Merge branch 'main' into on-error-abort

Author: AlexTate

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/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)

cwltool/workflow.py

@@ -153,7 +153,7 @@ def make_workflow_step(
     def job(
         self,
         job_order: CWLObjectType,
-        output_callbacks: Optional[OutputCallbackType],
+        output_callbacks: OutputCallbackType,
         runtimeContext: RuntimeContext,
     ) -> JobsGeneratorType:
         builder = self._init_job(job_order, runtimeContext)
@@ -421,7 +421,7 @@ def receive_output(
     def job(
         self,
         job_order: CWLObjectType,
-        output_callbacks: Optional[OutputCallbackType],
+        output_callbacks: OutputCallbackType,
         runtimeContext: RuntimeContext,
     ) -> JobsGeneratorType:
         """Initialize sub-workflow as a step in the parent profile."""

cwltool/workflow_job.py

@@ -65,7 +65,7 @@ def __init__(self, step: "WorkflowStep") -> None:
     def job(
         self,
         joborder: CWLObjectType,
-        output_callback: Optional[OutputCallbackType],
+        output_callback: OutputCallbackType,
         runtimeContext: RuntimeContext,
     ) -> JobsGeneratorType:
         runtimeContext = runtimeContext.copy()
@@ -585,7 +585,7 @@ def receive_output(
     def try_make_job(
         self,
         step: WorkflowJobStep,
-        final_output_callback: Optional[OutputCallbackType],
+        final_output_callback: OutputCallbackType,
         runtimeContext: RuntimeContext,
     ) -> JobsGeneratorType:
         container_engine = "docker"
@@ -774,7 +774,7 @@ def run(
     def job(
         self,
         joborder: CWLObjectType,
-        output_callback: Optional[OutputCallbackType],
+        output_callback: OutputCallbackType,
         runtimeContext: RuntimeContext,
     ) -> JobsGeneratorType:
         self.state = {}
@@ -849,7 +849,7 @@ def job(
                 else:
                     yield None
 
-        if not self.did_callback and output_callback:
+        if not self.did_callback:
             # could have called earlier on line 336;
             self.do_output_callback(output_callback)
             # depends which one comes first. All steps are completed

lint-requirements.txt

@@ -1,3 +1,3 @@
 flake8-bugbear<24.3
-black~=24.4
+black~=24.8
 codespell

mypy-requirements.txt

@@ -1,4 +1,4 @@
-mypy==1.10.1  # also update pyproject.toml
+mypy==1.11.1  # also update pyproject.toml
 ruamel.yaml>=0.16.0,<0.19
 cwl-utils>=0.32
 types-requests

tests/test_context.py

@@ -14,8 +14,8 @@ def test_replace_default_stdout_stderr() -> None:
     original_stdout = sys.stdout
     original_stderr = sys.stderr
 
-    sys.stdout = ""  # type: ignore
-    sys.stderr = ""  # type: ignore
+    sys.stdout = ""
+    sys.stderr = ""
 
     runtime_context = RuntimeContext()
     runtime_context.default_stdout = subprocess.DEVNULL  # type: ignore

tests/test_load_tool.py

@@ -30,13 +30,13 @@ def test_check_version() -> None:
     joborder: CWLObjectType = {"inp": "abc"}
     loadingContext = LoadingContext({"do_update": True})
     tool = load_tool(get_data("tests/echo.cwl"), loadingContext)
-    for _ in tool.job(joborder, None, RuntimeContext()):
+    for _ in tool.job(joborder, lambda output, process_status: None, RuntimeContext()):
         pass
 
     loadingContext = LoadingContext({"do_update": False})
     tool = load_tool(get_data("tests/echo.cwl"), loadingContext)
     with pytest.raises(WorkflowException):
-        for _ in tool.job(joborder, None, RuntimeContext()):
+        for _ in tool.job(joborder, lambda output, process_status: None, RuntimeContext()):
             pass
 
 

tests/test_streaming.py

@@ -61,7 +61,7 @@ def test_regular_file() -> None:
         }
     }
 
-    job = next(clt.job(joborder, None, runtime_context))
+    job = next(clt.job(joborder, lambda output, process_status: None, runtime_context))
     assert isinstance(job, JobBase)
 
     job._setup(runtime_context)
@@ -99,7 +99,7 @@ def test_input_can_be_named_pipe(
         }
     }
 
-    job = next(clt.job(joborder, None, runtime_context))
+    job = next(clt.job(joborder, lambda output, process_status: None, runtime_context))
     assert isinstance(job, JobBase)
 
     if raise_exception: