From ed12c4316b2fe0045edfe1d608122e2792c20499 Mon Sep 17 00:00:00 2001 From: Vecko <36369090+VeckoTheGecko@users.noreply.github.com> Date: Tue, 10 Mar 2026 12:51:36 +0100 Subject: [PATCH 01/12] MAINT: Update `make clean` Some jupyter cache results were being saved here causing desync --- docs/Makefile | 1 + 1 file changed, 1 insertion(+) diff --git a/docs/Makefile b/docs/Makefile index 580347a22c..3bc6174db0 100755 --- a/docs/Makefile +++ b/docs/Makefile @@ -50,6 +50,7 @@ help: clean: rm -rf $(BUILDDIR)/* + rm -rf .jupyter_cache html: $(SPHINXBUILD) -b html $(ALLSPHINXOPTS) $(BUILDDIR)/html From 34e9076930e73856fa9b484f6a2208ac89361955 Mon Sep 17 00:00:00 2001 From: Vecko <36369090+VeckoTheGecko@users.noreply.github.com> Date: Tue, 10 Mar 2026 12:56:05 +0100 Subject: [PATCH 02/12] Update community page --- docs/community/index.md | 91 ++++++++++++++++++++++++++++++----------- 1 file changed, 66 insertions(+), 25 deletions(-) diff --git a/docs/community/index.md b/docs/community/index.md index a4bc1d5992..b320e8e55b 100644 --- a/docs/community/index.md +++ b/docs/community/index.md @@ -1,30 +1,5 @@ # Community -```{toctree} -:caption: CLAM Community -:maxdepth: 1 -:hidden: - -Website -``` - -```{toctree} -:caption: GitHub -:maxdepth: 1 -:hidden: - -Discussions -Issues -``` - -```{toctree} -:caption: Community examples -:maxdepth: 1 -:hidden: - -Repository -``` - Parcels users and developers interact in a vibrant community on a few different platforms. Check out the cards below to see how you can interact with us. `````{grid} 1 2 2 2 @@ -78,6 +53,10 @@ Report a bug with an Issue Curious to see if someone has already written the custom `Kernel` you are thinking of or runs **Parcels** with the same hydrodynamic data? Check out the parcels_contributions repository and share examples with other users! +```{image} https://img.shields.io/badge/maintainer_needed-red +:width: 40% +``` + +++ ```{button-link} https://github.com/Parcels-code/parcels_contributions @@ -94,6 +73,10 @@ Share custom Parcels code Are you interested in advanced analysis and diagnostics of Parcels output or Lagrangian trajectories in general? The Lagrangian Diagnostics project provides code and descriptions of different analyses. +```{image} https://img.shields.io/badge/maintainer_needed-red +:width: 40% +``` + +++ ```{button-link} https://lagrangian-diags.readthedocs.io/en/latest/ @@ -105,3 +88,61 @@ Visit Lagrangian Diagnostics ``` ```` ````` + +(analysis-code)= + +## Analysis code + +Tools for analysing Lagrangian trajectory output. + +`````{grid} 1 2 2 2 +:gutter: 4 +:padding: 2 2 0 0 +:class-container: sd-text-center + +````{grid-item-card} Trajan +:shadow: md + +A Python package for analysing and plotting ocean drifter and trajectory data stored, developed as part of the OpenDrift project. This library assumes trajectories are stored as CF-compliant Netcdf/Zarr output. + ++++ + +```{button-link} https://github.com/OpenDrift/trajan +:click-parent: +:color: secondary +:expand: + +Visit Trajan +``` +```` +````{grid-item-card} Lagrangian Trajectories Toolbox +:shadow: md + +A Python library dedicated to the post-processing, visualisation and analysis of Lagrangian particle trajectories. This library assumes trajectories are stored as tabular output (e..g, Parquet or CSV). + +A Python package providing a suite of tools for working with Lagrangian trajectory data stored in NetCDF and Zarr formats. + ++++ + +```{button-link} https://github.com/oj-tooth/lt_toolbox +:click-parent: +:color: secondary +:expand: + +Visit LT Toolbox +``` +```` +````` + +(other-lagrangian-software)= + +## Other Lagrangian software + +The following is a list of other Lagrangian ocean modelling and analysis software: + +- [connectivity-modeling-system (CMS)](https://github.com/beatrixparis/connectivity-modeling-system) +- [Drifters.jl](https://github.com/JuliaClimate/Drifters.jl) +- [oceantracker](https://github.com/oceantracker/oceantracker) +- [OpenDrift](https://github.com/OpenDrift/opendrift) +- [TrackMPD](https://github.com/IJalonRojas/TrackMPD) +- [TRACMASS](https://www.tracmass.org/) From 