Fix typos and wrong pip version range (#147)

Co-authored-by: Michael R. Crusoe <[email protected]>

Author: kinow

cwl_utils/cwl_expression_refactor.py

@@ -59,7 +59,7 @@ def __call__(
 
 
 def arg_parser() -> argparse.ArgumentParser:
-    """Build the arrgument parser."""
+    """Build the argument parser."""
     parser = argparse.ArgumentParser(
         description="Tool to refactor CWL documents so that any CWL expression "
         "are separate steps as either ExpressionTools or CommandLineTools. Exit code 7 "
@@ -154,7 +154,7 @@ def run(args: argparse.Namespace) -> int:
                 for result_item in result
             ]
         yaml.scalarstring.walk_tree(result_json)
-        # ^ converts multine line strings to nice multiline YAML
+        # ^ converts multiline strings to nice multiline YAML
         with open(output, "w", encoding="utf-8") as output_filehandle:
             output_filehandle.write(
                 "#!/usr/bin/env cwl-runner\n"

cwl_utils/cwl_v1_0_expression_refactor.py

@@ -216,7 +216,7 @@ def traverse(
     skip_command_line1: bool,
     skip_command_line2: bool,
 ) -> Tuple[Union[cwl.CommandLineTool, cwl.ExpressionTool, cwl.Workflow], bool]:
-    """Convert the given process and any subprocesess."""
+    """Convert the given process and any subprocesses."""
     if not inside and isinstance(process, cwl.CommandLineTool):
         process = expand_stream_shortcuts(process)
         wf_inputs = []
@@ -1488,7 +1488,7 @@ def traverse_CommandLineTool(
                     )
                     new_clt_step = copy.copy(
                         step
-                    )  # a deepcopy would be convienant, but params2.cwl gives it problems
+                    )  # a deepcopy would be convenient, but params2.cwl gives it problems
                     new_clt_step.id = cast(str, new_clt_step.id).split("#")[-1]
                     new_clt_step.run = copy.copy(step.run)
                     new_clt_step.run.id = None
@@ -1515,7 +1515,7 @@ def traverse_CommandLineTool(
                                 )
                             else:
                                 raise Exception(
-                                    "Unimplemented OutputParamter type: %s",
+                                    "Unimplemented OutputParameter type: %s",
                                     type(new_outp),
                                 )
                     new_clt_step.in_ = copy.deepcopy(step.in_)
@@ -1595,7 +1595,7 @@ def remove_JSReq(
     process: Union[cwl.CommandLineTool, cwl.WorkflowStep, cwl.Workflow],
     skip_command_line1: bool,
 ) -> None:
-    """Since the InlineJavascriptRequiment is longer needed, remove it."""
+    """Since the InlineJavascriptRequirement is longer needed, remove it."""
     if skip_command_line1 and isinstance(process, cwl.CommandLineTool):
         return
     if process.hints:
@@ -1958,7 +1958,7 @@ def traverse_step(
 def workflow_step_to_InputParameters(
     step_ins: List[cwl.WorkflowStepInput], parent: cwl.Workflow, except_in_id: str
 ) -> List[cwl.InputParameter]:
-    """Create InputParametes to match the given WorkflowStep inputs."""
+    """Create InputParameters to match the given WorkflowStep inputs."""
     params = []
     for inp in step_ins:
         if not inp.id:

cwl_utils/cwl_v1_1_expression_refactor.py

@@ -216,7 +216,7 @@ def traverse(
     skip_command_line1: bool,
     skip_command_line2: bool,
 ) -> Tuple[Union[cwl.CommandLineTool, cwl.ExpressionTool, cwl.Workflow], bool]:
-    """Convert the given process and any subprocesess."""
+    """Convert the given process and any subprocesses."""
     if not inside and isinstance(process, cwl.CommandLineTool):
         process = expand_stream_shortcuts(process)
         wf_inputs = []
@@ -1488,7 +1488,7 @@ def traverse_CommandLineTool(
                     )
                     new_clt_step = copy.copy(
                         step
-                    )  # a deepcopy would be convienant, but params2.cwl gives it problems
+                    )  # a deepcopy would be convenient, but params2.cwl gives it problems
                     new_clt_step.id = cast(str, new_clt_step.id).split("#")[-1]
                     new_clt_step.run = copy.copy(step.run)
                     new_clt_step.run.id = None
@@ -1515,7 +1515,7 @@ def traverse_CommandLineTool(
                                 )
                             else:
                                 raise Exception(
-                                    "Unimplemented OutputParamter type: %s",
+                                    "Unimplemented OutputParameter type: %s",
                                     type(new_outp),
                                 )
                     new_clt_step.in_ = copy.deepcopy(step.in_)
@@ -1595,7 +1595,7 @@ def remove_JSReq(
     process: Union[cwl.CommandLineTool, cwl.WorkflowStep, cwl.Workflow],
     skip_command_line1: bool,
 ) -> None:
-    """Since the InlineJavascriptRequiment is longer needed, remove it."""
+    """Since the InlineJavascriptRequirement is longer needed, remove it."""
     if skip_command_line1 and isinstance(process, cwl.CommandLineTool):
         return
     if process.hints:
@@ -1958,7 +1958,7 @@ def traverse_step(
 def workflow_step_to_WorkflowInputParameters(
     step_ins: List[cwl.WorkflowStepInput], parent: cwl.Workflow, except_in_id: str
 ) -> List[cwl.WorkflowInputParameter]:
-    """Create WorkflowInputParametes to match the given WorkflowStep inputs."""
+    """Create WorkflowInputParameters to match the given WorkflowStep inputs."""
     params = []
     for inp in step_ins:
         if not inp.id:

