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Update black requirement from ~=22.0 to ~=23.1 #1796

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Merged
merged 8 commits into from
Feb 1, 2023
Merged

Update black requirement from ~=22.0 to ~=23.1 #1796

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22aa582
Update black requirement from ~=22.0 to ~=23.1
dependabot[bot] Feb 1, 2023
ae9fa45
black: target Python 3.6; longer lines to match flake8 config
mr-c Feb 1, 2023
364fc12
mass-format with longer lines
mr-c Feb 1, 2023
fc9fea3
git-blame-ignore-revs: ignore the black 23.1 reformatting
mr-c Feb 1, 2023
3b7360b
appease flake8
mr-c Feb 1, 2023
6ca79fb
add missing docstrings
mr-c Feb 1, 2023
c2eb875
CI: skip lint on Py3.6, black requires Py3.7+
mr-c Feb 1, 2023
b2b23e9
lintreadme: the README is ReST, not Markdown
mr-c Feb 1, 2023
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3 changes: 3 additions & 0 deletions .git-blame-ignore-revs
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Original file line number Diff line number Diff line change
Expand Up @@ -3,3 +3,6 @@

# upgrade to black 20.8b1
6fd6fdb381fe3f347627fd517a8f2dba7b0a7029

# upgrade to black 23.1, longer lines (100)
7fe8c0739b0515d00daabc7db87bc5fad926d345
3 changes: 3 additions & 0 deletions .github/workflows/ci-tests.yml
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Expand Up @@ -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) }}
Expand Down
13 changes: 7 additions & 6 deletions cwltool.Dockerfile
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Expand Up @@ -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
Expand Down
41 changes: 11 additions & 30 deletions cwltool/argparser.py
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Expand Up @@ -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,
)

Expand Down Expand Up @@ -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",
Expand Down Expand Up @@ -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",
Expand Down Expand Up @@ -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",
Expand All @@ -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",
Expand All @@ -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,
)

Expand Down Expand Up @@ -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",
)

Expand Down Expand Up @@ -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
Expand Down
51 changes: 13 additions & 38 deletions cwltool/builder.py
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Original file line number Diff line number Diff line change
Expand Up @@ -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))
Expand Down Expand Up @@ -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"
Expand Down Expand Up @@ -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:
Expand All @@ -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:
Expand All @@ -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:
Expand All @@ -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
Expand All @@ -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

Expand All @@ -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],
Expand Down Expand Up @@ -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 "
Expand Down Expand Up @@ -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):
Expand All @@ -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:
Expand Down
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