forked from galaxyproject/planemo
-
Notifications
You must be signed in to change notification settings - Fork 0
/
Makefile
179 lines (136 loc) · 6.6 KB
/
Makefile
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
# Default tests run with make test and make quick-tests
TESTS?=tests planemo
# Default environment for make tox
ENV?=py27
# Extra arguments supplied to tox command
ARGS?=
# Location of virtualenv used for development.
VENV?=.venv
VENV3?=.venv3
# Open resource on Mac OS X or Linux
OPEN_RESOURCE=bash -c 'open $$0 || xdg-open $$0'
# Source virtualenv to execute command (flake8, sphinx, twine, etc...)
IN_VENV=if [ -f $(VENV)/bin/activate ]; then . $(VENV)/bin/activate; fi;
IN_VENV3=if [ -f $(VENV3)/bin/activate ]; then . $(VENV3)/bin/activate; fi;
# TODO: add this upstream as a remote if it doesn't already exist.
UPSTREAM?=galaxyproject
SOURCE_DIR?=planemo
SOURCE_DOC_EXCLUDE=$(SOURCE_DIR)/cwl/cwl2script
BUILD_SCRIPTS_DIR=scripts
VERSION?=$(shell python $(BUILD_SCRIPTS_DIR)/print_version_for_release.py $(SOURCE_DIR))
DOC_URL?=https://planemo.readthedocs.org
PROJECT_URL?=https://github.com/galaxyproject/planemo
PROJECT_NAME?=planemo
TEST_DIR?=tests
DOCS_DIR?=docs
BUILD_SLIDESHOW?=$(IN_VENV) python $(BUILD_SCRIPTS_DIR)/build_slideshow.py
SLIDESHOW_TO_PDF?=bash -c 'docker run --rm -v `pwd`:/cwd astefanutti/decktape /cwd/$$0 /cwd/`dirname $$0`/`basename -s .html $$0`.pdf'
.PHONY: clean-pyc clean-build docs clean
help:
@egrep '^[a-zA-Z_-]+:.*?## .*$$' $(MAKEFILE_LIST) | sort | awk 'BEGIN {FS = ":.*?## "}; {printf "\033[36m%-30s\033[0m %s\n", $$1, $$2}'
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 *.egg-info
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/
submodule:
git submodule init
git submodule update
install: submodule ## install into Python envirnoment
python setup.py install && cd cwl-runner && python setup.py install
setup-venv: ## setup a development virtualenv in current directory
if [ ! -d $(VENV) ]; then virtualenv $(VENV); exit; fi;
$(IN_VENV) pip install --upgrade pip && pip install -r dev-requirements.txt -r requirements.txt
setup-venv3: ## setup a development virtualenv in current directory
if [ ! -d $(VENV3) ]; then virtualenv -p python3 $(VENV3); exit; fi;
$(IN_VENV3) pip install --upgrade pip && pip install -r dev-requirements.txt -r requirements.txt
setup-git-hook-lint: ## setup precommit hook for linting project
cp $(BUILD_SCRIPTS_DIR)/pre-commit-lint .git/hooks/pre-commit
setup-git-hook-lint-and-test: ## setup precommit hook for linting and testing project
cp $(BUILD_SCRIPTS_DIR)/pre-commit-lint-and-test .git/hooks/pre-commit
flake8: ## check style using flake8 for current Python (faster than lint)
$(IN_VENV) flake8 $(SOURCE_DIR) $(TEST_DIR)
lint: ## check style using tox and flake8 for Python 2 and Python 3
$(IN_VENV) tox -e py37-lint
test: ## run tests with the default Python (faster than tox)
$(IN_VENV) pytest $(TESTS)
quick-test: ## run quickest tests with the default Python
$(IN_VENV) PLANEMO_SKIP_SLOW_TESTS=1 PLANEMO_SKIP_GALAXY_TESTS=1 pytest $(TESTS)
gxwf-test-test: ## run test of workflow testing script
bash $(BUILD_SCRIPTS_DIR)/test_workflow_tests.sh
tox: ## run tests with tox in the specified ENV, defaults to py27
$(IN_VENV) tox -e $(ENV) -- $(ARGS)
_coverage-report: ## build coverage report with the default Python
coverage run --source $(SOURCE_DIR) setup.py $(TEST_DIR)
coverage report -m
coverage html
_open-coverage: ## open coverage report using open
open htmlcov/index.html || xdg-open htmlcov/index.html
coverage: _coverage-report open-coverage ## check code coverage quickly with the default Python
open-history: # view HISTORY.rst as HTML.
