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michaeldenesmichaeldenes
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Renaming the 'add your own kernel' tutorial, removing unnecessary imports, fixing kernel flag printing, and fixing the warning of repeated variables names in the kernel.
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Lines changed: 48 additions & 55 deletions

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‎docs/examples.rst‎

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@@ -12,4 +12,4 @@ PlasticParcels has a few example notebooks, see below.
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examples/example_Italy_coast.ipynb
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examples/example_Greece_coast.ipynb
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examples/example_Croatian_fisheries.ipynb
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examples/example_make_your_own_kernel.ipynb
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examples/example_add_your_own_kernel.ipynb

docs/examples/example_make_your_own_kernel.ipynb renamed to docs/examples/example_add_your_own_kernel.ipynb

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@@ -4,7 +4,7 @@
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"cell_type": "markdown",
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"metadata": {},
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"source": [
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"# Make your own behaviour kernel\n",
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"# Add your own behaviour kernels\n",
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"In this example, we will show how to turn on/off existing behaviour kernels, and how to create and include your own behaviour kernel to use in `plasticparcels` simulations. We will start by importing some necessary packages."
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]
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},
@@ -16,16 +16,18 @@
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"source": [
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"# Library imports\n",
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"from datetime import datetime, timedelta\n",
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"import os\n",
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"os.chdir('../../')\n",
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"\n",
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"# Parcels and PlasticParcels imports\n",
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"import plasticparcels as pp\n",
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"\n",
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"# Plotting imports\n",
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"import matplotlib.pyplot as plt\n",
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"import cartopy.crs as ccrs\n",
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"import cartopy.feature as cfeature\n",
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"import xarray as xr"
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"\n",
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"# Other imports\n",
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"import xarray as xr\n",
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"import math"
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]
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},
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{
@@ -43,7 +45,7 @@
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"outputs": [],
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"source": [
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"# Load the model settings\n",
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"settings_file = 'docs/examples/example_make_your_own_kernel_settings.json'\n",
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"settings_file = 'docs/examples/example_add_your_own_kernel_settings.json'\n",
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"settings = pp.utils.load_settings(settings_file)"
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]
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},
@@ -88,12 +90,17 @@
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"name": "stdout",
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"output_type": "stream",
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"text": [
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"[('use_3D', True), ('use_mixing', False), ('use_biofouling', False), ('use_stokes', False), ('use_wind', False)]\n"
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"('use_3D', True)\n",
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"('use_mixing', False)\n",
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"('use_biofouling', False)\n",
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"('use_stokes', False)\n",
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"('use_wind', False)\n"
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]
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}
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],
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"source": [
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"print([(key, value) for key, value in settings.items() if 'use_' in key.lower()])"
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"for key_value in [(key, value) for key, value in settings.items() if 'use_' in key.lower()]:\n",
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" print(key_value)"
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]
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},
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{
@@ -203,15 +210,15 @@
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"name": "stdout",
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"output_type": "stream",
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"text": [
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"<function PolyTEOS10_bsq at 0x7f30a098b910>\n",
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"<function AdvectionRK4_3D at 0x7f30a15d6d40>\n",
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"<function Biofouling at 0x7f30a098b880>\n",
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"<function StokesDrift at 0x7f30a098b6d0>\n",
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"<function unbeaching at 0x7f30a098ba30>\n",
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"<function checkThroughBathymetry at 0x7f30a098bac0>\n",
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"<function checkErrorThroughSurface at 0x7f30a098bbe0>\n",
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"<function periodicBC at 0x7f30a098bb50>\n",
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"<function deleteParticle at 0x7f30a098bc70>\n"
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"<function PolyTEOS10_bsq at 0x7f38b955f910>\n",
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"<function AdvectionRK4_3D at 0x7f38ba1b2d40>\n",
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"<function Biofouling at 0x7f38b955f880>\n",
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"<function StokesDrift at 0x7f38b955f6d0>\n",
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"<function unbeaching at 0x7f38b955fa30>\n",
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"<function checkThroughBathymetry at 0x7f38b955fac0>\n",
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"<function checkErrorThroughSurface at 0x7f38b955fbe0>\n",
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"<function periodicBC at 0x7f38b955fb50>\n",
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"<function deleteParticle at 0x7f38b955fc70>\n"
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]
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}
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],
@@ -238,7 +245,7 @@
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"output_type": "stream",
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"text": [
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"INFO: Output files are stored in example_Tunisia_fisheries_prebuilt.zarr.\n",
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"100%|██████████| 2592000.0/2592000.0 [34:50<00:00, 1240.09it/s]\n"
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"100%|██████████| 2592000.0/2592000.0 [14:30<00:00, 2977.08it/s]\n"
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]
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}
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],