6d70e452c69ab1b8e07279fdb4d5517de2916737 Mon Sep 17 00:00:00 2001 From: Vecko <36369090+VeckoTheGecko@users.noreply.github.com> Date: Tue, 10 Mar 2026 12:59:57 +0100 Subject: [PATCH 03/12] Move lagrangian diagnostics --- docs/community/index.md | 40 ++++++++++++++++++++-------------------- 1 file changed, 20 insertions(+), 20 deletions(-) diff --git a/docs/community/index.md b/docs/community/index.md index b320e8e55b..7692613608 100644 --- a/docs/community/index.md +++ b/docs/community/index.md @@ -67,26 +67,6 @@ Curious to see if someone has already written the custom `Kernel` you are thinki Share custom Parcels code ``` ```` -````{grid-item-card} Lagrangian Diagnostics -:img-top: ../_static/LAdiag-logo.svg -:shadow: md - -Are you interested in advanced analysis and diagnostics of Parcels output or Lagrangian trajectories in general? The Lagrangian Diagnostics project provides code and descriptions of different analyses. - -```{image} https://img.shields.io/badge/maintainer_needed-red -:width: 40% -``` - -+++ - -```{button-link} https://lagrangian-diags.readthedocs.io/en/latest/ -:click-parent: -:color: secondary -:expand: - -Visit Lagrangian Diagnostics -``` -```` ````` (analysis-code)= @@ -132,6 +112,26 @@ A Python package providing a suite of tools for working with Lagrangian trajecto Visit LT Toolbox ``` ```` +````{grid-item-card} Lagrangian Diagnostics +:img-top: ../_static/LAdiag-logo.svg +:shadow: md + +Are you interested in advanced analysis and diagnostics of Parcels output or Lagrangian trajectories in general? The Lagrangian Diagnostics project provides code and descriptions of different analyses. + +```{image} https://img.shields.io/badge/maintainer_needed-red +:width: 40% +``` + ++++ + +```{button-link} https://lagrangian-diags.readthedocs.io/en/latest/ +:click-parent: +:color: secondary +:expand: + +Visit Lagrangian Diagnostics +``` +```` ````` (other-lagrangian-software)= From 388da400eb7ac8b8c3e6c5c1ccadb570e0135e35 Mon Sep 17 00:00:00 2001 From: Vecko <36369090+VeckoTheGecko@users.noreply.github.com> Date: Tue, 10 Mar 2026 13:00:04 +0100 Subject: [PATCH 04/12] Update reference --- docs/getting_started/explanation_concepts.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/getting_started/explanation_concepts.md b/docs/getting_started/explanation_concepts.md index 35d91ec69b..d8b2850392 100644 --- a/docs/getting_started/explanation_concepts.md +++ b/docs/getting_started/explanation_concepts.md @@ -188,7 +188,7 @@ pset.execute(kernels=kernels, dt=dt, runtime=runtime) To analyse the particle data generated in the simulation, we need to define a `parcels.ParticleFile` and add it as an argument to `parcels.ParticleSet.execute()`. The output will be written in a [zarr format](https://zarr.readthedocs.io/en/stable/), which can be opened as an `xarray.Dataset`. The dataset will contain the particle data with at least `time`, `z`, `lat` and `lon`, for each particle at timesteps defined by the `outputdt` argument. -There are many ways to analyze particle output, and although we provide [a short tutorial to get started](./tutorial_output.ipynb), we recommend writing your own analysis code and checking out other projects such as [trajan](https://opendrift.github.io/trajan/index.html) and [Lagrangian Diagnostics](https://lagrangian-diags.readthedocs.io/en/latest/). +There are many ways to analyze particle output, and although we provide [a short tutorial to get started](./tutorial_output.ipynb), we recommend writing your own analysis code and checking out [related Lagrangian analysis projects in our community page](../community/index.md#analysis-code). ```{admonition} 🖥️ Learn how to run a simulation :class: seealso From a579a1d4e5919aecbffad62d73322e3c2b13245b Mon Sep 17 00:00:00 2001 From: Vecko <36369090+VeckoTheGecko@users.noreply.github.com> Date: Tue, 10 Mar 2026 13:05:42 +0100 Subject: [PATCH 05/12] typo --- docs/community/index.md | 6 ++---- 1 file changed, 2 insertions(+), 4 deletions(-) diff --git a/docs/community/index.md b/docs/community/index.md index 7692613608..d4e620de95 100644 --- a/docs/community/index.md +++ b/docs/community/index.md @@ -80,7 +80,7 @@ Tools for analysing Lagrangian trajectory output. :padding: 2 2 0 0 :class-container: sd-text-center -````{grid-item-card} Trajan +````{grid-item-card} TrajAn :shadow: md A Python package for analysing and plotting ocean drifter and trajectory data stored, developed as part of the OpenDrift project. This library assumes trajectories are stored as CF-compliant Netcdf/Zarr output. @@ -92,7 +92,7 @@ A Python package for analysing and plotting ocean drifter and trajectory data st :color: secondary :expand: -Visit Trajan +Visit TrajAn ``` ```` ````{grid-item-card} Lagrangian Trajectories Toolbox @@ -100,8 +100,6 @@ Visit Trajan A Python library dedicated to the post-processing, visualisation and analysis of Lagrangian particle trajectories. This library assumes trajectories are stored as tabular output (e..g, Parquet or CSV). -A Python package providing a suite of tools for working with Lagrangian trajectory data stored in NetCDF and Zarr formats. - +++ ```{button-link} https://github.com/oj-tooth/lt_toolbox From 8355239077ca57aa86813ca33417fdefa9273048 Mon Sep 17 00:00:00 2001 From: Vecko <36369090+VeckoTheGecko@users.noreply.github.com> Date: Tue, 10 Mar 2026 13:15:22 +0100 Subject: [PATCH 06/12] Add "projects that use Parcels" section --- docs/community/index.md | 10 ++++++++++ 1 file changed, 10 insertions(+) diff --git a/docs/community/index.md b/docs/community/index.md index d4e620de95..604d3bb474 100644 --- a/docs/community/index.md +++ b/docs/community/index.md @@ -132,6 +132,16 @@ Visit Lagrangian Diagnostics ```` ````` +## Projects that use Parcels + +The following is a list of projects that use Parcels: + +- [LOCATE](https://github.com/UPC-LOCATE/LOCATE/): A collection of numerical tools developed within LOCATE ESA-funded project to build simulations of plastic particle dispersion in nearshore water. +- [PlasticParcels](https://github.com/Parcels-code/plasticparcels): A tool - based on Parcels - providing a modular and customisable collection of methods, notebooks, and tutorials for advecting virtual plastic particles with a wide range of physical properties. +- [pyPlume](https://codeocean.com/capsule/9735287/tree/v1): A collection of notebooks and methods made unifying the process of loading two-dimensional oceanic current vector fields from models and observations, simulating trajectory models, and analyzing and visualizing particle trajectories. +- [VirtualFleet](https://github.com/euroargodev/VirtualFleet): Make and analyse simulations of virtual Argo float trajectories +- [VirtualShip](https://virtualship.parcels-code.org/): A framework to plan and conduct a virtual research expedition, receiving measurements as if they were coming from actual oceanographic instruments. + (other-lagrangian-software)= ## Other Lagrangian software From 599ae7999fd1c7cbc0f36f0327ad75a205cbddd0 Mon Sep 17 00:00:00 2001 From: Vecko <36369090+VeckoTheGecko@users.noreply.github.com> Date: Tue, 10 Mar 2026 13:17:09 +0100 Subject: [PATCH 07/12] copy edit --- docs/community/index.md | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/docs/community/index.md b/docs/community/index.md index 604d3bb474..611fedad21 100644 --- a/docs/community/index.md +++ b/docs/community/index.md @@ -134,7 +134,7 @@ Visit Lagrangian Diagnostics ## Projects that use Parcels -The following is a list of projects that use Parcels: +The following is an alphabetically sorted list of projects that use Parcels: - [LOCATE](https://github.com/UPC-LOCATE/LOCATE/): A collection of numerical tools developed within LOCATE ESA-funded project to build simulations of plastic particle dispersion in nearshore water. - [PlasticParcels](https://github.com/Parcels-code/plasticparcels): A tool - based on Parcels - providing a modular and customisable