Unify config files to expedition.yaml

.github/ISSUE_TEMPLATE/bug_report.md

@@ -1,7 +1,7 @@
 ---
 name: Bug report
 about: Create a report to help us improve
-title: ""
+title: ["needs-triage"]
 labels: bug
 assignees: ""
 ---

.github/ISSUE_TEMPLATE/feature_request.md

@@ -1,7 +1,7 @@
 ---
 name: Feature request
 about: Suggest an idea for this project
-title: ""
+title: ["needs-triage"]
 labels: enhancement
 assignees: ""
 ---

docs/user-guide/quickstart.md

@@ -46,10 +46,10 @@ virtualship init EXPEDITION_NAME --from-mfp CoordinatesExport.xlsx
 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.
+This will create a folder/directory called `EXPEDITION_NAME` with a single file: `expedition.yaml` containing details on the ship and instrument configurations, as well as the expedition schedule based on the sampling site coordinates that you specified in your MFP export. The `--from-mfp` flag indicates that the exported coordinates will be used.
 
 ```{note}
-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.
+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 an example `expedition.yaml` file in the `EXPEDITION_NAME` folder/directory. This file contains example waypoints, timings, instrument selections, and ship configuration, but can be edited or propagated through the rest of the workflow unedited to run a sample expedition.
 ```
 
 ## Expedition scheduling & ship configuration
@@ -61,7 +61,7 @@ virtualship plan EXPEDITION_NAME
 ```
 
 ```{tip}
-Using the `virtualship plan` tool is optional. Advanced users can also edit the `schedule.yaml` and `ship_config.yaml` files directly if preferred.
+Using the `virtualship plan` tool is optional. Advanced users can also edit the `expedition.yaml` file directly if preferred.
 ```
 
 The planning tool should look something like this and offers an intuitive way to make your selections:
@@ -111,7 +111,7 @@ For advanced users: you can also make further customisations to behaviours of al
 When you are happy with your ship configuration and schedule plan, press _Save Changes_.
 
