mass-format with longer lines

Author: mr-c

cwltool/argparser.py

@@ -126,9 +126,7 @@ def arg_parser() -> argparse.ArgumentParser:
         help="Path prefix for temporary directories. If --tmpdir-prefix is not "
         "provided, then the prefix for temporary directories is influenced by "
         "the value of the TMPDIR, TEMP, or TMP environment variables. Taking "
-        "those into consideration, the current default is {}.".format(
-            DEFAULT_TMP_PREFIX
-        ),
+        "those into consideration, the current default is {}.".format(DEFAULT_TMP_PREFIX),
         default=DEFAULT_TMP_PREFIX,
     )
 
@@ -318,12 +316,8 @@ def arg_parser() -> argparse.ArgumentParser:
         action="store_true",
         help="Combine components into single document and print.",
     )
-    printgroup.add_argument(
-        "--version", action="store_true", help="Print version and exit"
-    )
-    printgroup.add_argument(
-        "--validate", action="store_true", help="Validate CWL document only."
-    )
+    printgroup.add_argument("--version", action="store_true", help="Print version and exit")
+    printgroup.add_argument("--validate", action="store_true", help="Validate CWL document only.")
     printgroup.add_argument(
         "--print-supported-versions",
         action="store_true",
@@ -384,12 +378,8 @@ def arg_parser() -> argparse.ArgumentParser:
 
     volumegroup = parser.add_mutually_exclusive_group()
     volumegroup.add_argument("--verbose", action="store_true", help="Default logging")
-    volumegroup.add_argument(
-        "--quiet", action="store_true", help="Only print warnings and errors."
-    )
-    volumegroup.add_argument(
-        "--debug", action="store_true", help="Print even more logging"
-    )
+    volumegroup.add_argument("--quiet", action="store_true", help="Only print warnings and errors.")
+    volumegroup.add_argument("--debug", action="store_true", help="Print even more logging")
 
     parser.add_argument(
         "--write-summary",
@@ -494,12 +484,9 @@ def arg_parser() -> argparse.ArgumentParser:
             "Default root directory used by dependency resolvers configuration."
         )
         use_biocontainers_help = (
-            "Use biocontainers for tools without an "
-            "explicitly annotated Docker container."
-        )
-        conda_dependencies = (
-            "Short cut to use Conda to resolve 'SoftwareRequirement' packages."
+            "Use biocontainers for tools without an " "explicitly annotated Docker container."
         )
+        conda_dependencies = "Short cut to use Conda to resolve 'SoftwareRequirement' packages."
 
     parser.add_argument(
         "--beta-dependency-resolvers-configuration",
@@ -522,9 +509,7 @@ def arg_parser() -> argparse.ArgumentParser:
         action="store_true",
     )
 
-    parser.add_argument(
-        "--tool-help", action="store_true", help="Print command line help for tool"
-    )
+    parser.add_argument("--tool-help", action="store_true", help="Print command line help for tool")
 
     parser.add_argument(
         "--relative-deps",
@@ -537,8 +522,7 @@ def arg_parser() -> argparse.ArgumentParser:
     parser.add_argument(
         "--enable-dev",
         action="store_true",
-        help="Enable loading and running unofficial development versions of "
-        "the CWL standards.",
+        help="Enable loading and running unofficial development versions of " "the CWL standards.",
         default=False,
     )
 
@@ -647,8 +631,7 @@ def arg_parser() -> argparse.ArgumentParser:
         "--relax-path-checks",
         action="store_true",
         default=False,
-        help="Relax requirements on path names to permit "
-        "spaces and hash characters.",
+        help="Relax requirements on path names to permit " "spaces and hash characters.",
         dest="relax_path_checks",
     )
 
