# -*- coding: utf-8 -*- """ /*************************************************************************** GeoPublicHealth A QGIS plugin ------------------- begin : 2026-01-24 copyright : (C) 2026 by Manuel Vidaurre email : manuel.vidaurre@gmail.com ***************************************************************************/ /*************************************************************************** * * * This program is free software; you can redistribute it and/or modify * * it under the terms of the GNU General Public License as published by * * the Free Software Foundation; either version 2 of the License, or * * (at your option) any later version. * * * ***************************************************************************/ Installation script for GeoPublicHealth dependencies on macOS. This script installs all required dependencies for the GeoPublicHealth QGIS plugin. IMPORTANT: This script MUST be run using QGIS's Python, not your system Python. QGIS has its own isolated Python environment separate from: - macOS system Python (/usr/bin/python3) - Homebrew Python (/opt/homebrew/bin/python3 or /usr/local/bin/python3) - Anaconda/Miniconda Python - Any other Python installation USAGE: Method 1 - Run from QGIS Python Console (RECOMMENDED - Always uses correct Python): 1. Open QGIS 2. Go to Plugins > Python Console 3. Click the "Show Editor" button (icon in console toolbar) 4. Open this file (install_mac_dependencies.py) 5. Click "Run Script" button 6. Restart QGIS when complete Method 2 - Run from Terminal (ONLY if you use the full QGIS Python path): /Applications/QGIS.app/Contents/MacOS/bin/python3 install_mac_dependencies.py Optional arguments: --python-path PATH Override Python executable path --yes, -y Skip interactive prompts (for automation) --timeout SECONDS Timeout for each package install (default: none) --log PATH Log file path (default: auto-generated) Example for automation: /Applications/QGIS.app/Contents/MacOS/bin/python3 install_mac_dependencies.py --yes --log /tmp/install.log WARNING: Do NOT run with just "python3" or "python". This will use the wrong Python. Method 3 - Paste into QGIS Python Console: Copy and paste the entire script into the console """ import subprocess import sys import argparse import datetime from pathlib import Path def verify_qgis_python(python_exe): """Verify we're running with QGIS Python, not system Python.""" # Check if this looks like QGIS Python is_qgis_python = "QGIS.app" in python_exe or "qgis" in python_exe.lower() return is_qgis_python def parse_args(): """Parse command line arguments.""" parser = argparse.ArgumentParser( description="Install GeoPublicHealth dependencies for macOS", formatter_class=argparse.RawDescriptionHelpFormatter, epilog=""" Examples: # Run with QGIS Python (recommended): /Applications/QGIS.app/Contents/MacOS/bin/python3 install_mac_dependencies.py # Non-interactive mode for automation: /Applications/QGIS.app/Contents/MacOS/bin/python3 install_mac_dependencies.py --yes --log /tmp/install.log # Override QGIS Python path: python3 install_mac_dependencies.py --python-path /Applications/QGIS-LTR.app/Contents/MacOS/bin/python3 """, ) parser.add_argument( "--python-path", help="Path to Python executable to use (default: current Python)", default=sys.executable, ) parser.add_argument( "--yes", "-y", action="store_true", help="Skip interactive prompts (assume yes)", ) parser.add_argument( "--timeout", type=int, default=None, help="Timeout in seconds for each pip install (default: none)", ) parser.add_argument( "--log", help=("Log file path (default: geopublichealth_install_.log)"), ) return parser.parse_args() def install_dependencies(): """Install all required dependencies for GeoPublicHealth on macOS.""" # Parse arguments (only when run from command line, not when pasted in # console) try: args = parse_args() python_exe = args.python_path non_interactive = args.yes timeout = args.timeout log_file = args.log except SystemExit: # When pasted into QGIS console, argparse may fail - use defaults python_exe = sys.executable non_interactive = False timeout = None log_file = None # Determine log file path if not log_file: timestamp = datetime.datetime.now().strftime("%Y%m%d_%H%M%S") log_filename = f"geopublichealth_install_{timestamp}.log" log_path = Path(f"./{log_filename}").absolute() else: log_path = Path(log_file).absolute() print("=" * 70) print("GeoPublicHealth macOS Dependency Installer") print("=" * 70) # Verify we're using QGIS Python is_qgis_python = verify_qgis_python(python_exe) print(f"\nPython executable: {python_exe}") print(f"Python version: {sys.version.split()[0]}") print(f"Log file: {log_path}") if is_qgis_python: print("✓ Running with QGIS Python (correct!)") else: print("\n" + "!" * 70) print("⚠️ WARNING: This may NOT be QGIS's Python!") print("!" * 70) print("\nYou appear to be running system/Homebrew/Anaconda Python.") print("Dependencies installed here will NOT be available in QGIS.") print("\nQGIS Python is usually located at:") print(" /Applications/QGIS.app/Contents/MacOS/bin/python3") print("\nRECOMMENDED: Run this from QGIS Python Console.") print("See installation instructions in README.md or INSTALL_MAC.md") print("\n" + "!" * 70) if not non_interactive: response = input("\nContinue anyway? (yes/no): ").strip().lower() if response not in ["yes", "y"]: print("\nInstallation cancelled. Use QGIS Python Console.") return False