Updated logging (informative log messages, spinners for progress, suppressing Parcels INFO messages) (#191)

j-atkins · web-flow · commit 56424ede0260 · 2025-05-27T15:26:50.000+02:00
* add ctd_bgc to list

* new log output messages

* add yaspin as dependency

* add ship spinner to log messages

* update test to reflect new log output
diff --git a/environment.yml b/environment.yml
@@ -13,6 +13,7 @@ dependencies:
   - pyyaml
   - copernicusmarine >= 2
   - openpyxl
+  - yaspin
 
   # linting
   - pre-commit
diff --git a/pyproject.toml b/pyproject.toml
@@ -34,6 +34,7 @@ dependencies = [
     "pydantic >=2, <3",
     "PyYAML",
     "copernicusmarine >= 2",
+    "yaspin",
 ]
 
 [project.urls]
diff --git a/src/virtualship/expedition/do_expedition.py b/src/virtualship/expedition/do_expedition.py
@@ -31,6 +31,10 @@ def do_expedition(expedition_dir: str | Path, input_data: Path | None = None) ->
     :param expedition_dir: The base directory for the expedition.
     :param input_data: Input data folder (override used for testing).
     """
+    print("\n╔═════════════════════════════════════════════════╗")
+    print("║          VIRTUALSHIP EXPEDITION STATUS          ║")
+    print("╚═════════════════════════════════════════════════╝")
+
     if isinstance(expedition_dir, str):
         expedition_dir = Path(expedition_dir)
 
@@ -56,6 +60,8 @@ def do_expedition(expedition_dir: str | Path, input_data: Path | None = None) ->
         input_data=input_data,
     )
 
+    print("\n---- WAYPOINT VERIFICATION ----")
+
     # verify schedule is valid
     schedule.verify(ship_config.ship_speed_knots, loaded_input_data)
 
@@ -82,6 +88,8 @@ def do_expedition(expedition_dir: str | Path, input_data: Path | None = None) ->
         shutil.rmtree(expedition_dir.joinpath("results"))
     os.makedirs(expedition_dir.joinpath("results"))
 
+    print("\n----- EXPEDITION SUMMARY ------")
+
     # calculate expedition cost in US$
     assert schedule.waypoints[0].time is not None, (
         "First waypoint has no time. This should not be possible as it should have been verified before."
@@ -90,20 +98,26 @@ def do_expedition(expedition_dir: str | Path, input_data: Path | None = None) ->
     cost = expedition_cost(schedule_results, time_past)
     with open(expedition_dir.joinpath("results", "cost.txt"), "w") as file:
         file.writelines(f"cost: {cost} US$")
-    print(f"This expedition took {time_past} and would have cost {cost:,.0f} US$.")
+    print(f"\nExpedition duration: {time_past}\nExpedition cost: US$ {cost:,.0f}.")
+
+    print("\n--- MEASUREMENT SIMULATIONS ---")
 
     # simulate measurements
-    print("Simulating measurements. This may take a while..")
+    print("\nSimulating measurements. This may take a while...\n")
     simulate_measurements(
         expedition_dir,
         ship_config,
         loaded_input_data,
         schedule_results.measurements_to_simulate,
     )
-    print("Done simulating measurements.")
+    print("\nAll measurement simulations are complete.")
 
-    print("Your expedition has concluded successfully!")
-    print("Your measurements can be found in the results directory.")
+    print("\n----- EXPEDITION RESULTS ------")
+    print("\nYour expedition has concluded successfully!")
+    print(
+        f"Your measurements can be found in the '{expedition_dir}/results' directory."
+    )
+    print("\n------------- END -------------\n")
 
 
 def _load_input_data(
diff --git a/src/virtualship/expedition/simulate_measurements.py b/src/virtualship/expedition/simulate_measurements.py
@@ -2,10 +2,13 @@
 
 from __future__ import annotations
 
+import logging
 from datetime import timedelta
 from pathlib import Path
 from typing import TYPE_CHECKING
 
+from yaspin import yaspin
+
 from virtualship.instruments.adcp import simulate_adcp
 from virtualship.instruments.argo_float import simulate_argo_floats
 from virtualship.instruments.ctd import simulate_ctd
@@ -14,12 +17,17 @@
 from virtualship.instruments.ship_underwater_st import simulate_ship_underwater_st
 from virtualship.instruments.xbt import simulate_xbt
 from virtualship.models import ShipConfig
+from virtualship.utils import ship_spinner
 
 from .simulate_schedule import MeasurementsToSimulate
 
 if TYPE_CHECKING:
     from .input_data import InputData
 
+# parcels logger (suppress INFO messages to prevent log being flooded)
+external_logger = logging.getLogger("parcels.tools.loggers")
+external_logger.setLevel(logging.WARNING)
+
 
 def simulate_measurements(
     expedition_dir: str | Path,
@@ -42,61 +50,91 @@ def simulate_measurements(
         expedition_dir = Path(expedition_dir)
 
