diff --git a/docs/classroom-surf-environment.yml b/docs/classroom-surf-environment.yml index 4feda79a..51f33f18 100644 --- a/docs/classroom-surf-environment.yml +++ b/docs/classroom-surf-environment.yml @@ -45,8 +45,11 @@ miniconda: - opensimplex ==0.4.5 - numpy >=1,<2 - pydantic >=2,<3 - - copernicusmarine >=2 + - pyyaml + - copernicusmarine >= 2.2.2 - openpyxl + - yaspin + - textual # extra - xarray diff --git a/docs/user-guide/tutorials/surf_research_cloud_setup.ipynb b/docs/user-guide/tutorials/surf_research_cloud_setup.ipynb index 299d9cb0..a0a28fbf 100644 --- a/docs/user-guide/tutorials/surf_research_cloud_setup.ipynb +++ b/docs/user-guide/tutorials/surf_research_cloud_setup.ipynb @@ -2,18 +2,16 @@ "cells": [ { "cell_type": "markdown", - "metadata": { - "vscode": { - "languageId": "plaintext" - } - }, + "id": "98770716", + "metadata": {}, "source": [ - "# SURF Resarch Cloud: Virtualship environment setup\n", + "# SURF Resarch Cloud: VirtualShip environment setup\n", "\n", - "> Note: \n", - "> This guide is specific to students who are enrolled at UU in the Dynamical Oceanography course.\n", + "```\n", + "Note: This guide is specific to students who are enrolled at Utrecht University.\n", + "```\n", "\n", - "In the class, we use virtualship in the cloud (in this case, SURF Research Cloud - called SURF RC from here-on). This has several advantages:\n", + "In the class, we will use VirtualShip in the cloud (in this case, SURF Research Cloud - called SURF RC from here-on). This has several advantages:\n", "\n", "- You aren't limited to the power of your laptop\n", "- Input datasets are downloaded faster, as they're downloaded to the cloud instance (and not to your laptop)\n", @@ -29,9 +27,12 @@ "\n", "## 3. Jupyter workspace layout and additional config\n", "\n", - "> Note: This only needs to be done once during setup.\n", + "```\n", + "Note: This only needs to be done once during setup.\n", + "```\n", "\n", "In the Jupyter workspace, you'll see the following in your file explorer:\n", + "\n", "```\n", ".\n", "├── KERNEL-README.ipynb\n", @@ -45,24 +46,24 @@ "\n", "---\n", "\n", - "To be able to run virtualship from the terminal, we need to take some additional steps which are detailed in the `KERNEL-README.ipynb` contains important information for configuring your environment. Namely, for our uses, the \"Initialize conda\" section. Do the following.\n", - "\n", - "> #### Initialize conda\n", - "> \n", - "> To make the already installed conda-tool available for yourself, you have to initialize your terminal shell.\n", - "> \n", - "> Start a \"Terminal\" tab in the Jupyter Lab launcher and type:\n", - "> ```\n", - "> /etc/miniconda/bin/conda init\n", - "> ```\n", - "> Close the terminal tab and start a new one.\n", - "> You will see that the terminal prompt has changed to something like\n", - "> ```\n", - "> (base) metheuser@mywsp:\n", - "> ```\n", - "> This is conda telling you that you are currently in the \"base\" environment.\n", - "\n", - "From here, you already have another environment set up for you. Running `conda env list` in the terminal, you should see:\n", + "To be able to run VirtualShip from the Terminal, we need to take some additional steps which are detailed in the `KERNEL-README.ipynb`. This contains important information for configuring your environment. Namely, for our uses, the \"Initialize conda\" section. Do the following:\n", + "\n", + "#### Initialize conda\n", + "\n", + "To make the already installed conda-tool available for yourself, you have to initialize your Terminal shell.\n", + "\n", + "Start a \"Terminal\" tab in the Jupyter Lab launcher and type: `/etc/miniconda/bin/conda init`\n", + "\n", + "Close the Terminal tab and start a new one.\n", + "You will see that the Terminal prompt has changed to something like\n", + "\n", + "```\n", + "(base) metheuser@mywsp:\n", + "```\n", + "\n", + "This is conda telling you that you are currently in the \"base\" environment.\n", + "\n", + "From here, you already have another environment set up for you. Running `conda env list` in the Terminal, you should see:\n", "\n", "```bash\n", "conda env list\n", @@ -73,27 +74,28 @@ "virtualship /etc/miniconda/envs/virtualship`\n", "```\n", "\n", - "Here you can do `conda activate virtualship` to activate the environment called \"virtualship\". This environment is a shared environment among all workspace users that can be centrally updated. If you want you can create and manage your own environments by running the relevant conda commands.\n", + "Here you can do `conda activate virtualship` to activate the environment called \"virtualship\". This environment is a shared environment among all workspace users that can be centrally updated. If you want, you can create and manage your own environments by running the relevant conda commands.\n", "\n", - "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.\n", + "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.\n", "\n", "---\n", - "Finally, when you're working in Jupyter Notebooks, you are able to access the Conda environment with `virtualship` and related dependencies by switching the Kernel in the top right of the UI.\n", "\n", + "Finally, when you're working in Jupyter Notebooks, you are able to access the Conda environment with `virtualship` and related dependencies by switching the Kernel in the top right of the UI.\n", "\n", "\n", "## Course facilitator notes\n", "\n", - "If `virtualship` is updated on GitHub, and you want to update the shared environment, you can do so by running the following commands in the terminal:\n", + "If `virtualship` is updated on GitHub, and you want to update the shared environment, you can do so by running the following commands in the Terminal:\n", "\n", "```bash\n", "conda activate virtualship\n", "sudo /etc/miniconda/envs/virtualship/bin/pip install --upgrade git+https://github.com/OceanParcels/virtualship@main\n", - "```" + "```\n" ] }, { "cell_type": "markdown", + "id": "3926833e", "metadata": {}, "source": [] } @@ -104,5 +106,5 @@ } }, "nbformat": 4, - "nbformat_minor": 2 + "nbformat_minor": 5 }