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galaxy/Makefile
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Alireza Heidari ceb562bcdd Build the documentation in parallel by default 
The docs job takes ~83m on a pull request, ~82m of which is a single serial sphinx-build. Making `-j auto` the default in doc/Makefile speeds up every caller — CI, `make docs`, and a local build — and `SPHINXOPTS=` still gives a serial build. `docs-develop` no longer needs to pass `-j 4` of its own.

sphinx.ext.viewcode is not parallelized (see 45ed317832, which added GALAXY_DOCS_SKIP_VIEW_CODE for exactly that reason), so it is skipped for pull request builds, which only need to prove the documentation still builds. Pushes, which are what gets deployed to docs.galaxyproject.org, keep the embedded highlighted source.

Measured on a pull request run: 83m to 15m.
2026-07-29 10:26:50 +02:00

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Makefile
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# Location of virtualenv used for development.
VENV?=.venv
# Source virtualenv to execute command (black, isort, sphinx, twine, etc...)
IN_VENV=if [ -f "$(VENV)/bin/activate" ]; then . "$(VENV)/bin/activate"; fi;
RELEASE_CURR:=26.2
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'
PNPM := $(shell $(IN_VENV) command -v pnpm 2> /dev/null)
PNPM_INSTALL_OPTS=--frozen-lockfile
# Default to not fail on error, set to 1 to fail client builds on a plugin error.
GALAXY_PLUGIN_BUILD_FAIL_ON_ERROR?=0
# Respect predefined NODE_OPTIONS, otherwise set maximum heap size low for
# compatibility with smaller machines.
NODE_OPTIONS ?= --max-old-space-size=4096
NODE_ENV = env NODE_OPTIONS=$(NODE_OPTIONS) GALAXY_PLUGIN_BUILD_FAIL_ON_ERROR=$(GALAXY_PLUGIN_BUILD_FAIL_ON_ERROR)
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
NO_PNPM_MSG="Could not find pnpm, which is required to build the Galaxy client.\nIt should be shipped with Galaxy's virtualenv, but to install pnpm manually please visit \033[0;34mhttps://pnpm.io/installation\033[0m for instructions.\n"
SPACE := $() $()
NEVER_PYUPGRADE_PATHS := .venv/ .tox/ lib/galaxy/schema/bco/ \
lib/galaxy/schema/drs/ lib/tool_shed_client/schema/trs \
scripts/check_python.py tools/ test/functional/tools/cwl_tools/
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 requirements.txt -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 $(MAKE) -C doc html
setup-venv:
if [ ! -f $(VENV)/bin/activate ]; then bash scripts/common_startup.sh --dev-wheels; fi
diff-format: ## Format Python code changes since last commit
$(IN_VENV) darker .
format: ## Format Python code base
$(IN_VENV) isort .
$(IN_VENV) black .
remove-unused-imports: ## Remove unused imports in Python code base
$(IN_VENV) autoflake --in-place --remove-all-unused-imports --recursive --verbose lib/ test/
pyupgrade: ## Convert older code patterns to Python 3.10+ idiomatic ones
ack --type=python -f | grep -v '^$(subst $(SPACE),\|^,$(NEVER_PYUPGRADE_PATHS))' | xargs pyupgrade --py310-plus
ack --type=python -f | grep -v '^$(subst $(SPACE),\|^,$(NEVER_PYUPGRADE_PATHS))' | xargs auto-walrus
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)
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, RST files, and type stubs 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_config_types galaxy
$(CONFIG_MANAGE) build_sample_yaml reports --add-comments
$(CONFIG_MANAGE) build_rst reports > doc/source/admin/reports_options.rst
$(CONFIG_MANAGE) build_config_types reports
$(CONFIG_MANAGE) build_sample_yaml tool_shed --add-comments
$(CONFIG_MANAGE) build_config_types tool_shed
config-lint: ## lint galaxy YAML configuration file
$(CONFIG_MANAGE) lint galaxy
client-gen-markdown-directives: ## Regenerate Galaxy Markdown directive artifacts from directives.yml (reference, requirements, validator registry)
$(IN_VENV) python scripts/markdown_directives_doc.py
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) galaxy-release-util create-release-issue $(RELEASE_CURR)
release-check-blocking-issues: ## Check github for release blocking issues
$(IN_VENV) galaxy-release-util check-blocking-issues $(RELEASE_CURR)
release-check-blocking-prs: ## Check github for release blocking PRs
$(IN_VENV) galaxy-release-util check-blocking-prs $(RELEASE_CURR)
