Updating oceanparcels links and references to parcels-code

README.md

@@ -21,7 +21,7 @@ This project uses a combination of Javascript and Typescript (Javascript - as th
 ### 1. Clone the repository
 
 ```bash
-git clone https://github.com/OceanParcels/oceanparcels_website
+git clone https://github.com/Parcels-code/parcels-code.org
 ```
 
 ### 2. Install dependencies

package.json

@@ -1,5 +1,5 @@
 {
-  "name": "oceanparcels_website",
+  "name": "parcels-code.org",
   "version": "1.0.0",
   "private": true,
   "scripts": {
@@ -11,7 +11,7 @@
   },
   "repository": {
     "type": "git",
-    "url": "git+https://github.com/OceanParcels/oceanparcels_website.git"
+    "url": "git+https://github.com/Parcels-code/parcels-code.org.git"
   },
   "author": "Parcels Developers & Contributors",
   "license": "Apache 2.0",

src/data/footer-items.js

@@ -11,7 +11,7 @@ export const footerItems = {
     { label: 'Blog', href: '/blog' },
     {
       label: 'Brand Assets',
-      href: 'https://github.com/OceanParcels/oceanparcels_website/tree/main/public/parcels-assets',
+      href: 'https://github.com/Parcels-code/parcels-code.org/tree/main/public/parcels-assets',
     },
     { label: 'Accessibility', href: '/accessibility' },
   ],
@@ -38,11 +38,11 @@ export const footerItems = {
     },
     {
       label: 'GitHub Discussions',
-      href: 'https://github.com/OceanParcels/parcels/discussions',
+      href: 'https://github.com/Parcels-code/parcels/discussions',
     },
     {
       label: 'Issue Tracker',
-      href: 'https://github.com/OceanParcels/parcels/issues',
+      href: 'https://github.com/Parcels-code/parcels/issues',
     },
     { label: 'Utrecht Team', href: '/utrechtteam' },
   ],

src/data/projects.js

@@ -3,7 +3,7 @@ export const Projects = [
     name: 'PlasticParcels',
     description:
       'PlasticParcels simulates the transport and dispersion of plastics in the ocean.',
-    repo: 'https://github.com/OceanParcels/plasticparcels',
+    repo: 'https://github.com/Parcels-code/plasticparcels',
     homepage: 'https://plastic.parcels-code.org/en/latest/',
     logo_light: '/projects/plasticparcelslogo.png',
     logo_dark: '/projects/plasticparcelslogo_dia.png',
@@ -12,7 +12,7 @@ export const Projects = [
     name: 'VirtualShip Parcels',
     description:
       'VirtualShipParcels is a command-line simulator to plan and conduct a virtual research expedition.',
-    repo: 'https://github.com/OceanParcels/virtualship',
+    repo: 'https://github.com/Parcels-code/virtualship',
     homepage: 'https://virtualship.parcels-code.org',
     logo_light: '/projects/virtual_ship_logo.png',
     logo_dark: '/projects/virtual_ship_logo_dia.png',

src/pages/accessibility.js

@@ -7,7 +7,7 @@ const Accessibility = () => {
     <Layout
       title={'Accessibility'}
       card={
-        'https://raw.githubusercontent.com/OceanParcels/oceanparcels_website/main/public/parcels-assets/logo-no-text.png'
+        'https://raw.githubusercontent.com/Parcels-code/parcels-code.org/main/public/parcels-assets/logo-no-text.png'
       }
       url={`/accessibility`}
     >

src/pages/blog/index.js

@@ -81,7 +81,7 @@ export default function Blog({ allPostsData }) {
       title={'Blog | Parcels'}
       url={`/blog`}
       card={
-        'https://raw.githubusercontent.com/OceanParcels/oceanparcels_website/main/public/parcels-assets/logo-no-text.png'
+        'https://raw.githubusercontent.com/Parcels-code/parcels-code.org/main/public/parcels-assets/logo-no-text.png'
       }
     >
       <Box as='section'>

src/pages/index.js

@@ -8,7 +8,7 @@ export default function IndexPage() {
       url={`/`}
       title={'Parcels: A highly customisable Lagrangian simulation framework'}
       card={
-        'https://raw.githubusercontent.com/OceanParcels/oceanparcels_website/main/public/parcels-assets/logo-no-text.png'
+        'https://raw.githubusercontent.com/Parcels-code/parcels-code.org/main/public/parcels-assets/logo-no-text.png'
       }
       // enableBanner
     >