 ```{note}
-On pressing _Save Changes_ the tool will check the selections are valid (for example that the ship will be able to reach each waypoint in time). If they are, the changes will be saved to the `ship_config.yaml` and `schedule.yaml` files, ready for the next steps. If your selections are invalid you should be provided with information on how to fix them.
+On pressing _Save Changes_ the tool will check the selections are valid (for example that the ship will be able to reach each waypoint in time). If they are, the changes will be saved to the `expedition.yaml` file, ready for the next steps. If your selections are invalid you should be provided with information on how to fix them.
 ```
 
 ## Fetch the data

docs/user-guide/tutorials/Argo_data_tutorial.ipynb

@@ -14,7 +14,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 1,
+   "execution_count": null,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -28,33 +28,34 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "We have downloaded the data from Copernicus Marine Service, using `virtualship fetch` and the information in following `schedule.yaml` file:\n",
+    "We have downloaded the data from Copernicus Marine Service, using `virtualship fetch` and the information in following `schedule` section of the `expedition.yaml` file:\n",
     "```yaml\n",
-    "space_time_region:\n",
-    "  spatial_range:\n",
-    "    minimum_longitude: -5\n",
-    "    maximum_longitude: 5\n",
-    "    minimum_latitude: -5\n",
-    "    maximum_latitude: 5\n",
-    "    minimum_depth: 0\n",
-    "    maximum_depth: 2000\n",
-    "  time_range:\n",
-    "    start_time: 2023-01-01 00:00:00\n",
-    "    end_time: 2023-02-01 00:00:00\n",
-    "waypoints:\n",
-    "  - instrument: ARGO_FLOAT\n",
-    "    location:\n",
-    "      latitude: 0.02\n",
-    "      longitude: 0.02\n",
-    "    time: 2023-01-01 02:00:00\n",
+    "schedule:\n",
+    "  space_time_region:\n",
+    "    spatial_range:\n",
+    "      minimum_longitude: -5\n",
+    "      maximum_longitude: 5\n",
+    "      minimum_latitude: -5\n",
+    "      maximum_latitude: 5\n",
+    "      minimum_depth: 0\n",
+    "      maximum_depth: 2000\n",
+    "    time_range:\n",
+    "      start_time: 2023-01-01 00:00:00\n",
+    "      end_time: 2023-02-01 00:00:00\n",
+    "  waypoints:\n",
+    "    - instrument: ARGO_FLOAT\n",
+    "      location:\n",
+    "        latitude: 0.02\n",
+    "        longitude: 0.02\n",
+    "      time: 2023-01-01 02:00:00\n",
     "```\n",
     "\n",
     "After running `virtualship run`, we have a `results/argo_floats.zarr` file with the data from the float."
    ]
   },
   {
    "cell_type": "code",
-   "execution_count": 2,
+   "execution_count": null,
    "metadata": {},
    "outputs": [
     {
@@ -79,7 +80,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 3,
+   "execution_count": null,
    "metadata": {},
    "outputs": [
     {
@@ -111,7 +112,7 @@
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "parcels",
+   "display_name": "ship",
    "language": "python",
    "name": "python3"
   },
@@ -125,7 +126,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.12.3"
+   "version": "3.12.9"
   }
  },
  "nbformat": 4,

src/virtualship/cli/_fetch.py

@@ -12,8 +12,7 @@
 from virtualship.utils import (
     _dump_yaml,
     _generic_load_yaml,
-    _get_schedule,
-    _get_ship_config,
+    _get_expedition,
 )
 
 if TYPE_CHECKING:
@@ -24,7 +23,7 @@
 from copernicusmarine.core_functions.credentials_utils import InvalidUsernameOrPassword
 
 import virtualship.cli._creds as creds
-from virtualship.utils import SCHEDULE
+from virtualship.utils import EXPEDITION
 
 DOWNLOAD_METADATA = "download_metadata.yaml"
 
@@ -49,17 +48,18 @@ def _fetch(path: str | Path, username: str | None, password: str | None) -> None
     data_folder = path / "data"
     data_folder.mkdir(exist_ok=True)
 
-    schedule = _get_schedule(path)
-    ship_config = _get_ship_config(path)
+    expedition = _get_expedition(path)
 
-    schedule.verify(
-        ship_config.ship_speed_knots,
+    expedition.schedule.verify(
+        expedition.ship_config.ship_speed_knots,
         input_data=None,
         check_space_time_region=True,
         ignore_missing_fieldsets=True,
     )
 
-    space_time_region_hash = get_space_time_region_hash(schedule.space_time_region)
+    space_time_region_hash = get_space_time_region_hash(
+        expedition.schedule.space_time_region
+    )
 
     existing_download = get_existing_download(data_folder, space_time_region_hash)
     if existing_download is not None:
@@ -72,27 +72,27 @@ def _fetch(path: str | Path, username: str | None, password: str | None) -> None
     username, password = creds.get_credentials_flow(username, password, creds_path)
 
     # Extract space_time_region details from the schedule
-    spatial_range = schedule.space_time_region.spatial_range
-    time_range = schedule.space_time_region.time_range
+    spatial_range = expedition.schedule.space_time_region.spatial_range
+    time_range = expedition.schedule.space_time_region.time_range
     start_datetime = time_range.start_time
     end_datetime = time_range.end_time
-    instruments_in_schedule = schedule.get_instruments()
+    instruments_in_schedule = expedition.schedule.get_instruments()
 
     # Create download folder and set download metadata
     download_folder = data_folder / hash_to_filename(space_time_region_hash)
     download_folder.mkdir()
     DownloadMetadata(download_complete=False).to_yaml(
         download_folder / DOWNLOAD_METADATA
     )
-    shutil.copyfile(path / SCHEDULE, download_folder / SCHEDULE)
+    shutil.copyfile(path / EXPEDITION, download_folder / EXPEDITION)
 
     if (
         (
             {"XBT", "CTD", "CDT_BGC", "SHIP_UNDERWATER_ST"}
             & set(instrument.name for instrument in instruments_in_schedule)
         )
-        or ship_config.ship_underwater_st_config is not None
-        or ship_config.adcp_config is not None
+        or expedition.instruments_config.ship_underwater_st_config is not None
+        or expedition.instruments_config.adcp_config is not None
     ):
         print("Ship data will be downloaded. Please wait...")