Skip to content

Commit

Permalink
flake8 cleanup
Browse files Browse the repository at this point in the history 
Bonus type modernizing and some docstrings
  • Loading branch information
@mr-c
mr-c committed Jan 26, 2023
1 parent 8978ca2 commit 666a212
Show file tree
Hide file tree
Showing 49 changed files with 498 additions and 456 deletions.
8 changes: 8 additions & 0 deletions .flake8
View file
Original file line number Diff line number Diff line change
@@ -0,0 +1,8 @@
[flake8]
ignore = E203,W503
max-line-length = 100
select = B,C,E,F,W,T4
exclude = cwltool/schemas
extend-ignore = E501,B905
# when Python 3.10 is the minimum version, re-enable check B905 for zip + strict
extend-select = B9
13 changes: 7 additions & 6 deletions cwltool/argparser.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -42,7 +42,8 @@ def arg_parser() -> argparse.ArgumentParser:
type=str,
default="",
help="Log your tools stdout/stderr to this location outside of container "
"This will only log stdout/stderr if you specify stdout/stderr in their respective fields or capture it as an output",
"This will only log stdout/stderr if you specify stdout/stderr in their "
"respective fields or capture it as an output",
)

parser.add_argument(
Expand Down Expand Up @@ -741,7 +742,7 @@ def get_default_args() -> Dict[str, Any]:


class FSAction(argparse.Action):
objclass = None # type: str
objclass: str

def __init__(
self,
Expand Down Expand Up @@ -777,7 +778,7 @@ def __call__(


class FSAppendAction(argparse.Action):
objclass = None # type: str
objclass: str

def __init__(
self,
Expand Down Expand Up @@ -900,9 +901,9 @@ def add_argument(
return None

ahelp = description.replace("%", "%%")
action = None # type: Optional[Union[Type[argparse.Action], str]]
atype = None # type: Any
typekw = {} # type: Dict[str, Any]
action: Optional[Union[Type[argparse.Action], str]] = None
atype: Optional[Any] = None
typekw: Dict[str, Any] = {}

if inptype == "File":
action = FileAction
Expand Down
54 changes: 27 additions & 27 deletions cwltool/builder.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -2,29 +2,31 @@
import copy
import logging
import math
from typing import (
from typing import ( # pylint: disable=unused-import
IO,
TYPE_CHECKING,
Any,
Callable,
Dict,
List,
MutableMapping,
MutableSequence,
Optional,
Type,
Union,
cast,
)

from cwl_utils import expression
from cwl_utils.file_formats import check_format
from rdflib import Graph
from ruamel.yaml.comments import CommentedMap
from schema_salad.avro.schema import Names, Schema, make_avsc_object
from schema_salad.exceptions import ValidationException
from schema_salad.sourceline import SourceLine
from schema_salad.utils import convert_to_dict, json_dumps
from schema_salad.validate import validate
from typing_extensions import TYPE_CHECKING, Type # pylint: disable=unused-import

from ruamel.yaml.comments import CommentedMap

from .errors import WorkflowException
from .loghandler import _logger
Expand Down Expand Up @@ -186,10 +188,8 @@ def bind_input(
if lead_pos is None:
lead_pos = []

bindings = [] # type: List[MutableMapping[str, Union[str, List[int]]]]
binding = (
{}
) # type: Union[MutableMapping[str, Union[str, List[int]]], CommentedMap]
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
Expand All @@ -208,7 +208,7 @@ def bind_input(
).makeError(
"'position' expressions must evaluate to an int, "
f"not a {type(result)}. Expression {position} "
f"resulted in '{result}'."
f"resulted in {result!r}."
)
binding["position"] = result
bp.append(result)
Expand All @@ -227,7 +227,7 @@ def bind_input(
if isinstance(schema["type"], MutableSequence):
bound_input = False
for t in schema["type"]:
avsc = None # type: Optional[Schema]
avsc: Optional[Schema] = None
if isinstance(t, str) and self.names.has_name(t, None):
avsc = self.names.get_name(t, None)
elif (
Expand Down Expand Up @@ -336,10 +336,10 @@ def bind_input(
if binding:
b2 = cast(CWLObjectType, copy.deepcopy(binding))
b2["datum"] = item
itemschema = {
itemschema: CWLObjectType = {
"type": schema["items"],
"inputBinding": b2,
} # type: CWLObjectType
}
for k in ("secondaryFiles", "format", "streamable"):
if k in schema:
itemschema[k] = schema[k]
Expand All @@ -362,9 +362,9 @@ def _capture_files(f: CWLObjectType) -> CWLObjectType:
datum = cast(CWLObjectType, datum)
self.files.append(datum)

