Provide global exception handling through sys.excepthook

Catch unhandled exceptions globally through the except hook. Log these exceptions to file, ideally using the existing logger file handler. In case this handler does not exist, also output to a standard Python temporary file path, which avoids the need to load libraries to identify the user app directory.

docs/release/release_v1.4.md

@@ -134,6 +134,7 @@ Code base and docs
 - Python APIs
     - Previously Python APIs compatible with both Python 2 and 3 have been used when possible, but much of the package requires Python 3, and testing has been on Python >= 3.6
     - For a more consistent and modern codebase, we are initiating use of Python 3 APIs such as `pathlib` and specifically 3.6+ features such as f-strings
+- Unhandled exceptions are now logged (saved to a temp file if caught before logging is set up)
 - More links to external packages in API docs
 - Instructions on building the API docs
 - `Blobs` and `Image5d` are being migrated to class structures for better encapsulation and additional metadata

run.py

@@ -23,11 +23,13 @@
 
 """
 
+import logging
 import multiprocessing
 import os
 import platform
 import subprocess
 import sys
+import tempfile
 
 #: str: Name of Conda or Venv environment
 ENV_NAME = "mag"
@@ -126,6 +128,35 @@ def launch_magmap():
     visualizer.main()
 
 
+def log_uncaught_exception(exc_type, exc, trace):
+    """Handle uncaught exceptions globally with logging.
+    
+    Args:
+        exc_type: Exception class. 
+        exc: Exception instance.
+        trace: Traceback object.
+
+    Returns:
+
+    """
+    logger = logging.getLogger()
+    if not (any([isinstance(h, logging.StreamHandler)
+                 for h in logger.handlers])):
+        # add stream handler to output to terminal if not set up yet
+        logger.addHandler(logging.StreamHandler())
+
+    # log to temp file in case file logging has not been set up yet,
+    # in additional to any existing log file handler
+    log_file = tempfile.NamedTemporaryFile(
+        prefix="magellanmapper_error_", suffix=".log", delete=False)
+    logger.addHandler(logging.FileHandler(log_file.name))
+
+    # log the exception
+    logger.critical(
+        "Unhandled exception. Additional log saved to: %s", log_file.name,
+        exc_info=(exc_type, exc, trace))
+
+
 def main():
     """Launch MagellanMapper with environment activation.
 
@@ -197,6 +228,9 @@ def main():
     # support multiprocessing in frozen environments, necessary for Windows;
     # no effect on other platforms or non-frozen environments
     multiprocessing.freeze_support()
+
+    # log any unhandled exception
+    sys.excepthook = log_uncaught_exception
 
     # start MagellanMapper
     print("Starting MagellanMapper run script...")