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mr-cmr-c
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modernize part 1
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‎.coveragerc‎

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[run]
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branch = True
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source = cwlprov
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[report]
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exclude_lines =
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if self.debug:
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pragma: no cover
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raise NotImplementedError
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if __name__ == .__main__.:
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ignore_errors = True

‎Makefile‎

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# This file is part of cwlprov-py,
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# https://github.com/common-workflow-language/cwlprov-py/, 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: common-workflow-language@googlegroups.com
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# make format to fix most python formatting 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=cwlprov
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PACKAGE=cwlprov
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# `SHELL=bash` doesn't work for some, so don't use BASH-isms like
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# `[[` conditional expressions.
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PYSOURCES=$(wildcard ${MODULE}/**.py) setup.py
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DEVPKGS=diff_cover black pylint pep257 pydocstyle flake8 tox tox-pyenv \
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isort wheel autoflake flake8-bugbear pyupgrade bandit \
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-rtest-requirements.txt -rmypy-requirements.txt
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COVBASE=coverage run --append
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# Updating the Major & Minor version below?
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# Don't forget to update setup.py as well
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#VERSION=8.2.$(shell date +%Y%m%d%H%M%S --utc --date=`git log --first-parent \
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# --max-count=1 --format=format:%cI`)
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## all : default task
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all: dev
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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: FORCE
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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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pip install .
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## dev : install the ${MODULE} module in dev mode
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dev: install-dep
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pip install -e .
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## dist : create a module package for distribution
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dist: dist/${MODULE}-$(VERSION).tar.gz
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dist/${MODULE}-$(VERSION).tar.gz: $(SOURCES)
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python setup.py sdist bdist_wheel
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## docs : make the docs
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docs: FORCE
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cd docs && $(MAKE) html
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## clean : clean up all temporary / machine-generated files
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clean: FORCE
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rm -rf ${MODULE}/__pycache__
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python 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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# Linting and code style related targets
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## sorting imports using isort: https://github.com/timothycrosley/isort
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sort_imports: $(PYSOURCES)
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isort $^
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remove_unused_imports: $(PYSOURCES)
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autoflake --in-place --remove-all-unused-imports $^
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pep257: pydocstyle
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## pydocstyle : check Python code style
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pydocstyle: $(PYSOURCES)
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pydocstyle --add-ignore=D100,D101,D102,D103 $^ || true
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pydocstyle_report.txt: $(PYSOURCES)
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pydocstyle setup.py $^ > $@ 2>&1 || true
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diff_pydocstyle_report: pydocstyle_report.txt
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diff-quality --compare-branch=main --violations=pydocstyle --fail-under=100 $^
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## format : check/fix all code indentation and formatting (runs black)
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format: $(PYSOURCES)
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black $^
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format-check: $(PYSOURCES)
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black --diff --check $^
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## pylint : run static code analysis on Python code
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pylint: $(PYSOURCES)
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pylint --msg-template="{path}:{line}: [{msg_id}({symbol}), {obj}] {msg}" \
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$^ -j0|| true
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pylint_report.txt: $(PYSOURCES)
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pylint --msg-template="{path}:{line}: [{msg_id}({symbol}), {obj}] {msg}" \
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$^ -j0> $@ || true
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diff_pylint_report: pylint_report.txt
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diff-quality --violations=pylint pylint_report.txt
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.coverage:
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$(foreach RO,$(shell ls test),coverage run -m cwlprov.tool -d test/$(RO) validate && ) true
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$(foreach RO,$(shell ls test),coverage run -m cwlprov.tool -d test/$(RO) info && ) true
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$(foreach RO,$(shell ls test),coverage run -m cwlprov.tool -d test/$(RO) who && ) true
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$(foreach RO,$(shell ls test),coverage run -m cwlprov.tool -d test/$(RO) prov && ) true
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$(foreach RO,$(shell ls test),coverage run -m cwlprov.tool -d test/$(RO) inputs && ) true
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$(foreach RO,$(shell ls test),coverage run -m cwlprov.tool -d test/$(RO) outputs && ) true
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$(foreach RO,$(shell ls test),coverage run -m cwlprov.tool -d test/$(RO) runs && ) true
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#$(foreach RO,$(shell ls test),coverage run -m cwlprov.tool -d test/$(RO) derived && ) true
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#$(foreach RO,$(shell ls test),coverage run -m cwlprov.tool -d test/$(RO) runtimes && ) true
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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: $(PYSOURCES) FORCE
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$(foreach RO,$(shell ls test),python -m cwlprov.tool -d test/$(RO) validate && ) true
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$(foreach RO,$(shell ls test),python -m cwlprov.tool -d test/$(RO) info && ) true
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$(foreach RO,$(shell ls test),python -m cwlprov.tool -d test/$(RO) who && ) true
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$(foreach RO,$(shell ls test),python -m cwlprov.tool -d test/$(RO) prov && ) true
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$(foreach RO,$(shell ls test),python -m cwlprov.tool -d test/$(RO) inputs && ) true
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$(foreach RO,$(shell ls test),python -m cwlprov.tool -d test/$(RO) outputs && ) true
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$(foreach RO,$(shell ls test),python -m cwlprov.tool -d test/$(RO) runs && ) true
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#$(foreach RO,$(shell ls test),python -m cwlprov.tool -d test/$(RO) derived && ) true
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#$(foreach RO,$(shell ls test),python -m cwlprov.tool -d test/$(RO) runtimes && ) true
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## testcov : run the ${MODULE} test suite and collect coverage
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testcov: $(PYSOURCES)
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python setup.py test --addopts "--cov" ${PYTEST_EXTRA}
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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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mypy3: mypy
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mypy: $(filter-out setup.py,$(PYSOURCES))
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mypy $^
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pyupgrade: $(filter-out schema_salad/metaschema.py,$(PYSOURCES))
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pyupgrade --exit-zero-even-if-changed --py36-plus $^
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release-test: FORCE
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git diff-index --quiet HEAD -- || ( echo You have uncommited changes, please commit them and try again; false )
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./release-test.sh
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release: release-test
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. testenv2/bin/activate && \
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python testenv2/src/${PACKAGE}/setup.py sdist bdist_wheel
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. testenv2/bin/activate && \
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pip install twine && \
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twine upload testenv2/src/${PACKAGE}/dist/* && \
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git tag ${VERSION} && git push --tags
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flake8: $(PYSOURCES)
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flake8 $^
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FORCE:
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# Use this to print the value of a Makefile variable
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# Example `make print-VERSION`
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# From https://www.cmcrossroads.com/article/printing-value-makefile-variable
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print-% : ; @echo $* = $($*)

