Parcels v3.1.4: a Lagrangian Ocean Analysis tool for the petascale age

This is a minor update from Parcels v3.1.3, fixing dependency metadata for Parcels builds available via pip on pypi.

What's Changed

• Update dependency metadata by @VeckoTheGecko in #2139

Full Changelog: v3.1.3...v3.1.4

Parcels v3.1.3: a Lagrangian Ocean Analysis tool for the petascale age

This is a minor update from Parcels v3.1.2, with one very important change: It fixes a bug in the polyTEOS10-bsq kernel, discovered and patched by @michaeldenes in #2133. See also our blog post that describes the impact of this bug.

Apart, from that, this PR features mostly very minor changes to the documentation; as well as a fix to the partition_function (#1953) by @JamiePringle.

What's Changed

• Update CITATION.cff by @erikvansebille in #1845
• Add PR template by @VeckoTheGecko in #1852
• Fix broken 'output in zarr' hyperlinks by @michaeldenes in #1864
• Adding link to v4 documentation on stable docs too by @erikvansebille in #1865
• DOC: update link to v4 docs by @VeckoTheGecko in #1866
• Also storing the output from test_scipy_vs_jit() by @erikvansebille in #1871
• Install parcels in RTD (for main) by @VeckoTheGecko in #1884
• Fixes error raised when using multiple files for fields with no time dimension by @andrew-s28 in #1886
• Bump codecov/codecov-action from 5.3.1 to 5.4.0 by @dependabot[bot] in #1903
• Update particleset.py to make partition_function with repeatdt by @JamiePringle in #1953
• Update dark-theme docs by @erikvansebille in #1954
• DOC: Add 10 year anniversary announcement by @VeckoTheGecko in #1956
• Bump codecov/codecov-action from 5.4.0 to 5.4.2 by @dependabot[bot] in #1997
• Disallow numpydoc 1.9.0 by @VeckoTheGecko in #2086
• Fix PolyTEOS10-bsq kernel by @michaeldenes in #2133

Full Changelog: v3.1.2...v3.1.3

Parcels v3.1.2: a Lagrangian Ocean Analysis tool for the petascale age

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

New Contributors

• @observingClouds made their first contribution in #1805

Full Changelog: v3.1.1...v3.2.0

Parcels v3.1.1: a Lagrangian Ocean Analysis tool for the petascale age

Parcels v3.1.1 is a minor update based on v3.1.0. It improves the implementation of Croco and ROMS 3D vertical velocities (#1772)

Important

• Implementing correct depth-to-sigma calculation by @erikvansebille in #1772
• Adding new tutorial on the impact of grid and velocity interpolation scheme on trajectories by @erikvansebille in #1769
• Adding support for grid.negate_depth() method by @erikvansebille in #1778
• Add Python 3.13 support by @VeckoTheGecko in #1785

Other

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

Full Changelog: v3.1.0...v3.1.1

Parcels v3.1.0: a Lagrangian Ocean Analysis tool for the petascale age

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 #1696
• Support for CROCO 3D velocities by @erikvansebille in #1641
• API changes: Field and FieldSet by @VeckoTheGecko in #1709
• API changes: particlefile.py and other touchups by @VeckoTheGecko in #1727
• API changes: particleset.py and grid.py by @VeckoTheGecko in #1713
• New and updated reprs for Variable, ParticleFile, Field, VectorField, and ParticleSet by @VeckoTheGecko in #1743

Other

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

Full Changelog: v3.0.5...v3.1.0

Parcels v3.0.6: a Lagrangian Ocean Analysis tool for the petascale age

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: v3.0.5...v3.0.6

Parcels v3.0.5: a Lagrangian Ocean Analysis tool for the petascale age

Parcels v3.0.5 is a minor update to 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 #1672
• Type annotations by @VeckoTheGecko in #1660
• added: FieldSet.from_a_grid_dataset by @KOMPALALOKESH in #1650
• Drop Python 3.8, 3.9 support by @VeckoTheGecko in #1658
• Support use of parcels.rng in Kernels by @erikvansebille in #1618 and update import statements #1610
• Fix bug in JIT when interpolation overrides error of previous interpolation by @erikvansebille in #1645

Other minor changes

• Add deprecation decorators by @VeckoTheGecko in #1683
• Updates properties for xarray API change by @andrew-s28 in #1596
• Fixing customed_Cfunc_header_test to use particle_dlon by @erikvansebille in #1606
• Documentation updates and numpy randint bugfix by @VeckoTheGecko in #1604
• Fixing bug when executing a breaking pset by @erikvansebille in #1630

