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galaxy/Makefile
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John Chilton 9a586a58b9 Add CWL conformance API tests 
1) Download conformance tests to `test/functional/tools/cwl_tools` where
  they can be used also by framework and unit tests in the future.
2) Add populators to enable executing CWL conformance tests
3) Generate CWL conformance API tests only when needed for tests
2021-11-23 14:10:21 +00:00

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Makefile
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# 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;
RELEASE_CURR:=22.01
RELEASE_UPSTREAM:=upstream
CONFIG_MANAGE=$(IN_VENV) python lib/galaxy/config/config_manage.py
PROJECT_URL?=https://github.com/galaxyproject/galaxy
DOCS_DIR=doc
DOC_SOURCE_DIR=$(DOCS_DIR)/source
SLIDESHOW_DIR=$(DOC_SOURCE_DIR)/slideshow
OPEN_RESOURCE=bash -c 'open $$0 || xdg-open $$0'
SLIDESHOW_TO_PDF?=bash -c 'docker run --rm -v `pwd`:/cwd astefanutti/decktape /cwd/$$0 /cwd/`dirname $$0`/`basename -s .html $$0`.pdf'
YARN := $(shell command -v yarn 2> /dev/null)
YARN_INSTALL_OPTS=--network-timeout 300000 --check-files
CWL_TARGETS := test/functional/tools/cwl_tools/v1.0/conformance_tests.yaml \
test/functional/tools/cwl_tools/v1.1/conformance_tests.yaml \
test/functional/tools/cwl_tools/v1.2/conformance_tests.yaml \
lib/galaxy_test/api/cwl/test_cwl_conformance_v1_0.py \
lib/galaxy_test/api/cwl/test_cwl_conformance_v1_1.py \
lib/galaxy_test/api/cwl/test_cwl_conformance_v1_2.py
all: help
@echo "This makefile is used for building Galaxy's JS client, documentation, and drive the release process. A sensible all target is not implemented."
docs: ## Generate HTML documentation.
# Run following commands to setup the Python portion of the requirements:
# $ ./scripts/common_startup.sh
# $ . .venv/bin/activate
# $ pip install -r lib/galaxy/dependencies/dev-requirements.txt
$(IN_VENV) $(MAKE) -C doc clean
$(IN_VENV) $(MAKE) -C doc html
docs-develop: ## Fast doc generation and more warnings (for development)
$(IN_VENV) GALAXY_DOCS_SKIP_VIEW_CODE=1 SPHINXOPTS='-j 4' $(MAKE) -C doc html
setup-venv:
if [ ! -f $(VENV)/bin/activate ]; then bash scripts/common_startup.sh --dev-wheels; fi
list-dependency-updates: setup-venv
$(IN_VENV) pip list --outdated --format=columns
docs-slides-ready:
test -f plantuml.jar || wget http://jaist.dl.sourceforge.net/project/plantuml/plantuml.jar
java -jar plantuml.jar -c $(DOC_SOURCE_DIR)/slideshow/architecture/images/plantuml_options.txt -tsvg $(SLIDESHOW_DIR)/architecture/images/ *.plantuml.txt
$(IN_VENV) python scripts/slideshow/build_slideshow.py 'Galaxy Architecture' $(SLIDESHOW_DIR)/architecture/galaxy_architecture.md
docs-slides-export: docs-slides-ready
$(SLIDESHOW_TO_PDF) $(SLIDESHOW_DIR)/galaxy_architecture/galaxy_architecture.html
_open-docs:
$(OPEN_RESOURCE) $(DOCS_DIR)/_build/html/index.html
open-docs: docs _open-docs ## generate Sphinx HTML documentation and open in browser
open-project: ## open project on github
$(OPEN_RESOURCE) $(PROJECT_URL)
uwsgi-rebuild-validation: ## rebuild uwsgi_config.yml kwalify schema against latest uwsgi master.
$(CONFIG_MANAGE) build_uwsgi_yaml
tool-shed-config-validate: ## validate tool shed YAML configuration file
$(CONFIG_MANAGE) validate tool_shed
tool-shed-config-lint: ## lint tool shed YAML configuration file
$(CONFIG_MANAGE) lint tool_shed
tool-shed-config-convert-dry-run: ## convert old style tool shed ini to yaml (dry run)
$(CONFIG_MANAGE) convert tool_shed --dry-run
tool-shed-config-convert: ## convert old style tool shed ini to yaml
$(CONFIG_MANAGE) convert tool_shed
reports-config-validate: ## validate reports YAML configuration file
$(CONFIG_MANAGE) validate reports
reports-config-convert-dry-run: ## convert old style reports ini to yaml (dry run)
$(CONFIG_MANAGE) convert reports --dry-run
reports-config-convert: ## convert old style reports ini to yaml
$(CONFIG_MANAGE) convert reports
reports-config-lint: ## lint reports YAML configuration file
$(CONFIG_MANAGE) lint reports
config-validate: ## validate galaxy YAML configuration file
$(CONFIG_MANAGE) validate galaxy
config-convert-dry-run: ## convert old style galaxy ini to yaml (dry run)
$(CONFIG_MANAGE) convert galaxy --dry-run
config-convert: ## convert old style galaxy ini to yaml
$(CONFIG_MANAGE) convert galaxy
config-rebuild: ## Rebuild all sample YAML and RST files from config schema
$(CONFIG_MANAGE) build_sample_yaml galaxy --add-comments
$(CONFIG_MANAGE) build_rst galaxy > doc/source/admin/galaxy_options.rst
$(CONFIG_MANAGE) build_sample_yaml reports --add-comments
$(CONFIG_MANAGE) build_rst reports > doc/source/admin/reports_options.rst
$(CONFIG_MANAGE) build_sample_yaml tool_shed --add-comments
config-lint: ## lint galaxy YAML configuration file
$(CONFIG_MANAGE) lint galaxy
release-ensure-upstream: ## Ensure upstream branch for release commands setup
ifeq (shell git remote -v | grep $(RELEASE_UPSTREAM), )
git remote add $(RELEASE_UPSTREAM) git@github.com:galaxyproject/galaxy.git
else
@echo "Remote $(RELEASE_UPSTREAM) already exists."
