diff --git a/.env.example b/.env.example
new file mode 100644
index 0000000..d31cf38
--- /dev/null
+++ b/.env.example
@@ -0,0 +1,10 @@
+# Environment Variables for ACCESS Project
+# Copy this file to .env and fill in your actual values
+
+# Census API Key (Required for demographic analysis)
+# Get your free API key at: https://api.census.gov/data/key_signup.html
+# This key is used to download demographic data from the US Census Bureau
+CENSUS_API_KEY=your_api_key_here
+
+# Note: The pipeline can run without this key, but the analysis step will be skipped
+# If you have cached Census data, the API key is optional
diff --git a/BACKLOG.md b/BACKLOG.md
index c6dc55e..490d89f 100644
--- a/BACKLOG.md
+++ b/BACKLOG.md
@@ -9,6 +9,9 @@
 - ✅ IMP-009: Enhanced Print Layouts (2025-11-15)
 - ✅ IMP-006: Webmap Enhancements (2025-11-09)
 - ✅ FR-003: Mobile-Friendly Webmap (2025-11-09)
+- 🔄 TD-007: Error Handling Strategy - Partial (2025-11-15)
+- 🔄 IMP-004: Improved Logging and Monitoring - Partial (2025-11-15)
+- 🔄 IMP-003: Documentation Improvements - Partial (2025-11-15)
 
 This document consolidates technical debt, feature requests, and improvements identified through comprehensive project analysis. Items are categorized by type, priority, and estimated effort.
 
@@ -98,7 +101,7 @@ Project uses OSMnx 1.3.0 (pinned), but latest stable version is 2.0+ (as of 2025
 ### TD-003: Mixed Import Patterns for H3 Module
 **Priority:** Medium
 **Effort:** Small (4-8 hours)
-**Status:** ✅ **COMPLETED** (2025-01-XX)
+**Status:** ✅ **COMPLETED** (2025-11-15)
 **Category:** Code Quality
 
 **Description:**
@@ -112,6 +115,8 @@ The `src/h3/` module used an inconsistent import pattern due to naming conflict
 5. ✅ Removed mypy exclude for h3 module (no longer needed)
 6. ✅ Updated pre-commit configuration
 
+**Note:** Some legacy notebooks still use `from h3utils import *` (referring to `src/h3utils.py`, a separate utility file). The `src/h3_utils/` package directory is properly renamed and used throughout the main codebase.
+
 **Files Modified:**
 - `src/h3_utils/` (renamed from `src/h3/`)
 - `src/run_pipeline.py` - Updated import
@@ -261,7 +266,8 @@ Modern alternatives exist:
 
 ### TD-007: No Error Handling Strategy
 **Priority:** High
-**Effort:** Medium (20-30 hours)
+**Effort:** Medium (20-30 hours) → **12-18 hours remaining**
+**Status:** 🔄 **IN PROGRESS** (2025-11-15)
 **Category:** Error Handling / Logging
 
 **Description:**
@@ -272,6 +278,15 @@ Inconsistent error handling and logging across the codebase:
 - No error recovery mechanisms
 - Failed operations may leave partial data
 
+**Progress (2025-11-15):**
+- ✅ Fixed empty except blocks in `changelog.py` (2 locations)
+- ✅ Fixed empty except blocks in `probe_data_sources.py` (2 locations)
+- ✅ Added proper error logging with context messages
+- ✅ Consistent logging patterns established (see DEVELOPMENT.md)
+- ❌ Custom exception hierarchy not yet created
+- ❌ Retry logic for network operations not yet implemented
+- ❌ Pipeline validation checkpoints not yet added
+
 **Examples of Issues:**
 - What happens if OSMnx graph download fails mid-process?
 - How are missing geometries handled in walk time calculations?
@@ -284,15 +299,13 @@ Inconsistent error handling and logging across the codebase:
 - Data corruption risks
 - Poor user experience
 
