Merge pull request #164 from deeptools/release_docs

Release docs

Makefile

@@ -0,0 +1,143 @@
+# Default tests run with make test and make quick-tests
+NOSE_TESTS?=tests HiCExplorer
+# Default environment for make tox
+ENV?=py27
+# Extra arguments supplied to tox command
+ARGS?=
+# Location of virtualenv used for development.
+VENV?=.venv
+# Source virtualenv to execute command (flake8, sphinx, twine, etc...)
+IN_VENV=if [ -f $(VENV)/bin/activate ]; then . $(VENV)/bin/activate; fi;
+# TODO: add this upstream as a remote if it doesn't already exist.
+UPSTREAM?=galaxyproject
+SOURCE_DIR?=HiCExplorer
+BUILD_SCRIPTS_DIR=scripts
+VERSION?=$(shell python $(BUILD_SCRIPTS_DIR)/print_version_for_release.py $(SOURCE_DIR))
+DOC_URL?=https://hicexplorer.readthedocs.org
+PROJECT_URL?=https://github.com/deeptools/HiCExplorer
+PROJECT_NAME?=hicexplorer
+TEST_DIR?=tests
+
+
+
+.PHONY: clean-pyc clean-build docs clean
+
+help:
+	@echo "clean - remove all build, test, coverage and Python artifacts"
+	@echo "clean-build - remove build artifacts"
+	@echo "clean-pyc - remove Python file artifacts"
+	@echo "clean-test - remove test and coverage artifacts"
+	@echo "setup-venv - setup a development virutalenv in current directory."
+	@echo "lint - check style using tox and flake8 for Python 2 and Python 3"
+	@echo "lint-readme - check README formatting for PyPI"
+	@echo "flake8 - check style using flake8 for current Python (faster than lint)"
+	@echo "test - run tests with the default Python (faster than tox)"
+	@echo "quick-test - run quickest tests with the default Python"
+	@echo "coverage - check code coverage quickly with the default Python"
+	@echo "docs - generate Sphinx HTML documentation, including API docs"
+	@echo "open-docs - generate Sphinx HTML documentation and open in browser"
+	@echo "open-rtd - open docs on readthedocs.org"
+	@echo "open-project - open project on github"
+	@echo "release - package, review, and upload a release"
+	@echo "dist - package"
+	@echo "setup-git-hook-lint - setup precommit hook for linting project"
+	@echo "setup-git-hook-lint-and-test - setup precommit hook for linting and testing project"
+	@echo "update-extern - update external artifacts copied locally"
+
+clean: clean-build clean-pyc clean-test
+
+clean-build:
+	rm -fr build/
+	rm -fr dist/
+	rm -fr *.egg-info
+
+clean-pyc:
+	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:
+	rm -fr .tox/
+	rm -f .coverage
+	rm -fr htmlcov/
+
+setup-venv:
+	if [ ! -d $(VENV) ]; then virtualenv $(VENV); exit; fi;
+	$(IN_VENV) pip install -r requirements.txt && pip install -r dev-requirements.txt
+
+setup-git-hook-lint:
+	cp $(BUILD_SCRIPTS_DIR)/pre-commit-lint .git/hooks/pre-commit
+
+setup-git-hook-lint-and-test:
+	cp $(BUILD_SCRIPTS_DIR)/pre-commit-lint-and-test .git/hooks/pre-commit
+
+flake8:
+	$(IN_VENV) flake8 --max-complexity 15 $(SOURCE_DIR)  $(TEST_DIR)
+
+lint:
+	$(IN_VENV) tox -e py27-lint && tox -e py36-lint
+
+lint-readme:
+	$(IN_VENV) python setup.py check -r -s
+
+test:
+	$(IN_VENV) nosetests $(NOSE_TESTS)
+
+tox:
+	$(IN_VENV) tox -e $(ENV) -- $(ARGS)
+
+coverage:
+	coverage run --source $(SOURCE_DIR) setup.py $(TEST_DIR)
+	coverage report -m
+	coverage html
+	open htmlcov/index.html || xdg-open htmlcov/index.html
+
+docs:
+	$(IN_VENV) sphinx-apidoc -f -o docs/ hicexplorer
+	$(IN_VENV) $(MAKE) -C docs clean
+	$(IN_VENV) $(MAKE) -C docs html
+
+_open-docs:
+	open docs/_build/html/index.html || xdg-open docs/_build/html/index.html
+
+open-docs: docs _open-docs
+
+open-rtd: docs
+	open $(DOC_URL) || xdg-open $(PROJECT_URL)
+
+open-project:
+	open $(PROJECT_URL) || xdg-open $(PROJECT_URL)
+
+dist: clean
+	$(IN_VENV) python setup.py sdist bdist_egg bdist_wheel
+	ls -l dist
+
+release-test-artifacts: dist
+	$(IN_VENV) twine upload -r test dist/*
+	open https://testpypi.python.org/pypi/$(PROJECT_NAME) || xdg-open https://testpypi.python.org/pypi/$(PROJECT_NAME)
+
+release-aritfacts: release-test-artifacts
+	@while [ -z "$$CONTINUE" ]; do \
+		read -r -p "Have you executed release-test and reviewed results? [y/N]: " CONTINUE; \
+	done ; \
+	[ $$CONTINUE = "y" ] || [ $$CONTINUE = "Y" ] || (echo "Exiting."; exit 1;)
+	@echo "Releasing"
+	$(IN_VENV) twine upload dist/*
+
+commit-version:
+	$(IN_VENV) python $(BUILD_SCRIPTS_DIR)/commit_version.py $(SOURCE_DIR) $(VERSION)
+
+new-version:
+	$(IN_VENV) python $(BUILD_SCRIPTS_DIR)/new_version.py $(SOURCE_DIR) $(VERSION) 2
+
+release-local: commit-version release-aritfacts new-version
+
+push-release:
+	git push $(UPSTREAM) master
+	git push --tags $(UPSTREAM)
+
+release: release-local push-release
+
+add-history:
+	$(IN_VENV) python scripts/bootstrap_history.py $(ITEM)

dev-requirements.txt

@@ -0,0 +1,26 @@
+# For testing
+tox
+nose
+coverage
+
+#Building Docs
+mock
+sphinx_rtd_theme
+sphinx-argparse==0.2.1
+sphinx>=1.2.0
+CommonMark>=0.5.6
+
+# Used to check readme.
+readme
+
+# For Python 2.6 tests
+unittest2
+
+# Used for code checking.
+pyflakes
+flake8
+flake8-import-order
+
+# For release
+wheel
+twine