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‎Makefile‎

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# This file is part of cwl-upgrader
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# https://github.com/common-workflow-language/cwl-upgrader/, and is
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#
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# Licensed under the Apache License, Version 2.0 (the "License");
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# you may not use this file except in compliance with the License.
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# You may obtain a copy of the License at
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#
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# http://www.apache.org/licenses/LICENSE-2.0
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#
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# Unless required by applicable law or agreed to in writing, software
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# distributed under the License is distributed on an "AS IS" BASIS,
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# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
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# See the License for the specific language governing permissions and
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# limitations under the License.
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#
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# Contact: [email protected]
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# make pep8 to check for basic Python code compliance
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# make autopep8 to fix most pep8 errors
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# make pylint to check Python code for enhanced compliance including naming
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# and documentation
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# make coverage-report to check coverage of the python scripts by the tests
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MODULE=cwl-upgrader
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# `SHELL=bash` Will break Titus's laptop, so don't use BASH-isms like
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# `[[` conditional expressions.
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PYSOURCES=$(wildcard ${MODULE}/**.py tests/*.py) setup.py
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DEVPKGS=pep8 diff_cover autopep8 pylint coverage pep257
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MYPYPATH=typeshed/2or3
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MYPYFLAGS=--disallow-untyped-calls --disallow-untyped-defs \
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--warn-incomplete-stub --warn-redundant-casts
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VERSION=$(shell git describe --tags --dirty | sed s/v//)
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## all : default task
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all: ./setup.py develop
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## help : print this help message and exit
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help: Makefile
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@sed -n 's/^##//p' $<
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## install-dep : install most of the development dependencies via pip
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install-dep: install-dependencies
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install-dependencies:
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pip install --upgrade $(DEVPKGS)
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pip install -r requirements.txt
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## install : install the ${MODULE} module and schema-salad-tool
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install: FORCE
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./setup.py build install
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## dist : create a module package for distribution
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dist: dist/${MODULE}-$(VERSION).tar.gz
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dist/${MODULE}-$(VERSION).tar.gz: $(SOURCES)
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./setup.py sdist
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## clean : clean up all temporary / machine-generated files
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clean: FORCE
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rm -f ${MODILE}/*.pyc tests/*.pyc
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./setup.py clean --all || true
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rm -Rf .coverage
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rm -f diff-cover.html
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## pep8 : check Python code style
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pep8: $(PYSOURCES)
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pep8 --exclude=_version.py --show-source --show-pep8 $^ || true
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pep8_report.txt: $(PYSOURCES)
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pep8 --exclude=_version.py $^ > $@ || true
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diff_pep8_report: pep8_report.txt
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diff-quality --violations=pep8 pep8_report.txt
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## pep257 : check Python code style
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pep257: $(PYSOURCES)
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pep257 --ignore=D100,D101,D102,D103 $^ || true
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pep257_report.txt: $(PYSOURCES)
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pep257 setup.py $^ > $@ 2>&1 || true
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diff_pep257_report: pep257_report.txt
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diff-quality --violations=pep8 pep257_report.txt
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## autopep8 : fix most Python code indentation and formatting
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autopep8: $(PYSOURCES)
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autopep8 --recursive --in-place --ignore E309 $^
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# A command to automatically run astyle and autopep8 on appropriate files
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## format : check/fix all code indentation and formatting (runs autopep8)
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format: autopep8
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# Do nothing
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## pylint : run static code analysis on Python code
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pylint: $(PYSOURCES)
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pylint --msg-template="{path}:{line}: [{msg_id}({symbol}), {obj}] {msg}" \
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$^ || true
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pylint_report.txt: ${PYSOURCES}
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pylint --msg-template="{path}:{line}: [{msg_id}({symbol}), {obj}] {msg}" \
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$^ > $@ || true
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diff_pylint_report: pylint_report.txt
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diff-quality --violations=pylint pylint_report.txt
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.coverage: $(PYSOURCES)
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coverage run --branch --source=${MODULE} setup.py test
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coverage.xml: .coverage
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coverage xml
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coverage.html: htmlcov/index.html
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htmlcov/index.html: .coverage
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coverage html
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@echo Test coverage of the Python code is now in htmlcov/index.html
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coverage-report: .coverage
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coverage report
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diff-cover: coverage.xml
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diff-cover $^
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diff-cover.html: coverage.xml
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diff-cover $^ --html-report $@
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## test : run the ${MODULE} test suite
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test: FORCE
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python setup.py test
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sloccount.sc: ${PYSOURCES} Makefile
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sloccount --duplicates --wide --details $^ > $@
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## sloccount : count lines of code
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sloccount: ${PYSOURCES} Makefile
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sloccount $^
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list-author-emails:
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@echo 'name, E-Mail Address'
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@git log --format='%aN,%aE' | sort -u | grep -v 'root'
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mypy: ${PYSOURCES}
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MYPYPATH=${MYPYPATH} mypy ${MYPYFLAGS} cwlupgrader/
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MYPYPATH=${MYPYPATH} mypy --py2 ${MYPYFLAGS} cwlupgrader/
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jenkins:
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rm -Rf env && virtualenv env
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. env/bin/activate ; \
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pip install -U setuptools pip wheel ; \
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${MAKE} install-dep coverage.html coverage.xml pep257_report.txt \
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sloccount.sc pep8_report.txt pylint_report.txt
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if ! test -d env3 ; then virtualenv -p python3 env3 ; fi
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. env3/bin/activate ; \
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pip install -U mypy-lang; ${MAKE} mypy
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FORCE:

