Supporting list of instruments in yaml (#147)

* Supporting list of instruments

* Adding unit tests for schedule.yaml

* Fix schedule bug

* Fixing another error in the yaml

* Updating locations without instruments

* Creating get_instruments_in_schedule() function

* Update test schedule

Author: erikvansebille

src/virtualship/cli/commands.py

@@ -20,7 +20,12 @@
     _get_ship_config,
     do_expedition,
 )
-from virtualship.utils import SCHEDULE, SHIP_CONFIG, mfp_to_yaml
+from virtualship.utils import (
+    SCHEDULE,
+    SHIP_CONFIG,
+    get_instruments_in_schedule,
+    mfp_to_yaml,
+)
 
 
 @click.command()
@@ -135,12 +140,7 @@ def fetch(path: str | Path, username: str | None, password: str | None) -> None:
     time_range = schedule.space_time_region.time_range
     start_datetime = time_range.start_time
     end_datetime = time_range.end_time
-    instruments_in_schedule = [
-        waypoint.instrument[0].name
-        if isinstance(waypoint.instrument, list)
-        else waypoint.instrument.name
-        for waypoint in schedule.waypoints  # TODO check why instrument is a list here
-    ]
+    instruments_in_schedule = get_instruments_in_schedule(schedule)
 
     # Create download folder and set download metadata
     download_folder = data_folder / hash_to_filename(space_time_region_hash)

src/virtualship/expedition/do_expedition.py

@@ -7,7 +7,12 @@
 import pyproj
 
 from virtualship.cli._fetch import get_existing_download, get_space_time_region_hash
-from virtualship.utils import CHECKPOINT, SCHEDULE, SHIP_CONFIG
+from virtualship.utils import (
+    CHECKPOINT,
+    SCHEDULE,
+    SHIP_CONFIG,
+    get_instruments_in_schedule,
+)
 
 from .checkpoint import Checkpoint
 from .expedition_cost import expedition_cost
@@ -33,11 +38,7 @@ def do_expedition(expedition_dir: str | Path, input_data: Path | None = None) ->
     schedule = _get_schedule(expedition_dir)
 
     # remove instrument configurations that are not in schedule
-    instruments_in_schedule = [
-        waypoint.instrument.name
-        for waypoint in schedule.waypoints
-        if waypoint.instrument
-    ]
+    instruments_in_schedule = get_instruments_in_schedule(schedule)
 
     for instrument in [
         "ARGO_FLOAT",

src/virtualship/static/schedule.yaml

@@ -10,23 +10,32 @@ space_time_region:
     start_time: 2023-01-01 00:00:00
     end_time: 2023-02-01 00:00:00
 waypoints:
-  - instrument: CTD
+  - instrument:
+      - CTD
     location:
       latitude: 0
       longitude: 0
     time: 2023-01-01 00:00:00
-  - instrument: DRIFTER
+  - instrument:
+      - DRIFTER
+      - CTD
     location:
       latitude: 0.01
       longitude: 0.01
     time: 2023-01-01 01:00:00
-  - instrument: ARGO_FLOAT
+  - instrument:
+      - ARGO_FLOAT
     location:
       latitude: 0.02
       longitude: 0.02
     time: 2023-01-01 02:00:00
-  - instrument: XBT
+  - instrument:
+      - XBT
     location:
       latitude: 0.03
       longitude: 0.03
     time: 2023-01-01 03:00:00
+  - location:
+      latitude: 0.03
+      longitude: 0.03
+    time: 2023-01-01 03:00:00

src/virtualship/utils.py

@@ -173,3 +173,13 @@ def _validate_numeric_mins_to_timedelta(value: int | float | timedelta) -> timed
     if isinstance(value, timedelta):
         return value
     return timedelta(minutes=value)
+
+
+def get_instruments_in_schedule(schedule):
+    instruments_in_schedule = []
+    for waypoint in schedule.waypoints:
+        if waypoint.instrument:
+            for instrument in waypoint.instrument:
+                if instrument:
+                    instruments_in_schedule.append(instrument.name)
+    return instruments_in_schedule

tests/expedition/expedition_dir/schedule.yaml

@@ -1,16 +1,18 @@
 waypoints:
-  - instrument: CTD
+  - instrument:
+      - CTD
     location:
       latitude: 0
       longitude: 0
     time: 2023-01-01 00:00:00
-  - instrument: DRIFTER
+  - instrument:
+      - DRIFTER
+      - ARGO_FLOAT
     location:
       latitude: 0.01
       longitude: 0.01
-    time: 2023-01-01 01:00:00
-  - instrument: ARGO_FLOAT
-    location:
+    time: 2023-01-02 00:00:00
+  - location: # empty waypoint
       latitude: 0.02
-      longitude: 0.02
-    time: 2023-01-01 02:00:00
+      longitude: 0.01
+    time: 2023-01-02 03:00:00