Merge pull request #450 from common-workflow-language/manu-chroma-patch-1

setup.py: pin ruamel.yaml package version

Author: mr-c

cwltool/main.py

@@ -434,7 +434,7 @@ def load_job_order(args, t, stdin, print_input_deps=False, relative_deps=False,
     if len(args.job_order) == 1 and args.job_order[0][0] != "-":
         job_order_file = args.job_order[0]
     elif len(args.job_order) == 1 and args.job_order[0] == "-":
-        job_order_object = yaml.round_trip_load(stdin)  # type: ignore
+        job_order_object = yaml.round_trip_load(stdin)
         job_order_object, _ = loader.resolve_all(job_order_object, file_uri(os.getcwd()) + "/")
     else:
         job_order_file = None

cwltool/workflow.py

@@ -684,7 +684,7 @@ def __init__(self, toolpath_object, pos, **kwargs):
                 for tool_entry in self.embedded_tool.tool[toolfield]:
                     frag = shortname(tool_entry["id"])
                     if frag == shortinputid:
-                        param.update(tool_entry)  # type: ignore
+                        param.update(tool_entry)
                         found = True
                         bound.add(frag)
                         break

mypy.ini

@@ -1,2 +1,5 @@
+[mypy-ruamel.*]
+ignore_errors = True
+
 [mypy-schema_salad.*]
 ignore_errors = True

requirements.txt

@@ -1,5 +1,5 @@
 requests>=1.0
-ruamel.yaml==0.13.7
+ruamel.yaml>=0.12.4,<0.15
 rdflib==4.2.2
 rdflib-jsonld==0.4.0
 shellescape==3.4.1

setup.py

@@ -54,7 +54,7 @@
       install_requires=[
           'setuptools',
           'requests >= 1.0',
-          'ruamel.yaml >= 0.12.4',
+          'ruamel.yaml >= 0.12.4, < 0.15',
           'rdflib >= 4.2.2, < 4.3.0',
           'shellescape >= 3.4.1, < 3.5',
           'schema-salad >= 2.6, < 3',