@@ -329,8 +336,6 @@
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"metadata": {},
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"outputs": [],
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"source": [
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"import math\n",
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"\n",
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"# An example kernel that applies a constant northward drift to particles\n",
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"def NorthwardDrift(particle, fieldset, time):\n",
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" # Only apply Northward drift if the particle is moving in the ocean\n",
@@ -340,8 +345,8 @@
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"\n",
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"def EastwardDrift(particle, fieldset, time):\n",
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" # Only apply Eastward drift if the particle is moving in the ocean\n",
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" (ocean_u, ocean_v) = fieldset.UV[time, particle.depth, particle.lat, particle.lon]\n",
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" if math.sqrt(ocean_u**2 + ocean_v**2) > 1e-10:\n",
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" (ocean_U, ocean_V) = fieldset.UV[time, particle.depth, particle.lat, particle.lon]\n",
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" if math.sqrt(ocean_U**2 + ocean_V**2) > 1e-10:\n",
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" particle_dlon += 1e-3 # Units of degrees"
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]
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},
@@ -354,15 +359,15 @@
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"name": "stdout",
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"output_type": "stream",
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"text": [
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"<function PolyTEOS10_bsq at 0x7f30a098b910>\n",
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"<function AdvectionRK4_3D at 0x7f30a15d6d40>\n",
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"<function Biofouling at 0x7f30a098b880>\n",
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"<function StokesDrift at 0x7f30a098b6d0>\n",
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"<function unbeaching at 0x7f30a098ba30>\n",
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"<function checkThroughBathymetry at 0x7f30a098bac0>\n",
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"<function checkErrorThroughSurface at 0x7f30a098bbe0>\n",
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"<function periodicBC at 0x7f30a098bb50>\n",
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"<function deleteParticle at 0x7f30a098bc70>\n"
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"<function PolyTEOS10_bsq at 0x7f38b955f910>\n",
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"<function AdvectionRK4_3D at 0x7f38ba1b2d40>\n",
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"<function Biofouling at 0x7f38b955f880>\n",
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"<function StokesDrift at 0x7f38b955f6d0>\n",
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"<function unbeaching at 0x7f38b955fa30>\n",
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"<function checkThroughBathymetry at 0x7f38b955fac0>\n",
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"<function checkErrorThroughSurface at 0x7f38b955fbe0>\n",
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"<function periodicBC at 0x7f38b955fb50>\n",
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"<function deleteParticle at 0x7f38b955fc70>\n"
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]
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}
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],
@@ -387,17 +392,17 @@
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"name": "stdout",
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"output_type": "stream",
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"text": [
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"<function PolyTEOS10_bsq at 0x7f30a098b910>\n",
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"<function AdvectionRK4_3D at 0x7f30a15d6d40>\n",
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"<function Biofouling at 0x7f30a098b880>\n",
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"<function StokesDrift at 0x7f30a098b6d0>\n",
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"<function NorthwardDrift at 0x7f307007e830>\n",
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"<function EastwardDrift at 0x7f307007e7a0>\n",
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"<function unbeaching at 0x7f30a098ba30>\n",
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"<function checkThroughBathymetry at 0x7f30a098bac0>\n",
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"<function checkErrorThroughSurface at 0x7f30a098bbe0>\n",
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"<function periodicBC at 0x7f30a098bb50>\n",
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"<function deleteParticle at 0x7f30a098bc70>\n"
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"<function PolyTEOS10_bsq at 0x7f38b955f910>\n",
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"<function AdvectionRK4_3D at 0x7f38ba1b2d40>\n",
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"<function Biofouling at 0x7f38b955f880>\n",
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"<function StokesDrift at 0x7f38b955f6d0>\n",
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"<function NorthwardDrift at 0x7f38889ba440>\n",
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"<function EastwardDrift at 0x7f38889ba290>\n",
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"<function unbeaching at 0x7f38b955fa30>\n",
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"<function checkThroughBathymetry at 0x7f38b955fac0>\n",
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"<function checkErrorThroughSurface at 0x7f38b955fbe0>\n",
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"<function periodicBC at 0x7f38b955fb50>\n",
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"<function deleteParticle at 0x7f38b955fc70>\n"
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]
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}
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],
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"name": "stdout",
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"output_type": "stream",
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"text": [
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"WARNING: ocean_u declared in multiple Kernels\n",
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"WARNING: ocean_v declared in multiple Kernels\n",
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"WARNING: ocean_u declared in multiple Kernels\n",
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"WARNING: ocean_v declared in multiple Kernels\n",
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"WARNING: ocean_u declared in multiple Kernels\n",
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"WARNING: ocean_v declared in multiple Kernels\n",
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"WARNING: ocean_u declared in multiple Kernels\n",
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"WARNING: ocean_v declared in multiple Kernels\n",
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"WARNING: ocean_u declared in multiple Kernels\n",
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"WARNING: ocean_v declared in multiple Kernels\n",
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"WARNING: ocean_u declared in multiple Kernels\n",
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"WARNING: ocean_v declared in multiple Kernels\n",
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"INFO: Output files are stored in example_Tunisia_fisheries_custom.zarr.\n",
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"100%|██████████| 2592000.0/2592000.0 [25:23<00:00, 1701.47it/s]\n"
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"100%|██████████| 2592000.0/2592000.0 [15:12<00:00, 2839.68it/s]\n"
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]
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}
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],

docs/examples/example_make_your_own_kernel_settings.json renamed to docs/examples/example_add_your_own_kernel_settings.json

File renamed without changes.

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