Merge branch 'master' into multiprocess

Author: tetron

README.rst

@@ -18,7 +18,7 @@ CWL conformance tests: |Conformance Status| |Linux Status| |Windows Status| |Cov
   :target: https://codecov.io/gh/common-workflow-language/cwltool
 
 This is the reference implementation of the Common Workflow Language.  It is
-intended to feature complete and provide comprehensive validation of CWL
+intended to be feature complete and provide comprehensive validation of CWL
 files as well as provide other tools related to working with CWL.
 
 This is written and tested for `Python <https://www.python.org/>`_ ``2.7 and 3.x {x = 4, 5, 6}``
@@ -113,7 +113,7 @@ the default cwl-runner use::
 
 Use with boot2docker
 --------------------
-boot2docker is running docker inside a virtual machine and it only mounts ``Users``
+boot2docker runs Docker inside a virtual machine and it only mounts ``Users``
 on it. The default behavior of CWL is to create temporary directories under e.g.
 ``/Var`` which is not accessible to Docker containers.
 
@@ -126,7 +126,7 @@ Using user-space replacements for Docker
 ----------------------------------------
 
 Some shared computing environments don't support Docker software containers for technical or policy reasons.
-As a work around, the CWL reference runner supports using a alternative ``docker`` implementations on Linux
+As a work around, the CWL reference runner supports using alternative ``docker`` implementations on Linux
 with the ``--user-space-docker-cmd`` option.
 
 One such "user space" friendly docker replacement is ``udocker`` https://github.com/indigo-dc/udocker and another
@@ -176,7 +176,7 @@ Use with GA4GH Tool Registry API
 
 Cwltool can launch tools directly from `GA4GH Tool Registry API`_ endpoints.
 
-By default, cwltool searches https://dockstore.org/ .  Use --add-tool-registry to add other registries to the search path.
+By default, cwltool searches https://dockstore.org/ .  Use ``--add-tool-registry`` to add other registries to the search path.
 
 For example ::
 
@@ -229,7 +229,7 @@ installing cwltool. For instance::
 
 Installing cwltool in this fashion enables several new command line options.
 The most general of these options is ``--beta-dependency-resolvers-configuration``.
-This option allows one to specify a dependency resolvers configuration file.
+This option allows one to specify a dependency resolver's configuration file.
 This file may be specified as either XML or YAML and very simply describes various
 plugins to enable to "resolve" ``SoftwareRequirement`` dependencies.
 

cwltool/validate_js.py

@@ -20,7 +20,7 @@
 from .utils import json_dumps
 
 def is_expression(tool, schema):
-    # type: (Union[CommentedMap, Any], Schema) -> bool
+    # type: (Union[CommentedMap, Any], Optional[Schema]) -> bool
     return isinstance(schema, avro.schema.EnumSchema) \
         and schema.name == "Expression" and isinstance(tool, string_types)
 
@@ -37,7 +37,7 @@ def filter(self, record):
 _logger_validation_warnings.addFilter(SuppressLog("cwltool.validation_warnings"))
 
 def get_expressions(tool,             # type: Union[CommentedMap, Any]
-                    schema,           # type: avro.schema.Schema
+                    schema,           # type: Optional[avro.schema.Schema]
                     source_line=None  # type: Optional[SourceLine]
                    ):  # type: (...) -> List[Tuple[Text, Optional[SourceLine]]]
     if is_expression(tool, schema):
@@ -52,7 +52,6 @@ def get_expressions(tool,             # type: Union[CommentedMap, Any]
                              logger=_logger_validation_warnings):
                 valid_schema = possible_schema
 
-        assert valid_schema is not None
         return get_expressions(tool, valid_schema, source_line)
     elif isinstance(schema, avro.schema.ArraySchema):
         if not isinstance(tool, list):