Try to fix logger issues in Python 3.5 ad 3.6

clade/extensions/abstract.py

@@ -57,7 +57,8 @@ def __init__(self, work_dir, conf=None):
         self.temp_dir = ""
 
         self.conf = conf if conf else dict()
-        self.logger = get_logger("clade", with_name=False, conf=self.conf)
+
+        self.logger = None
 
         if not hasattr(self, "requires"):
             self.requires = []
@@ -563,6 +564,7 @@ def log(self, message):
 
         self.conf["log_level"] must be set to INFO or DEBUG in order to see the message.
         """
+        self.__get_logger()
         self.logger.info("{}: {}".format(self.name, message))
 
     def debug(self, message):
@@ -572,18 +574,30 @@ def debug(self, message):
 
         WARNING: debug messages can have a great impact on the performance.
         """
+        self.__get_logger()
         self.logger.debug("{}: [DEBUG] {}".format(self.name, message))
 
     def warning(self, message):
         """Print warning message.
 
         self.conf["log_level"] must be set to WARNING, INFO or DEBUG in order to see the message.
         """
+        self.__get_logger()
         self.logger.warning("{}: [WARNING] {}".format(self.name, message))
 
     def error(self, message):
         """Print error message.
 
         self.conf["log_level"] must be set to ERROR, WARNING, INFO or DEBUG in order to see the message.
         """
+        self.__get_logger()
         self.logger.error("{}: [ERROR] {}".format(self.name, message))
+
+    def __get_logger(self):
+        # Initializing logger this way serves two purposes:
+        #   - as a workaround for multiprocessing not supporting passing logger
+        #     objects in Python 3.5 and 3.6
+        #   - and to setup logger in subprocesses
+
+        if not self.logger:
+            self.logger = get_logger("clade", with_name=False, conf=self.conf)

clade/extensions/common.py

@@ -22,12 +22,9 @@
 from clade.extensions.abstract import Extension
 from clade.extensions.opts import requires_value
 from clade.cmds import iter_cmds_by_which, number_of_cmds_by_which
-from clade.utils import get_logger
 
 
 def unwrap(self, cmd):
-    # Subprocesses need to setup logger again
-    self.logger = get_logger("clade", with_name=False, conf=self.conf)
     return self.parse_cmd(cmd)