release-bootstrap-history: ## bootstrap history for a new release
$(IN_VENV) galaxy-release-util create-changelog $(RELEASE_CURR)
update-lint-requirements:
./lib/galaxy/dependencies/update_lint_requirements.sh
update-dependencies: update-lint-requirements ## update pinned, dev and typecheck 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
skip-client: ## Run only the server, skipping the client build.
GALAXY_SKIP_CLIENT_BUILD=1 sh run.sh
client-node-deps: ## Install NodeJS dependencies for the client.
ifndef PNPM
corepack enable pnpm;
endif
$(IN_VENV) cd client && pnpm install $(PNPM_INSTALL_OPTS)
format-xsd:
xmllint --format --output galaxy-tmp.xsd lib/galaxy/tool_util/xsd/galaxy.xsd
mv galaxy-tmp.xsd lib/galaxy/tool_util/xsd/galaxy.xsd
build-api-schema:
$(IN_VENV) python scripts/dump_openapi_schema.py _schema.yaml
$(IN_VENV) python scripts/dump_openapi_schema.py --app shed _shed_schema.yaml
remove-api-schema:
rm _schema.yaml
rm _shed_schema.yaml
update-client-api-schema: client-node-deps build-api-schema ## Update client API schema
$(IN_VENV) cd client && pnpm openapi-typescript ../_schema.yaml -o packages/api-client/src/schema/schema.ts && pnpm prettier --write packages/api-client/src/schema/schema.ts
$(IN_VENV) cd client && pnpm openapi-typescript ../_shed_schema.yaml -o ../lib/tool_shed/webapp/frontend/src/schema/schema.ts && pnpm prettier --write ../lib/tool_shed/webapp/frontend/src/schema/schema.ts
$(MAKE) remove-api-schema
lint-api-schema: build-api-schema
$(IN_VENV) npx --yes @redocly/cli lint _schema.yaml
$(IN_VENV) npx --yes @redocly/cli lint _shed_schema.yaml
$(IN_VENV) codespell -I .ci/ignore-spelling.txt _schema.yaml
$(IN_VENV) codespell -I .ci/ignore-spelling.txt _shed_schema.yaml
$(MAKE) remove-api-schema
update-navigation-schema: client-node-deps
$(IN_VENV) cd client && node navigation_to_schema.mjs
install-client: ## Install prebuilt client wheel from PyPI matching the current Galaxy version
$(IN_VENV) pip install "galaxy-web-client==$$(PYTHONPATH=lib python -c 'from galaxy.version import VERSION; print(VERSION)')"
client: client-node-deps ## Rebuild client-side artifacts for local development.
$(IN_VENV) cd client && $(NODE_ENV) pnpm run build
client-production: client-node-deps ## Rebuild client-side artifacts for a production deployment without sourcemaps.
$(IN_VENV) cd client && $(NODE_ENV) pnpm run build-production
client-production-maps: client-node-deps ## Rebuild client-side artifacts for a production deployment with sourcemaps.
$(IN_VENV) cd client && $(NODE_ENV) pnpm run build-production-maps
client-lint-autofix: client-node-deps ## Automatically fix linting errors in client code
$(IN_VENV) cd client && pnpm run eslint --quiet --fix
client-format: client-node-deps client-lint-autofix ## Reformat client code, ensures autofixes are applied first
$(IN_VENV) cd client && pnpm run format
client-dev-server: client-node-deps ## Starts a Vite dev server for client development (HMR enabled)
$(IN_VENV) cd client && $(NODE_ENV) pnpm run develop
client-test: client-node-deps ## Run JS unit tests
$(IN_VENV) cd client && pnpm run test
client-eslint-precommit: client-node-deps # Client linting for pre-commit hook; skips glob input and takes specific paths
$(IN_VENV) cd client && pnpm run eslint-precommit
client-eslint: client-node-deps # Run client linting
$(IN_VENV) cd client && pnpm run eslint
client-format-check: client-node-deps # Run client formatting check
$(IN_VENV) cd client && pnpm run format-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
$(IN_VENV) cd client && pnpm run test:watch
serve-selenium-notebooks: ## Serve testing notebooks for Jupyter
cd lib && export PYTHONPATH=`pwd`; jupyter notebook --notebook-dir=galaxy_test/selenium/jupyter
files-sources-lint: ## Validate file sources configuration
$(IN_VENV) cd lib && PYTHONPATH=`pwd` python galaxy/files/validate/script.py
files-sources-lint-verbose: ## Validate file sources configuration (verbose)
$(IN_VENV) cd lib && PYTHONPATH=`pwd` python galaxy/files/validate/script.py --verbose
# 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
mypy:
cd lib && mypy . ../test
.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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