Mypy tooling and some mypy fixes

.github/workflows/ci.yml

@@ -52,3 +52,28 @@ jobs:
         uses: codecov/codecov-action@v5.4.0
         with:
           token: ${{ secrets.CODECOV_TOKEN }}
+  typechecking:
+    name: mypy
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
+      - uses: mamba-org/setup-micromamba@v2
+        with:
+          environment-name: ship
+          environment-file: environment.yml
+          create-args: >-
+            python=3.12
+
+      - run: pip install . --no-deps
+      - run: conda install lxml # dep for report generation
+      - name: Typechecking
+        run: |
+          mypy --install-types --non-interactive src/virtualship --html-report mypy-report
+      - name: Upload test results
+        if: ${{ always() }} # Upload even on mypy error
+        uses: actions/upload-artifact@v4
+        with:
+          name: Mypy report
+          path: mypy-report

environment.yml

@@ -16,6 +16,7 @@ dependencies:
 
   # linting
   - pre-commit
+  - mypy
 
   # Testing
   - pytest

src/virtualship/expedition/do_expedition.py

@@ -50,15 +50,15 @@ def do_expedition(expedition_dir: str | Path, input_data: Path | None = None) ->
     checkpoint.verify(schedule)
 
     # load fieldsets
-    input_data = _load_input_data(
+    loaded_input_data = _load_input_data(
         expedition_dir=expedition_dir,
         schedule=schedule,
         ship_config=ship_config,
         input_data=input_data,
     )
 
     # verify schedule is valid
-    schedule.verify(ship_config.ship_speed_knots, input_data)
+    schedule.verify(ship_config.ship_speed_knots, loaded_input_data)
 
     # simulate the schedule
     schedule_results = simulate_schedule(
@@ -98,7 +98,7 @@ def do_expedition(expedition_dir: str | Path, input_data: Path | None = None) ->
     simulate_measurements(
         expedition_dir,
         ship_config,
-        input_data,
+        loaded_input_data,
         schedule_results.measurements_to_simulate,
     )
     print("Done simulating measurements.")
@@ -131,6 +131,10 @@ def _load_input_data(
         space_time_region_hash = get_space_time_region_hash(schedule.space_time_region)
         input_data = get_existing_download(expedition_dir, space_time_region_hash)
 
+    assert input_data is not None, (
+        "Input data hasn't been found. Have you run the `virtualship fetch` command?"
+    )
+
     return InputData.load(
         directory=input_data,
         load_adcp=ship_config.adcp_config is not None,

src/virtualship/expedition/input_data.py

@@ -43,6 +43,7 @@ def load(
         :param load_ship_underwater_st: Whether to load the ship underwater ST fieldset.
         :returns: An instance of this class with loaded fieldsets.
         """
+        directory = Path(directory)
         if load_drifter:
             drifter_fieldset = cls._load_drifter_fieldset(directory)
         else:
@@ -152,7 +153,7 @@ def _load_drifter_fieldset(cls, directory: Path) -> FieldSet:
         return fieldset
 
     @classmethod
-    def _load_argo_float_fieldset(cls, directory: str | Path) -> FieldSet:
+    def _load_argo_float_fieldset(cls, directory: Path) -> FieldSet:
         filenames = {
             "U": directory.joinpath("argo_float_uv.nc"),
             "V": directory.joinpath("argo_float_uv.nc"),

src/virtualship/expedition/schedule.py

@@ -5,17 +5,19 @@
 import itertools
 from datetime import datetime, timedelta
 from pathlib import Path
+from typing import TYPE_CHECKING
 
 import pydantic
 import pyproj
 import yaml
 from parcels import FieldSet
 
 from ..location import Location
-from .input_data import InputData
 from .ship_config import InstrumentType
 from .space_time_region import SpaceTimeRegion
 
+if TYPE_CHECKING:
+    from .input_data import InputData
 projection: pyproj.Geod = pyproj.Geod(ellps="WGS84")
 
 

src/virtualship/expedition/simulate_measurements.py

@@ -1,18 +1,23 @@
 """simulate_measurements function."""
 
+from __future__ import annotations
+
 from datetime import timedelta
 from pathlib import Path
+from typing import TYPE_CHECKING
 
 from ..instruments.adcp import simulate_adcp
 from ..instruments.argo_float import simulate_argo_floats
 from ..instruments.ctd import simulate_ctd
 from ..instruments.drifter import simulate_drifters
 from ..instruments.ship_underwater_st import simulate_ship_underwater_st
 from ..instruments.xbt import simulate_xbt
-from .input_data import InputData
 from .ship_config import ShipConfig
 from .simulate_schedule import MeasurementsToSimulate
 
+if TYPE_CHECKING:
+    from .input_data import InputData
+
 
 def simulate_measurements(
     expedition_dir: str | Path,