Updates to surf docs and virtual environment dependencies

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

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
 }