collection of methods, notebooks, and tutorials for advecting virtual plastic particles with a wide range of physical properties. @@ -146,7 +146,7 @@ The following is a list of projects that use Parcels: ## Other Lagrangian software -The following is a list of other Lagrangian ocean modelling and analysis software: +The following is an alphabetically sorted list of other Lagrangian ocean modelling and analysis software: - [connectivity-modeling-system (CMS)](https://github.com/beatrixparis/connectivity-modeling-system) - [Drifters.jl](https://github.com/JuliaClimate/Drifters.jl) From 8ff6b831708bd836fcbbcf26563529312e4d4a10 Mon Sep 17 00:00:00 2001 From: Vecko <36369090+VeckoTheGecko@users.noreply.github.com> Date: Tue, 10 Mar 2026 13:17:38 +0100 Subject: [PATCH 08/12] copy edits --- docs/community/index.md | 2 -- 1 file changed, 2 deletions(-) diff --git a/docs/community/index.md b/docs/community/index.md index 611fedad21..4f23aa0251 100644 --- a/docs/community/index.md +++ b/docs/community/index.md @@ -142,8 +142,6 @@ The following is an alphabetically sorted list of projects that use Parcels: - [VirtualFleet](https://github.com/euroargodev/VirtualFleet): Make and analyse simulations of virtual Argo float trajectories - [VirtualShip](https://virtualship.parcels-code.org/): A framework to plan and conduct a virtual research expedition, receiving measurements as if they were coming from actual oceanographic instruments. -(other-lagrangian-software)= - ## Other Lagrangian software The following is an alphabetically sorted list of other Lagrangian ocean modelling and analysis software: From f624c0a64191d71c7c606a0215d9a536eac0a8af Mon Sep 17 00:00:00 2001 From: Vecko <36369090+VeckoTheGecko@users.noreply.github.com> Date: Tue, 10 Mar 2026 13:28:56 +0100 Subject: [PATCH 09/12] Disable left sidebar --- docs/community/index.md | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/docs/community/index.md b/docs/community/index.md index 4f23aa0251..e13bbe810a 100644 --- a/docs/community/index.md +++ b/docs/community/index.md @@ -1,3 +1,7 @@ +--- +html_theme.sidebar_secondary.remove: true +--- + # Community Parcels users and developers interact in a vibrant community on a few different platforms. Check out the cards below to see how you can interact with us. From 9ffb243167e310e6566b1690b1638656c96e19b8 Mon Sep 17 00:00:00 2001 From: Vecko <36369090+VeckoTheGecko@users.noreply.github.com> Date: Tue, 10 Mar 2026 14:47:52 +0100 Subject: [PATCH 10/12] Revert "Disable left sidebar" This reverts commit f624c0a64191d71c7c606a0215d9a536eac0a8af. --- docs/community/index.md | 4 ---- 1 file changed, 4 deletions(-) diff --git a/docs/community/index.md b/docs/community/index.md index e13bbe810a..4f23aa0251 100644 --- a/docs/community/index.md +++ b/docs/community/index.md @@ -1,7 +1,3 @@ ---- -html_theme.sidebar_secondary.remove: true ---- - # Community Parcels users and developers interact in a vibrant community on a few different platforms. Check out the cards below to see how you can interact with us. From 6026a1fbb35b1c03869d9b4a1fcb223e81883bca Mon Sep 17 00:00:00 2001 From: Vecko <36369090+VeckoTheGecko@users.noreply.github.com> Date: Thu, 12 Mar 2026 15:07:43 +0100 Subject: [PATCH 11/12] Convert cards to list --- docs/community/index.md | 61 +++-------------------------------------- 1 file changed, 4 insertions(+), 57 deletions(-) diff --git a/docs/community/index.md b/docs/community/index.md index 4f23aa0251..e39c695cb8 100644 --- a/docs/community/index.md +++ b/docs/community/index.md @@ -73,64 +73,11 @@ Share custom Parcels code ## Analysis code -Tools for analysing Lagrangian trajectory output. +The following is an alphabetically sorted list of tools for analysing Lagrangian trajectory output: -`````{grid} 1 2 2 2 -:gutter: 4 -:padding: 2 2 0 0 -:class-container: sd-text-center - -````{grid-item-card} TrajAn -:shadow: md - -A Python package for analysing and plotting ocean drifter and trajectory data stored, developed as part of the OpenDrift