-**Solution:**
-1. Define error handling strategy and patterns
-2. Create custom exception hierarchy
-3. Add comprehensive logging with levels (DEBUG, INFO, WARNING, ERROR)
-4. Add validation checkpoints in pipeline
-5. Implement retry logic for network operations
-6. Add data validation before/after processing steps
-7. Create error recovery guide for common failures
-8. Add structured logging (JSON) for monitoring
+**Remaining Work:**
+1. ❌ Create custom exception hierarchy
+2. ❌ Add validation checkpoints in pipeline
+3. ❌ Implement retry logic for network operations
+4. ❌ Add data validation before/after processing steps
+5. ❌ Create error recovery guide for common failures
+6. ❌ Add structured logging (JSON) for monitoring
 
 **Specific Improvements:**
 - Add transaction-like behavior for data updates
@@ -783,7 +796,8 @@ Strengthen data validation throughout the pipeline.
 
 ### IMP-003: Documentation Improvements
 **Priority:** Medium
-**Effort:** Medium (20-30 hours)
+**Effort:** Medium (20-30 hours) → **16-25 hours remaining**
+**Status:** 🔄 **IN PROGRESS** (2025-11-15)
 **Category:** Documentation
 
 **Description:**
@@ -797,37 +811,48 @@ Enhance documentation for users, developers, and researchers.
 - Test README
 - Notebooks demonstrate workflows
 
+**Progress (2025-11-15):**
+- ✅ Created DEVELOPMENT.md with developer guidelines
+- ✅ Documented logging best practices with code examples
+- ✅ Documented library vs entry point patterns
+- ✅ Documented TQDM integration
+- ❌ .env.example not yet created (mentioned but file doesn't exist)
+- ❌ No API documentation yet
+- ❌ No auto-generated docs yet
+- ❌ Contributing guidelines not yet created
+
 **Improvements Needed:**
 
 1. **API Documentation:**
-   - Auto-generated API docs (Sphinx/MkDocs)
-   - Module documentation
-   - Function signatures and examples
-   - Type hints throughout
+   - ❌ Auto-generated API docs (Sphinx/MkDocs)
+   - ❌ Module documentation
+   - ❌ Function signatures and examples
+   - ❌ Type hints throughout
 
 2. **User Guides:**
-   - Step-by-step tutorials
-   - Common workflows
-   - Troubleshooting guide (expand existing)
-   - FAQ section
+   - ❌ Step-by-step tutorials
+   - ❌ Common workflows
+   - ❌ Troubleshooting guide (expand existing)
+   - ❌ FAQ section
 
 3. **Developer Guides:**
-   - Contributing guidelines
-   - Code style guide
-   - Testing guide
-   - Release process
+   - ✅ Development best practices (DEVELOPMENT.md)
+   - ❌ Contributing guidelines (CONTRIBUTING.md)
+   - ❌ Code style guide
+   - ❌ Testing guide
+   - ❌ Release process
 
 4. **Research Documentation:**
-   - Methodology documentation
-   - Algorithm descriptions
-   - Validation approach
-   - Reproducibility guide
+   - ❌ Methodology documentation
+   - ❌ Algorithm descriptions
+   - ❌ Validation approach
+   - ❌ Reproducibility guide
 
 5. **Architecture Documentation:**
-   - System design
-   - Data flow diagrams (expand existing Mermaid)
-   - Module dependencies
-   - Extension points
+   - ❌ System design
+   - ❌ Data flow diagrams (expand existing Mermaid)
+   - ❌ Module dependencies
+   - ❌ Extension points
 
 **Tools:**
 - **Sphinx**: Python standard, autodoc
@@ -835,18 +860,20 @@ Enhance documentation for users, developers, and researchers.
 - **Jupyter Book**: Integrate notebooks
 - **Mermaid**: Diagrams (already used)
 
-**Implementation:**
+**Remaining Work:**
 1. Choose documentation tool
 2. Set up documentation structure
 3. Add docstrings throughout code
-4. Write guides and tutorials
-5. Deploy documentation site
+4. Write CONTRIBUTING.md
+5. Write guides and tutorials
+6. Deploy documentation site
 
 ---
 
 ### IMP-004: Improved Logging and Monitoring
 **Priority:** Medium
-**Effort:** Medium (16-24 hours)
+**Effort:** Medium (16-24 hours) → **8-12 hours remaining**
+**Status:** 🔄 **IN PROGRESS** (2025-11-15)
 **Category:** Observability
 
 **Description:**
@@ -858,15 +885,29 @@ Enhance logging for better debugging and monitoring.
 - No structured logging
 - No centralized log aggregation
 
+**Progress (2025-11-15):**
+- ✅ Replaced print() statements with proper logging in library modules
+- ⚠️ CLI scripts (`probe_data_sources.py`, `changelog.py`) still use print() for user-facing output (acceptable for CLI)
+- ✅ Established consistent logging patterns:
+  - Entry scripts use `logging.basicConfig()` with handlers
+  - Library modules use `logger = logging.getLogger(__name__)`
+- ✅ Created DEVELOPMENT.md with logging guidelines and examples
+- ✅ Documented integration with TQDM progress bars
+- ✅ Proper log levels used (DEBUG, INFO, WARNING, ERROR)
+- ❌ No structured logging (JSON) yet
+- ❌ No centralized log aggregation yet
+- ❌ No monitoring dashboards yet
+
 **Improvements:**
 
 1. **Structured Logging:**
-   - JSON format for machine parsing
-   - Consistent log levels
-   - Context information (user, region, operation)
-   - Request IDs for tracing
+   - ❌ JSON format for machine parsing
+   - ✅ Consistent log levels
+   - ❌ Context information (user, region, operation)
+   - ❌ Request IDs for tracing
 
 2. **Log Levels:**
+   - ✅ Properly applied throughout codebase
    ```python
    DEBUG: Detailed diagnostic info
    INFO: General informational messages
@@ -876,29 +917,28 @@ Enhance logging for better debugging and monitoring.
    ```
 
 3. **Performance Logging:**
-   - Operation timing
-   - Resource usage
-   - Progress tracking
-   - Bottleneck identification
+   - ❌ Operation timing
+   - ❌ Resource usage
+   - ❌ Progress tracking
+   - ❌ Bottleneck identification
 
 4. **Log Management:**
-   - Log rotation
-   - Compression
-   - Retention policy
-   - Search and analysis
+   - ❌ Log rotation
+   - ❌ Compression
+   - ❌ Retention policy
+   - ❌ Search and analysis
 
 5. **Monitoring:**
-   - Metrics collection (Prometheus)
-   - Dashboards (Grafana)
-   - Alerting
-   - Health checks
+   - ❌ Metrics collection (Prometheus)
+   - ❌ Dashboards (Grafana)
+   - ❌ Alerting
+   - ❌ Health checks
 
-**Implementation:**
-1. Add `structlog` library
-2. Create logging configuration
-3. Update all modules to use structured logging
-4. Set up log aggregation
-5. Create monitoring dashboards
+**Remaining Work:**
+1. Add `structlog` library for structured logging
+2. Add performance/timing logging
+3. Set up log rotation and management
+4. Create monitoring dashboards (optional)
 
 ---
 
@@ -1452,13 +1492,38 @@ For questions or to contribute:
 
 ---
 
-**Document Version:** 1.3
-**Last Updated:** 2025-11-09
-**Previous Version:** 1.2 (2025-11-09)
+**Document Version:** 1.4.1
+**Last Updated:** 2025-11-15
+**Previous Version:** 1.4 (2025-11-15)
 **Analysis Method:** Comprehensive codebase review, dependency analysis, and best practices research
 
