Merge branch 'v4-dev' into bugfix/2260-vectorize-pwlinear-node

Author: fluidnumerics-joe

docs/community/contributing.rst

@@ -6,7 +6,7 @@ Why contribute?
 
 `Lagrangian Ocean Analysis <https://doi.org/10.1016/j.ocemod.2017.11.008>`_ is one of the primary modelling tools available to oceanographers to understand how ocean currents transport material. This modelling approach allows researchers to model the ocean and understand the `movement of water <https://doi.org/10.1029/2023GL105662>`_ in the ocean itself (or even `on other planets <https://doi.org/10.3847/1538-4357/ac9d94>`_), as well as the transport of `nutrients <https://doi.org/10.1029/2023GL108001>`_, `marine organisms <https://doi.org/10.3354/meps14526>`_, `oil <https://doi.org/10.1590/0001-3765202220210391>`_, `plastic <https://doi.org/10.1038/s41561-023-01216-0>`_, as well as `almost <https://doi.org/10.1016/j.robot.2024.104730>`_ `anything <https://doi.org/10.1111/cobi.14295>`_ `else <https://doi.org/10.1016/j.marpolbul.2023.115254>`_ that would be adrift at sea. Since ocean currents play a key role in climate by storing heat and carbon, and also in the formation of the 'plastic soup', understanding transport phenomena in the ocean is crucial to support a more sustainable future.
 
-The Parcels code, for which development started in 2015, is now one of the most widely used tools for Lagrangian Ocean Analysis. It's used by dozens of groups around the world - see `this list <https://oceanparcels.org/articles.html>`_ for a full list of the peer-reviewed articles using Parcels. Its flexibility for users to create new, custom 'behaviours' (i.e. let virtual particles be controlled by other mechanics than only the ocean flow) and its compatibility with many different types of hydrodynamic input data are the two key features.
+The Parcels code, for which development started in 2015, is now one of the most widely used tools for Lagrangian Ocean Analysis. It's used by dozens of groups around the world - see `this list <https://oceanparcels.org/papers-citing-parcels#papers-citing-parcels>`_ for a full list of the peer-reviewed articles using Parcels. Its flexibility for users to create new, custom 'behaviours' (i.e. let virtual particles be controlled by other mechanics than only the ocean flow) and its compatibility with many different types of hydrodynamic input data are the two key features.
 
 .. note::
 

docs/examples/documentation_MPI.ipynb

@@ -176,7 +176,7 @@
     "\n",
     "With load-balancing we mean that `Particles` that are close together are ideally on the same MPI processor. Practically, it means that we need to take care how `Particles` are spread over chunks and processors. See for example the two figures below:\n",
     "\n",
-    "![](http://oceanparcels.org/images/parcelsParallel.png)\n",
+    "![](images/ParcelsParallel.png)\n",
     "_Example of load-balancing for Particles. The domain is chunked along the thick lines, and the orange and blue particles are on separate MPI processors. Before load-balancing (left panel), two chuncks in the centre of the domain have both orange and blue particles. After the load-balancing (right panel), the Particles are redistributed over the processors so that the number of chunks and particles per processor is optimised._\n",
     "\n",
     "The difficulty is that since we don't know how the `ParticleSet` will disperse over time, we need to do this load-balancing 'on the fly'. If you to contribute to the optimisation of the load-balancing, please leave a message on [github](https://github.com/OceanParcels/parcels/issues)!\n"

docs/examples/documentation_advanced_zarr.ipynb

@@ -19,8 +19,8 @@
     "\n",
     "Topics:\n",
     "\n",
-    "- Capturing output in memory using the `MemoryStore` of `zarr` ([link](https://zarr.readthedocs.io/en/stable/api/storage.html#zarr.storage.MemoryStore))\n",
-    "- Transferring data from a `MemoryStore` into a directory (via `DirectoryStore`; [link](https://zarr.readthedocs.io/en/stable/api/storage.html#zarr.storage.DirectoryStore)) or a zip file (via `ZipStore`; [link](https://zarr.readthedocs.io/en/stable/api/storage.html#zarr.storage.ZipStore)).\n",
+    "- Capturing output in memory using the `MemoryStore` of `zarr` ([link](https://zarr.readthedocs.io/en/v2.18.5/api/storage.html#zarr.storage.MemoryStore))\n",
+    "- Transferring data from a `MemoryStore` into a directory (via `DirectoryStore`; [link](https://zarr.readthedocs.io/en/v2.18.5/api/storage.html#zarr.storage.DirectoryStore)) or a zip file (via `ZipStore`; [link](https://zarr.readthedocs.io/en/v2.18.5/api/storage.html#zarr.storage.ZipStore)).\n",
     "- Re-chunking output to better align with specific analyses (time vs. spatial filtering).\n"
    ]
   },

docs/examples/images/ParcelsParallel.png

@@ -153,7 +153,7 @@
     "\n",
     "- [Understanding **stuck particles** at land boundaries](https://docs.oceanparcels.org/en/latest/examples/documentation_stuck_particles.html)\n",
     "- [**Preventing stuck particles** at land boundaries](https://docs.oceanparcels.org/en/latest/examples/documentation_unstuck_Agrid.html)\n",
-    "- Or download and use the [data on the **original C-grid**](https://www.mercator-ocean.eu/en/solutions-expertise/accessing-digital-data/) from [Mercator Ocean International](https://www.mercator-ocean.eu) directly\n",
+    "- Or download and use the [data on the **original C-grid**](https://www.mercator-ocean.eu/ocean-data/explore-ocean-data/access-data/#elementor-toc__heading-anchor-0) from [Mercator Ocean International](https://www.mercator-ocean.eu) directly\n",
     "\n",
     "### If you are working with field data on different grids:\n",
     "\n",

docs/examples/tutorial_parcels_structure.ipynb

@@ -545,6 +545,7 @@ def execute(
 
         if verbose_progress:
             pbar = tqdm(total=(end_time - start_time) / np.timedelta64(1, "s"), file=sys.stdout)
+            pbar.set_description("Integration time: " + str(start_time))
 
         next_output = start_time + sign_dt * outputdt if output_file else None
 
@@ -566,6 +567,7 @@ def execute(
                         next_output += outputdt
 
             if verbose_progress:
+                pbar.set_description("Integration time: " + str(time))
                 pbar.update((next_time - time) / np.timedelta64(1, "s"))
 
             time = next_time