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create a mediterannean subset of fisheries data and give logo to workshop tutorial
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‎src/DRAKKAR workshop code/PlasticParcels_DRAKKAR_tutorial.ipynb‎

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"id": "8hmSW7UJUdO8",
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"outputId": "5a03f29c-ae96-48f0-a045-0e37e228e7d3"
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},
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"outputs": [
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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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"cgen\n",
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"jupyter\n",
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"matplotlib-base>=2.0.2\n",
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"netcdf4>=1.1.9\n",
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"numpy>=1.9.1\n",
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"platformdirs\n",
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"psutil\n",
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"py>=1.4.27\n",
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"pymbolic\n",
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"scipy\n",
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"tqdm\n",
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"trajan\n",
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"xarray>=0.10.8\n",
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"cftime>=1.3.1\n",
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"dask>=2.0\n",
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"nbval\n",
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"scikit-learn\n",
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"pykdtree\n",
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"zarr>=2.11.0\n",
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"black\n",
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"isort\n",
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"pytest\n",
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"pytest-html\n",
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"coverage\n",
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"flake8>=2.1.0\n",
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"pre_commit\n",
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"pydocsty;e\n",
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"ipython\n",
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"numpydoc\n",
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"nbsphinx\n",
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"sphinx<6\n",
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"pandoc>1.12.1,<3\n",
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"pydata-sphinx-theme\n",
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"sphinx-autobuild\n",
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"myst-parser\n",
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"parcels\n"
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]
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}
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],
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"outputs": [],
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"source": [
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"packages = ['cgen',\n",
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" 'netcdf4>=1.1.9',\n",
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"id": "hoW6ozA04wue",
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"outputId": "cdf7ef3d-c0d1-4da1-99b3-73373b1bb0c4"
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},
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"outputs": [
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{
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"ename": "FileURLRetrievalError",
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"evalue": "Failed to retrieve file url:\n\n\tCannot retrieve the public link of the file. You may need to change\n\tthe permission to 'Anyone with the link', or have had many accesses.\n\nYou may still be able to access the file from the browser:\n\n\thttps://drive.google.com/uc?id=1DMtK76aCZxUOHdJFv1mI_EPTTHz_HIIN\n\nbut Gdown can't. Please check connections and permissions.",
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"output_type": "error",
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"traceback": [
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"\u001b[0;31m---------------------------------------------------------------------------\u001b[0m",
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"\u001b[0;31mFileURLRetrievalError\u001b[0m Traceback (most recent call last)",
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"\u001b[0;32m/usr/local/lib/python3.10/dist-packages/gdown/download.py\u001b[0m in \u001b[0;36mdownload\u001b[0;34m(url, output, quiet, proxy, speed, use_cookies, verify, id, fuzzy, resume, format, user_agent)\u001b[0m\n\u001b[1;32m 231\u001b[0m \u001b[0;32mtry\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 232\u001b[0;31m \u001b[0murl\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mget_url_from_gdrive_confirmation\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mres\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mtext\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 233\u001b[0m \u001b[0;32mexcept\u001b[0m \u001b[0mFileURLRetrievalError\u001b[0m \u001b[0;32mas\u001b[0m \u001b[0me\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
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"\u001b[0;32m/usr/local/lib/python3.10/dist-packages/gdown/download.py\u001b[0m in \u001b[0;36mget_url_from_gdrive_confirmation\u001b[0;34m(contents)\u001b[0m\n\u001b[1;32m 48\u001b[0m \u001b[0;32mif\u001b[0m \u001b[0;32mnot\u001b[0m \u001b[0murl\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m---> 49\u001b[0;31m raise FileURLRetrievalError(\n\u001b[0m\u001b[1;32m 50\u001b[0m \u001b[0;34m\"Cannot retrieve the public link of the file. \"\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
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"\u001b[0;31mFileURLRetrievalError\u001b[0m: Cannot retrieve the public link of the file. You may need to change the permission to 'Anyone with the link', or have had many accesses.",
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"\nDuring handling of the above exception, another exception occurred:\n",
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"\u001b[0;31mFileURLRetrievalError\u001b[0m Traceback (most recent call last)",
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"\u001b[0;32m<ipython-input-6-ff46f8bfe9e1>\u001b[0m in \u001b[0;36m<cell line: 23>\u001b[0;34m()\u001b[0m\n\u001b[1;32m 28\u001b[0m \u001b[0;31m#except:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 29\u001b[0m \u001b[0;31m# print(os.system('wget https://drive.google.com/uc?id='+file_id+' -P '+output))\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m---> 30\u001b[0;31m \u001b[0mgdown\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mdownload\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0murl\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0moutput\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mquiet\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0;32mFalse\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m",
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"\u001b[0;32m/usr/local/lib/python3.10/dist-packages/gdown/download.py\u001b[0m in \u001b[0;36mdownload\u001b[0;34m(url, output, quiet, proxy, speed, use_cookies, verify, id, fuzzy, resume, format, user_agent)\u001b[0m\n\u001b[1;32m 241\u001b[0m \u001b[0murl_origin\u001b[0m\u001b[0;34m,\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 242\u001b[0m )\n\u001b[0;32m--> 243\u001b[0;31m \u001b[0;32mraise\u001b[0m \u001b[0mFileURLRetrievalError\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mmessage\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 244\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 245\u001b[0m \u001b[0;32mif\u001b[0m \u001b[0mgdrive_file_id\u001b[0m \u001b[0;32mand\u001b[0m \u001b[0mis_gdrive_download_link\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
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"\u001b[0;31mFileURLRetrievalError\u001b[0m: Failed to retrieve file url:\n\n\tCannot retrieve the public link of the file. You may need to change\n\tthe permission to 'Anyone with the link', or have had many accesses.\n\nYou may still be able to access the file from the browser:\n\n\thttps://drive.google.com/uc?id=1DMtK76aCZxUOHdJFv1mI_EPTTHz_HIIN\n\nbut Gdown can't. Please check connections and permissions."
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]
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}
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],
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"outputs": [],
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"source": [
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"## Download required data for the tutorial\n",
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"files = [\"coordinates.zip\",\n",
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"id": "l4rWBopK4-33",
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"outputId": "ca64b20d-82aa-4a58-d614-7aa0b9f951ed"
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},
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"outputs": [
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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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"daily_V.zip unzipped\n",
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"daily_W.zip unzipped\n",
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"PlasticParcels.zip unzipped\n",
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"ERA5.zip unzipped\n",
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"coordinates.zip unzipped\n",
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"unbeaching.zip unzipped\n",
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"release.zip unzipped\n",
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"daily_U.zip unzipped\n"
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]
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}
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],
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"outputs": [],
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"source": [
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"## Unzip data and delete the .zip file\n",
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"download_files = os.listdir('./data_download/')\n",
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},
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"source": [
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"# PlasticParcels DRAKKAR Tutorial\n",
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"\n",
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"![PlasticParcels](https://github.com/OceanParcels/PlasticParcels/blob/main/logo.png)\n",
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"\n",
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"In this tutorial we will introduce you to some of the basic Parcels functions, as well as utilise the PlasticParcels tool for simulating microplastic pollution in the Mediterranean sea.\n",
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"\n",
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"By the end of this tutorial you should be able to create and visual hydrodynamic (and other) fields, create particle sets that represent marine microplastic pollution release locations, and apply physics parameterisations to simulate the dispersal of microplastics in the ocean.\n",

