[pre-commit.ci] pre-commit autoupdate

.pre-commit-config.yaml

@@ -5,13 +5,13 @@ repos:
       - id: check-merge-conflict
       - id: debug-statements
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.12.12
+    rev: v0.13.0
     hooks:
       - id: ruff-check   #  Run the linter.
         args: [--fix, --exit-non-zero-on-fix]
       - id: ruff-format  #  Run the formatter.
   - repo: https://github.com/pre-commit/mirrors-mypy
-    rev: "v1.17.1"
+    rev: "v1.18.1"
     hooks:
       - id: mypy
         additional_dependencies: [types-jsonschema, xarray, types-tabulate, numpy]

tests/core/data/example_netcdf_generator.py

@@ -23,8 +23,6 @@ def generate_files() -> None:
     x = x_off + x_idx * res + res / 2
     y = y_off + y_idx * res + res / 2
 
-    xx, yy = np.meshgrid(x, y)
-
     # Cell IDs
     cell_id = np.arange(x_n * y_n)
 

tests/core/test_variables.py

@@ -176,7 +176,7 @@ class TestModel:
         model_name = "TestModel"
         vars_populated_by_init = ("test_var",)
 
-    with pytest.raises(ValueError, match="not in the known variables registry."):
+    with pytest.raises(ValueError, match=r"not in the known variables registry."):
         variables._collect_vars_populated_by_init([TestModel])
 
     variables.Variable(
@@ -207,7 +207,7 @@ class TestModel:
         vars_populated_by_first_update = ("test_var",)
         vars_populated_by_init = ("test_var",)
 
-    with pytest.raises(ValueError, match="not in the known variables registry."):
+    with pytest.raises(ValueError, match=r"not in the known variables registry."):
         variables._collect_vars_populated_by_first_update([TestModel])
 
     variables.Variable(
@@ -245,7 +245,7 @@ class TestModel:
         model_name = "TestModel"
         vars_updated = ("test_var",)
 
-    with pytest.raises(ValueError, match="not in the known variables registry."):
+    with pytest.raises(ValueError, match=r"not in the known variables registry."):
         variables._collect_updated_by_vars([TestModel])
 
     var = variables.Variable(
@@ -282,7 +282,7 @@ class TestModel:
         model_name = "TestModel"
         vars_required_for_update = ("test_var",)
 
-    with pytest.raises(ValueError, match="not in the known variables registry."):
+    with pytest.raises(ValueError, match=r"not in the known variables registry."):
         variables._collect_vars_required_for_update([TestModel])
 
     var = variables.Variable(
@@ -313,7 +313,7 @@ class TestModel:
         model_name = "TestModel"
         vars_required_for_init = ("test_var",)
 
-    with pytest.raises(ValueError, match="not in the known variables registry."):
+    with pytest.raises(ValueError, match=r"not in the known variables registry."):
         variables._collect_vars_required_for_init([TestModel])
 
     var = variables.Variable(
@@ -416,7 +416,7 @@ def test_get_variable(known_variables, run_variables):
     """Test the get_variable function."""
     from virtual_ecosystem.core import variables
 
-    with pytest.raises(KeyError, match="not a known variable."):
+    with pytest.raises(KeyError, match=r"not a known variable."):
         variables.get_variable("test_var")
 
     var = variables.Variable(
@@ -500,7 +500,7 @@ def test_get_model_order(run_variables):
 
     # Test wrong stage
     with pytest.raises(
-        ConfigurationError, match="Stage must be either 'init' or 'update'."
+        ConfigurationError, match=r"Stage must be either 'init' or 'update'."
     ):
         variables.get_model_order("wrong_stage")
 

tests/models/animals/test_animal_cohorts.py

@@ -464,7 +464,7 @@ def test_die_individual(
         # Handle zero-death cases separately
         if number_of_deaths == 0:
             with pytest.raises(
-                ValueError, match="Number of deaths must be a positive integer."
+                ValueError, match=r"Number of deaths must be a positive integer."
             ):
                 herbivore_cohort_instance.die_individual(number_of_deaths, [])
             return

tests/models/hydrology/test_hydrology_model.py

@@ -204,7 +204,7 @@ def test_generate_hydrology_model(
                 mock_setup.assert_called_once()
 
                 # Check arguments passed to _setup
-                called_args, called_kwargs = mock_setup.call_args
+                _called_args, called_kwargs = mock_setup.call_args
                 assert (
                     called_kwargs["initial_soil_moisture"]
                     == config["hydrology"]["initial_soil_moisture"]

tests/models/hydrology/test_hydrology_tools.py

@@ -173,8 +173,8 @@ def test_check_precipitation_surface_raises_error():
 
     with pytest.raises(
         ValueError,
-        match="Surface precipitation should not be negative! Consider checking that the"
-        " canopy water balance is correct.",
+        match=r"Surface precipitation should not be negative! "
+        r"Consider checking that the canopy water balance is correct.",
     ):
         check_precipitation_surface(test_array)
 

tests/models/plants/test_exporter.py

@@ -326,7 +326,7 @@ def test_CommunityDataExporter_dump_cohort_data(
     )
 
     # First dump in write mode with no allocations: expected behaviour in setup
-    communities, canopies, stem_allocations = fixture_exporter_components
+    communities, canopies, _stem_allocations = fixture_exporter_components
     exporter._dump_cohort_data(
         communities=communities,
         canopies=canopies,
@@ -639,7 +639,7 @@ def test_CommunityDataExporter_through_config(
         assert exporter._write_header
 
         # First dump in write mode with no allocations: expected behaviour in setup
-        communities, canopies, stem_allocations = fixture_exporter_components
+        communities, canopies, _stem_allocations = fixture_exporter_components
         exporter.dump(
             communities=communities,
             canopies=canopies,

virtual_ecosystem/models/abiotic/wind.py

@@ -369,7 +369,6 @@ def mix_and_ventilate(
 
     # Copy the input to update with mixing
     input_variable_mixed = input_variable.copy()
-    n_layers, n_cells = input_variable_mixed.shape
 
     # Extract the layer thickness and current value for the canopy layers, excluding the
     # surface layer and above canopy values