add collaborative workspace setup guide to index

Author: j-atkins

docs/user-guide/tutorials/index.md

@@ -6,6 +6,7 @@ maxdepth: 1
 caption: Tutorials
 ---
 surf_research_cloud_setup.ipynb
+surf_collaborative_setup.ipynb
 ADCP_data_tutorial.ipynb
 CTD_data_tutorial.ipynb
 Drifter_data_tutorial.ipynb

docs/user-guide/tutorials/surf_collaborative_setup.ipynb

@@ -5,7 +5,7 @@
    "id": "98770716",
    "metadata": {},
    "source": [
-    "# SURF Resarch Cloud: VirtualShip environment setup\n",
+    "# SURF Resarch Cloud: Collaborative Workspace Setup Guide\n",
     "\n",
     "```\n",
     "Note: This guide is specific to students who are enrolled at Utrecht University.\n",
@@ -34,9 +34,12 @@
     "\n",
     "## 4. Launch VirtualShip environment\n",
     "\n",
-    "❗️ Before proceeding any further, you should type the following command in the Terminal: `bash` and then hit Enter. This will ensure that you are in a bash shell for the rest of the setup.\n",
+    "❗️ Before proceeding any further, you should type the following command in the Terminal and then hit Enter: `bash` ❗️\n",
     "\n",
-    "You will see that the Terminal prompt has changed to something like\n",
+    "\n",
+    "This will ensure that you are in a bash shell for the rest of the setup.\n",
+    "\n",
+    "You will see that the Terminal prompt has changed to something like:\n",
     "\n",
     "```bash\n",
     "(base) metheuser@mywsp:\n",
@@ -55,27 +58,43 @@
     "virtualship            /etc/miniconda3/envs/virtualship\n",
     "```\n",
     "\n",
-    "Next, to launch the VirtualShip environment, type the following command in the Terminal and hit Enter:\n",
+    "Next, to launch the VirtualShip environment, type the following command in the Terminal and hit Enter: `conda activate virtualship`\n",
+    "\n",
+    "This will activate the VirtualShip conda environment, which has all the necessary dependencies installed. You can confirm that you are in the correct environment by checking that your Terminal prompt now looks something like:\n",
     "\n",
     "```bash\n",
-    "conda activate virtualship\n",
+    "(virtualship) metheuser@mywsp:\n",
     "```\n",
     "\n",
-    "This will activate the VirtualShip conda environment, which has all the necessary dependencies installed. You can confirm that you are in the correct environment by checking that your Terminal prompt now starts with `(virtualship)`.\n",
+    "With the `virtualship` environment, you now have access to the `virtualship` command in your Terminal.\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`.\n",
+    "This can be confirmed by typing the following command in the Terminal and hitting Enter: `virtualship --help`.\n",
     "\n",
-    "## 5. Navigate to the shared storage folder\n",
-    "\n",
-    "We will be working from a shared storage folder in the workspace. To navigate to this folder, type the following command in the Terminal and hit Enter:\n",
+    "You should see something like:\n",
     "\n",
-    "```bash\n",
-    "cd data/virtualship-storage/\n",
     "```\n",
+    "virtualship --help\n",
+    "\n",
+    "Usage: virtualship [OPTIONS] COMMAND [ARGS]...\n",
+    "\n",
+    "Options:\n",
+    "  --version  Show the version and exit.\n",
+    "  --help     Show this message and exit.\n",
+    "\n",
+    "Commands:\n",
+    "  fetch  Download input data for an expedition.\n",
+    "  init   Initialize a directory for a new expedition, with an example...\n",
+    "  plan   Launch UI to help build schedule and ship config files.\n",
+    "  run    Run the expedition.\n",
+    "  ```\n",
+    "\n",
+    "## 5. Navigate to the shared storage folder\n",
+    "\n",
+    "We will be working from a shared storage folder in the workspace. To navigate to this folder, type the following command in the Terminal and hit Enter: `cd data/virtualship-storage/`\n",
     "\n",
-    "Depending on the specific set-up for the course you are taking, if you now enter `ls` to list the contents of the directory, you should see various group folders, for example: `group_1`, `group_2`, ... and so on.\n",
+    "Depending on the specific set-up for the course you are taking, if you now enter `ls` to list the contents of the directory, you may see various group folders, for example: `group_1`, `group_2`, ... and so on.\n",
     "\n",
-    "This is where will be working from for the rest of the course, with the group name for each folder corresponding to your assigned group.\n",
+    "If you have been pre-assigned into groups, this is where will be working from for the rest of the course, with the group name for each folder corresponding to your assigned group.\n",
     "\n",
     "You are ready to continue with the VirtualShip analysis workflow as described in the course materials and/or VirtualShip [quickstart guide](https://virtualship.readthedocs.io/en/latest/user-guide/quickstart.html)."
    ]