‎src/data_subsets/create_fisheries_subset.ipynb‎

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{
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"cells": [
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{
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"cell_type": "code",
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"execution_count": 4,
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"metadata": {},
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"outputs": [],
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"source": [
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"import numpy as np\n",
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"import xarray as xr\n",
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"import pandas as pd\n"
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]
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},
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{
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"cell_type": "code",
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"execution_count": 5,
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"metadata": {},
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"outputs": [],
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"source": [
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"## Create a subset of the fisheries data for the tutorial\n",
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"file = '../../data/release/generated_files/agg_data_fisheries_info.csv'\n",
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"df = pd.read_csv(file)"
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]
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},
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{
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"cell_type": "code",
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"execution_count": 6,
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"metadata": {},
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"outputs": [],
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"source": [
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"left_lim, right_lim = [-10, 42]\n",
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"bottom_lim, top_lim = [30, 48]"
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]
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},
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{
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"cell_type": "code",
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"execution_count": 12,
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"metadata": {},
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"outputs": [],
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"source": [
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"inside_longitudes = np.logical_and((df['Longitude']>= left_lim), (df['Longitude'] <= right_lim))"
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]
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},
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{
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"cell_type": "code",
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"execution_count": 13,
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"metadata": {},
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"outputs": [],
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"source": [
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"inside_latitudes = np.logical_and((df['Latitude']>= bottom_lim), (df['Latitude'] <= top_lim))"
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]
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},
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{
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"cell_type": "code",
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"execution_count": 14,
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"metadata": {},
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"outputs": [],
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"source": [
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"id_to_keep = np.logical_and(inside_longitudes, inside_latitudes)"
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]
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},
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{
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"cell_type": "code",
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"execution_count": 16,
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"metadata": {},
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"outputs": [],
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"source": [
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"subset = df[id_to_keep]"
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]
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},
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{
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"cell_type": "code",
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"execution_count": 17,
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"metadata": {},
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"outputs": [],
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"source": [
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"# Store datafile\n",
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"output_data = '../../data/release/generated_files/'\n",
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"subset.to_csv(output_data+'agg_data_fisheries_info_subset.csv')"
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]
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"metadata": {},
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"outputs": [],
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"source": []
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}
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],
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"metadata": {
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"kernelspec": {
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"display_name": "py3_parcels",
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"language": "python",
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"name": "python3"
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},
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"language_info": {
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"codemirror_mode": {
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"name": "ipython",
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"version": 3
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},
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"file_extension": ".py",
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"mimetype": "text/x-python",
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"name": "python",
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"nbconvert_exporter": "python",
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"pygments_lexer": "ipython3",
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"version": "3.11.4"
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}
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},
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"nbformat": 4,
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"nbformat_minor": 2
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}

‎src/release/create_fisheries_release.ipynb‎

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"outputs": [],
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"source": [
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"# Store datafile\n",
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"#agg_data_fisheries.to_csv(output_data+'fleet_monthly_aggregated.csv')\n",
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"agg_data_fisheries.to_csv(output_data+'fleet_monthly_aggregated.csv')\n",
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"## This chops it down from 70gb for one year to 2gb!"
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]
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},
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"## This chops it down from 70gb for one year to 2gb!"
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]
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},
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{
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"cell_type": "markdown",
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"metadata": {},
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"source": []
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},
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{
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"cell_type": "code",
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"execution_count": 12,

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