print("\nProceeding with current Python (you have been warned)...") print("\n" + "=" * 70) # Define dependencies to install # IMPORTANT: Order matters! numba must be installed before libpysal/esda # because those packages may use numba during build/installation dependencies = [ ("pip", ["pip", "--upgrade"], "Package installer"), ("numpy", ["numpy"], "Numerical computing"), ("scipy", ["scipy"], "Scientific computing"), ("pandas", ["pandas"], "Data analysis"), ("numba", ["numba"], "Performance optimization (Required)"), ( "libpysal & esda", ["libpysal", "esda", "--no-build-isolation"], "Spatial analysis (Required)", ), ("matplotlib", ["matplotlib"], "Plotting (Optional)"), ] print("\nThe following packages will be installed:") for name, _, description in dependencies: print(f" • {name}: {description}") print("\n" + "=" * 70) print("Starting installation...") print("=" * 70) installed = [] failed = [] for name, packages, description in dependencies: print( ( f"\n[{len(installed) + len(failed) + 1}/{len(dependencies)}] " f"Installing {name}..." ) ) print("-" * 70) try: # Build the pip install command cmd = [python_exe, "-m", "pip", "install"] + packages print(f"Running: {' '.join(cmd)}") # Write to log with open(log_path, "a", encoding="utf-8") as log: log.write(f"\n{'=' * 70}\n") log.write(f">>> {' '.join(cmd)}\n") log.write(f"{'=' * 70}\n") # Run pip install result = subprocess.run( cmd, capture_output=True, text=True, timeout=timeout, ) # Write full output to log with open(log_path, "a", encoding="utf-8") as log: log.write(result.stdout or "") log.write(result.stderr or "") # Show abbreviated output to console if result.stdout: # Only show last few lines to avoid clutter lines = result.stdout.strip().split("\n") for line in lines[-3:]: if line.strip(): print(f" {line}") if result.returncode == 0: print(f"✓ {name} installed successfully") installed.append(name) else: print(f"✗ {name} installation failed") print(f" See full log: {log_path}") if result.stderr: print(" Error snippet:") for line in result.stderr.strip().split("\n")[-3:]: if line.strip(): print(f" {line}") failed.append(name) except subprocess.TimeoutExpired: error_msg = f"✗ {name} installation timed out (> {timeout}s)" print(error_msg) with open(log_path, "a", encoding="utf-8") as log: log.write(f"\n{error_msg}\n") failed.append(name) except Exception as e: error_msg = f"✗ Error installing {name}: {str(e)}" print(error_msg) with open(log_path, "a", encoding="utf-8") as log: log.write(f"\n{error_msg}\n") failed.append(name) # Summary print("\n" + "=" * 70) print("INSTALLATION SUMMARY") print("=" * 70) print(f"\nLog file: {log_path}") if installed: print(f"\n✓ Successfully installed ({len(installed)}):") for name in installed: print(f" • {name}") if failed: print(f"\n✗ Failed to install ({len(failed)}):") for name in failed: print(f" • {name}") print(f"\nFull installation log: {log_path}") # Verify critical dependencies print("\n" + "=" * 70) print("VERIFYING REQUIRED DEPENDENCIES") print("=" * 70) critical = { "libpysal": "Spatial analysis", "esda": "Exploratory spatial data analysis", "numba": "Performance optimization", } def check_module(module_name): cmd = [ python_exe, "-c", ( "import importlib; " f"module = importlib.import_module('{module_name}'); " "print(getattr(module, '__version__', 'unknown'))" ), ] result = subprocess.run(cmd, capture_output=True, text=True) if result.returncode == 0: return True, result.stdout.strip() return False, result.stderr.strip() all_critical_ok = True for module, description in critical.items(): ok, version = check_module(module) if ok: print(f"✓ {module} {version} is available - {description}") else: print(f"✗ {module} is NOT available - {description}") all_critical_ok = False # Check optional dependencies print("\nOptional dependencies:") ok, version = check_module("matplotlib") if ok: print(f"✓ matplotlib is available (version {version})") else: print("○ matplotlib not available (plotting disabled)") # Final message print("\n" + "=" * 70) if all_critical_ok and not failed: print("SUCCESS! All dependencies installed successfully.") print("\nNext steps:") print("1. Restart QGIS for changes to take effect") print("2. Install the GeoPublicHealth plugin from Plugins menu") print("3. Start using GeoPublicHealth!") print(f"\nInstallation log: {log_path}") exit_code = 0 elif all_critical_ok: print("PARTIAL SUCCESS - Core dependencies are installed.") print( "\nSome optional packages failed, but the plugin should work for " "basic features." ) print("\nNext steps:") print("1. Restart QGIS for changes to take effect") print("2. Install the GeoPublicHealth plugin from Plugins menu") print(f"\nInstallation log: {log_path}") exit_code = 0 else: print("INSTALLATION INCOMPLETE") print("\nSome required dependencies failed to install.") print(f"\nFull installation log: {log_path}") print( "\nPlease try running install_dependencies_console.py from QGIS " "Python Console" ) print("See INSTALL_MAC.md and MAC_INSTALL_TECHNICAL.md for help.") print("\nIf reporting an issue, please attach:") print(f" - Log file: {log_path}") print( " - QGIS version: (run in QGIS console: from qgis.core import " "QgsApplication; print(QgsApplication.version()))" ) print(f" - macOS version: (run in terminal: sw_vers)") exit_code = 1 print("=" * 70) return exit_code if __name__ == "__main__": # Run the installation exit_code = install_dependencies() sys.exit(exit_code)