loadContents_sourceline = (
None
) # type: Union[None, MutableMapping[str, Union[str, List[int]]], CWLObjectType]
loadContents_sourceline: Union[
None, MutableMapping[str, Union[str, List[int]]], CWLObjectType
] = None
if binding and binding.get("loadContents"):
loadContents_sourceline = binding
elif schema.get("loadContents"):
Expand All @@ -385,7 +385,7 @@ def _capture_files(f: CWLObjectType) -> CWLObjectType:
except Exception as e:
raise Exception(
"Reading {}\n{}".format(datum["location"], e)
)
) from e

if "secondaryFiles" in schema:
if "secondaryFiles" not in datum:
Expand Down Expand Up @@ -415,8 +415,8 @@ def _capture_files(f: CWLObjectType) -> CWLObjectType:
"The result of a expression in the field "
"'required' must "
f"be a bool or None, not a {type(required_result)}. "
f"Expression '{sf_entry['required']}' resulted "
f"in '{required_result}'."
f"Expression {sf_entry['required']!r} resulted "
f"in {required_result!r}."
)
sf_required = required_result
else:
Expand Down Expand Up @@ -454,7 +454,7 @@ def _capture_files(f: CWLObjectType) -> CWLObjectType:
"Expected secondaryFile expression to "
"return type 'str', a 'File' or 'Directory' "
"dictionary, or a list of the same. Received "
f"'{type(sfname)} from '{sf_entry['pattern']}'."
f"{type(sfname)!r} from {sf_entry['pattern']!r}."
)

for d in cast(
Expand Down Expand Up @@ -529,9 +529,9 @@ def addsf(
"An expression in the 'format' field must "
"evaluate to a string, or list of strings. "
"However a non-string item was received: "
f"'{entry}' of type '{type(entry)}'. "
f"The expression was '{schema['format']}' and "
f"its fully evaluated result is '{eval_format}'."
f"{entry!r} of type {type(entry)!r}. "
f"The expression was {schema['format']!r} and "
f"its fully evaluated result is {eval_format!r}."
)
if expression.needs_parsing(entry):
message = (
Expand All @@ -542,7 +542,7 @@ def addsf(
"Expressions or CWL Parameter References. List "
f"entry number {index+1} contains the following "
"unallowed CWL Parameter Reference or Expression: "
f"'{entry}'."
f"{entry!r}."
)
if message:
raise SourceLine(
Expand All @@ -557,8 +557,8 @@ def addsf(
"evaluate to a string, or list of strings. "
"However the type of the expression result was "
f"{type(eval_format)}. "
f"The expression was '{schema['format']}' and "
f"its fully evaluated result is 'eval_format'."
f"The expression was {schema['format']!r} and "
f"its fully evaluated result is {eval_format!r}."
)
try:
check_format(
Expand All @@ -568,8 +568,8 @@ def addsf(
)
except ValidationException as ve:
raise WorkflowException(
"Expected value of '%s' to have format %s but\n "
" %s" % (schema["name"], schema["format"], ve)
f"Expected value of {schema['name']!r} to have "
f"format {schema['format']!r} but\n {ve}"
) from ve

visit_class(
Expand Down Expand Up @@ -646,7 +646,7 @@ def generate_arg(self, binding: CWLObjectType) -> List[str]:
"'separate' option can not be specified without prefix"
)

argl = [] # type: MutableSequence[CWLOutputType]
argl: MutableSequence[CWLOutputType] = []
if isinstance(value, MutableSequence):
if binding.get("itemSeparator") and value:
itemSeparator = cast(str, binding["itemSeparator"])
Expand Down
6 changes: 3 additions & 3 deletions cwltool/checker.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -62,7 +62,7 @@ def check_types(
return check_types(
merge_flatten_type(_get_type(srctype)), _get_type(sinktype), None, None
)
raise WorkflowException(f"Unrecognized linkMerge enum '{linkMerge}'")
raise WorkflowException(f"Unrecognized linkMerge enum {linkMerge!r}")


def merge_flatten_type(src: SinkType) -> CWLOutputType:
Expand Down Expand Up @@ -561,8 +561,8 @@ def loop_checker(steps: Iterator[MutableMapping[str, Any]]) -> None:
"""
Check http://commonwl.org/cwltool#Loop requirement compatibility with other directives.
:raises:
ValidationException: If there is an incompatible combination between cwltool:loop and 'scatter' or 'when'.
:raises ValidationException: If there is an incompatible combination between
cwltool:loop and 'scatter' or 'when'.
"""
exceptions = []
for step in steps:
Expand Down
Loading

0 comments on commit 666a212

Please sign in to comment.