Parcels v3.0.0: a Lagrangian Ocean Analysis tool for the petascale age

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.

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 #1402
• Create tutorial_kernelloop.ipynb by @erikvansebille in #1421
• Update collectionsoa.py to allow user defined MPI partitioning by @JamiePringle in #1414
• Repeatdt small chunksize warning by @erikvansebille in #1430
• Compilation info as metadata by @erikvansebille in #1433
• Adding support for OperationCode.StopAllExecution by @erikvansebille in #1115
• Storing particle.xi in output files by @erikvansebille in #1147

Deprecated features

• Removing inbuilt plotting methods by @erikvansebille in #1397
• Retiring AoS support by @erikvansebille in #1423

Code clean-ups

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

Other minor fixes to code, installation and Continuous Integration

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

New Contributors

• @ammedd made their first contribution in #1415

Full Changelog: v2.4.2...v3.0.0