Merge pull request #2045 from common-workflow-language/main

Sync Updates to prov_data_input_output branch

Author: ElderMedic

.github/workflows/ci-tests.yml

@@ -32,7 +32,7 @@ jobs:
     strategy:
       matrix:
         py-ver-major: [3]
-        py-ver-minor: [8, 9, 10, 11, 12]
+        py-ver-minor: [8, 9, 10, 11, 12, 13]
         step: [lint, unit, bandit, mypy]
 
     env:

.gitignore

@@ -1,6 +1,8 @@
 # Generated during tests
 pytestdebug.log
 tmp/
+*.sif
+involucro
 
 # Python temps
 __pycache__/
@@ -59,4 +61,3 @@ cwltool/_version.py
 cwltool_deps
 docs/_build/
 docs/autoapi/
-

README.rst

@@ -1,5 +1,5 @@
 #############################################################################################
-``cwltool``: The reference reference implementation of the Common Workflow Language standards
+``cwltool``: The reference implementation of the Common Workflow Language standards
 #############################################################################################
 
 |Linux Status| |Coverage Status| |Docs Status|

cwltool/argparser.py

@@ -921,6 +921,11 @@ def add_argument(
             action = DirectoryAppendAction
         else:
             action = AppendAction
+            items = inptype["items"]
+            if items == "int" or items == "long":
+                atype = int
+            elif items == "double" or items == "float":
+                atype = float
     elif isinstance(inptype, MutableMapping) and inptype["type"] == "enum":
         atype = str
     elif isinstance(inptype, MutableMapping) and inptype["type"] == "record":

cwltool/builder.py

@@ -282,7 +282,7 @@ def bind_input(
                 and "itemSeparator" not in binding
             ):
                 st["inputBinding"] = {}
-            for k in ("secondaryFiles", "format", "streamable"):
+            for k in ("secondaryFiles", "format", "streamable", "loadContents"):
                 if k in schema:
                     st[k] = schema[k]
             if value_from_expression:
@@ -349,7 +349,7 @@ def bind_input(
                         "type": schema["items"],
                         "inputBinding": b2,
                     }
-                    for k in ("secondaryFiles", "format", "streamable"):
+                    for k in ("secondaryFiles", "format", "streamable", "loadContents"):
                         if k in schema:
                             itemschema[k] = schema[k]
                     bindings.extend(

cwltool/checker.py

@@ -517,10 +517,13 @@ def is_conditional_step(param_to_step: Dict[str, CWLObjectType], parm_id: str) -
 
 
 def is_all_output_method_loop_step(param_to_step: Dict[str, CWLObjectType], parm_id: str) -> bool:
-    """Check if a step contains a `loop` directive with `all` outputMethod."""
+    """Check if a step contains a `loop` directive with `all_iterations` outputMethod."""
     source_step: Optional[MutableMapping[str, Any]] = param_to_step.get(parm_id)
     if source_step is not None:
-        if source_step.get("loop") is not None and source_step.get("outputMethod") == "all":
+        if (
+            source_step.get("loop") is not None
+            and source_step.get("outputMethod") == "all_iterations"
+        ):
             return True
     return False
 

cwltool/command_line_tool.py

@@ -806,7 +806,7 @@ def remove_dirname(d: CWLObjectType) -> None:
     def job(
         self,
         job_order: CWLObjectType,
-        output_callbacks: Optional[OutputCallbackType],
+        output_callbacks: OutputCallbackType,
         runtimeContext: RuntimeContext,
     ) -> Generator[Union[JobBase, CallbackJob], None, None]:
         workReuse, _ = self.get_requirement("WorkReuse")

cwltool/errors.py

@@ -8,10 +8,8 @@
 
 # flake8: noqa: F401
 
-from cwl_utils.errors import WorkflowException as WorkflowException
-
-
 from cwl_utils.errors import GraphTargetMissingException as GraphTargetMissingException
+from cwl_utils.errors import WorkflowException as WorkflowException
 
 
 class UnsupportedRequirement(WorkflowException):

cwltool/process.py

@@ -1075,7 +1075,7 @@ def visit(self, op: Callable[[CommentedMap], None]) -> None:
     def job(
         self,
         job_order: CWLObjectType,
-        output_callbacks: Optional[OutputCallbackType],
+        output_callbacks: OutputCallbackType,
         runtimeContext: RuntimeContext,
     ) -> JobsGeneratorType:
         pass

cwltool/procgenerator.py

@@ -30,7 +30,7 @@ def receive_output(self, jobout: Optional[CWLObjectType], processStatus: str) ->
     def job(
         self,
         job_order: CWLObjectType,
-        output_callbacks: Optional[OutputCallbackType],
+        output_callbacks: OutputCallbackType,
         runtimeContext: RuntimeContext,
     ) -> JobsGeneratorType:
         try:
@@ -41,7 +41,7 @@ def job(
             while self.processStatus is None:
                 yield None
 
-            if self.processStatus != "success" and output_callbacks:
+            if self.processStatus != "success":
                 output_callbacks(self.jobout, self.processStatus)
                 return
 
@@ -89,7 +89,7 @@ def __init__(
     def job(
         self,
         job_order: CWLObjectType,
-        output_callbacks: Optional[OutputCallbackType],
+        output_callbacks: OutputCallbackType,
         runtimeContext: RuntimeContext,
     ) -> JobsGeneratorType:
         return ProcessGeneratorJob(self).job(job_order, output_callbacks, runtimeContext)