‎cwlupgrader/main.py‎

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#!/usr/bin/env python
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from __future__ import print_function, unicode_literals
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from __future__ import print_function
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import ruamel.yaml
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from typing import Any, Dict
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from collections import Mapping, Sequence
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from typing import Any, Dict, Union
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from collections import Mapping, MutableMapping, Sequence
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import sys
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import copy
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print(ruamel.yaml.round_trip_dump(document))
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return 0
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def draft3_to_v1_0(document): # type: (Dict[unicode, Any]) -> None
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def draft3_to_v1_0(document): # type: (Dict[str, Any]) -> None
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_draft3_to_v1_0(document)
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document['cwlVersion'] = 'v1.0'
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def _draft3_to_v1_0(document):
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# type: (Dict[unicode, Any]) -> Dict[unicode, Any]
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# type: (MutableMapping[str, Any]) -> MutableMapping[str, Any]
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if "class" in document:
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if document["class"] == "Workflow":
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for out in document["outputs"]:
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del document["description"]
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for key, value in document.items():
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if isinstance(value, Mapping):
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if isinstance(value, MutableMapping):
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document[key] = _draft3_to_v1_0(value)
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return document
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def setupCLTMappings(document): # type: (Dict[unicode, Any]) -> None
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def setupCLTMappings(document): # type: (MutableMapping[str, Any]) -> None
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for paramType in ['inputs', 'outputs']:
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params = {}
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for param in document[paramType]:
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document[paramType] = params
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def shortenType(typeObj):
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# type: (List[Any]) -> Union[Unicode, List[Any]]
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# type: (List[Any]) -> Union[str, List[Any]]
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if isinstance(typeObj, str) or not isinstance(typeObj, Sequence):
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return typeObj
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newType = []

‎typeshed/2or3/ruamel/__init__.py‎

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‎typeshed/2or3/ruamel/yaml/__init__.pyi‎

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# Stubs for ruamel.yaml (Python 2)
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#
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# NOTE: This dynamically typed stub was automatically generated by stubgen.
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from typing import Any
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from .cyaml import *
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from .main import *

‎typeshed/2or3/ruamel/yaml/cyaml.pyi‎

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# Stubs for ruamel.yaml.cyaml (Python 2)
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#
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# NOTE: This dynamically typed stub was automatically generated by stubgen.
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from .loader import SafeLoader
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class CSafeLoader(SafeLoader):
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pass

‎typeshed/2or3/ruamel/yaml/error.pyi‎

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# Stubs for ruamel.yaml.error (Python 2)
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#
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# NOTE: This dynamically typed stub was automatically generated by stubgen.
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from typing import Any
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class YAMLError(Exception): ...
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class MarkedYAMLError(YAMLError): ...

‎typeshed/2or3/ruamel/yaml/loader.pyi‎

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# Stubs for ruamel.yaml.loader (Python 2)
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#
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# NOTE: This dynamically typed stub was automatically generated by stubgen.
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class Loader():
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pass
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class SafeLoader(Loader):
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pass

‎typeshed/2or3/ruamel/yaml/main.pyi‎

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# Stubs for ruamel.yaml.main (Python 2)
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#
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# NOTE: This dynamically typed stub was automatically generated by stubgen.
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from typing import Any, AnyStr, BinaryIO, IO, List, Tuple, Union
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from ruamel.yaml.loader import *
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VersionType = Union[List[int], str, Tuple[int, int]]
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StreamType = Union[BinaryIO, IO[str]]
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def load(stream: StreamType,
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Loader: Any =...,
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version: VersionType = None) -> Any: ...
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def round_trip_load(stream: StreamType,
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version: VersionType = None) -> Any: ...
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def dump(data: Any) -> Any: ...
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def round_trip_dump(data: Any) -> Any: ...

‎typeshed/2or3/ruamel/yaml/parser.pyi‎

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# Stubs for ruamel.yaml.parser (Python 2)
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#
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# NOTE: This dynamically typed stub was automatically generated by stubgen.
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from typing import Any
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from ruamel.yaml.error import MarkedYAMLError
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class ParserError(MarkedYAMLError): ...

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