project. This library assumes trajectories are stored as CF-compliant Netcdf/Zarr output. - -+++ - -```{button-link} https://github.com/OpenDrift/trajan -:click-parent: -:color: secondary -:expand: - -Visit TrajAn -``` -```` -````{grid-item-card} Lagrangian Trajectories Toolbox -:shadow: md - -A Python library dedicated to the post-processing, visualisation and analysis of Lagrangian particle trajectories. This library assumes trajectories are stored as tabular output (e..g, Parquet or CSV). - -+++ - -```{button-link} https://github.com/oj-tooth/lt_toolbox -:click-parent: -:color: secondary -:expand: - -Visit LT Toolbox -``` -```` -````{grid-item-card} Lagrangian Diagnostics -:img-top: ../_static/LAdiag-logo.svg -:shadow: md - -Are you interested in advanced analysis and diagnostics of Parcels output or Lagrangian trajectories in general? The Lagrangian Diagnostics project provides code and descriptions of different analyses. - -```{image} https://img.shields.io/badge/maintainer_needed-red -:width: 40% -``` - -+++ - -```{button-link} https://lagrangian-diags.readthedocs.io/en/latest/ -:click-parent: -:color: secondary -:expand: - -Visit Lagrangian Diagnostics -``` -```` -````` +- [Lagrangian Diagnostics](https://lagrangian-diags.readthedocs.io/en/latest/) (![maintainer needed](https://img.shields.io/badge/maintainer_needed-red)): Are you interested in advanced analysis and diagnostics of Parcels output or Lagrangian trajectories in general? The Lagrangian Diagnostics project provides code and descriptions of different analyses. +- [Lagrangian Trajectories Toolbox](https://github.com/oj-tooth/lt_toolbox): A Python library dedicated to the post-processing, visualisation and analysis of Lagrangian particle trajectories. This library assumes trajectories are stored as tabular output (e..g, Parquet or CSV). +- [TrajAn](https://github.com/OpenDrift/trajan): A Python package for analysing and plotting ocean drifter and trajectory data stored, developed as part of the OpenDrift project. This library assumes trajectories are stored as CF-compliant Netcdf/Zarr output. ## Projects that use Parcels From 433b45d6bd91a5cbb76403b0fa2aa1d2629def10 Mon Sep 17 00:00:00 2001 From: Vecko <36369090+VeckoTheGecko@users.noreply.github.com> Date: Thu, 12 Mar 2026 15:09:18 +0100 Subject: [PATCH 12/12] update link --- docs/community/index.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/community/index.md b/docs/community/index.md index e39c695cb8..669d209322 100644 --- a/docs/community/index.md +++ b/docs/community/index.md @@ -85,7 +85,7 @@ The following is an alphabetically sorted list of projects that use Parcels: - [LOCATE](https://github.com/UPC-LOCATE/LOCATE/): A collection of numerical tools developed within LOCATE ESA-funded project to build simulations of plastic particle dispersion in nearshore water. - [PlasticParcels](https://github.com/Parcels-code/plasticparcels): A tool - based on Parcels - providing a modular and customisable collection of methods, notebooks, and tutorials for advecting virtual plastic particles with a wide range of physical properties. -- [pyPlume](https://codeocean.com/capsule/9735287/tree/v1): A collection of notebooks and methods made unifying the process of loading two-dimensional oceanic current vector fields from models and observations, simulating trajectory models, and analyzing and visualizing particle trajectories. +- [pyPlume](https://github.com/jerukan/PyPlume): A collection of notebooks and methods made unifying the process of loading two-dimensional oceanic current vector fields from models and observations, simulating trajectory models, and analyzing and visualizing particle trajectories. - [VirtualFleet](https://github.com/euroargodev/VirtualFleet): Make and analyse simulations of virtual Argo float trajectories - [VirtualShip](https://virtualship.parcels-code.org/): A framework to plan and conduct a virtual research expedition, receiving measurements as if they were coming from actual oceanographic instruments.