Cosmetic: auto reset to 1 thread on macOS and Python 3.8 to prevent the crash #175

Author: alexeigurevich

Diff for: CHANGES.txt

@@ -16,6 +16,7 @@
        - proper assembly coloring in the MetaQUAST HTML report for more than 14 assemblies;
        - catching the Krona charts crashes prematurely;
        - proper checking of user BED files in the read alignment mode;
+       - prevent crashes due to multi-threading on macOS and Python 3.8+ (switch to single-thread);
        - cosmetic changes in warning/error messages.
 
       5. Documentation:

Diff for: quast_libs/log.py

@@ -201,29 +201,11 @@ def error(self, message='', exit_with_code=0, to_stderr=False, indent='', fake_i
             self._num_nf_errors += 1
 
     def exception(self, e, exit_code=0):
-        # FIXME: special case: handling the known bug of macOS & Python3.8+ & joblib
-        # see: https://github.com/ablab/quast/issues/175
-        extra_message = ''
-        if type(e) == TypeError and 'NoneType' in str(e) and 'int' in str(e):
-            if qconfig.max_threads and qconfig.max_threads > 1 and qconfig.platform_name == 'macosx' and \
-                    sys.version_info.major == 3 and sys.version_info.minor >= 8:
-                extra_message = '\n\nThis seems to be a known bug when using multi-threading in Python 3.8+ on macOS!\n' \
-                                'The current workarounds are\n' \
-                                '  to switch to single-thread execution (-t 1)\n' \
-                                'or\n' \
-                                '  to downgrade your Python to 3.7 or below.\n' \
-                                'Sorry for the inconvenience!\n' \
-                                'Please find more details in https://github.com/ablab/quast/issues/175\n'
-
         if self._logger.handlers:
             self._logger.error('')
             self._logger.exception(e)
-            if extra_message:
-                self._logger.info(extra_message)
         else:
             sys.stderr.write(str(e) + '\n')
-            if extra_message:
-                sys.stderr.write(extra_message + '\n')
 
         if exit_code:
             exit(exit_code)

Diff for: quast_libs/qconfig.py

@@ -314,6 +314,14 @@ def set_max_threads(logger):
             max_threads = DEFAULT_MAX_THREADS
         logger.notice('Maximum number of threads is set to ' + str(max_threads) +
                       ' (use --threads option to set it manually)')
+    # FIXME: special case: handling the known bug of macOS & Python3.8+ & joblib
+    # see: https://github.com/ablab/quast/issues/175
+    if max_threads > 1 and platform_name == 'macosx' and sys.version_info.major == 3 and sys.version_info.minor >= 8:
+        max_threads = 1
+        logger.warning('Maximum number of threads is reset to 1 to prevent the crash '
+                       'due to a known bug when using multi-threading in Python 3.8+ on macOS! '
+                       'For multi-threading please downgrade your Python to 3.7. Sorry for the inconvenience! '
+                       'Please find more details in https://github.com/ablab/quast/issues/175')
 
 
 def quast_version():