update tutorial for Friday (#135)

* update tutorial for Friday

* code into markdown cells

* formatting

* move to assignments

* thumbnail

Author: ammedd

docs/conf.py

@@ -76,5 +76,5 @@
     "user-guide/assignments/Research_Proposal_only": "user-guide/_images/MFP.jpg",
     "user-guide/assignments/Virtualship_research_proposal": "user-guide/_images/AnnaWeber.jpeg",
     "user-guide/assignments/sciencecommunication_assignment": "user-guide/_images/marine_ss.jpg",
-    "user-guide/tutorials/Sail_the_ship": "user-guide/_images/vessel.jpg",
+    "user-guide/assignments/Sail_the_ship": "user-guide/_images/vessel.jpg",
 }

docs/user-guide/tutorials/Sail_the_ship.ipynb renamed to docs/user-guide/assignments/Sail_the_ship.ipynb

@@ -4,7 +4,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "### Time has come to start your expedition!\n",
+    "### Start your expedition!\n",
     "\n",
     "https://www.youtube.com/watch?v=G82kIgc1imk\n",
     "\n",
@@ -15,22 +15,14 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "Create a folder for your expedition where the results will be saved. Initialize the virtualship using a `!` to use the tool directly from this notebook or copy the commands (without the `!`) directly into your terminal\n",
-    "```\n",
-    "Usage: virtualship init [OPTIONS] PATH\n",
+    "On your (virtual) machine change directory into the folder where your expedition will be run. Initialize the virtualship by copying the commands directly into a terminal.\n",
     "\n",
-    "  Initialize a directory for a new expedition, with an example schedule and\n",
-    "  ship config files.\n",
-    "  ```"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "!virtualship init EXPEDITION_NAME"
+    ">Usage: virtualship init [OPTIONS] PATH\n",
+    ">\n",
+    ">  Initialize a directory for a new expedition, with an example schedule and\n",
+    ">  ship config files.\n",
+    "\n",
+    "```virtualship init EXPEDITION_NAME```"
    ]
   },
   {
@@ -39,46 +31,56 @@
    "source": [
     "This will create a folder `EXPEDITION_NAME` with two files: `schedule.yaml` and\t`ship_config.yaml`.\n",
     "\n",
-    "Populate the `schedule.yaml` file manually with each sampling CTD station and drifer/argo float deployment position. The route between points will be sailed as the shortest great-cirlce distance.  \n",
-    "[TODO: or initialize from a MFP csv file and correct where needed]\n",
-    "\n",
-    "When you have finished your schedule, run the fetch command to download input data for the virtual ship from the Copernicus marine data store. \n",
-    "You will need to register via: https://data.marine.copernicus.eu/register and provide your username and password as command line arguments:\n",
-    "```\n",
-    "Usage: virtualship fetch [OPTIONS] PATH\n",
+    "You can populate the `schedule.yaml` file manually with each sampling CTD station and XBT/DRIFTER/ARGO_FLOAT deployment position. Or use the exported cruise coordinates from MFP. In that case, add an extra column to the .xlsx file called `Instrument` and on each line write which instruments you want to use or deploy there. Multiple instrument are allowed, e.g. `DRIFTER, CTD` or `DRIFTER, ARGO_FLOAT`. If you want to use your MFP export, make sure your directory is clean and run:\n",
     "\n",
-    "  Download input data for an expedition.\n",
-    "  ```"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "!virtualship fetch EXPEDITION_NAME --username <USERNAME> --password <PASSWORD>"
+    "```virtualship init EXPEDITION_NAME --from-mfp CoordinatesExport.xlsx```"
    ]
   },
   {
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "After your input data has been downloaded you can begin your expedition:\n",
-    "```\n",
-    "Usage: virtualship run [OPTIONS] PATH\n",
     "\n",
-    "  Run the expedition.\n",
-    "  ```"
+    "Mind that the route between points will be sailed as the shortest great-cirlce distance.  \n",
+    "\n",
+    "Instrument configurations can be provided in `ship_config`. \n",
+    "\n",
+    "Under `adcp_config` provide the configuration of your ADCP, so either `max_depth_meter: -1000.0` if you want to use the OceanObserver or `max_depth_meter: -150.0` if you want to use the SeaSeven. \n",
+    "\n",
+    "If you don't need the ADCP to measure, remove the `adcp_config` and underlying lines from the configuration file. \n",
+    "\n",
+    "If you do not want to collect underway data, remove `ship_underwater_st_config` from the configuration file.\n",
+    "\n",
+    "Change the xbt, drifter and argo_float configurations if you want.\n",
+    "\n",
+    "For the CTD, provide the maximum depth you will want to measure at. All other CTD casts will be done to approximately 20 meter of the ocean floor. \n",
+    "\n",
+    "When you have finished your schedule and config, run the fetch command to download input data for the virtual ship from the Copernicus marine data store. \n",
+    "You will need to register via: https://data.marine.copernicus.eu/register \n",
+    "You can provide your username and password as command line arguments. If you don't you will be prompted for your credentials.\n",
+    "\n",
+    "> Usage: virtualship fetch [OPTIONS] PATH\n",
+    ">\n",
+    ">  Download input data for an expedition.\n",
+    "\n",
+    "```virtualship fetch EXPEDITION_NAME --username <USERNAME> --password <PASSWORD>```\n",
+    "\n",
+    "```virtualship fetch EXPEDITION_NAME```"
    ]
   },
   {
-   "cell_type": "code",
-   "execution_count": null,
+   "cell_type": "markdown",
    "metadata": {},
-   "outputs": [],
    "source": [
-    "!virtualship run EXPEDITION_NAME"
+    "Waiting for your data download is a great time to practice your level of patience. A skill much needed in oceanographic fieldwork ;-)\n",
+    "\n",
+    "After your input data has been downloaded you can do your expedition:\n",
+    "\n",
+    "> Usage: virtualship run [OPTIONS] PATH\n",
+    ">\n",
+    "> Run the expedition.\n",
+    "\n",
+    "```virtualship run EXPEDITION_NAME```"
    ]
   },
   {