src/pages/papers-citing-parcels.js

@@ -48,7 +48,7 @@ const PapersCitingParcels = () => {
     <Layout
       title={'Papers citing Parcels'}
       card={
-        'https://raw.githubusercontent.com/OceanParcels/oceanparcels_website/main/public/parcels-assets/logo-no-text.png'
+        'https://raw.githubusercontent.com/Parcels-code/parcels-code.org/main/public/parcels-assets/logo-no-text.png'
       }
       url={`/papers-citing-parcels`}
     >

src/pages/utrechtteam.js

@@ -9,7 +9,7 @@ const UtrechtTeam = () => {
     <Layout
       title={'Utrecht Team'}
       card={
-        'https://raw.githubusercontent.com/OceanParcels/oceanparcels_website/main/public/parcels-assets/logo-no-text.png'
+        'https://raw.githubusercontent.com/Parcels-code/parcels-code.org/main/public/parcels-assets/logo-no-text.png'
       }
       url={`/utrechtteam`}
     >

src/posts/10year-event/index.md

@@ -21,19 +21,19 @@ The event ended with a party on Friday evening 3 October 2025, in Utrecht. This
 
 All times in the schedules below are in Central European Summer Time (GMT+2).
 
-Some sessions have accompanying interactive notebooks. These - along with instructions - can be found [here](https://github.com/OceanParcels/10year-anniversary-event).
+Some sessions have accompanying interactive notebooks. These - along with instructions - can be found [here](https://github.com/Parcels-code/10year-anniversary-event).
 
 ### Wednesday 1 October: Workshops
 
 - Session 1a: How to get started with Parcels [[Video](https://surfdrive.surf.nl/index.php/s/2UTneRPQd6OFPJ0)] - _Erik van Sebille_
 - Session 1b: The Parcels internals: how to get started with code-development - _Nick Hodgskin_
-- Session 2: Making custom kernels [[Notebook](https://github.com/OceanParcels/10year-anniversary-session2) & [Video](https://surfdrive.surf.nl/index.php/s/tbRmcWjUqGuuM01)] - _Michael Denes_
-- Session 3: Lagrangian Diagnostics [[Notebook](https://github.com/OceanParcels/Lagrangian_diags) & [Video](https://surfdrive.surf.nl/index.php/s/MEuGgibPLvxdoiw)] - _Jimena Medina Rubio, Laura Gomez Navarro, Siren Rühs, Nick Hodgskin_
+- Session 2: Making custom kernels [[Notebook](https://github.com/Parcels-code/10year-anniversary-session2) & [Video](https://surfdrive.surf.nl/index.php/s/tbRmcWjUqGuuM01)] - _Michael Denes_
+- Session 3: Lagrangian Diagnostics [[Notebook](https://github.com/Parcels-code/Lagrangian_diags) & [Video](https://surfdrive.surf.nl/index.php/s/MEuGgibPLvxdoiw)] - _Jimena Medina Rubio, Laura Gomez Navarro, Siren Rühs, Nick Hodgskin_
 
 ### Thursday 2 October: Workshops
 
-- Session 4: What is Parcels v4? And how to get ready for it? [[Notebook](https://github.com/OceanParcels/10year-anniversary-session4) & [Video](https://surfdrive.surf.nl/index.php/s/VtnUMPFAGDz2UPR)]- _Nick Hodgskin, Joe Schoonover, Erik van Sebille_
-- Session 5: Particle animations [[Notebook](https://github.com/OceanParcels/10year-anniversary-session5) & [Video](https://surfdrive.surf.nl/index.php/s/WsO8wySLhBemW76)] and colormaps [[Notebook](https://github.com/OceanParcels/10year-anniversary-session5) & [Video](https://surfdrive.surf.nl/index.php/s/5b6tvF6xgX1cN0G)] - _Vesna Bertoncelj, Christian Kehl, Nick Hodgskin_
+- Session 4: What is Parcels v4? And how to get ready for it? [[Notebook](https://github.com/Parcels-code/10year-anniversary-session4) & [Video](https://surfdrive.surf.nl/index.php/s/VtnUMPFAGDz2UPR)]- _Nick Hodgskin, Joe Schoonover, Erik van Sebille_
+- Session 5: Particle animations [[Notebook](https://github.com/Parcels-code/10year-anniversary-session5) & [Video](https://surfdrive.surf.nl/index.php/s/WsO8wySLhBemW76)] and colormaps [[Notebook](https://github.com/Parcels-code/10year-anniversary-session5) & [Video](https://surfdrive.surf.nl/index.php/s/5b6tvF6xgX1cN0G)] - _Vesna Bertoncelj, Christian Kehl, Nick Hodgskin_
 
 ### Friday 3 October: Mini-conference
 
@@ -70,7 +70,7 @@ number VI.C.222.025.
 
 ## Background of the event
 
-Michael Lange committed [b2ae2fd](https://github.com/OceanParcels/Parcels/commit/b2ae2fd44979c125fbc21f2c939289db62dc4816) on 29 September 2015, and we’ve come a long way since then (we didn’t even have an acronym at that point!).
+Michael Lange committed [b2ae2fd](https://github.com/Parcels-code/Parcels/commit/b2ae2fd44979c125fbc21f2c939289db62dc4816) on 29 September 2015, and we’ve come a long way since then (we didn’t even have an acronym at that point!).
 
 [More than 200 articles have been published using Parcels](/papers-citing-parcels#papers-citing-parcels), on topics ranging from winds on Jupiter (the planet) and iceberg melt to AUV steering and tuna (the fish) behaviour.
 

src/posts/polyteos10-kernel/index.md

@@ -12,11 +12,11 @@ summary: 'An issue with the `PolyTEOS10_bsq` kernel has been identified, where i
 In recent days we’ve come across a bug in an application kernel of `parcels`. The `PolyTEOS10_bsq` kernel is used to calculate the density of seawater from the temperature and salinity fields. The kernel is based on equation (13) from
 [Roquet et al. (2014)](https://doi.org/10.1016/j.ocemod.2015.04.002) where the density $\rho$ is determined from the summation of a vertical reference profile $r_0$ and a residual function or density anomaly $r$. That is, $\rho(S,T,z) = r_0(z) + r(S,T,z)$.
 
-Up until the fix in [v3.1.3](https://github.com/OceanParcels/Parcels/releases/tag/v3.1.3) (see [PR #2133](https://github.com/OceanParcels/Parcels/pull/2133)), the kernel only computed the density anomaly $r$, and did not include the vertical reference profile. At the ocean surface this isn’t a problem, as $r_0(z=0) = 0$ and so the computed density was correct. However, $r_0(z)>0$ below the ocean surface, and at relatively deep depths, this value can be significant. For example, at 100 m depth this value is 0.46443 kg/m$^3$ and at 500 m depth this value is 2.31175 kg/m$^3$, see the figure below.
+Up until the fix in [v3.1.3](https://github.com/Parcels-code/Parcels/releases/tag/v3.1.3) (see [PR #2133](https://github.com/Parcels-code/Parcels/pull/2133)), the kernel only computed the density anomaly $r$, and did not include the vertical reference profile. At the ocean surface this isn’t a problem, as $r_0(z=0) = 0$ and so the computed density was correct. However, $r_0(z)>0$ below the ocean surface, and at relatively deep depths, this value can be significant. For example, at 100 m depth this value is 0.46443 kg/m$^3$ and at 500 m depth this value is 2.31175 kg/m$^3$, see the figure below.
 
 ![Vertical reference profile as a function of depth](/posts/polyteos10-kernel/depth_vs_r0.png)
 
-By using the kernel implementation before the fix in PR [#2133](https://github.com/OceanParcels/Parcels/pull/2133), the seawater density at depths below the ocean surface were being underestimated, as the actual seawater density would have otherwise been higher. Simulations that computed vertical velocities (such as sinking/rise velocities) using density differences between a particle and its surrounding seawater may have been impacted.
+By using the kernel implementation before the fix in PR [#2133](https://github.com/Parcels-code/Parcels/pull/2133), the seawater density at depths below the ocean surface were being underestimated, as the actual seawater density would have otherwise been higher. Simulations that computed vertical velocities (such as sinking/rise velocities) using density differences between a particle and its surrounding seawater may have been impacted.
 
 Below we’ve compiled a list of several papers that may be impacted, but we urge the community to check their own projects for use of this kernel at depth. This list may be updated as we become aware of other potentially impacted papers.