diff --git a/docs/conf.py b/docs/conf.py index 15f8ee9f..85fbb484 100644 --- a/docs/conf.py +++ b/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", } diff --git a/docs/user-guide/tutorials/Sail_the_ship.ipynb b/docs/user-guide/assignments/Sail_the_ship.ipynb similarity index 75% rename from docs/user-guide/tutorials/Sail_the_ship.ipynb rename to docs/user-guide/assignments/Sail_the_ship.ipynb index a21b39f5..3105607d 100644 --- a/docs/user-guide/tutorials/Sail_the_ship.ipynb +++ b/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 --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 --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```" ] }, {