@@ -933,9 +916,7 @@ def add_argument(
                 fieldtype,
                 records,
                 fielddescription,
-                default=default.get(shortname(field["name"]), None)
-                if default
-                else None,
+                default=default.get(shortname(field["name"]), None) if default else None,
                 input_required=required,
             )
         return

cwltool/builder.py

@@ -191,9 +191,7 @@ def bind_input(
         bindings: List[MutableMapping[str, Union[str, List[int]]]] = []
         binding: Union[MutableMapping[str, Union[str, List[int]]], CommentedMap] = {}
         value_from_expression = False
-        if "inputBinding" in schema and isinstance(
-            schema["inputBinding"], MutableMapping
-        ):
+        if "inputBinding" in schema and isinstance(schema["inputBinding"], MutableMapping):
             binding = CommentedMap(schema["inputBinding"].items())
 
             bp = list(aslist(lead_pos))
@@ -303,8 +301,7 @@ def bind_input(
                     else:
                         schema["type"] = "record"
                         schema["fields"] = [
-                            {"name": field_name, "type": "Any"}
-                            for field_name in datum.keys()
+                            {"name": field_name, "type": "Any"} for field_name in datum.keys()
                         ]
                 elif isinstance(datum, list):
                     schema["type"] = "array"
@@ -378,14 +375,10 @@ def _capture_files(f: CWLObjectType) -> CWLObjectType:
                         debug,
                     ):
                         try:
-                            with self.fs_access.open(
-                                cast(str, datum["location"]), "rb"
-                            ) as f2:
+                            with self.fs_access.open(cast(str, datum["location"]), "rb") as f2:
                                 datum["contents"] = content_limit_respected_read(f2)
                         except Exception as e:
-                            raise Exception(
-                                "Reading {}\n{}".format(datum["location"], e)
-                            ) from e
+                            raise Exception("Reading {}\n{}".format(datum["location"], e)) from e
 
                 if "secondaryFiles" in schema:
                     if "secondaryFiles" not in datum:
@@ -398,13 +391,8 @@ def _capture_files(f: CWLObjectType) -> CWLObjectType:
 
                     for num, sf_entry in enumerate(sf_schema):
                         if "required" in sf_entry and sf_entry["required"] is not None:
-                            required_result = self.do_eval(
-                                sf_entry["required"], context=datum
-                            )
-                            if not (
-                                isinstance(required_result, bool)
-                                or required_result is None
-                            ):
+                            required_result = self.do_eval(sf_entry["required"], context=datum)
+                            if not (isinstance(required_result, bool) or required_result is None):
                                 if sf_schema == schema["secondaryFiles"]:
                                     sf_item: Any = sf_schema[num]
                                 else:
@@ -425,9 +413,7 @@ def _capture_files(f: CWLObjectType) -> CWLObjectType:
                         if "$(" in sf_entry["pattern"] or "${" in sf_entry["pattern"]:
                             sfpath = self.do_eval(sf_entry["pattern"], context=datum)
                         else:
-                            sfpath = substitute(
-                                cast(str, datum["basename"]), sf_entry["pattern"]
-                            )
+                            sfpath = substitute(cast(str, datum["basename"]), sf_entry["pattern"])
 
                         for sfname in aslist(sfpath):
                             if not sfname:
@@ -438,8 +424,7 @@ def _capture_files(f: CWLObjectType) -> CWLObjectType:
                                 d_location = cast(str, datum["location"])
                                 if "/" in d_location:
                                     sf_location = (
-                                        d_location[0 : d_location.rindex("/") + 1]
-                                        + sfname
+                                        d_location[0 : d_location.rindex("/") + 1] + sfname
                                     )
                                 else:
                                     sf_location = d_location + sfname
@@ -462,9 +447,7 @@ def _capture_files(f: CWLObjectType) -> CWLObjectType:
                                 datum["secondaryFiles"],
                             ):
                                 if not d.get("basename"):
-                                    d["basename"] = d["location"][
-                                        d["location"].rindex("/") + 1 :
-                                    ]
+                                    d["basename"] = d["location"][d["location"].rindex("/") + 1 :]
                                 if d["basename"] == sfbasename:
                                     found = True
 
@@ -488,9 +471,7 @@ def addsf(
                                         ),
                                         sfname,
                                     )
-                                elif discover_secondaryFiles and self.fs_access.exists(
-                                    sf_location
-                                ):
+                                elif discover_secondaryFiles and self.fs_access.exists(sf_location):
                                     addsf(
                                         cast(
                                             MutableSequence[CWLObjectType],
@@ -550,9 +531,7 @@ def addsf(
                                 ).makeError(message)
                         evaluated_format = cast(List[str], eval_format)
                     else:
-                        raise SourceLine(
-                            schema, "format", WorkflowException, debug
-                        ).makeError(
+                        raise SourceLine(schema, "format", WorkflowException, debug).makeError(
                             "An expression in the 'format' field must "
                             "evaluate to a string, or list of strings. "
                             "However the type of the expression result was "
@@ -642,9 +621,7 @@ def generate_arg(self, binding: CWLObjectType) -> List[str]:
                 WorkflowException,
                 debug,
             ):
-                raise WorkflowException(
-                    "'separate' option can not be specified without prefix"
-                )
+                raise WorkflowException("'separate' option can not be specified without prefix")
 
         argl: MutableSequence[CWLOutputType] = []
         if isinstance(value, MutableSequence):
@@ -653,9 +630,7 @@ def generate_arg(self, binding: CWLObjectType) -> List[str]:
                 argl = [itemSeparator.join([self.tostr(v) for v in value])]
             elif binding.get("valueFrom"):
                 value = [self.tostr(v) for v in value]
-                return cast(List[str], ([prefix] if prefix else [])) + cast(
-                    List[str], value
-                )
+                return cast(List[str], ([prefix] if prefix else [])) + cast(List[str], value)
             elif prefix and value:
                 return [prefix]
             else:

cwltool/checker.py

@@ -59,9 +59,7 @@ def check_types(
             None,
         )
     if linkMerge == "merge_flattened":
-        return check_types(
-            merge_flatten_type(_get_type(srctype)), _get_type(sinktype), None, None
-        )
+        return check_types(merge_flatten_type(_get_type(srctype)), _get_type(sinktype), None, None)
     raise WorkflowException(f"Unrecognized linkMerge enum {linkMerge!r}")
 
 
@@ -74,9 +72,7 @@ def merge_flatten_type(src: SinkType) -> CWLOutputType:
     return {"items": src, "type": "array"}
 
 
-def can_assign_src_to_sink(
-    src: SinkType, sink: Optional[SinkType], strict: bool = False
-) -> bool:
+def can_assign_src_to_sink(src: SinkType, sink: Optional[SinkType], strict: bool = False) -> bool:
     """
     Check for identical type specifications, ignoring extra keys like inputBinding.
 
@@ -104,9 +100,7 @@ def can_assign_src_to_sink(
             for sinksf in cast(List[CWLObjectType], sink.get("secondaryFiles", [])):
                 if not [
                     1
-                    for srcsf in cast(
-                        List[CWLObjectType], src.get("secondaryFiles", [])
-                    )
+                    for srcsf in cast(List[CWLObjectType], src.get("secondaryFiles", []))
                     if sinksf == srcsf
                 ]:
                     if strict:
@@ -122,9 +116,7 @@ def can_assign_src_to_sink(
                     return False
             return True
         for this_src in src:
-            if this_src != "null" and can_assign_src_to_sink(
-                cast(SinkType, this_src), sink
-            ):
+            if this_src != "null" and can_assign_src_to_sink(cast(SinkType, this_src), sink):
                 return True
         return False
     if isinstance(sink, MutableSequence):
@@ -135,9 +127,7 @@ def can_assign_src_to_sink(
     return bool(src == sink)
 
 
-def _compare_records(
-    src: CWLObjectType, sink: CWLObjectType, strict: bool = False
-) -> bool:
+def _compare_records(src: CWLObjectType, sink: CWLObjectType, strict: bool = False) -> bool:
     """
     Compare two records, ensuring they have compatible fields.
 