     if len(measurements.ship_underwater_sts) > 0:
-        print("Simulating onboard salinity and temperature measurements.")
         if ship_config.ship_underwater_st_config is None:
             raise RuntimeError("No configuration for ship underwater ST provided.")
         if input_data.ship_underwater_st_fieldset is None:
             raise RuntimeError("No fieldset for ship underwater ST provided.")
-        simulate_ship_underwater_st(
-            fieldset=input_data.ship_underwater_st_fieldset,
-            out_path=expedition_dir.joinpath("results", "ship_underwater_st.zarr"),
-            depth=-2,
-            sample_points=measurements.ship_underwater_sts,
-        )
+        with yaspin(
+            text="Simulating onboard temperature and salinity measurements... ",
+            side="right",
+            spinner=ship_spinner,
+        ) as spinner:
+            simulate_ship_underwater_st(
+                fieldset=input_data.ship_underwater_st_fieldset,
+                out_path=expedition_dir.joinpath("results", "ship_underwater_st.zarr"),
+                depth=-2,
+                sample_points=measurements.ship_underwater_sts,
+            )
+            spinner.ok("✅")
 
     if len(measurements.adcps) > 0:
-        print("Simulating onboard ADCP.")
         if ship_config.adcp_config is None:
             raise RuntimeError("No configuration for ADCP provided.")
         if input_data.adcp_fieldset is None:
             raise RuntimeError("No fieldset for ADCP provided.")
-        simulate_adcp(
-            fieldset=input_data.adcp_fieldset,
-            out_path=expedition_dir.joinpath("results", "adcp.zarr"),
-            max_depth=ship_config.adcp_config.max_depth_meter,
-            min_depth=-5,
-            num_bins=ship_config.adcp_config.num_bins,
-            sample_points=measurements.adcps,
-        )
+        with yaspin(
+            text="Simulating onboard ADCP... ", side="right", spinner=ship_spinner
+        ) as spinner:
+            simulate_adcp(
+                fieldset=input_data.adcp_fieldset,
+                out_path=expedition_dir.joinpath("results", "adcp.zarr"),
+                max_depth=ship_config.adcp_config.max_depth_meter,
+                min_depth=-5,
+                num_bins=ship_config.adcp_config.num_bins,
+                sample_points=measurements.adcps,
+            )
+            spinner.ok("✅")
 
     if len(measurements.ctds) > 0:
-        print("Simulating CTD casts.")
         if ship_config.ctd_config is None:
             raise RuntimeError("No configuration for CTD provided.")
         if input_data.ctd_fieldset is None:
             raise RuntimeError("No fieldset for CTD provided.")
-        simulate_ctd(
-            out_path=expedition_dir.joinpath("results", "ctd.zarr"),
-            fieldset=input_data.ctd_fieldset,
-            ctds=measurements.ctds,
-            outputdt=timedelta(seconds=10),
-        )
+        with yaspin(
+            text="Simulating CTD casts... ", side="right", spinner=ship_spinner
+        ) as spinner:
+            simulate_ctd(
+                out_path=expedition_dir.joinpath("results", "ctd.zarr"),
+                fieldset=input_data.ctd_fieldset,
+                ctds=measurements.ctds,
+                outputdt=timedelta(seconds=10),
+            )
+            spinner.ok("✅")
 
     if len(measurements.ctd_bgcs) > 0:
-        print("Simulating BGC CTD casts.")
         if ship_config.ctd_bgc_config is None:
             raise RuntimeError("No configuration for CTD_BGC provided.")
         if input_data.ctd_bgc_fieldset is None:
             raise RuntimeError("No fieldset for CTD_BGC provided.")
-        simulate_ctd_bgc(
-            out_path=expedition_dir.joinpath("results", "ctd_bgc.zarr"),
-            fieldset=input_data.ctd_bgc_fieldset,
-            ctd_bgcs=measurements.ctd_bgcs,
-            outputdt=timedelta(seconds=10),
-        )
+        with yaspin(
+            text="Simulating BGC CTD casts... ", side="right", spinner=ship_spinner
+        ) as spinner:
+            simulate_ctd_bgc(
+                out_path=expedition_dir.joinpath("results", "ctd_bgc.zarr"),
+                fieldset=input_data.ctd_bgc_fieldset,
+                ctd_bgcs=measurements.ctd_bgcs,
+                outputdt=timedelta(seconds=10),
+            )
+            spinner.ok("✅")
+
+    if len(measurements.xbts) > 0:
+        if ship_config.xbt_config is None:
+            raise RuntimeError("No configuration for XBTs provided.")
+        if input_data.xbt_fieldset is None:
+            raise RuntimeError("No fieldset for XBTs provided.")
+        with yaspin(
+            text="Simulating XBTs... ", side="right", spinner=ship_spinner
+        ) as spinner:
+            simulate_xbt(
+                out_path=expedition_dir.joinpath("results", "xbts.zarr"),
+                fieldset=input_data.xbt_fieldset,
+                xbts=measurements.xbts,
+                outputdt=timedelta(seconds=1),
+            )
+            spinner.ok("✅")
 
     if len(measurements.drifters) > 0:
-        print("Simulating drifters")
+        print("Simulating drifters... ")
         if ship_config.drifter_config is None:
             raise RuntimeError("No configuration for drifters provided.")
         if input_data.drifter_fieldset is None:
@@ -111,7 +149,7 @@ def simulate_measurements(
         )
 