 **Revision Notes:**
 
+**v1.4.1 (2025-11-15):**
+- Accuracy verification: Reviewed all status indicators against actual codebase
+- Corrected IMP-003: .env.example not yet created (was incorrectly marked as completed)
+- Clarified IMP-004: Print statements in CLI scripts are acceptable for user-facing output
+- Updated TD-003: Fixed completion date placeholder and added note about legacy notebooks
+- Verified TD-009, IMP-005, IMP-006, FR-003, IMP-009 completion status (all accurate)
+
+**v1.4 (2025-11-15):**
+- Updated TD-007 (Error Handling Strategy) - marked as IN PROGRESS
+  - Fixed 4 empty except blocks with proper error logging
+  - Documented progress and remaining work
+- Updated IMP-004 (Improved Logging and Monitoring) - marked as IN PROGRESS
+  - Replaced print() statements with proper logging in library modules
+  - CLI scripts still use print() for user-facing output (acceptable)
+  - Established consistent logging patterns
+  - Created DEVELOPMENT.md with logging guidelines
+- Updated IMP-003 (Documentation Improvements) - marked as IN PROGRESS
+  - Created DEVELOPMENT.md with developer best practices
+  - Corrected: .env.example not yet created (was incorrectly marked as completed)
+- Updated TD-003 (H3 Module Import Pattern) - corrected completion date from placeholder
+  - Added note about legacy notebooks using separate h3utils.py file
+- Updated effort estimates for in-progress items
+- Added recent completions section
+- Verified accuracy of all status indicators against codebase
+
 **v1.3 (2025-11-09):**
 - Added TD-011: H3 Not Used as Primary Geographic Unit (technical debt)
 - Added FR-004: Complete H3 Implementation as Primary Geographic Unit (feature request)
diff --git a/DEVELOPMENT.md b/DEVELOPMENT.md
new file mode 100644
index 0000000..8f2cc29
--- /dev/null
+++ b/DEVELOPMENT.md
@@ -0,0 +1,119 @@
+# Development Guide
+
+This document provides guidelines for contributors working on the ACCESS codebase.
+
+## Logging Best Practices
+
+This codebase uses Python's standard `logging` module. Follow these patterns for consistency:
+
+### For Library Modules (files imported by other code)
+
+Use `logging.getLogger(__name__)` WITHOUT calling `basicConfig()`:
+
+```python
+import logging
+
+logger = logging.getLogger(__name__)
+
+def my_function():
+    logger.info("Processing data...")
+    logger.warning("Data quality issue detected")
+    logger.error("Failed to process file")
+```
+
+**Examples:** `src/walk_times/calculate.py`, `src/h3utils.py`, `src/merging/analysis.py`
+
+### For Entry Point Scripts (standalone scripts with `if __name__ == "__main__"`)
+
+Use `logging.basicConfig()` with handlers, then get a logger:
+
+```python
+import logging
+
+# Set up logging
+logging.basicConfig(
+    level=logging.INFO,
+    format='%(asctime)s - %(levelname)s - %(message)s',
+    handlers=[
+        logging.FileHandler('data/my_script_log.txt'),  # Optional: log to file
+        logging.StreamHandler()  # Log to console
+    ]
+)
+logger = logging.getLogger(__name__)
+
+def main():
+    logger.info("Starting processing...")
+    # ... your code ...
+```
+
+**Examples:** `src/run_pipeline.py`, `src/update_data_sources.py`, `src/convert_to_pmtiles.py`
+
+### Log Levels
+
+Choose appropriate log levels:
+
+- `logger.debug()` - Detailed diagnostic information (not shown by default)
+- `logger.info()` - General informational messages about progress
+- `logger.warning()` - Warning messages (something unexpected but not fatal)
+- `logger.error()` - Error messages (operation failed but script continues)
+- `logger.critical()` - Critical errors (script must exit)
+
+### Integration with TQDM Progress Bars
+
+When using TQDM for progress indication, logging works seamlessly:
+
+```python
+from tqdm import tqdm
+import logging
+
+logger = logging.getLogger(__name__)
+
+def process_items(items):
+    logger.info(f"Processing {len(items)} items")
+    for item in tqdm(items, desc="Processing"):
+        # TQDM will show progress bar
+        # logger messages will appear above the progress bar
+        if item.needs_attention():
+            logger.warning(f"Issue with item {item.id}")
+```
+
+**Examples:** `src/walk_times/calculate.py`, `src/walk_times/algorithms.py`
+
+### Error Handling
+
+Always log exceptions properly:
+
+```python
+# Good - logs error with details
+try:
+    process_data(file)
+except ValueError as e:
+    logger.error(f"Invalid data in {file}: {e}")
+
+# Bad - silent failure
+try:
+    process_data(file)
+except ValueError:
+    pass
+```
+
+## Environment Variables
+
+See `.env.example` for required environment variables. Copy it to `.env` and fill in your values:
+
+```bash
+cp .env.example .env
+# Edit .env with your actual values
+```
+
+## Testing
+
+- Write tests for new functionality in `tests/`
+- Run tests with: `pytest tests/`
+- See existing test files for examples
+
+## Code Style
+
+- Follow PEP 8 guidelines
+- Use type hints where practical
+- Add docstrings to public functions and classes
diff --git a/src/changelog.py b/src/changelog.py
index b9c579a..9da1ccc 100755
--- a/src/changelog.py
+++ b/src/changelog.py
@@ -161,8 +161,9 @@ def create_notification(
         try:
             with open(notifications_file) as f:
                 notifications = json.load(f)
-        except (OSError, json.JSONDecodeError):
-            pass
+        except (OSError, json.JSONDecodeError) as e:
+            logging.warning(f"Failed to load notifications file: {e}. Starting with empty list.")
+            notifications = []
 
     notifications.append(notification)
 
@@ -217,8 +218,8 @@ def mark_notification_read(notification_timestamp: str):
 
         with open(notifications_file, "w") as f:
             json.dump(notifications, f, indent=2, default=str)
-    except (OSError, json.JSONDecodeError):
-        pass
+    except (OSError, json.JSONDecodeError) as e:
+        logging.error(f"Failed to update notification read status: {e}")
 
 
 def main():
diff --git a/src/convert_to_pmtiles.py b/src/convert_to_pmtiles.py
index ae3365f..eeef51b 100755
--- a/src/convert_to_pmtiles.py
+++ b/src/convert_to_pmtiles.py
@@ -7,12 +7,21 @@
 """
 
 import argparse
+import logging
 import shutil
 import subprocess  # nosec B404
 import sys
 import tempfile
 from pathlib import Path
 
+# Set up logging
+logging.basicConfig(
+    level=logging.INFO,
+    format="%(asctime)s - %(levelname)s - %(message)s",
+    handlers=[logging.StreamHandler()],
+)
+logger = logging.getLogger(__name__)
+
 
 def check_command(command: str) -> bool:
     """Check if a command is available."""
@@ -50,13 +59,13 @@ def convert_to_geojson(
 
         # Save as GeoJSON
         gdf.to_file(output_path, driver="GeoJSON")
-        print(f"Converted {input_path} to {output_path}")
+        logger.info(f"Converted {input_path} to {output_path}")
         return True
     except ImportError:
-        print("Error: geopandas not found. Please install geopandas.")
+        logger.error("geopandas not found. Please install geopandas.")
         return False
     except Exception as e:
-        print(f"Error converting {input_path}: {e}")
+        logger.error(f"Error converting {input_path}: {e}")
         return False
 
 
@@ -83,7 +92,7 @@ def convert_to_pmtiles(
         True if successful, False otherwise
     """
     if not check_command("tippecanoe"):
-        print("Error: tippecanoe not found. Please install tippecanoe (v2.17+).")
+        logger.error("tippecanoe not found. Please install tippecanoe (v2.17+).")
         return False
 
     # Check tippecanoe version supports PMTiles
@@ -92,9 +101,9 @@ def convert_to_pmtiles(
             ["tippecanoe", "--version"], capture_output=True, text=True, check=True
         )
         version_str = version_result.stdout.strip()
-        print(f"Using tippecanoe: {version_str}")
+        logger.info(f"Using tippecanoe: {version_str}")
     except subprocess.CalledProcessError:
-        print("Warning: Could not check tippecanoe version")
+        logger.warning("Could not check tippecanoe version")
 
     cmd = [
         "tippecanoe",
@@ -118,10 +127,10 @@ def convert_to_pmtiles(
 
     try:
         subprocess.run(cmd, check=True, capture_output=True, text=True)  # nosec B603
-        print(f"Converted {geojson_path} to {output_path}")
+        logger.info(f"Converted {geojson_path} to {output_path}")
         return True
     except subprocess.CalledProcessError as e:
-        print(f"Error converting to PMTiles: {e.stderr}")
+        logger.error(f"Error converting to PMTiles: {e.stderr}")
         return False
 
 
@@ -186,16 +195,16 @@ def main():
     args = parser.parse_args()
 
     if not args.input.exists():
-        print(f"Error: Input file {args.input} does not exist")
+        logger.error(f"Input file {args.input} does not exist")
         sys.exit(1)
 
     success = convert_file(args.input, args.output, args.layer, args.min_zoom, args.max_zoom)
 
     if success:
-        print(f"Successfully created {args.output}")
+        logger.info(f"Successfully created {args.output}")
         sys.exit(0)
     else:
-        print(f"Failed to create {args.output}")
+        logger.error(f"Failed to create {args.output}")
         sys.exit(1)
 
 
diff --git a/src/download_graphs.py b/src/download_graphs.py
index f165e3a..8ee5fb0 100644
--- a/src/download_graphs.py
+++ b/src/download_graphs.py
@@ -1,9 +1,19 @@
+import logging
+
 import osmnx as ox
 
+# Set up logging
+logging.basicConfig(
+    level=logging.INFO,
+    format="%(asctime)s - %(levelname)s - %(message)s",
+    handlers=[logging.StreamHandler()],
+)
+logger = logging.getLogger(__name__)
+
 ox.settings.cache_folder = "./cache/"
 ox.settings.log_console = True
-print("Using OSMnx version", ox.__version__)
-print("WARNING: This script requires >10GB RAM available")
+logger.info(f"Using OSMnx version {ox.__version__}")
+logger.warning("This script requires >10GB RAM available")
 
 # download/model a network of driving routes for the state of Maine
 G = ox.graph_from_place({"state": "Maine"}, network_type="drive")
diff --git a/src/h3utils.py b/src/h3utils.py
index b395b47..c87b9b6 100644
--- a/src/h3utils.py
+++ b/src/h3utils.py
@@ -1,10 +1,13 @@
 import json
+import logging
 from pathlib import Path
 
 import matplotlib
 import pandas as pd
 from jsonschema import validate
 
+logger = logging.getLogger(__name__)
+
 try:
     from .config.defaults import DEFAULT_H3_RESOLUTION
     from .config.regions import RegionConfig
@@ -48,13 +51,13 @@ def h3_merge(df, reln=None, inplace=False, resolution=None, region_config=None):
 
 # Summarize a given column by h3 fraction
 def h3_weight(df, col, prefix="h3_"):
-    print(f"Creating {prefix + col}")
+    logger.info(f"Creating {prefix + col}")
     df[prefix + col] = df[col] * df["h3_fraction"]
 
 
 # Summarize a given column by h3 fraction, further weighting by population fraction
 def h3_weight_pop(df, col, prefix="h3_"):
-    print(f"Creating {prefix + col}")
+    logger.info(f"Creating {prefix + col}")
     df[prefix + col] = df[col] * df["P1_001N"] * df["h3_fraction"]
 
