Refactor CLI output messages for consistency and clarity; enhance type hints in tests

Author: emmanuelmathot

eopf_geozarr/cli.py

@@ -120,7 +120,7 @@ def info_command(args: argparse.Namespace) -> None:
         print(f"Total groups: {len(dt.children)}")
 
         print("\nGroup structure:")
-        for group_name, group in dt.children.items():
+        for group_name, group in dt.groups.items():
             print(f"  {group_name}:")
             if hasattr(group, "data_vars") and group.data_vars:
                 print(f"    Variables: {list(group.data_vars.keys())}")
@@ -221,14 +221,14 @@ def validate_command(args: argparse.Namespace) -> None:
         print(f"Non-compliant variables: {total_variables - compliant_variables}")
 
         if compliance_issues:
-            print(f"\n❌ Dataset is NOT GeoZarr compliant")
+            print("\n❌ Dataset is NOT GeoZarr compliant")
             print(f"Issues found: {len(compliance_issues)}")
             if args.verbose:
                 print("Detailed issues:")
                 for issue in set(compliance_issues):
                     print(f"  - {issue}")
         else:
-            print(f"\n✅ Dataset appears to be GeoZarr compliant")
+            print("\n✅ Dataset appears to be GeoZarr compliant")
 
     except Exception as e:
         print(f"❌ Error validating dataset: {e}")
@@ -316,7 +316,7 @@ def create_parser() -> argparse.ArgumentParser:
 
 
 def main() -> None:
-    """Main entry point for the CLI."""
+    """Execute main entry point for the CLI."""
     parser = create_parser()
 
     if len(sys.argv) == 1:

eopf_geozarr/conversion/geozarr.py

@@ -518,7 +518,7 @@ def write_geozarr_group(
     zarr_group = zarr.open_group(group_path, mode="r+", zarr_format=3)
     consolidate_metadata(zarr_group.store)
 
-    print(f"  ✅ Metadata consolidated")
+    print("  ✅ Metadata consolidated")
 
     ds = xr.open_dataset(
         group_path, engine="zarr", zarr_format=3, decode_coords="all"
@@ -645,7 +645,7 @@ def create_geozarr_compliant_multiscales(
 
         # Skip level 0 - native resolution is in the root group
         if level == 0:
-            print(f"Skipping level 0 - native resolution is already in group 0")
+            print("Skipping level 0 - native resolution is already in group 0")
             continue
 
         print(f"\nCreating overview level {level} (1:{scale_factor} scale)...")

eopf_geozarr/tests/test_cli_e2e.py

@@ -19,15 +19,15 @@ class TestCLIEndToEnd:
     """End-to-end CLI tests with real data."""
 
     @pytest.fixture
-    def temp_output_dir(self) -> str:
+    def temp_output_dir(self):  # type: ignore[no-untyped-def]
         """Create a temporary directory for test outputs."""
         temp_dir = tempfile.mkdtemp()
         yield temp_dir
         shutil.rmtree(temp_dir)
 
     @pytest.mark.slow
     @pytest.mark.network
-    def test_cli_convert_real_sentinel2_data(self, temp_output_dir) -> None:
+    def test_cli_convert_real_sentinel2_data(self, temp_output_dir: str) -> None:
         """
         Test CLI conversion using real Sentinel-2 data from the notebook.
 
@@ -111,8 +111,9 @@ def test_cli_convert_real_sentinel2_data(self, temp_output_dir) -> None:
 
         # Verify info output contains expected information
         info_output = result_info.stdout
-        assert "Groups found:" in info_output, "Info should list groups"
-        assert "measurements/reflectance/r10m" in info_output, "Should find r10m group"
+        assert "Total groups:" in info_output, "Info should show total groups count"
+        assert "Group structure:" in info_output, "Info should show group structure"
+        assert "measurements:" in info_output, "Should find measurements group"
 
         # Test 3: CLI validate command
         print("\n=== Testing CLI validate command ===")
@@ -136,7 +137,7 @@ def test_cli_convert_real_sentinel2_data(self, temp_output_dir) -> None:
 
         # Verify validation output
         validate_output = result_validate.stdout
-        assert "GeoZarr compliance validation" in validate_output, "Should show validation header"
+        assert "Validation Results:" in validate_output, "Should show validation header"
         assert "✅" in validate_output, "Should show successful validations"
 
         # Test 4: Verify data structure and compliance
@@ -146,9 +147,8 @@ def test_cli_convert_real_sentinel2_data(self, temp_output_dir) -> None:
 
         print("✅ All CLI end-to-end tests passed!")
 
-    def _verify_converted_data_structure(self, output_path, groups) -> None:
+    def _verify_converted_data_structure(self, output_path: Path, groups: list[str]) -> None:
         """Verify the structure and compliance of converted data."""
-
         # Check each group was converted
         for group in groups:
             group_path = output_path / group.lstrip("/")
@@ -195,7 +195,7 @@ def _verify_converted_data_structure(self, output_path, groups) -> None:
                 assert (
                     "_ARRAY_DIMENSIONS" in ds["spatial_ref"].attrs
                 ), f"Missing _ARRAY_DIMENSIONS in spatial_ref for {group}"
-                print(f"    ✅ spatial_ref variable verified")
+                print("    ✅ spatial_ref variable verified")
 
             ds.close()
 
@@ -204,11 +204,10 @@ def _verify_converted_data_structure(self, output_path, groups) -> None:
             print(f"    Overview levels: {sorted([d.name for d in level_dirs])}")
 
             if len(level_dirs) > 1:
-                print(f"    ✅ Multiscale structure created")
+                print("    ✅ Multiscale structure created")
 
     def test_cli_help_commands(self) -> None:
         """Test that all CLI help commands work."""
-
         # Test main help
         result = subprocess.run(
             ["python", "-m", "eopf_geozarr", "--help"], capture_output=True, text=True

eopf_geozarr/tests/test_conversion.py

@@ -1,6 +1,6 @@
 """Tests for the conversion module."""
 
-from unittest.mock import Mock, patch
+from unittest.mock import patch
 
 import numpy as np
 import pytest
@@ -20,7 +20,7 @@
 class TestUtilityFunctions:
     """Test utility functions."""
 
-    def test_downsample_2d_array_block_averaging(self):
+    def test_downsample_2d_array_block_averaging(self) -> None:
         """Test downsampling with block averaging."""
         # Create a 4x4 array
         source_data = np.array(
@@ -40,7 +40,7 @@ def test_downsample_2d_array_block_averaging(self):
 
         np.testing.assert_array_equal(result, expected)
 
-    def test_downsample_2d_array_subsampling(self):
+    def test_downsample_2d_array_subsampling(self) -> None:
         """Test downsampling with subsampling when block size is 1."""
         source_data = np.array([[1, 2, 3], [4, 5, 6], [7, 8, 9]], dtype=float)
 
@@ -52,27 +52,27 @@ def test_downsample_2d_array_subsampling(self):
 
         np.testing.assert_array_equal(result, expected)
 
-    def test_calculate_aligned_chunk_size_perfect_divisor(self):
+    def test_calculate_aligned_chunk_size_perfect_divisor(self) -> None:
         """Test chunk size calculation with perfect divisor."""
         # 1000 dimension, want 256 chunks
         result = calculate_aligned_chunk_size(1000, 256)
         # Should find 250 as the largest divisor <= 256
         assert result == 250
         assert 1000 % result == 0
 
-    def test_calculate_aligned_chunk_size_larger_than_dimension(self):
+    def test_calculate_aligned_chunk_size_larger_than_dimension(self) -> None:
         """Test chunk size calculation when desired size is larger than dimension."""
         result = calculate_aligned_chunk_size(100, 256)
         assert result == 100
 
-    def test_calculate_aligned_chunk_size_no_perfect_divisor(self):
+    def test_calculate_aligned_chunk_size_no_perfect_divisor(self) -> None:
         """Test chunk size calculation when no perfect divisor exists."""
         # Prime number dimension
         result = calculate_aligned_chunk_size(97, 50)
         # Should return 1 as the only divisor when no good divisor is found
         assert result == 1
 
-    def test_is_grid_mapping_variable(self):
+    def test_is_grid_mapping_variable(self) -> None:
         """Test grid mapping variable detection."""
         # Create a dataset with a grid mapping variable
         ds = xr.Dataset(
@@ -86,10 +86,10 @@ def test_is_grid_mapping_variable(self):
             }
         )
 
-        assert is_grid_mapping_variable(ds, "spatial_ref") == True
-        assert is_grid_mapping_variable(ds, "temperature") == False
+        assert is_grid_mapping_variable(ds, "spatial_ref") is True
+        assert is_grid_mapping_variable(ds, "temperature") is False
 
-    def test_validate_existing_band_data_valid(self):
+    def test_validate_existing_band_data_valid(self) -> None:
         """Test validation of existing valid band data."""
         # Create datasets
         existing_ds = xr.Dataset(
@@ -108,16 +108,16 @@ def test_validate_existing_band_data_valid(self):
 
         expected_ds = xr.Dataset({"B04": (["y", "x"], np.random.rand(100, 100))})
 
-        assert validate_existing_band_data(existing_ds, "B04", expected_ds) == True
+        assert validate_existing_band_data(existing_ds, "B04", expected_ds) is True
 
-    def test_validate_existing_band_data_missing(self):
+    def test_validate_existing_band_data_missing(self) -> None:
         """Test validation of missing band data."""
         existing_ds = xr.Dataset({})
         expected_ds = xr.Dataset({"B04": (["y", "x"], np.random.rand(100, 100))})
 
-        assert validate_existing_band_data(existing_ds, "B04", expected_ds) == False
+        assert validate_existing_band_data(existing_ds, "B04", expected_ds) is False
 
-    def test_calculate_overview_levels(self):
+    def test_calculate_overview_levels(self) -> None:
         """Test overview levels calculation."""
         levels = calculate_overview_levels(1024, 1024, min_dimension=256, tile_width=256)
 
@@ -142,7 +142,7 @@ def test_calculate_overview_levels(self):
 class TestMetadataSetup:
     """Test metadata setup functions."""
 
-    def test_setup_datatree_metadata_geozarr_spec_compliant(self):
+    def test_setup_datatree_metadata_geozarr_spec_compliant(self) -> None:
         """Test GeoZarr metadata setup."""
         # Create a real DataTree with measurement groups
         # Create datasets for different resolution groups
@@ -189,7 +189,7 @@ def test_setup_datatree_metadata_geozarr_spec_compliant(self):
 class TestIntegration:
     """Integration tests."""
 
-    def test_create_simple_geozarr_metadata(self):
+    def test_create_simple_geozarr_metadata(self) -> None:
         """Test creating simple GeoZarr metadata structure."""
         # Create a simple dataset
         data = np.random.rand(10, 10)

eopf_geozarr/tests/test_integration_sentinel2.py

@@ -6,7 +6,6 @@
 docs/analysis/eopf-geozarr/EOPF_Sentinel2_ZarrV3_geozarr_compliant.ipynb
 """
 
-import os
 import shutil
 import tempfile
 from pathlib import Path
@@ -24,7 +23,7 @@ class TestSentinel2Integration:
     """Integration tests for Sentinel-2 EOPF to GeoZarr conversion."""
 
     @pytest.fixture
-    def sample_sentinel2_datatree(self):
+    def sample_sentinel2_datatree(self) -> xr.DataTree:
         """
         Create a sample Sentinel-2 EOPF DataTree structure for testing.
 
@@ -217,15 +216,15 @@ def sample_sentinel2_datatree(self):
         return dt
 
     @pytest.fixture
-    def temp_output_dir(self):
+    def temp_output_dir(self) -> str:
         """Create a temporary directory for test outputs."""
         temp_dir = tempfile.mkdtemp()
         yield temp_dir
         shutil.rmtree(temp_dir)
 
     def test_complete_sentinel2_conversion_notebook_workflow(
         self, sample_sentinel2_datatree, temp_output_dir
-    ):
+    ) -> None:
         """
         Test complete conversion following the notebook workflow.
 
@@ -247,7 +246,7 @@ def test_complete_sentinel2_conversion_notebook_workflow(
             "/quality/l1c_quicklook/r10m",
         ]
 
-        print(f"Converting Sentinel-2 EOPF DataTree to GeoZarr format...")
+        print("Converting Sentinel-2 EOPF DataTree to GeoZarr format...")
         print(f"Input groups: {groups}")
         print(f"Output path: {output_path}")
 
@@ -283,7 +282,7 @@ def test_complete_sentinel2_conversion_notebook_workflow(
 
         print("✅ All integration tests passed!")
 
-    def _verify_basic_structure(self, output_path, groups):
+    def _verify_basic_structure(self, output_path, groups) -> None:
         """Verify the basic Zarr store structure."""
         print("Verifying basic structure...")
 
@@ -301,7 +300,7 @@ def _verify_basic_structure(self, output_path, groups):
             assert level_0_path.exists(), f"Level 0 not found for {group}"
             assert (level_0_path / "zarr.json").exists(), f"Level 0 missing zarr.json for {group}"
 
-    def _verify_geozarr_spec_compliance(self, output_path, group):
+    def _verify_geozarr_spec_compliance(self, output_path, group) -> None:
         """
         Verify GeoZarr specification compliance following the notebook verification.
 
@@ -380,13 +379,13 @@ def _verify_geozarr_spec_compliance(self, output_path, group):
         if "GeoTransform" in ds["spatial_ref"].attrs:
             print(f"    ✅ GeoTransform: {ds['spatial_ref'].attrs['GeoTransform']}")
         else:
-            print(f"    ⚠️  Missing GeoTransform attribute")
+            print("    ⚠️  Missing GeoTransform attribute")
 
         # Check 6: CRS information (from notebook verification)
         if "crs_wkt" in ds["spatial_ref"].attrs:
-            print(f"    ✅ CRS WKT present")
+            print("    ✅ CRS WKT present")
         else:
-            print(f"    ⚠️  Missing CRS WKT")
+            print("    ⚠️  Missing CRS WKT")
 
         # Check 7: Coordinate standard names (from notebook verification)
         for coord in ["x", "y"]:
@@ -402,7 +401,7 @@ def _verify_geozarr_spec_compliance(self, output_path, group):
 
         ds.close()
 
-    def _verify_multiscale_structure(self, output_path, group):
+    def _verify_multiscale_structure(self, output_path, group) -> None:
         """Verify multiscale structure following notebook patterns."""
         print(f"Verifying multiscale structure for {group}...")
 
@@ -475,15 +474,15 @@ def _verify_multiscale_structure(self, output_path, group):
                         f"    Level {prev_level}→{level} downsampling ratio: {height_ratio:.2f}x{width_ratio:.2f}"
                     )
 
-    def _verify_rgb_data_access(self, output_path, groups):
+    def _verify_rgb_data_access(self, output_path, groups) -> None:
         """Verify RGB data access patterns from the notebook."""
         print("Verifying RGB data access patterns...")
 
         # Find groups with RGB bands (following notebook logic)
         rgb_groups = []
         for group in groups:
-            group_path = str(output_path / group.lstrip("/") / "0")
-            ds = xr.open_dataset(group_path, engine="zarr", zarr_format=3)
+            group_path_str = str(output_path / group.lstrip("/") / "0")
+            ds = xr.open_dataset(group_path_str, engine="zarr", zarr_format=3)
 
             # Check for RGB bands (b04=red, b03=green, b02=blue for Sentinel-2)
             has_rgb = all(band in ds.data_vars for band in ["b04", "b03", "b02"])
@@ -530,7 +529,7 @@ def _verify_rgb_data_access(self, output_path, groups):
                 ds.close()
 
     @pytest.mark.slow
-    def test_performance_characteristics(self, sample_sentinel2_datatree, temp_output_dir):
+    def test_performance_characteristics(self, sample_sentinel2_datatree, temp_output_dir) -> None:
         """
         Test performance characteristics following notebook analysis.
 
@@ -546,7 +545,7 @@ def test_performance_characteristics(self, sample_sentinel2_datatree, temp_outpu
         groups = ["/measurements/reflectance/r10m"]  # Focus on one group for performance testing
 
         with patch("eopf_geozarr.conversion.geozarr.print"):
-            dt_geozarr = create_geozarr_dataset(
+            create_geozarr_dataset(
                 dt_input=dt_input,
                 groups=groups,
                 output_path=str(output_path),