rst2html HISTORY.rst > /tmp/planemo_history.html
$(OPEN_RESOURCE) /tmp/planemo_history.html
ready-docs: ## rebuild docs folder ahead of running docs or lint-docs
rm -f $(DOCS_DIR)/$(SOURCE_DIR).rst
rm -f $(DOCS_DIR)/modules.rst
$(BUILD_SLIDESHOW) 'Galaxy Tool Framework Changes' $(DOCS_DIR)/galaxy_changelog.md
$(BUILD_SLIDESHOW) 'Planemo: A Scientific Workflow SDK' $(DOCS_DIR)/presentations/2016_workflows.md
$(IN_VENV) sphinx-apidoc -f -o $(DOCS_DIR)/ $(SOURCE_DIR) $(SOURCE_DOC_EXCLUDE)
$(IN_VENV) python scripts/commands_to_rst.py
docs: ready-docs ## generate Sphinx HTML documentation, including API docs
$(IN_VENV) $(MAKE) -C $(DOCS_DIR) clean
$(IN_VENV) $(MAKE) -C $(DOCS_DIR) html
lint-docs: ready-docs
$(IN_VENV) $(MAKE) -C $(DOCS_DIR) clean
$(IN_VENV) $(MAKE) -C $(DOCS_DIR) html 2>&1 | python $(BUILD_SCRIPTS_DIR)/lint_sphinx_output.py
_open-docs:
$(OPEN_RESOURCE) $(DOCS_DIR)/_build/html/index.html
open-slides-galaxy-changelog: ready-docs
$(OPEN_RESOURCE) $(DOCS_DIR)/galaxy_changelog.html
open-slides-workflows: ready-docs
$(OPEN_RESOURCE) $(DOCS_DIR)/presentations/2016_workflows.html
export-slides-workflows: ready-docs
$(SLIDESHOW_TO_PDF) $(DOCS_DIR)/presentations/2016_workflows.html
open-docs: docs _open-docs ## generate Sphinx HTML documentation and open in browser
open-rtd: docs ## open docs on readthedocs.org
$(OPEN_RESOURCE) $(PROJECT_URL)
open-project: ## open project on github
$(OPEN_RESOURCE) $(PROJECT_URL)
dist: clean submodule ## create and check packages
$(IN_VENV) python setup.py sdist bdist_wheel
$(IN_VENV) twine check dist/*
ls -l dist
release-test-artifacts: dist
$(IN_VENV) twine upload -r test dist/*
$(OPEN_RESOURCE) https://testpypi.python.org/pypi/$(PROJECT_NAME)
release-artifacts: release-test-artifacts ## Package and Upload to PyPi
@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: ## Update version and history, commit and add tag
$(IN_VENV) python $(BUILD_SCRIPTS_DIR)/commit_version.py $(SOURCE_DIR) $(VERSION)
new-version: ## Mint a new version
$(IN_VENV) python $(BUILD_SCRIPTS_DIR)/new_version.py $(SOURCE_DIR) $(VERSION)
release-local: commit-version new-version
release-brew: ## Mint a new homebrew release
bash $(BUILD_SCRIPTS_DIR)/update_planemo_recipe.bash $(VERSION)
push-release: ## Push a tagged release to github
git push $(UPSTREAM) master
git push --tags $(UPSTREAM)
release: release-local push-release ## package, review, and upload a release
add-history: ## Reformat HISTORY.rst with data from Github's API
$(IN_VENV) python $(BUILD_SCRIPTS_DIR)/bootstrap_history.py $(ITEM)
update-extern: ## update external artifacts copied locally
sh scripts/update_extern.sh