add Makefile to measure coverage

.coveragerc

@@ -0,0 +1,3 @@
+[run]
+branch = True
+source = cwltool

Makefile

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+# This file is part of cwltool,
+# https://github.com/common-workflow-language/cwltool/, and is
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#     http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+#
+# Contact: common-workflow-language@googlegroups.com
+
+# make pep8 to check for basic Python code compliance
+# make autopep8 to fix most pep8 errors
+# make pylint to check Python code for enhanced compliance including naming
+#  and documentation
+# make coverage-report to check coverage of the python scripts by the tests
+
+MODULE=cwltool
+
+# `SHELL=bash` doesn't work for some, so don't use BASH-isms like
+# `[[` conditional expressions.
+PYSOURCES=$(wildcard ${MODULE}/**.py tests/*.py) setup.py
+DEVPKGS=pep8 diff_cover autopep8 pylint coverage pep257
+DEBDEVPKGS=pep8 python-autopep8 pylint python-coverage pep257 sloccount
+VERSION=1.0.$(shell date +%Y%m%d%H%M%S --date=`git log --first-parent \
+	--max-count=1 --format=format:%cI`)
+mkfile_dir := $(dir $(abspath $(lastword $(MAKEFILE_LIST))))
+
+## all         : default task
+all:
+	./setup.py develop
+
+## help        : print this help message and exit
+help: Makefile
+	@sed -n 's/^##//p' $<
+
+## install-dep : install most of the development dependencies via pip
+install-dep:
+	pip install --upgrade $(DEVPKGS)
+
+## install-deb-dep: install most of the dev dependencies via apt-get
+install-deb-dep:
+	sudo apt-get install $(DEBDEVPKGS)
+
+## install     : install the ${MODULE} module and schema-salad-tool
+install: FORCE
+	./setup.py build install
+
+## dist        : create a module package for distribution
+dist: dist/${MODULE}-$(VERSION).tar.gz
+
+dist/${MODULE}-$(VERSION).tar.gz: $(SOURCES)
+	./setup.py sdist
+
+## clean       : clean up all temporary / machine-generated files
+clean: FORCE
+	rm -f ${MODILE}/*.pyc tests/*.pyc
+	./setup.py clean --all || true
+	rm -Rf .coverage
+	rm -f diff-cover.html
+
+## pep8        : check Python code style
+pep8: $(PYSOURCES)
+	pep8 --exclude=_version.py  --show-source --show-pep8 $^ || true
+
+pep8_report.txt: $(PYSOURCES)
+	pep8 --exclude=_version.py $^ > pep8_report.txt || true
+
+diff_pep8_report: pep8_report.txt
+	diff-quality --violations=pep8 pep8_report.txt
+
+## pep257      : check Python code style
+pep257: $(PYSOURCES)
+	pep257 --ignore=D100,D101,D102,D103 $^ || true
+
+pep257_report.txt: $(PYSOURCES)
+	pep257 setup.py $^ > pep257_report.txt 2>&1 || true
+
+diff_pep257_report: pep257_report.txt
+	diff-quality --violations=pep8 pep257_report.txt
+
+## autopep8    : fix most Python code indentation and formatting
+autopep8: $(PYSOURCES)
+	autopep8 --recursive --in-place --ignore E309 $^
+
+# A command to automatically run astyle and autopep8 on appropriate files
+## format      : check/fix all code indentation and formatting (runs autopep8)
+format: autopep8
+	# Do nothing
+
+## pylint      : run static code analysis on Python code
+pylint: $(PYSOURCES)
+	pylint --msg-template="{path}:{line}: [{msg_id}({symbol}), {obj}] {msg}" \
+                $^ || true
+
+pylint_report.txt: ${PYSOURCES}
+	pylint --msg-template="{path}:{line}: [{msg_id}({symbol}), {obj}] {msg}" \
+		$^ > pylint_report.txt || true
+
+diff_pylint_report: pylint_report.txt
+	diff-quality --violations=pylint pylint_report.txt
+
+.coverage: $(PYSOURCES) all
+	export COVERAGE_PROCESS_START=${mkfile_dir}.coveragerc; \
+	       cd ${CWL}; ./run_test.sh RUNNER=cwltool
+	coverage run setup.py test
+	coverage combine ${CWL} ${CWL}/draft-3/ ./
+
+coverage.xml: .coverage
+	python-coverage xml
+
+coverage.html: htmlcov/index.html
+
+htmlcov/index.html: .coverage
+	python-coverage html
+	@echo Test coverage of the Python code is now in htmlcov/index.html
+
+coverage-report: .coverage
+	python-coverage report
+
+diff-cover: coverage-gcovr.xml coverage.xml
+	diff-cover coverage-gcovr.xml coverage.xml
+
+diff-cover.html: coverage-gcovr.xml coverage.xml
+	diff-cover coverage-gcovr.xml coverage.xml \
+		--html-report diff-cover.html
+
+## test        : run the ${MODULE} test suite
+test: FORCE
+	python tests/test_examples.py 
+
+sloccount.sc: ${PYSOURCES} Makefile
+	sloccount --duplicates --wide --details $^ > sloccount.sc
+
+## sloccount   : count lines of code
+sloccount: ${PYSOURCES} Makefile
+	sloccount $^
+
+list-author-emails:
+	@echo 'name, E-Mail Address'
+	@git log --format='%aN,%aE' | sort -u | grep -v 'root'
+
+FORCE: