mirror of
https://github.com/chanzuckerberg/cellxgene.git
synced 2026-09-17 05:47:58 +08:00
907cc634f5
This PR contains a refactoring to make adding new features easier. The new features include supporting the tiledb format, and the multi dataset application. The refactoring includes Simplifying the directory structure and files. a class structure to handle annotations (currently one type: AnnotationsLocalFile). a class to handle application configuration a class structure to handle matrix data (currently AnndataAdaptor and CxgAdaptor). CxgAdaptor uses tiledb. Algorithms that were previously dependent on the scanpy anndata object are now generalized to work with an abstract interface. The multi dataset option is not fully supported yet, and so the option to use it is hidden. Use "cli launch --dataroot ..." To access this feature. All combinations of app single dataset/ app multi dataset and AnndataAdaptor/CxgAdaptor work with all the features, such as annotations, ontologies, diffexp.
194 lines
4.6 KiB
Makefile
194 lines
4.6 KiB
Makefile
include common.mk
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BUILDDIR := build
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CLIENTBUILD := $(BUILDDIR)/client
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SERVERBUILD := $(BUILDDIR)/server
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CLEANFILES := $(BUILDDIR)/ client/build build dist cellxgene.egg-info
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PART ?= patch
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# CLEANING
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.PHONY: clean
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clean: clean-lite clean-server clean-client
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# cleaning the client's node_modules is the longest one, so we avoid that if possible
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.PHONY: clean-lite
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clean-lite:
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rm -rf $(CLEANFILES)
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clean-%:
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cd $(*) && $(MAKE) clean
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# BUILDING PACKAGE
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.PHONY: build
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build: clean build-cli
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@echo "done"
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.PHONY: build-client
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build-client:
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cd client && $(MAKE) ci build
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.PHONY: build-cli
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build-cli: build-client
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git ls-files server/ | cpio -pdm $(BUILDDIR)
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cp -r client/build/ $(CLIENTBUILD)
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mkdir -p $(SERVERBUILD)/common/web/static/img
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mkdir -p $(SERVERBUILD)/common/web/templates/
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cp $(CLIENTBUILD)/index.html $(SERVERBUILD)/common/web/templates/
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cp -r $(CLIENTBUILD)/static $(SERVERBUILD)/common/web/
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cp $(CLIENTBUILD)/favicon.png $(SERVERBUILD)/common/web/static/img
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cp $(CLIENTBUILD)/service-worker.js $(SERVERBUILD)/common/web/static/js/
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cp MANIFEST.in README.md setup.cfg setup.py $(BUILDDIR)
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# If you are actively developing in the server folder use this, dirties the source tree
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.PHONY: build-for-server-dev
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build-for-server-dev: clean-server build-client
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mkdir -p server/common/web/static/img
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mkdir -p server/common/web/static/js
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mkdir -p server/common/web/templates/
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cp client/build/index.html server/common/web/templates/
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cp -r client/build/static server/common/web/
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cp client/build/favicon.png server/common/web/static/img
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cp client/build/service-worker.js server/common/web/static/js/
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# TESTING
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.PHONY: test
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test: unit-test smoke-test
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.PHONY: unit-test
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unit-test: unit-test-server unit-test-client
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unit-test-%:
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cd $(*) && $(MAKE) unit-test
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.PHONY: smoke-test
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smoke-test:
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cd client && $(MAKE) smoke-test
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.PHONY: smoke-test-annotations
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smoke-test-annotations:
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cd client && $(MAKE) smoke-test-annotations
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# FORMATTING CODE
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.PHOHY: fmt
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fmt: fmt-client fmt-py
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.PHONY: fmt-client
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fmt-client:
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cd client && $(MAKE) fmt
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.PHONY: fmt
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fmt-py:
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black .
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.PHONY: lint
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lint:
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flake8 server
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# CREATING DISTRIBUTION RELEASE
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.PHONY: pydist
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pydist: build
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cd $(BUILDDIR); python setup.py sdist -d ../dist
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@echo "done"
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# RELEASE HELPERS
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# create new version to commit to master
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.PHONY: release-stage-1
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release-stage-1: dev-env bump clean-lite gen-package-lock
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@echo "Version bumped part:$(PART) and client built. Ready to commit and push"
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# build dist and release to dev pypi
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.PHONY: release-stage-2
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release-stage-2: dev-env pydist twine
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@echo "Dist built and uploaded to test.pypi.org"
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@echo "Test the install:"
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@echo " make install-release-test"
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@echo "Then upload to Pypi prod:"
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@echo " make twine-prod"
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.PHONY: release-stage-final
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release-stage-final: twine-prod
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@echo "Release uploaded to pypi.org"
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# DANGER: releases directly to prod
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# use this if you accidently burned a test release version number,
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.PHONY: release-directly-to-prod
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release-directly-to-prod: dev-env pydist twine-prod
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@echo "Dist built and uploaded to pypi.org"
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@echo "Test the install:"
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@echo " make install-release"
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.PHONY: dev-env
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dev-env: dev-env-client dev-env-server
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.PHONY: dev-env-client
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dev-env-client:
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cd client && $(MAKE) ci
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.PHONY: dev-env-server
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dev-env-server:
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pip install -r server/requirements-dev.txt
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# give PART=[major, minor, part] as param to make bump
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.PHONY: bump
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bump:
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bumpversion --config-file .bumpversion.cfg $(PART)
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.PHONY: twine
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twine:
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twine upload --repository-url https://test.pypi.org/legacy/ dist/*
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.PHONY: twine-prod
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twine-prod:
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twine upload dist/*
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# quicker than re-building client
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.PHONY: gen-package-lock
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gen-package-lock:
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cd client && $(MAKE) install
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# INSTALL
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# setup.py sucks when you have your library in a separate folder, adding these in to help setup envs
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# install from build directory
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.PHONY: install
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install: uninstall
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cd $(BUILDDIR); pip install -e .
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# install from source tree for development
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.PHONY: install-dev
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install-dev: uninstall
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pip install -e .
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# install from test.pypi to test your release
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.PHONY: install-release-test
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install-release-test: uninstall
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pip install --no-cache-dir --index-url https://test.pypi.org/simple/ --extra-index-url https://pypi.org/simple cellxgene
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@echo "Installed cellxgene from test.pypi.org, now run and smoke test"
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# install from pypi to test your release
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.PHONY: install-release
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install-release: uninstall
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pip install --no-cache-dir cellxgene
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@echo "Installed cellxgene from pypi.org"
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# install from dist
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.PHONY: install-dist
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install-dist: uninstall
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pip install dist/cellxgene*.tar.gz
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.PHONY: uninstall
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uninstall:
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pip uninstall -y cellxgene || :
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