endif
release-merge-stable-to-next: release-ensure-upstream ## Merge last release into dev
git fetch $(RELEASE_UPSTREAM) && git checkout dev && git merge --ff-only $(RELEASE_UPSTREAM)/dev && git merge $(RELEASE_UPSTREAM)/$(RELEASE_PREVIOUS)
release-push-dev: release-ensure-upstream # Push local dev branch upstream
git push $(RELEASE_UPSTREAM) dev
release-issue: ## Create release issue on github
$(IN_VENV) python scripts/bootstrap_history.py --create-release-issue $(RELEASE_CURR)
release-check-metadata: ## check github PR metadata for target release
$(IN_VENV) python scripts/bootstrap_history.py --check-release $(RELEASE_CURR)
release-check-blocking-issues: ## Check github for release blocking issues
$(IN_VENV) python scripts/bootstrap_history.py --check-blocking-issues $(RELEASE_CURR)
release-check-blocking-prs: ## Check github for release blocking PRs
$(IN_VENV) python scripts/bootstrap_history.py --check-blocking-prs $(RELEASE_CURR)
release-bootstrap-history: ## bootstrap history for a new release
$(IN_VENV) python scripts/bootstrap_history.py --release $(RELEASE_CURR)
update-lint-requirements:
./lib/galaxy/dependencies/update_lint_requirements.sh
update-dependencies: update-lint-requirements ## update pinned and dev dependencies
$(IN_VENV) ./lib/galaxy/dependencies/update.sh
$(CWL_TARGETS):
./scripts/update_cwl_conformance_tests.sh
generate-cwl-conformance-tests: $(CWL_TARGETS) ## Initialise CWL conformance tests
clean-cwl-conformance-tests: # Clean CWL conformance tests
for f in $(CWL_TARGETS); do \
if [ $$(basename "$$f") = conformance_tests.yaml ]; then \
rm -rf $$(dirname "$$f"); \
else \
rm -f "$$f"; \
fi \
done
update-cwl-conformance-tests: ## update CWL conformance tests
$(MAKE) clean-cwl-conformance-tests
$(MAKE) generate-cwl-conformance-tests
node-deps: ## Install NodeJS dependencies.
ifndef YARN
@echo "Could not find yarn, which is required to build the Galaxy client.\nTo install yarn, please visit \033[0;34mhttps://yarnpkg.com/en/docs/install\033[0m for instructions, and package information for all platforms.\n"
false;
else
cd client && yarn install $(YARN_INSTALL_OPTS)
endif
client: node-deps ## Rebuild client-side artifacts for local development.
cd client && yarn run build
client-production: node-deps ## Rebuild client-side artifacts for a production deployment without sourcemaps.
cd client && yarn run build-production
client-production-maps: node-deps ## Rebuild client-side artifacts for a production deployment with sourcemaps.
cd client && yarn run build-production-maps
client-format: node-deps ## Reformat client code
cd client && yarn run prettier
client-watch: node-deps ## A useful target for parallel development building. See also client-dev-server.
cd client && yarn run watch
client-dev-server: node-deps ## Starts a webpack dev server for client development (HMR enabled)
cd client && yarn run serve
client-test: node-deps ## Run JS unit tests
cd client && yarn run test
client-eslint: node-deps # Run client linting
cd client && yarn run eslint
client-format-check: node-deps # Run client formatting check
cd client && yarn run prettier-check
client-lint: client-eslint client-format-check ## ES lint and check format of client
client-test-watch: client ## Watch and run all client unit tests on changes
cd client && yarn run jest-watch
serve-selenium-notebooks: ## Serve testing notebooks for Jupyter
cd lib && export PYTHONPATH=`pwd`; jupyter notebook --notebook-dir=galaxy_test/selenium/jupyter
# Release Targets
release-create-rc: ## Create a release-candidate branch or new release-candidate version
$(IN_VENV) ./scripts/release.sh -c
release-create: ## Create a release branch
$(IN_VENV) ./scripts/release.sh
release-create-point: release-create ## Create a point release
.PHONY: help
help:
@egrep '^[a-zA-Z_-]+:.*?## .*$$' $(MAKEFILE_LIST) | sort | awk 'BEGIN {FS = ":.*?## "}; {printf "\033[36m%-30s\033[0m %s\n", $$1, $$2}'
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