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

Parcels v3.0.1: a Lagrangian Ocean Analysis tool for the petascale age

Parcels v3.0.1 is a minor update to v3.0.0. It fixes a number of bugs and includes some important clarifications to the documentation and tutorials. Specifically:

What's Changed

Most relevant for users

• Adding support for using Field.from_netcdf() with variable as a dict by @erikvansebille in #1446
• Expanding explanation of output chunks parameter by @erikvansebille in #1494
• Running parcels in a grid with a coordinate grid with missing values (nans) by @dicaearchus in #1495

Refactoring, cleaning etc

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

New Contributors

• @dicaearchus made their first contribution in #1449

Full Changelog: v3.0.0...v3.0.1

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

Parcels v2.4.2: a Lagrangian Ocean Analysis tool for the petascale age

Parcels v2.4.2 is a minor update to the v2.4.1 release of February 2023; focussing mostly on a redesign of the documentation, notebooks and tutorial structure at docs.oceanparcels.org, using ReadTheDocs. This change was a fantastic effort by @VeckoTheGecko.

What's Changed

Documentation changes

• Cleaning the documentation and moving to ReadTheDocs in #1321, #1341, #1342, #1346, #1355 and #1371 (by @VeckoTheGecko)
• A new tutorial on how to use Parcels output in geospatial datatypes and software #1359 (by @VeckoTheGecko)

Code changes

• Create combined kernel from kernel function list in #1351 (by @VeckoTheGecko)
• Speedup C-contiguous arrays in #1074
• isort support in #1323 (by @VeckoTheGecko)
• Upgrade syntax to Python 3.8 in #1328 (by @VeckoTheGecko)

GitHub Continuous Integration changes

• Add black as dev dependency and intialise .git-blame-ignore-revs in #1327 (by @VeckoTheGecko)
• Configure pre-commit and pre-commit CI in #1286 (by @VeckoTheGecko)
• Update to use mamba in #1337 (by @VeckoTheGecko)
• Issue templates in #1361 (by @VeckoTheGecko)

Full Changelog: v2.4.1...v2.4.2

Parcels v2.4.1: a Lagrangian Ocean Analysis tool for the petascale age

Parcels v2.4.1 is a minor update to the v2.4.0 release of October 2022; with mostly bugfixes, cleanups of the code, and enhancements to the GitHub workflow. The most important ones are below

What's Changed

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

Full Changelog: v2.4.0...v2.4.1

Parcels v2.4.0: a Lagrangian Ocean Analysis tool for the petascale age

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.

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 (#1199)
• Updating documentation notebooks (#1237)
• Fixing 'fatal: not a git repository' warning (#1251)

Full Changelog: v2.3.2...v2.4.0

Parcels v2.3.2: a Lagrangian Ocean Analysis tool for the petascale age

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 (#1208)
• Updating the structure and particle-particle interaction tutorial (by @pdnooteboom, #1197)
• Clarification on the show_time parameter (by @VeckoTheGecko, #1215)
• Adding section to delaystart tutorial on adding particles during execution (#1223)
• Implementing fieldset.UV.eval for SummedVectorFields too (#1200)

Other fixes

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

New Contributors

• @VeckoTheGecko made their first contribution in #1215

Full Changelog: v2.3.1...v2.3.2

Parcels v2.3.1: a Lagrangian Ocean Analysis tool for the petascale age

Parcels v2.3.1 builds upon previous versions of Parcels and specifically introduces the following new (minor) features:

• 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)

Parcels v2.3.0: a Lagrangian Ocean Analysis tool for the petascale age

Parcels v2.3.0 builds upon previous versions of Parcels and specifically introduces four new features:

• Prototype implementation of Particle-Particle interaction in Scipy mode (#1031, thanks to @qubixes and @RoelBrouwer ).
• Implementation of Particle-Field interaction 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 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)

Parcels v2.2.2: a Lagrangian Ocean Analysis tool for the petascale age

Parcels v2.2.2 builds upon previous versions of Parcels and fixes a number of bugs. Furthermore, it also adds the following features:

• 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) (#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