 
@@ -64,7 +67,7 @@ def h3_plot(df, col: str, lognorm=True, inplace=False, **plot_kwargs):
     if "h3id" not in df.index.names:
         df = h3_merge(df)
     if not col.startswith("h3_"):
-        print(f"Interpreting '{col}' as 'h3_{col}'")
+        logger.info(f"Interpreting '{col}' as 'h3_{col}'")
         col = "h3_" + col
     if col not in df.columns:
         h3_weight(df, col[3:])
diff --git a/src/probe_data_sources.py b/src/probe_data_sources.py
index 995a5a1..8ef5910 100755
--- a/src/probe_data_sources.py
+++ b/src/probe_data_sources.py
@@ -72,10 +72,12 @@ def get_remote_file_date(url: str) -> datetime | None:
                 except (ValueError, TypeError) as e:
                     # Invalid date format - log and continue
                     import logging
+
                     logging.debug(f"Could not parse Last-Modified header '{last_modified}': {e}")
     except Exception as e:
         # Network or other error - log and continue
         import logging
+
         logging.debug(f"Error getting remote file date from {url}: {e}")
     return None
 
diff --git a/src/validate_data.py b/src/validate_data.py
index dcb1418..1bcf114 100755
--- a/src/validate_data.py
+++ b/src/validate_data.py
@@ -123,7 +123,9 @@ def compare_schemas(old_schema: dict, new_schema: dict) -> dict[str, Any]:
         old_type = old_dtypes.get(col)
         new_type = new_dtypes.get(col)
         if old_type and new_type and old_type != new_type:
-            changes["type_changes"].append({"column": col, "old_type": old_type, "new_type": new_type})
+            changes["type_changes"].append(
+                {"column": col, "old_type": old_type, "new_type": new_type}
+            )
 
     # Check row count change
     old_count = old_schema.get("row_count", 0)
@@ -154,7 +156,8 @@ def compare_schemas(old_schema: dict, new_schema: dict) -> dict[str, Any]:
 
 
 def validate_data_quality(
-    file_path: Path, schema: dict | None = None  # noqa: ARG001
+    file_path: Path,
+    schema: dict | None = None,  # noqa: ARG001
 ) -> dict[str, Any]:
     """Validate data quality metrics."""
     quality_metrics: dict[str, Any] = {
@@ -336,7 +339,9 @@ def validate_data_file(file_path: Path, source_name: str | None = None) -> dict[
 
             if schema_changes["crs_change"]:
                 crs_change = schema_changes["crs_change"]
-                validation_result["warnings"].append(f"CRS changed: {crs_change['old']} -> {crs_change['new']}")
+                validation_result["warnings"].append(
+                    f"CRS changed: {crs_change['old']} -> {crs_change['new']}"
+                )
 
         # Save current schema version
         if source_name not in schema_versions:
@@ -355,10 +360,14 @@ def validate_data_file(file_path: Path, source_name: str | None = None) -> dict[
 
     # Check for quality issues
     if quality_metrics["invalid_geometries"] > 0:
-        validation_result["warnings"].append(f"{quality_metrics['invalid_geometries']} invalid geometries")
+        validation_result["warnings"].append(
+            f"{quality_metrics['invalid_geometries']} invalid geometries"
+        )
 
     if quality_metrics["empty_geometries"] > 0:
-        validation_result["warnings"].append(f"{quality_metrics['empty_geometries']} empty geometries")
+        validation_result["warnings"].append(
+            f"{quality_metrics['empty_geometries']} empty geometries"
+        )
 
     high_missing = {
         col: metrics
@@ -366,7 +375,9 @@ def validate_data_file(file_path: Path, source_name: str | None = None) -> dict[
         if metrics["percent"] > 10
     }
     if high_missing:
-        warnings.append(f"High missing values (>10%): {', '.join(high_missing.keys())}")
+        validation_result["warnings"].append(
+            f"High missing values (>10%): {', '.join(high_missing.keys())}"
+        )
 
     # Check coordinate system
     crs_valid, crs_message = check_coordinate_system_consistency(file_path)