Fix linter/mypy warnings

Author: mdales

deltap/global_code_residents_pixel.py

@@ -50,7 +50,7 @@ def calc_persistence_value(
 
 def process_delta_p(
     current: yg.YirgacheffeLayer,
-    scenario: yg.YirgacheffeLayer,
+    scenario: yg.YirgacheffeLayer | float,
     current_aoh: float,
     historic_aoh: float,
     exponent: str | float
@@ -88,6 +88,7 @@ def global_code_residents_pixel_ae(
                 sys.exit(f"Failed to open current layer {current_aohs_path / filename}")
 
             try:
+                scenario: yg.YirgacheffeLayer | float
                 scenario, _ = open_layer(scenario_aohs_path / filename)
             except FileNotFoundError:
                 # If there is a current but now scenario file it's because the species went extinct under the scenario
@@ -143,8 +144,8 @@ def global_code_residents_pixel_ae(
                 non_breeding_scenario_path = scenario_aohs_path / nonbreeding_filename
                 breeding_scenario_path = scenario_aohs_path / breeding_filename
             else:
-                non_breeding_scenario_path = "nan"
-                breeding_scenario_path = "nan"
+                non_breeding_scenario_path = Path("nan") # nan path is the sentinel from csv inputs
+                breeding_scenario_path = Path("nan")
 
             try:
                 current_breeding, current_aoh_breeding = open_layer(current_aohs_path / breeding_filename)
@@ -155,11 +156,13 @@ def global_code_residents_pixel_ae(
             except FileNotFoundError:
                 sys.exit(f"Failed to open current non breeding {current_aohs_path / nonbreeding_filename}")
             try:
+                scenario_breeding: yg.YirgacheffeLayer | float
                 scenario_breeding, _ = open_layer(breeding_scenario_path)
             except FileNotFoundError:
                 # If there is a current but now scenario file it's because the species went extinct under the scenario
                 scenario_breeding = 0.0
             try:
+                scenario_non_breeding: yg.YirgacheffeLayer | float
                 scenario_non_breeding, _ = open_layer(non_breeding_scenario_path)
             except FileNotFoundError:
                 # If there is a current but now scenario file it's because the species went extinct under the scenario

local/merge_global_habitat.py

@@ -27,7 +27,7 @@ def merge_global_habitat(
         local_layer.set_window_for_union(global_layer.area)
         cleared = local_layer.nan_to_num()
         combined = yg.where(cleared != 0, local_layer, global_layer)
-        ctx = alive_bar(manual=True, title=str(lcc)) if show_progress else nullcontext()
+        ctx = alive_bar(manual=True) if show_progress else nullcontext()
         with ctx as bar:
             combined.to_geotiff(output_layer_path, callback=bar, parallelism=True)
 

prepare_layers/make_diff_map.py

@@ -1,7 +1,10 @@
 import argparse
+from contextlib import nullcontext
 from pathlib import Path
 
 import yirgacheffe as yg
+from alive_progress import alive_bar # type: ignore
+from snakemake_argparse_bridge import snakemake_compatible # type: ignore
 
 POSSIBLE_HABITAT_CLASSES = [100, 200, 300, 400, 500, 600, 700, 800, 900,
     1000, 1100, 1200, 1300, 1400, 1401, 1402, 1403, 1404,
@@ -21,15 +24,27 @@ def make_diff_map(
 
         if not current_habitat_filename.exists() and not scenario_habitat_filename.exists():
             continue
-        current_layer = yg.read_raster(current_habitat_filename) if current_habitat_filename.exists() else yg.constant(0.0)
-        scenario_layer = yg.read_raster(scenario_habitat_filename) if scenario_habitat_filename.exists() else yg.constant(0.0)
+        current_layer = yg.read_raster(current_habitat_filename) if current_habitat_filename.exists() \
+            else yg.constant(0.0)
+        scenario_layer = yg.read_raster(scenario_habitat_filename) if scenario_habitat_filename.exists() \
+            else yg.constant(0.0)
         habitat_diff = current_layer != scenario_layer
         layers.append(habitat_diff)
+
     diff = yg.any(layers)
     area = yg.area_raster(diff.map_projection)
     scaled_diff = diff * area
-    scaled_diff.to_geotiff(output_path, parallelism=parallelism)
 
+    ctx = alive_bar(manual=True) if show_progress else nullcontext()
+    with ctx as bar:
+        scaled_diff.to_geotiff(output_path, callback=bar, parallelism=parallelism)
+
+@snakemake_compatible(mapping={
+    "current_path": "input.current",
+    "scenario_path": "params.scenario",
+    "parallelism": "threads",
+    "output_path": "output[0]",
+})
 def main() -> None:
     parser = argparse.ArgumentParser(description="Generate an area difference map.")
     parser.add_argument(
@@ -51,7 +66,7 @@ def main() -> None:
         type=Path,
         help='Path where final map should be stored',
         required=True,
-        dest='results_path',
+        dest='output_path',
     )
     parser.add_argument(
         '-j',
@@ -74,7 +89,7 @@ def main() -> None:
     make_diff_map(
         args.current_path,
         args.scenario_path,
-        args.results_path,
+        args.output_path,
         args.parallelism,
         args.show_progress,
     )

prepare_layers/make_food_current_map.py

@@ -346,7 +346,9 @@ def make_food_current_map(
     os.makedirs(output_path.parent, exist_ok=True)
 
     lcc_list = get_lcc_list(current_lvl1_path)
-    result_queues: dict[int,multiprocessing.queues.Queue] = { lcc: multiprocessing.Queue(maxsize=10) for lcc in lcc_list}
+    result_queues: dict[int,multiprocessing.queues.Queue] = {
+        lcc: multiprocessing.Queue(maxsize=10) for lcc in lcc_list
+    }
 
     assembly_processes = [
         Process(target=assemble_map, args=(

tests/test_food_layer.py

@@ -1,20 +1,27 @@
 
 import numpy as np
 import pytest
-import yirgacheffe as yg
 
-from prepare_layers.make_food_current_map import TileInfo, process_tile, balance_crop_and_pasture_differences, \
+from prepare_layers.make_food_current_map import balance_crop_and_pasture_differences, \
     CROP_CODE, PASTURE_CODE, remove_land_cover, add_land_cover
 
-@pytest.mark.parametrize("initial_crop_diff,initial_pasture_diff,expected_crop_diff,expected_pasture_diff", [
-    (0.0, 0.0, 0.0, 0.0),
-    (0.8, 0.0, 0.8, 0.0),
-    (-0.8, 0.0, -0.8, 0.0),
-    (0.0, 0.8, 0.0, 0.8),
-    (0.0, -0.8, 0.0, -0.8),
-    (0.4, 0.2, 0.4, 0.2),
-    (-0.4, -0.2, -0.4, -0.2),
-])
+@pytest.mark.parametrize(
+    [
+        "initial_crop_diff",
+        "initial_pasture_diff",
+        "expected_crop_diff",
+        "expected_pasture_diff"
+    ],
+    [
+        (0.0, 0.0, 0.0, 0.0),
+        (0.8, 0.0, 0.8, 0.0),
+        (-0.8, 0.0, -0.8, 0.0),
+        (0.0, 0.8, 0.0, 0.8),
+        (0.0, -0.8, 0.0, -0.8),
+        (0.4, 0.2, 0.4, 0.2),
+        (-0.4, -0.2, -0.4, -0.2),
+    ]
+)
 def test_balance_not_needed(
     initial_crop_diff: float,
     initial_pasture_diff: float,
@@ -24,30 +31,35 @@ def test_balance_not_needed(
     result_crop_diff, result_pasture_diff = balance_crop_and_pasture_differences(
         initial_crop_diff,
         initial_pasture_diff,
-        dict(),
+        {},
     )
     assert expected_crop_diff == result_crop_diff
     assert expected_pasture_diff == result_pasture_diff
 
 
-def test_one_sided_balance() -> None:
+def test_brokend_balance() -> None:
+    # Testing that we spot if we've said to remove land where there isn't any
     lcc_data_map = {
         CROP_CODE: np.zeros((10, 10)),
         PASTURE_CODE: np.zeros((10, 10)),
     }
-    result_crop_diff, result_pasture_diff = balance_crop_and_pasture_differences(
-        0.5,
-        -0.1,
-        lcc_data_map,
-    )
-    # assert expected_crop_diff == result_crop_diff
-    # assert expected_pasture_diff == result_pasture_diff
-    # assert (lcc_data_map[CROP_CODE] == crop_cell_value).all()
-    # assert (lcc_data_map[PASTURE_CODE] == pasture_cell_value).all()
+    with pytest.raises(ValueError):
+        _ = balance_crop_and_pasture_differences(
+            0.5,
+            -0.1,
+            lcc_data_map,
+        )
 
 
 @pytest.mark.parametrize(
-    "initial_crop_diff,initial_pasture_diff,expected_crop_diff,expected_pasture_diff,crop_cell_value,pasture_cell_value",
+    [
+        "initial_crop_diff",
+        "initial_pasture_diff",
+        "expected_crop_diff",
+        "expected_pasture_diff",
+        "crop_cell_value",
+        "pasture_cell_value"
+    ],
     [
         (0.25, -0.5, 0.0, -0.25, 0.25, 0.75),
     ]
@@ -77,7 +89,14 @@ def test_simple_balance_transfer(
 
 
 @pytest.mark.parametrize(
-    "initial_crop_diff,initial_pasture_diff,expected_crop_diff,expected_pasture_diff,crop_cell_value,pasture_cell_value",
+    [
+        "initial_crop_diff",
+        "initial_pasture_diff",
+        "expected_crop_diff",
+        "expected_pasture_diff",
+        "crop_cell_value",
+        "pasture_cell_value"
+    ],
     [
         (0.25, -0.5, 0.0, -0.25, 0.5, 0.5),
         (0.5, -0.25, 0.25, 0.0, 0.5, 0.5),
@@ -110,9 +129,16 @@ def test_simple_half_balance_transfer(
     assert (expected_pasture_map == lcc_data_map[PASTURE_CODE]).all()
 
 
-@pytest.mark.parametrize("crop_diff,expected_crop_cell,expected_other_cell", [
-    (-0.5, 0.5, 0.5),
-])
+@pytest.mark.parametrize(
+    [
+        "crop_diff",
+        "expected_crop_cell",
+        "expected_other_cell",
+    ],
+    [
+        (-0.5, 0.5, 0.5),
+    ]
+)
 def test_remove_land_simple(
     crop_diff: float,
     expected_crop_cell: float,
@@ -138,13 +164,22 @@ def test_remove_land_simple(
     assert (expected_other_map == lcc_data_map[1]).all()
 
 
-@pytest.mark.parametrize("crop_diff,pnv_value,expected_crop_cell,expected_other_1_cell,expected_other_2_cell", [
-    (-0.5, 1, 0.0, 1.0, 0.0),
-    (-0.75, 1, 0.0, 1.0, 0.0), # too much
-    (-0.25, 1, 0.5, 0.5, 0.0),
-    (-0.5, 2, 0.0, 0.0, 1.0),
-    (-0.25, 2, 0.5, 0.0, 0.5),
-])
+@pytest.mark.parametrize(
+    [
+        "crop_diff",
+        "pnv_value",
+        "expected_crop_cell",
+        "expected_other_1_cell",
+        "expected_other_2_cell",
+    ],
+    [
+        (-0.5, 1, 0.0, 1.0, 0.0),
+        (-0.75, 1, 0.0, 1.0, 0.0), # too much
+        (-0.25, 1, 0.5, 0.5, 0.0),
+        (-0.5, 2, 0.0, 0.0, 1.0),
+        (-0.25, 2, 0.5, 0.0, 0.5),
+    ]
+)
 def test_remove_land_less_simple(
     crop_diff: float,
     pnv_value: int,
@@ -189,7 +224,6 @@ def test_add_land_simple(
         1: np.ones((10, 10)),
         CROP_CODE: np.zeros((10, 10)),
     }
-    pnv_data = np.full((10, 10), 1)
 
     add_land_cover(
         CROP_CODE,
@@ -217,7 +251,6 @@ def test_add_land_avoid_excluded(
         PASTURE_CODE: np.array([[i % 2] * 10 for i in range(10)]).astype(float),
         CROP_CODE: np.zeros((10, 10)),
     }
-    pnv_data = np.full((10, 10), 1)
 
     add_land_cover(
         CROP_CODE,

utils/footprint_of_humanity.py

@@ -24,7 +24,7 @@ def absolute(
     merge1 = pd.merge(current_cleaned, pnv_cleaned, on=["id_no", "season"], suffixes=["_current", "_pnv"])
     merge2 = pd.merge(merge1, scenario, on=["id_no", "season"], how="left", indicator=True)
     merged = merge2[["id_no", "season", "class_name", "aoh_total_current", "aoh_total_pnv", "aoh_total", "_merge"]].copy()
-    merged.aoh_total = merged.aoh_total.fillna(0)
+    merged["aoh_total"] = merged.aoh_total.fillna(0)
     merged.rename(columns={"aoh_total": "aoh_total_scenario"}, inplace=True)
 
     merged["current_persistence"] = (merged.aoh_total_current / merged.aoh_total_pnv) ** 0.25

utils/raster_sum.py

@@ -1,10 +1,10 @@
 import argparse
-import os
 import resource
 from pathlib import Path
 
 import yirgacheffe as yg
 from alive_progress import alive_bar # type: ignore
+from snakemake_argparse_bridge import snakemake_compatible # type: ignore
 
 def raster_sum(
     images_dir: Path,
@@ -20,6 +20,10 @@ def raster_sum(
     with alive_bar(manual=True) as bar:
         total.to_geotiff(output_filename, callback=bar, parallelism=True)
 
+@snakemake_compatible(mapping={
+    "rasters_directory": "input.rasters",
+    "output_filename": "output[0]",
+})
 def main() -> None:
     parser = argparse.ArgumentParser(description="Sums many rasters into a single raster")
     parser.add_argument(