Remove spacetime-region (#264)

* first round, delete SpaceTimeRegion object and related classes/methods

* remove space time region from _plan

* update base and instrument class logic to use waypoint extremes for spacetime domain

* clean up _plan methods

* extend latlon buffer for drifters

* set time buffer from drifter lifetime config

* shift testing to use waypoint space-times instead of space-time-region object

* fix assert error messaging

* remove spatial constraint on fieldset ingestion

* add control over whether to constrain spatial region in fieldset

* give argos a prescribed lifetime

* add lifetime field to expedition models and _plan

* update test with argo lifetime

* remove temporary debugging tools

* [pre-commit.ci] auto fixes from pre-commit.com hooks

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* update argo endtime and give depth lim in fieldset generation

* remove depth lim on fieldset generation

* clean up comment

* change lifetime in expedition model to be in days units

* update _plan logic (+ more changes to expedition model) to handle lifetime in minutes

* small refactor for readability

* [pre-commit.ci] auto fixes from pre-commit.com hooks

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* remove broken links

* update pre-downloaded data documentation to explain argo/drifter lifetime bounds

* fix docs build?

* another broken link

* add error messaging for unsuported time units

* [pre-commit.ci] auto fixes from pre-commit.com hooks

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---------

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

Author: j-atkins

docs/user-guide/assignments/Research_proposal_intro.ipynb

@@ -150,9 +150,15 @@
     "\n",
     "Finally, fit your equipment in the 20-foot container. The container will be sent to your port of departure ahead of time with a cargo boat, so make sure you are packed in time for this transfer. Remember there are no shops at sea, so think carefully and plan ahead. \n",
     "\n",
-    "![Equipment preparation NIOZ](https://www.nioz.nl/application/files/9116/7500/3457/2023-01-16-packing.jpg) \n",
-    "![Equipment loading](https://www.nioz.nl/application/files/7416/7810/2265/2023-03-06-container-shifting.jpg) "
+    "<!-- TODO: these images are no longer hosted -->\n",
+    "<!-- ![Equipment preparation NIOZ](https://www.nioz.nl/application/files/9116/7500/3457/2023-01-16-packing.jpg) \n",
+    "![Equipment loading](https://www.nioz.nl/application/files/7416/7810/2265/2023-03-06-container-shifting.jpg)  -->"
    ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": []
   }
  ],
  "metadata": {

docs/user-guide/assignments/Sail_the_ship.ipynb

@@ -259,7 +259,7 @@
     "\n",
     "Reporting your journey is an essential aspect of our oceanographic research expedition. It allows us to share our experiences, communicate our findings, and contribute to the broader scientific community. After each scientific expedition a cruise report should be written (or in the case of this course, a presentation).\n",
     "\n",
-    "You can find many cruise [reports](https://www.bodc.ac.uk/resources/inventories/cruise_inventory/reports/pe358.pdf) and [blogs](https://www.nioz.nl/en/blog/topic/1027) online from many different cruises.\n",
+    "You can find many cruise [reports](https://www.bodc.ac.uk/resources/inventories/cruise_inventory/reports/pe358.pdf) and [blogs](https://www.nioz.nl/en/news-and-blogs) online from many different cruises.\n",
     "\n",
     "Reporting our journey allows us to validate the data collected during our research activities. It provides context for our findings and helps ensure that our results are accurately interpreted and understood. Detailed reports enable us to cross-reference our observations with environmental conditions, sampling locations, and other relevant factors, enhancing the reliability and credibility of our data. \n",
     "\n",

docs/user-guide/documentation/pre_download_data.md

@@ -20,6 +20,10 @@ In addition, all pre-downloaded data must be split into separate files per times
 **Monthly data**: when using monthly data, ensure that your final .nc file download is for the month *after* your expedition schedule end date. This is to ensure that a Parcels FieldSet can be generated under-the-hood which fully covers the expedition period. For example, if your expedition runs from 1st May to 15th May, your final monthly data file should be in June. Daily data files only need to cover the expedition period exactly.
 ```
 
+```{note}
+**Argo and Drifter data**: if using Argo floats or Drifters in your expedition, ensure that: 1) the temporal extent of the downloaded data also accounts for the full *lifetime* of the instruments, not just the expedition period, and 2) the spatial bounds of the downloaded data also accounts for the likely drift distance of the instruments over their lifetimes. Otherwise, simulations will end prematurely (out-of-bounds errors) when the data runs out.
+```
+
 Further, VirtualShip expects pre-downloaded data to be organised in a specific directory & filename structure within the specified local data directory. The expected structure is as outlined in the subsequent sections.
 
 #### Directory structure

docs/user-guide/teacher-content/UU-ocean-of-future/Tutorial1.ipynb

@@ -59,7 +59,7 @@
     "\n",
     "- https://schmidtocean.org/cruise-log-post/four-unexpected-things-i-learned-while-working-on-a-research-vessel/\n",
     "\n",
-    "Or browse through some blogs from many different cruises, e.g. https://www.nioz.nl/en/blog/topic/1027\n",
+    "Or browse through some blogs from many different cruises, e.g. https://www.nioz.nl/en/news-and-blogs/blog/dust2025\n",
     "</div>\n",
     "\n",
     "\n",

docs/user-guide/tutorials/Drifter_data_tutorial.ipynb

@@ -17,7 +17,7 @@
    "source": [
     "## Set up\n",
     "\n",
-    "#### Imports\n",
+    "### Imports\n",
     "\n",
     "The first step is to import the Python packages required for post-processing the data and plotting. \n",
     "\n",
@@ -46,7 +46,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "#### Data directory\n",
+    "### Data directory\n",
     "\n",
     "Next, you should set `data_dir` to be the path to your expedition results in the code block below. You should replace `\"/path/to/EXPEDITION/results/\"` with the path for your machine.\n",
     "\n",
@@ -70,7 +70,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "#### Load data\n",
+    "### Load data\n",
     "\n",
     "We are now ready to read in the data using the `xarray` package. You can carry on executing the next cells without making changes to the code…"
    ]
@@ -311,7 +311,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "## Case study: Interpreting drifter trajectories\n",
+    "### Case study: Interpreting drifter trajectories\n",
     "\n",
     "<div class=\"alert alert-block alert-info\"> \n",
     "<b>**NOTE**:</b> This next section has no code to run and will likely look different from your own results - you will have run your own drifter simulations with different initial positions and times! This is just an example to demonstrate the kinds of drifter flow dynamics questions you can start to think about.\n",