cwl_utils/cwl_v1_2_expression_refactor.py

@@ -216,7 +216,7 @@ def traverse(
     skip_command_line1: bool,
     skip_command_line2: bool,
 ) -> Tuple[Union[cwl.CommandLineTool, cwl.ExpressionTool, cwl.Workflow], bool]:
-    """Convert the given process and any subprocesess."""
+    """Convert the given process and any subprocesses."""
     if not inside and isinstance(process, cwl.CommandLineTool):
         process = expand_stream_shortcuts(process)
         wf_inputs = []
@@ -1584,7 +1584,7 @@ def traverse_CommandLineTool(
                     )
                     new_clt_step = copy.copy(
                         step
-                    )  # a deepcopy would be convienant, but params2.cwl gives it problems
+                    )  # a deepcopy would be convenient, but params2.cwl gives it problems
                     new_clt_step.id = cast(str, new_clt_step.id).split("#")[-1]
                     new_clt_step.run = copy.copy(step.run)
                     new_clt_step.run.id = None
@@ -1611,7 +1611,7 @@ def traverse_CommandLineTool(
                                 )
                             else:
                                 raise Exception(
-                                    "Unimplemented OutputParamter type: %s",
+                                    "Unimplemented OutputParameter type: %s",
                                     type(new_outp),
                                 )
                     new_clt_step.in_ = copy.deepcopy(step.in_)
@@ -1691,7 +1691,7 @@ def remove_JSReq(
     process: Union[cwl.CommandLineTool, cwl.WorkflowStep, cwl.Workflow],
     skip_command_line1: bool,
 ) -> None:
-    """Since the InlineJavascriptRequiment is longer needed, remove it."""
+    """Since the InlineJavascriptRequirement is longer needed, remove it."""
     if skip_command_line1 and isinstance(process, cwl.CommandLineTool):
         return
     if process.hints:
@@ -2062,7 +2062,7 @@ def traverse_step(
 def workflow_step_to_WorkflowInputParameters(
     step_ins: List[cwl.WorkflowStepInput], parent: cwl.Workflow, except_in_id: str
 ) -> List[cwl.WorkflowInputParameter]:
-    """Create WorkflowInputParametes to match the given WorkflowStep inputs."""
+    """Create WorkflowInputParameters to match the given WorkflowStep inputs."""
     params = []
     for inp in step_ins:
         if not inp.id:

cwl_utils/docker_extract.py

@@ -57,7 +57,7 @@ def main(args: argparse.Namespace) -> None:
 def extract_docker_requirements(
     process: ProcessType,
 ) -> Iterator[cwl.DockerRequirement]:
-    """Yield an iterator of the docker reqs, normalizint the pull request."""
+    """Yield an iterator of the docker reqs, normalizing the pull request."""
     for req in extract_docker_reqs(process):
         if isinstance(req.dockerPull, str) and ":" not in req.dockerPull:
             req.dockerPull += ":latest"

cwl_utils/pack.py

@@ -261,12 +261,12 @@ def _add_req(_req_name: str) -> None:
             requirements += [{"class": _req_name}]
 
     if cwl.get("class") == "Workflow":
-        sub_worflow = False
+        sub_workflow = False
         for step in cwl["steps"]:
             if step["run"]["class"] == "Workflow":
-                sub_worflow = True
+                sub_workflow = True
                 break
-        if sub_worflow:
+        if sub_workflow:
             _add_req("SubworkflowFeatureRequirement")
     return cwl
 

docs/conf.py

@@ -18,8 +18,8 @@
 # -- Project information -----------------------------------------------------
 
 project = 'cwl-utils'
-copyright = '2019, CWL Commmunity'
-author = 'CWL Commmunity'
+copyright = '2019, CWL Community'
+author = 'CWL Community'
 
 
 # -- General configuration ---------------------------------------------------

mypy-requirements.txt

@@ -1,4 +1,4 @@
 mypy==0.971
 typing_extensions
 types-requests
-types-setuptools>==57.4.0
+types-setuptools>=57.4.0