‎cwlprov/tool.py‎

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_logger.fatal(e)
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return Status.IO_ERROR
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if __name__ == "__main__":
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main(sys.argv[1:])

‎mypy-requirements.txt‎

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mypy

‎requirements.txt‎

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wheel
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sphinx
3-
pytest

‎setup.py‎

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import cwlprov
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setup(
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name = 'cwlprov',
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packages = find_packages(exclude=['contrib', 'docs', 'tests']), # Required
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version = cwlprov.__version__,
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description = 'cwlprov API for Python',
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long_description=long_description,
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long_description_content_type="text/markdown",
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author = 'Stian Soiland-Reyes',
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author_email = 'stain@apache.org',
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include_package_data=True,
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# https://www.apache.org/licenses/LICENSE-2.0
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license = "Apache License, Version 2.0",
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url = 'https://github.com/common-workflow-language/cwlprov-py',
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# download_url = 'https://github.com/stain/arcp-py/archive/0.1.0.tar.gz',
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keywords = "cwl prov cwlprov provenance",
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install_requires=[
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'prov >= 1.5.1',
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'bdbag >= 1.4.1',
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#'bagit >= 1.6.4', # Transitive from bdbag
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'arcp >= 0.2.0',
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'rdflib-jsonld >= 0.4.0',
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'rdflib >= 4.2.2',
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],
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tests_require=['pytest'],
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entry_points={
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'console_scripts': ["cwlprov=cwlprov.tool:main"]
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},
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python_requires='>=3.6, <4',
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classifiers=[
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# https://pypi.python.org/pypi?%3Aaction=list_classifiers
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'Development Status :: 2 - Pre-Alpha',
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'Intended Audience :: Developers',
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'Topic :: Software Development :: Build Tools',
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# 'License :: OSI Approved :: Apache Software License',
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# https://github.com/pypa/pypi-legacy/issues/564
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#'License :: OSI Approved',
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# 'License :: OSI Approved :: Apache License, Version 2.0 (Apache-2.0)',
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'Programming Language :: Python :: 3',
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'Programming Language :: Python :: 3.6',
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'Topic :: Internet',
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'Topic :: System :: Archiving :: Packaging',
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],
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name="cwlprov",
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packages=find_packages(exclude=["contrib", "docs", "tests"]), # Required
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version=cwlprov.__version__,
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description="cwlprov API for Python",
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long_description=long_description,
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long_description_content_type="text/markdown",
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author="Stian Soiland-Reyes",
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author_email="stain@apache.org",
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include_package_data=True,
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# https://www.apache.org/licenses/LICENSE-2.0
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license="Apache License, Version 2.0",
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url="https://github.com/common-workflow-language/cwlprov-py",
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# download_url = 'https://github.com/stain/arcp-py/archive/0.1.0.tar.gz',
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keywords="cwl prov cwlprov provenance",
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install_requires=[
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"prov >= 1.5.1",
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"bdbag >= 1.4.1",
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#'bagit >= 1.6.4', # Transitive from bdbag
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"arcp >= 0.2.0",
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"rdflib-jsonld >= 0.4.0, < 0.6.2",
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"rdflib >= 4.2.2, <6.0",
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],
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tests_require=["pytest"],
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entry_points={"console_scripts": ["cwlprov=cwlprov.tool:main"]},
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python_requires=">=3.6, <4",
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classifiers=[
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# https://pypi.python.org/pypi?%3Aaction=list_classifiers
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"Development Status :: 2 - Pre-Alpha",
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"Intended Audience :: Developers",
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"Topic :: Software Development :: Build Tools",
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# 'License :: OSI Approved :: Apache Software License',
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# https://github.com/pypa/pypi-legacy/issues/564
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#'License :: OSI Approved',
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# 'License :: OSI Approved :: Apache License, Version 2.0 (Apache-2.0)',
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"Programming Language :: Python :: 3",
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"Programming Language :: Python :: 3.6",
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"Topic :: Internet",
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"Topic :: System :: Archiving :: Packaging",
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],
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)

‎test-requirements.txt‎

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coverage

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