     if len(measurements.argo_floats) > 0:
-        print("Simulating argo floats")
+        print("Simulating argo floats... ")
         if ship_config.argo_float_config is None:
             raise RuntimeError("No configuration for argo floats provided.")
         if input_data.argo_float_fieldset is None:
@@ -123,16 +161,3 @@ def simulate_measurements(
             outputdt=timedelta(minutes=5),
             endtime=None,
         )
-
-    if len(measurements.xbts) > 0:
-        print("Simulating XBTs")
-        if ship_config.xbt_config is None:
-            raise RuntimeError("No configuration for XBTs provided.")
-        if input_data.xbt_fieldset is None:
-            raise RuntimeError("No fieldset for XBTs provided.")
-        simulate_xbt(
-            out_path=expedition_dir.joinpath("results", "xbts.zarr"),
-            fieldset=input_data.xbt_fieldset,
-            xbts=measurements.xbts,
-            outputdt=timedelta(seconds=1),
-        )
diff --git a/src/virtualship/instruments/__init__.py b/src/virtualship/instruments/__init__.py
@@ -1,5 +1,13 @@
 """Measurement instrument that can be used with Parcels."""
 
-from . import adcp, argo_float, ctd, drifter, ship_underwater_st, xbt
+from . import adcp, argo_float, ctd, ctd_bgc, drifter, ship_underwater_st, xbt
 
-__all__ = ["adcp", "argo_float", "ctd", "drifter", "ship_underwater_st", "xbt"]
+__all__ = [
+    "adcp",
+    "argo_float",
+    "ctd",
+    "ctd_bgc",
+    "drifter",
+    "ship_underwater_st",
+    "xbt",
+]
diff --git a/src/virtualship/models/schedule.py b/src/virtualship/models/schedule.py
@@ -121,6 +121,8 @@ def verify(
         :raises NotImplementedError: If an instrument in the schedule is not implemented.
         :return: None. The method doesn't return a value but raises exceptions if verification fails.
         """
+        print("\nVerifying route... ")
+
         if check_space_time_region and self.space_time_region is None:
             raise ScheduleError(
                 "space_time_region not found in schedule, please define it to fetch the data."
@@ -145,8 +147,6 @@ def verify(
         # check if all waypoints are in water
         # this is done by picking an arbitrary provided fieldset and checking if UV is not zero
 
-        print("Verifying all waypoints are on water..")
-
         # get all available fieldsets
         available_fieldsets = []
         if input_data is not None:
@@ -184,7 +184,6 @@ def verify(
                 raise ScheduleError(
                     f"The following waypoints are on land: {['#' + str(wp_i) + ' ' + str(wp) for (wp_i, wp) in land_waypoints]}"
                 )
-            print("Good, all waypoints are on water.")
 
         # check that ship will arrive on time at each waypoint (in case no unexpected event happen)
         time = self.waypoints[0].time
@@ -215,6 +214,8 @@ def verify(
             else:
                 time = wp_next.time
 
+        print("... All good to go!")
+
 
 def _is_on_land_zero_uv(fieldset: FieldSet, waypoint: Waypoint) -> bool:
     """
diff --git a/src/virtualship/utils.py b/src/virtualship/utils.py
@@ -8,6 +8,8 @@
 from pathlib import Path
 from typing import TYPE_CHECKING, TextIO
 
+from yaspin import Spinner
+
 if TYPE_CHECKING:
     from virtualship.models import Schedule, ShipConfig
 
@@ -247,3 +249,21 @@ def _get_ship_config(expedition_dir: Path) -> ShipConfig:
         raise FileNotFoundError(
             f'Ship config not found. Save it to "{file_path}".'
         ) from e
+
+
+# custom ship spinner
+ship_spinner = Spinner(
+    interval=240,
+    frames=[
+        " 🚢    ",
+        "  🚢   ",
+        "   🚢  ",
+        "    🚢 ",
+        "     🚢",
+        "    🚢 ",
+        "   🚢  ",
+        "  🚢   ",
+        " 🚢    ",
+        "🚢     ",
+    ],
+)
diff --git a/tests/expedition/test_do_expedition.py b/tests/expedition/test_do_expedition.py
@@ -8,4 +8,6 @@
 def test_do_expedition(capfd: CaptureFixture) -> None:
     do_expedition("expedition_dir", input_data=Path("expedition_dir/input_data"))
     out, _ = capfd.readouterr()
-    assert "This expedition took" in out, "Expedition did not complete successfully."
+    assert "Your expedition has concluded successfully!" in out, (
+        "Expedition did not complete successfully."
+    )

Original file line number	Diff line number	Diff line change
`@@ -34,6 +34,7 @@ dependencies = [`
`34`	`34`	`"pydantic >=2, <3",`
`35`	`35`	`"PyYAML",`
`36`	`36`	`"copernicusmarine >= 2",`
	`37`	`+ "yaspin",`
`37`	`38`	`]`
`38`	`39`
`39`	`40`	`[project.urls]`