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Makefile
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Makefile
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.PHONY: clean clean-test clean-pyc clean-build docs help
.DEFAULT_GOAL := help
define BROWSER_PYSCRIPT
import os, webbrowser, sys
try:
from urllib import pathname2url
except:
from urllib.request import pathname2url
webbrowser.open("file://" + pathname2url(os.path.abspath(sys.argv[1])))
endef
export BROWSER_PYSCRIPT
define PRINT_HELP_PYSCRIPT
import re, sys
for line in sys.stdin:
match = re.match(r'^([a-zA-Z_-]+):.*?## (.*)$$', line)
if match:
target, help = match.groups()
print("%-20s %s" % (target, help))
endef
export PRINT_HELP_PYSCRIPT
BROWSER := python -c "$$BROWSER_PYSCRIPT"
help:
@python -c "$$PRINT_HELP_PYSCRIPT" < $(MAKEFILE_LIST)
clean: clean-build clean-pyc clean-test ## remove all build, test, coverage and Python artifacts
clean-build: ## remove build artifacts
rm -fr build/
rm -fr dist/
rm -fr .eggs/
rm -rf puticr/download
rm -rf puticr/bin
rm -rf puticr/lib
find . -name '*.egg-info' -exec rm -fr {} +
find . -name '*.egg' -exec rm -rf {} +
clean-pyc: ## remove Python file artifacts
find . -name '*.pyc' -exec rm -f {} +
find . -name '*.pyo' -exec rm -f {} +
find . -name '*~' -exec rm -f {} +
find . -name '__pycache__' -exec rm -fr {} +
clean-test: ## remove test and coverage artifacts
rm -fr .tox/
rm -f .coverage
rm -fr htmlcov/
rm -fr .pytest_cache
lint: ## check style with flake8
. puticr/bin/activate && \
flake8 puticr tests
test: ## run tests quickly with the default Python
py.test
test-all: ## run tests on every Python version with tox
. puticr/bin/activate && \
tox
coverage: ## check code coverage quickly with the default Python
. puticr/bin/activate && \
coverage run --source puticr -m pytest && \
coverage report -m && \
coverage html
$(BROWSER) htmlcov/index.html
docs: ## generate Sphinx HTML documentation, including API docs
rm -f docs/puticr.rst
rm -f docs/modules.rst
sphinx-apidoc -o docs/ puticr
$(MAKE) -C docs clean
$(MAKE) -C docs html
$(BROWSER) docs/_build/html/index.html
servedocs: docs ## compile the docs watching for changes
watchmedo shell-command -p '*.rst' -c '$(MAKE) -C docs html' -R -D .
release: dist ## package and upload a release
twine upload dist/*
dist: clean ## builds source and wheel package
python setup.py sdist
python setup.py bdist_wheel
ls -l dist
install: clean ## install the package to the active Python's site-packages
command -v virtualenv > /dev/null 2>&1 || pip install virtualenv --user
virtualenv puticr && \
. puticr/bin/activate && \
pip install -U Paver && \
pip install -r requirements_dev.txt && \
pip install -U sphinx_rtd_theme && \
mkdir -p puticr/download && \
mkdir -p puticr/files && \
python setup.py install && \
cp puticr/cgmaptools puticr/bin && \
cp puticr/update_CGmap2.py puticr/bin && \
cp puticr/identify_hotspot_V2.py puticr/bin && \
cd puticr/bin && ln -sf ../download/BSseeker2/Antisense.py Antisense.py && \
ln -sf ../download/BSseeker2/bs_seeker2-align.py bs_seeker2-align.py && \
ln -sf ../download/BSseeker2/bs_seeker2-build.py bs_seeker2-build.py && \
ln -sf ../download/BSseeker2/bs_seeker2-call_methylation.py bs_seeker2-call_methylation.py && \
ln -sf ../download/BSseeker2/FilterReads.py FilterReads.py && \
ln -sf ../download/cgmaptools-0.1.2/src/ASM.pl ASM && \
ln -sf ../download/cgmaptools-0.1.2/src/ATCGmapCovInBins.py ATCGmapCovInBins && \
ln -sf ../download/cgmaptools-0.1.2/src/ATCGmapStatCov.py ATCGmapStatCov && \
ln -sf ../download/cgmaptools-0.1.2/src/ATCGmapToCGmapWig.py ATCGmapToCGmapWig && \
ln -sf ../download/cgmaptools-0.1.2/src/BismarkToCGmap.py BismarkToCGmap && \
ln -sf ../download/cgmaptools-0.1.2/src/CGmapCovInBins.py CGmapCovInBins && \
ln -sf ../download/cgmaptools-0.1.2/src/CGmapFillContext.py CGmapFillContext && \
ln -sf ../download/cgmaptools-0.1.2/src/CGmapFillIndex.py CGmapFillIndex && \
ln -sf ../download/cgmaptools-0.1.2/src/CGmapInterDiffReg.py CGmapInterDiffReg && \
ln -sf ../download/cgmaptools-0.1.2/src/CGmapInterDiffSite.py CGmapInterDiffSite && \
ln -sf ../download/cgmaptools-0.1.2/src/CGmapIntersect.py CGmapIntersect && \
ln -sf ../download/cgmaptools-0.1.2/src/CGmapMerge.py CGmapMerge && \
ln -sf ../download/cgmaptools-0.1.2/src/CGmapMethInBins.py CGmapMethInBins && \
ln -sf ../download/cgmaptools-0.1.2/src/CGmapSelectBySite.py CGmapSelectBySite && \
ln -sf ../download/cgmaptools-0.1.2/src/CGmapsMethInBins.py CGmapsMethInBins && \
ln -sf ../download/cgmaptools-0.1.2/src/CGmapSplitByChr.py CGmapSplitByChr && \
ln -sf ../download/cgmaptools-0.1.2/src/CGmapStatCov.py CGmapStatCov && \
ln -sf ../download/cgmaptools-0.1.2/src/CGmapStatMeth.py CGmapStatMeth && \
ln -sf ../download/cgmaptools-0.1.2/src/CGmapToRegion.py CGmapToRegion && \
ln -sf ../download/cgmaptools-0.1.2/src/CGmapToWig.py CGmapToWig && \
ln -sf ../download/cgmaptools-0.1.2/src/FindCCGG.py FindCCGG && \
ln -sf ../download/cgmaptools-0.1.2/src/FragRegFromBED.py FragRegFromBED && \
ln -sf ../download/cgmaptools-0.1.2/src/mCBinHeatmap.R mCBinHeatmap && \
ln -sf ../download/cgmaptools-0.1.2/src/mCFragRegView.R mCFragRegView && \
ln -sf ../download/cgmaptools-0.1.2/src/mCLollipop.R mCLollipop && \
ln -sf ../download/cgmaptools-0.1.2/src/mCTanghulu.pl mCTanghulu && \
ln -sf ../download/cgmaptools-0.1.2/src/MergeListOfCGmap.py MergeListOfCGmap && \
ln -sf ../download/cgmaptools-0.1.2/src/SNVFromATCGmap.py SNVFromATCGmap && \
ln -sf ../download/cgmaptools-0.1.2/src/Sort_chr_pos.py Sort_chr_pos