@@ -219,9 +209,7 @@ def static_checker(
         sink = warning.sink
         linkMerge = warning.linkMerge
         sinksf = sorted(
-            p["pattern"]
-            for p in sink.get("secondaryFiles", [])
-            if p.get("required", True)
+            p["pattern"] for p in sink.get("secondaryFiles", []) if p.get("required", True)
         )
         srcsf = sorted(p["pattern"] for p in src.get("secondaryFiles", []))
         # Every secondaryFile required by the sink, should be declared
@@ -233,16 +221,13 @@ def static_checker(
                 missing,
             )
             msg3 = SourceLine(src, "id").makeError(
-                "source '%s' does not provide those secondaryFiles."
-                % (shortname(src["id"]))
+                "source '%s' does not provide those secondaryFiles." % (shortname(src["id"]))
             )
             msg4 = SourceLine(src.get("_tool_entry", src), "secondaryFiles").makeError(
                 "To resolve, add missing secondaryFiles patterns to definition of '%s' or"
                 % (shortname(src["id"]))
             )
-            msg5 = SourceLine(
-                sink.get("_tool_entry", sink), "secondaryFiles"
-            ).makeError(
+            msg5 = SourceLine(sink.get("_tool_entry", sink), "secondaryFiles").makeError(
                 "mark missing secondaryFiles in definition of '%s' as optional."
                 % shortname(sink["id"])
             )
@@ -303,17 +288,14 @@ def static_checker(
             )
             + "\n"
             + SourceLine(sink, "type").makeError(
-                "  with sink '%s' of type %s"
-                % (shortname(sink["id"]), json_dumps(sink["type"]))
+                "  with sink '%s' of type %s" % (shortname(sink["id"]), json_dumps(sink["type"]))
             )
         )
         if extra_message is not None:
             msg += "\n" + SourceLine(sink).makeError("  " + extra_message)
 
         if linkMerge is not None:
-            msg += "\n" + SourceLine(sink).makeError(
-                "  source has linkMerge method %s" % linkMerge
-            )
+            msg += "\n" + SourceLine(sink).makeError("  source has linkMerge method %s" % linkMerge)
         exception_msgs.append(msg)
 
     for sink in step_inputs:
@@ -358,7 +340,6 @@ def check_all_types(
     validation = {"warning": [], "exception": []}  # type: Dict[str, List[SrcSink]]
     for sink in sinks:
         if sourceField in sink:
-
             valueFrom = cast(Optional[str], sink.get("valueFrom"))
             pickValue = cast(Optional[str], sink.get("pickValue"))
 
@@ -371,11 +352,7 @@ def check_all_types(
                     Optional[str],
                     sink.get(
                         "linkMerge",
-                        (
-                            "merge_nested"
-                            if len(cast(Sized, sink[sourceField])) > 1
-                            else None
-                        ),
+                        ("merge_nested" if len(cast(Sized, sink[sourceField])) > 1 else None),
                     ),
                 )  # type: Optional[str]
 
@@ -385,10 +362,7 @@ def check_all_types(
                 srcs_of_sink = []  # type: List[CWLObjectType]
                 for parm_id in cast(MutableSequence[str], sink[sourceField]):
                     srcs_of_sink += [src_dict[parm_id]]
-                    if (
-                        is_conditional_step(param_to_step, parm_id)
-                        and pickValue is None
-                    ):
+                    if is_conditional_step(param_to_step, parm_id) and pickValue is None:
                         validation["warning"].append(
                             SrcSink(
                                 src_dict[parm_id],
@@ -490,9 +464,7 @@ def get_dependency_tree(step_inputs: List[CWLObjectType]) -> Dict[str, List[str]
     for step_input in step_inputs:
         if "source" in step_input:
             if isinstance(step_input["source"], list):
-                vertices_in = [
-                    get_step_id(cast(str, src)) for src in step_input["source"]
-                ]
+                vertices_in = [get_step_id(cast(str, src)) for src in step_input["source"]]
             else:
                 vertices_in = [get_step_id(cast(str, step_input["source"]))]
             vertex_out = get_step_id(cast(str, step_input["id"]))
@@ -542,9 +514,7 @@ def is_conditional_step(param_to_step: Dict[str, CWLObjectType], parm_id: str) -
     return False
 
 
-def is_all_output_method_loop_step(
-    param_to_step: Dict[str, CWLObjectType], parm_id: str
-) -> bool:
+def is_all_output_method_loop_step(param_to_step: Dict[str, CWLObjectType], parm_id: str) -> bool:
     """Check if a step contains a http://commonwl.org/cwltool#Loop requirement with `all` outputMethod."""
     source_step: Optional[MutableMapping[str, Any]] = param_to_step.get(parm_id)
     if source_step is not None: