github.com/OceanParcels/Parcels/pull/1604
* Fixing bug when executing a breaking pset by erikvansebille in https://github.com/OceanParcels/Parcels/pull/1630

Documentation updates
* Contributing documentation and issue/discussion templates changes by VeckoTheGecko in https://github.com/OceanParcels/Parcels/pull/1634
* Minor tutorial updates by erikvansebille in https://github.com/OceanParcels/Parcels/pull/1633
* Updating docstrings for advection kernels by erikvansebille in https://github.com/OceanParcels/Parcels/pull/1640

Code quality improvement
* https://github.com/OceanParcels/Parcels/pull/1603, https://github.com/OceanParcels/Parcels/pull/1605, https://github.com/OceanParcels/Parcels/pull/1614, https://github.com/OceanParcels/Parcels/pull/1615, https://github.com/OceanParcels/Parcels/pull/1635, https://github.com/OceanParcels/Parcels/pull/1638, https://github.com/OceanParcels/Parcels/pull/1644, https://github.com/OceanParcels/Parcels/pull/1648, https://github.com/OceanParcels/Parcels/pull/1652, https://github.com/OceanParcels/Parcels/pull/1655, https://github.com/OceanParcels/Parcels/pull/1666, https://github.com/OceanParcels/Parcels/pull/1667


New Contributors
* KOMPALALOKESH made their first contribution in https://github.com/OceanParcels/Parcels/pull/1650
* dependabot made their first contribution in https://github.com/OceanParcels/Parcels/pull/1677

**Full Changelog**: https://github.com/OceanParcels/Parcels/compare/v3.0.4...v3.0.5

Most important changes
* Changing np.infty to np.inf for compatibility with NumPy 2.0 by andrew-s28 in https://github.com/OceanParcels/parcels/pull/1589
* Note in the Parcels structure tutorial on the `field[particle]` sampling speed by erikvansebille in https://github.com/OceanParcels/parcels/pull/1577

Other minor changes
* Fixing some AST deprecationwarnings by erikvansebille in https://github.com/OceanParcels/parcels/pull/1575
* Fix minor spelling grammar tutorials by michaeldenes in https://github.com/OceanParcels/parcels/pull/1582
* Renaming CMEMS to Copernicus Marine Service and CMS in documentation by erikvansebille in https://github.com/OceanParcels/parcels/pull/1583

New Contributors
* michaeldenes made their first contribution in https://github.com/OceanParcels/parcels/pull/1582

**Full Changelog**: https://github.com/OceanParcels/parcels/compare/v3.0.3...v3.0.4