Rename cltool to command_line_tool

* to avoid confusion with cwltool itself

Author: Anton Khodak

cwltool/cltool.py renamed to cwltool/command_line_tool.py

@@ -1,7 +1,6 @@
-# Do wildcard import of cltool
-from .cltool import *
+# Do wildcard import of command_line_tool
+from .command_line_tool import *
 
 _logger = logging.getLogger("cwltool")
-_logger.warning("'draft2tool.py' has been renamed to 'tool.py'" 
-	"and will be removed in the future.")
-
+_logger.warning("'draft2tool.py' has been renamed to 'command_line_tool.py'"
+                "and will be removed in the future.")

cwltool/draft2tool.py

@@ -23,7 +23,7 @@
 from schema_salad.ref_resolver import Fetcher, Loader, file_uri, uri_file_path
 from schema_salad.sourceline import strip_dup_lineno
 
-from . import cltool, workflow
+from . import command_line_tool, workflow
 from .builder import Builder
 from .cwlrdf import printdot, printrdf
 from .errors import UnsupportedRequirement, WorkflowException
@@ -822,7 +822,7 @@ def main(argsl=None,  # type: List[str]
                 arg_parser().print_help()
                 return 1
         if args.relax_path_checks:
-            cltool.ACCEPTLIST_RE = cltool.ACCEPTLIST_EN_RELAXED_RE
+            command_line_tool.ACCEPTLIST_RE = command_line_tool.ACCEPTLIST_EN_RELAXED_RE
 
         if args.ga4gh_tool_registries:
             ga4gh_tool_registries[:] = args.ga4gh_tool_registries

cwltool/main.py

@@ -12,7 +12,7 @@
 from ruamel.yaml.comments import CommentedMap, CommentedSeq
 from schema_salad.sourceline import SourceLine, cmap
 
-from . import cltool, expression
+from . import command_line_tool, expression
 from .errors import WorkflowException
 from .load_tool import load_tool
 from .process import Process, shortname, uniquename, get_overrides
@@ -33,9 +33,9 @@ def defaultMakeTool(toolpath_object,  # type: Dict[Text, Any]
         raise WorkflowException(u"Not a dict: `%s`" % toolpath_object)
     if "class" in toolpath_object:
         if toolpath_object["class"] == "CommandLineTool":
-            return cltool.CommandLineTool(toolpath_object, **kwargs)
+            return command_line_tool.CommandLineTool(toolpath_object, **kwargs)
         elif toolpath_object["class"] == "ExpressionTool":
-            return cltool.ExpressionTool(toolpath_object, **kwargs)
+            return command_line_tool.ExpressionTool(toolpath_object, **kwargs)
         elif toolpath_object["class"] == "Workflow":
             return Workflow(toolpath_object, **kwargs)
 

cwltool/workflow.py

@@ -2,14 +2,14 @@
 import unittest
 from mock import mock
 from cwltool.utils import windows_default_container_id
-from cwltool.cltool import DEFAULT_CONTAINER_MSG, CommandLineTool
+from cwltool.command_line_tool import DEFAULT_CONTAINER_MSG, CommandLineTool
 
 
 class TestDefaultDockerWarning(unittest.TestCase):
 
     # Test to check warning when default docker Container is used on Windows
-    @mock.patch("cwltool.cltool.onWindows",return_value = True)
-    @mock.patch("cwltool.cltool._logger")
+    @mock.patch("cwltool.command_line_tool.onWindows",return_value = True)
+    @mock.patch("cwltool.command_line_tool._logger")
     def test_default_docker_warning(self,mock_logger,mock_windows):
 
         class TestCommandLineTool(CommandLineTool):