Sail the ship notebook #248
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| "With the `virtualship` environment, you now have access to the `virtualship` command in your Terminal, which can be confirmed by running `virtualship --help`. From here you can `cd` into `data/shared-storage/{your-name}` and run `virtualship` commands as you would on your local machine (see the VirtualShip [quickstart guide](https://virtualship.readthedocs.io/en/latest/user-guide/quickstart.html)). \n", | ||
| "With the `virtualship` environment, you now have access to the `virtualship` command in your Terminal, which can be confirmed by running `virtualship --help`. \n", | ||
| "\n", | ||
| "From here you can `cd` ('change directory') into `data/storage-osl/{your-name}` and run `virtualship` commands as you would on your local machine (see the VirtualShip [quickstart guide](https://virtualship.readthedocs.io/en/latest/user-guide/quickstart.html)). \n", |
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In the past we had issues with their home directory being full. Is it even necessary now to cd into storage with streaming Copernicus data? If so, be more explicit that they should
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I think it's best they continue working from storage so that the results files are stored there + we don't lose all the groups' data if something goes wrong with the workspace.
Re: explicitly stating that they should cd into storage, I favour leaving it like this in the SURF set up notebook but then being explicit about it in the sail_the_ship notebook (right they actually start running commands), i.e.
Otherwise I can imagine there could be instances where students cd during the SURF set up but may have moved away before running virtualship commands.
But I'll make this line even more explicit in sail_the_ship, I agree it could otherwise be missed 👍
| "> Usage: virtualship fetch [OPTIONS] PATH\n", | ||
| ">\n", | ||
| "> Download input data for an expedition.\n", | ||
| "This guide will help you get started with running your VirtualShip expedition. Follow the steps below to set up your programming environment, configure your expedition, and launch your simulation. \n", |
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replace "This guide will help you get started with running" with "Now let's get started on"
remove "programming"?
change "configure" to plan?
| "```\n", | ||
| "virtualship fetch EXPEDITION_NAME\n", | ||
| "```" | ||
| "You will need to register for **Copernicus Marine Service** account (see [here](https://data.marine.copernicus.eu/register)), if you have not done so already. This is required to access the oceanographic data that VirtualShip uses to run your expedition." |
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add a
register for a Copernicus Marine Service
| "### Upload the coordinates to your virtual machine\n", | ||
| "\n", | ||
| "<div class=\"alert alert-block alert-success\"> \n", | ||
| "**TIP**: If you have not done so already, make sure you create a folder for your group's expedition data in your persistent storage on SURF RC (i.e. `mkdir data/storage-osl/{your-group-name}`).\n", |
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Make these into absolute paths with a / before data so it doesn't matter from which path they type this command
| "```" | ||
| "### NIOZ MFP tool\n", | ||
| "\n", | ||
| "The first step is to plan the expedition route for your chosen research question, bearing in mind where you will need to go to collect data for your research, what kind of sampling strategy you will use, and how long you want your expedition to last (remember, though, you have a three week ship time limit).\n", |
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replace with?
"The first step is to plan the expedition route for your chosen research, bearing in mind the time needed for your sampling strategy, and traveling to and from a port suitable for research vessels (remember, though, you have a three week ship time limit).\n"
| "## 5) Expedition scheduling & ship configuration\n", | ||
| "\n", | ||
| "<div class=\"alert alert-block alert-success\"> \n", | ||
| "**TIP**: From here, you should replace any references to `EXPEDITION_NAME` with the actual name you used for your expedition when running the `virtualship init` command.\n", |
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remove "when running the virtualship init command"
Revive the
sail_the_ship.ipynbnotebook, to be used in the Ocean and Sea Level UU course as an instruction document for students to run their VirtualShip expeditions for their given research question.This combines elements of the quickstart guide with pointers to the SURF set up as well as some more general ship-going information.