Documentation updates

• Contributing documentation and issue/discussion templates changes by @VeckoTheGecko in #1634
• Minor tutorial updates by @erikvansebille in #1633
• Updating docstrings for advection kernels by @erikvansebille in #1640

Code quality improvement

• #1603, #1605, #1614, #1615, #1635, #1638, #1644, #1648, #1652, #1655, #1666, #1667

New Contributors

• @KOMPALALOKESH made their first contribution in #1650
• @dependabot made their first contribution in #1677

Full Changelog: v3.0.4...v3.0.5

Parcels v3.0.4: a Lagrangian Ocean Analysis tool for the petascale age

Parcels v3.0.4 is a minor update to v3.0.3 that patches a compatibility issue with the new NumPy 2.0, where np.infty is not supported anymore.

Most important changes

• Changing np.infty to np.inf for compatibility with NumPy 2.0 by @andrew-s28 in #1589
• Note in the Parcels structure tutorial on the field[particle] sampling speed by @erikvansebille in #1577

Other minor changes

• Fixing some AST deprecationwarnings by @erikvansebille in #1575
• Fix minor spelling grammar tutorials by @michaeldenes in #1582
• Renaming CMEMS to Copernicus Marine Service and CMS in documentation by @erikvansebille in #1583

New Contributors

• @michaeldenes made their first contribution in #1582

Full Changelog: v3.0.3...v3.0.4

Parcels v3.0.3: a Lagrangian Ocean Analysis tool for the petascale age

Parcels v3.0.3 is a minor update to v3.0.2. It includes a new way to create a FieldSet using FieldSet.from_modulefile(), improves the implementation of the AdvectionRK45 Kernel, and implements a test for the pypi-package upon release. It also includes a number of updates to the tutorials and fixes a number of bugs.

What's Changed

Most relevant for users

• Creating a new Fieldset.from_modulefile() method by @erikvansebille in #1566
• Improve AdvectionRK45 Kernel implementation by @erikvansebille in #1539
• PyPi release updates by @andrew-s28 in #1574

Documentation improvements

• Adding note to Parcels tutorial on add_variable compatibility by @erikvansebille in #1505
• Moving the note on add_variables in the Parcels tutorial to its first use by @erikvansebille in #1506
• Explaining statuscode kernel order by @erikvansebille in #1508
• Updating Argo kernel to parcels v3 API by @erikvansebille in #1524
• Adding infobox on UnitConverter to sampling tutorial by @erikvansebille in #1540
• Fixing weblink to Ariane software page by @erikvansebille in #1543
• Adding section in parcels structure tutorial on optimisation and parallelisation by @erikvansebille in #1555
• Clarifying particle_dlon variable use in kernel loop tutorial by @erikvansebille in #1535
• Simplifying parcels structure note by @erikvansebille in #1556
• Fixing link to partition function in the parcels structure tutorial by @erikvansebille in #1572

Bug-fixes and code-cleaning etc

• Update particleset.py by @dicaearchus in #1547
• Adding support for delete_cfiles as pset.execute() keyword by @erikvansebille in #1551
• Compilation error message fix for local variable name that is also FieldSet constant by @erikvansebille in #1552
• Pinning zarr in environment files to !=2.18.0 by @erikvansebille in #1565 and @jamespolly in #1567
• Throwing an error when dt has too high precision by @erikvansebille in #1558

New Contributors

• @jamespolly made their first contribution in #1567
• @andrew-s28 made their first contribution in #1574

Full Changelog: v3.0.2...v3.0.3

Parcels v3.0.2: a Lagrangian Ocean Analysis tool for the petascale age

Parcels v3.0.2 is a minor update to v3.0.1. It includes a new, more intuitive way to add Variables to a ParticleSet class, using a new Particleset.add_variable() method (#1501). It also fixes a number of bugs.

What's Changed

Most relevant for users

• Implementing Particleset.add_variable() method by @erikvansebille in #1501
• Setting defaults for FieldSet.computeTimeChunk() by @erikvansebille in #1502

Bug-fixes and code cleaning etc

• make it possible to import dataset with single time instance by @dicaearchus in #1496
• Simplifying the NEMO curvilinear tutorial by @erikvansebille in #1499
• Bugfix for cgrid eval without applyConversion by @erikvansebille in #1500
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in #1490

Full Changelog: v3.0.1...v3.0.2