post review edits

Author: j-atkins

docs/user-guide/assignments/index.md

@@ -9,5 +9,5 @@ Research_proposal_intro.ipynb
 Research_Proposal_only.ipynb
 Virtualship_research_proposal.ipynb
 sciencecommunication_assignment.ipynb
-Sail_the_ship.ipynb
+<!-- Sail_the_ship.ipynb -->
 ```

docs/user-guide/quickstart.md

@@ -22,29 +22,28 @@ Feel free to design your expedition as you wish! There is no need to copy these
 
 ### Export the coordinates
 
-Once you have finalised your MFP expedition route, select "Export" on the right hand side of the window --> "Export Coordinates" --> "DD". This will download your coordinates as an .xslx (Excel) file, which we will later feed into the VirtualShip protocol to initialise the expedition.
+Once you have finalised your MFP expedition route, select "Export" on the right hand side of the window --> "Export Coordinates" --> "DD". This will download your coordinates as an .xlsx (Excel) file, which we will later feed into the VirtualShip protocol to initialise the expedition.
 
 ## Expedition initialisation
 
 ```{note}
-VirtualShip is a command line interface (CLI) based tool. From this point on in the Quickstart we will be working predominantly via the command line.
-If you are unfamiliar with what a CLI is, see [here](https://www.w3schools.com/whatis/whatis_cli.asp) for more information.
+VirtualShip is a command line interface (CLI) based tool. From this point on in the Quickstart we will be working predominantly via the command line in the Terminal. If you are unfamiliar with what a CLI is, see [here](https://www.w3schools.com/whatis/whatis_cli.asp) for more information.
 ```
 
 You should now navigate to where you would like your expedition to be run on your (virtual) machine (i.e. `cd path/to/expedition/dir/`). Then run the following command in your CLI:
 
 ```
-virtualship init EXPEDITION_NAME --from-mfp CoordinatesExport.xslx
+virtualship init EXPEDITION_NAME --from-mfp CoordinatesExport.xlsx
 ```
 
 ```{tip}
-The `CoordinatesExport.xslx` in the `virtualship init` command refers to the .xslx file exported from MFP. Replace the filename with the name of your exported .xslx file (and make sure to move it from the Downloads to the folder/directory in which you are running the expedition).
+The `CoordinatesExport.xlsx` in the `virtualship init` command refers to the .xlsx file exported from MFP. Replace the filename with the name of your exported .xlsx file (and make sure to move it from the Downloads to the folder/directory in which you are running the expedition).
 ```
 
 This will create a folder/directory called `EXPEDITION_NAME` with two files: `schedule.yaml` and `ship_config.yaml` based on the sampling site coordinates that you specified in your MFP export. The `--from-mfp` flag indictates that the exported coordinates will be used.
 
 ```{note}
-It is also possible to run the expedition initialisation step without an MFP .xslx export file. In this case you should simply run `virtualship init EXPEDITION_NAME` in the CLI. This will write example `schedule.yaml` and `ship_config.yaml` files in the `EXPEDITION_NAME` folder/directory. These files contain example waypoints, timings and instrument selections, but can be edited or propagated through the rest of the workflow unedited to run a sample expedition.
+For advanced users: it is also possible to run the expedition initialisation step without an MFP .xlsx export file. In this case you should simply run `virtualship init EXPEDITION_NAME` in the CLI. This will write example `schedule.yaml` and `ship_config.yaml` files in the `EXPEDITION_NAME` folder/directory. These files contain example waypoints, timings and instrument selections, but can be edited or propagated through the rest of the workflow unedited to run a sample expedition.
 ```
 
 ## Expedition scheduling & ship configuration
@@ -71,7 +70,7 @@ In the planning tool, under _Ship Config Editor_ > _Ship Speed & Onboard Measure
 
 VirtualShip is capable of taking underway temperature and salinity measurements, as well as onboard ADCP measurements, as the ship sails across the length of the expedition (see [here](https://virtualship.readthedocs.io/en/latest/user-guide/assignments/Research_proposal_intro.html#Underway-Data) for more detail). These underway measurements can be switched on/off under _Ship Config Editor_ > _Ship Speed & Onboard Measurements_ as well.
 
-For the underway ADCP, there is a choice of using the OceanObserver or SeaSeven version (see [here](https://virtualship.readthedocs.io/en/latest/user-guide/assignments/Research_proposal_intro.html#ADCP) for more detail on the two ADCP types).
+For the underway ADCP, there is a choice of using the 38 kHz OceanObserver or the 300 kHz SeaSeven version (see [here](https://virtualship.readthedocs.io/en/latest/user-guide/assignments/Research_proposal_intro.html#ADCP) for more detail on the two ADCP types).
 
 ### Waypoint datetimes
 
@@ -98,7 +97,7 @@ Click [here](https://virtualship.readthedocs.io/en/latest/user-guide/assignments
 Instrument selections can be made for each waypoint in the same sub-panels as the [waypoint time](#waypoint-datetimes) selection by simply switching each on or off. Multiple instruments are allowed at each waypoint.
 
 ```{note}
-For advanced users only: you can also make further customisations to behaviours of all instruments under _Ship Config Editor_ > _Instrument Configurations_.
+For advanced users: you can also make further customisations to behaviours of all instruments under _Ship Config Editor_ > _Instrument Configurations_.
 ```
 
 ### Save changes
@@ -141,12 +140,6 @@ It might take up to an hour to simulate the measurements depending on your choic
 
 Upon successfully completing the simulation, results from the expedition will be stored in the `EXPEDITION_NAME/results` directory, written as [Zarr](https://zarr.dev/) files.
 
-If you are a working on a remote machine, download your results by navigating to `EXPEDITION_NAME/results` and running:
-
-```
-zip -r results.zip results/
-```
-
-From here you can carry on your analysis offline. We encourage you to explore and analyse these data using [Xarray](https://docs.xarray.dev/en/stable/). We also provide various further [VirtualShip tutorials](https://virtualship.readthedocs.io/en/latest/user-guide/tutorials/index.html) which provide examples of how to visualise data recorded by the VirtualShip instruments.
+From here you can carry on your analysis (offline). We encourage you to explore and analyse these data using [Xarray](https://docs.xarray.dev/en/stable/). We also provide various further [VirtualShip tutorials](https://virtualship.readthedocs.io/en/latest/user-guide/tutorials/index.html) which provide examples of how to visualise data recorded by the VirtualShip instruments.
 
 <!-- TODO: Add a link to visualisation tool as an alternate option to own visualisation when/if this feature is implemented?! -->