Merge pull request #1796 from common-workflow-language/dependabot/pip/black-approx-eq-23.1

Update black requirement from ~=22.0 to ~=23.1

Author: mr-c

.git-blame-ignore-revs

@@ -3,3 +3,6 @@
 
 # upgrade to black 20.8b1
 6fd6fdb381fe3f347627fd517a8f2dba7b0a7029
+
+# upgrade to black 23.1, longer lines (100)
+7fe8c0739b0515d00daabc7db87bc5fad926d345

.github/workflows/ci-tests.yml

@@ -25,6 +25,9 @@ jobs:
           - py-ver-major: 3
             py-ver-minor: 6
             step: mypy
+          - py-ver-major: 3
+            py-ver-minor: 6
+            step: lint
 
     env:
       py-semver: ${{ format('{0}.{1}', matrix.py-ver-major, matrix.py-ver-minor) }}

cwltool.Dockerfile

@@ -4,14 +4,15 @@ RUN apk add --no-cache git gcc python3-dev libxml2-dev libxslt-dev libc-dev linu
 
 WORKDIR /cwltool
 COPY . .
-
-RUN pip install toml -rmypy-requirements.txt -rrequirements.txt
-RUN CWLTOOL_USE_MYPYC=1 MYPYPATH=mypy-stubs pip wheel --no-binary schema-salad --wheel-dir=/wheels .[deps]
+RUN CWLTOOL_USE_MYPYC=1 MYPYPATH=mypy-stubs pip wheel --no-binary schema-salad \
+	--wheel-dir=/wheels .[deps]  # --verbose
 RUN rm /wheels/schema_salad*
-RUN pip install black
+RUN pip install "black~=22.0"
+# galaxy-util 22.1.2 depends on packaging<22, but black 23.x needs packaging>22
 RUN SCHEMA_SALAD_USE_MYPYC=1 MYPYPATH=mypy-stubs pip wheel --no-binary schema-salad \
-	$(grep schema.salad requirements.txt) black --wheel-dir=/wheels
-RUN pip install --force-reinstall --no-index --no-warn-script-location --root=/pythonroot/ /wheels/*.whl
+	$(grep schema.salad requirements.txt) "black~=22.0" --wheel-dir=/wheels  # --verbose
+RUN pip install --force-reinstall --no-index --no-warn-script-location \
+	--root=/pythonroot/ /wheels/*.whl
 # --force-reinstall to install our new mypyc compiled schema-salad package
 
 FROM python:3.11-alpine as module

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: