Refactor CLI output messages and update pre-commit configuration for flake8

Author: emmanuelmathot

.github/README.md .github/CI.md.github/README.md renamed to .github/CI.md

@@ -27,7 +27,7 @@ repos:
     hooks:
       - id: flake8
         additional_dependencies: [flake8-docstrings]
-        args: [--max-line-length=88, --extend-ignore=E203,W503]
+        args: [--max-line-length=150, --extend-ignore=E203]
 
   - repo: https://github.com/pre-commit/mirrors-mypy
     rev: v1.5.1

.pre-commit-config.yaml

@@ -8,7 +8,6 @@
 import argparse
 import sys
 from pathlib import Path
-from typing import List, Optional
 
 import xarray as xr
 
@@ -72,7 +71,7 @@ def convert_command(args: argparse.Namespace) -> None:
             max_retries=args.max_retries,
         )
 
-        print(f"✅ Successfully converted EOPF dataset to GeoZarr format")
+        print("✅ Successfully converted EOPF dataset to GeoZarr format")
         print(f"Output saved to: {output_path}")
 
         if args.verbose:
@@ -116,11 +115,11 @@ def info_command(args: argparse.Namespace) -> None:
         print(f"Loading dataset from: {input_path}")
         dt = xr.open_datatree(input_path, engine="zarr")
 
-        print(f"\nDataset Information:")
-        print(f"==================")
+        print("\nDataset Information:")
+        print("==================")
         print(f"Total groups: {len(dt.children)}")
 
-        print(f"\nGroup structure:")
+        print("\nGroup structure:")
         for group_name, group in dt.children.items():
             print(f"  {group_name}:")
             if hasattr(group, "data_vars") and group.data_vars:
@@ -182,14 +181,14 @@ def validate_command(args: argparse.Namespace) -> None:
         total_variables = 0
         compliant_variables = 0
 
-        print(f"\nValidation Results:")
-        print(f"==================")
+        print("\nValidation Results:")
+        print("==================")
 
         for group_name, group in dt.children.items():
             print(f"\nGroup: {group_name}")
 
             if not hasattr(group, "data_vars") or not group.data_vars:
-                print(f"  ⚠️  No data variables found")
+                print("  ⚠️  No data variables found")
                 continue
 
             for var_name, var in group.data_vars.items():
@@ -215,8 +214,8 @@ def validate_command(args: argparse.Namespace) -> None:
                     print(f"  ✅ {var_name}: Compliant")
                     compliant_variables += 1
 
-        print(f"\nSummary:")
-        print(f"========")
+        print("\nSummary:")
+        print("========")
         print(f"Total variables checked: {total_variables}")
         print(f"Compliant variables: {compliant_variables}")
         print(f"Non-compliant variables: {total_variables - compliant_variables}")

eopf_geozarr/cli.py

@@ -18,13 +18,9 @@
 import os
 import shutil
 import time
-import warnings
-from pathlib import Path
 from typing import Any, Dict, List, Optional, Tuple
 
-import dask.array as da
 import numpy as np
-import rasterio
 import xarray as xr
 import zarr
 import zarr.api
@@ -502,7 +498,7 @@ def write_geozarr_group(
     # Create GeoZarr-spec compliant multiscales (overview levels as children groups)
     try:
         print(f"Creating GeoZarr-spec compliant multiscales for {group_name}")
-        multiscales_result = create_geozarr_compliant_multiscales(
+        create_geozarr_compliant_multiscales(
             ds=ds,
             output_path=output_path,
             group_name=group_name,
@@ -815,7 +811,6 @@ def create_native_crs_tile_matrix_set(
         level = overview["level"]
         width = overview["width"]
         height = overview["height"]
-        scale_factor = overview["scale_factor"]
 
         # Calculate cell size (pixel size in CRS units)
         cell_size_x = (right - left) / width

eopf_geozarr/conversion/geozarr.py

@@ -1,7 +1,7 @@
 """Utility functions for GeoZarr conversion."""
 
 import numpy as np
-import rasterio
+import rasterio  # noqa: F401  # Import to enable .rio accessor
 import xarray as xr
 
 

eopf_geozarr/conversion/utils.py

@@ -6,7 +6,6 @@
 docs/analysis/eopf-geozarr/EOPF_Sentinel2_ZarrV3_geozarr_compliant.ipynb
 """
 
-import os
 import shutil
 import subprocess
 import tempfile
@@ -20,15 +19,15 @@ class TestCLIEndToEnd:
     """End-to-end CLI tests with real data."""
 
     @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)
 
     @pytest.mark.slow
     @pytest.mark.network
-    def test_cli_convert_real_sentinel2_data(self, temp_output_dir):
+    def test_cli_convert_real_sentinel2_data(self, temp_output_dir) -> None:
         """
         Test CLI conversion using real Sentinel-2 data from the notebook.
 
@@ -39,7 +38,10 @@ def test_cli_convert_real_sentinel2_data(self, temp_output_dir):
         4. Tests CLI info and validate commands
         """
         # Dataset from the notebook
-        input_url = "https://objectstore.eodc.eu:2222/e05ab01a9d56408d82ac32d69a5aae2a:sample-data/tutorial_data/cpm_v253/S2B_MSIL1C_20250113T103309_N0511_R108_T32TLQ_20250113T122458.zarr"
+        input_url = (
+            "https://objectstore.eodc.eu:2222/e05ab01a9d56408d82ac32d69a5aae2a:sample-data/"
+            "tutorial_data/cpm_v253/S2B_MSIL1C_20250113T103309_N0511_R108_T32TLQ_20250113T122458.zarr"
+        )
         output_path = Path(temp_output_dir) / "s2b_geozarr_cli_test.zarr"
 
         # Groups to convert (from the notebook)
@@ -50,7 +52,7 @@ def test_cli_convert_real_sentinel2_data(self, temp_output_dir):
             "/quality/l1c_quicklook/r10m",
         ]
 
-        print(f"Testing CLI conversion with real Sentinel-2 data...")
+        print("Testing CLI conversion with real Sentinel-2 data...")
         print(f"Input URL: {input_url}")
         print(f"Output path: {output_path}")
 
@@ -144,7 +146,7 @@ def test_cli_convert_real_sentinel2_data(self, temp_output_dir):
 
         print("✅ All CLI end-to-end tests passed!")
 
-    def _verify_converted_data_structure(self, output_path, groups):
+    def _verify_converted_data_structure(self, output_path, groups) -> None:
         """Verify the structure and compliance of converted data."""
 
         # Check each group was converted
@@ -204,7 +206,7 @@ def _verify_converted_data_structure(self, output_path, groups):
             if len(level_dirs) > 1:
                 print(f"    ✅ Multiscale structure created")
 
-    def test_cli_help_commands(self):
+    def test_cli_help_commands(self) -> None:
         """Test that all CLI help commands work."""
 
         # Test main help
@@ -237,7 +239,7 @@ def test_cli_help_commands(self):
 
         print("✅ All CLI help commands work correctly")
 
-    def test_cli_version(self):
+    def test_cli_version(self) -> None:
         """Test CLI version command."""
         result = subprocess.run(
             ["python", "-m", "eopf_geozarr", "--version"], capture_output=True, text=True