fork/cellxgene
1
0
Fork 0
mirror of https://github.com/chanzuckerberg/cellxgene.git synced 2026-10-03 01:08:12 +08:00
Code Issues Packages Projects Releases Wiki Activity

server refactor (#1140)

Browse Source 
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.
This commit is contained in:
bmccandless
2020-02-19 10:22:35 -08:00
committed by GitHub
parent 349c413d8b
commit 907cc634f5
116 changed files with 2697 additions and 3252 deletions
Download Patch File Download Diff File Expand all files Collapse all files
Makefile
+13 -44
View File
@@ -34,24 +34,24 @@ build-client:
build-cli: build-client
git ls-files server/ | cpio -pdm $(BUILDDIR)
cp -r client/build/ $(CLIENTBUILD)
mkdir -p $(SERVERBUILD)/app/web/static/img
mkdir -p $(SERVERBUILD)/app/web/templates/
cp $(CLIENTBUILD)/index.html $(SERVERBUILD)/app/web/templates/
cp -r $(CLIENTBUILD)/static $(SERVERBUILD)/app/web/
cp $(CLIENTBUILD)/favicon.png $(SERVERBUILD)/app/web/static/img
cp $(CLIENTBUILD)/service-worker.js $(SERVERBUILD)/app/web/static/js/
mkdir -p $(SERVERBUILD)/common/web/static/img
mkdir -p $(SERVERBUILD)/common/web/templates/
cp $(CLIENTBUILD)/index.html $(SERVERBUILD)/common/web/templates/
cp -r $(CLIENTBUILD)/static $(SERVERBUILD)/common/web/
cp $(CLIENTBUILD)/favicon.png $(SERVERBUILD)/common/web/static/img
cp $(CLIENTBUILD)/service-worker.js $(SERVERBUILD)/common/web/static/js/
cp MANIFEST.in README.md setup.cfg setup.py $(BUILDDIR)
# If you are actively developing in the server folder use this, dirties the source tree
.PHONY: build-for-server-dev
build-for-server-dev: clean-server build-client
mkdir -p server/app/web/static/img
mkdir -p server/app/web/static/js
mkdir -p server/app/web/templates/
cp client/build/index.html server/app/web/templates/
cp -r client/build/static server/app/web/
cp client/build/favicon.png server/app/web/static/img
cp client/build/service-worker.js server/app/web/static/js/
mkdir -p server/common/web/static/img
mkdir -p server/common/web/static/js
mkdir -p server/common/web/templates/
cp client/build/index.html server/common/web/templates/
cp -r client/build/static server/common/web/
cp client/build/favicon.png server/common/web/static/img
cp client/build/service-worker.js server/common/web/static/js/
# TESTING
@@ -137,10 +137,6 @@ dev-env-client:
dev-env-server:
pip install -r server/requirements-dev.txt
.PHONY: gui-env
gui-env: dev-env
pip install -r server/requirements-gui.txt
# give PART=[major, minor, part] as param to make bump
.PHONY: bump
bump:
@@ -195,30 +191,3 @@ install-dist: uninstall
uninstall:
pip uninstall -y cellxgene || :
# GUI
.PHONY: build-assets
build-assets:
pyside2-rcc server/gui/cellxgene.qrc -o server/gui/cellxgene_rc.py
.PHONY: gui-spec-osx
gui-spec-osx: clean-lite gui-env
pip install -e .[gui]
pyi-makespec -D -w --additional-hooks-dir server/gui/ -n cellxgene --add-binary='/System/Library/Frameworks/Tk.framework/Tk':'tk' --add-binary='/System/Library/Frameworks/Tcl.framework/Tcl':'tcl' --add-data server/app/web/templates/:server/app/web/templates/ --add-data server/app/web/static/:server/app/web/static/ --icon server/gui/images/cxg_icons.icns server/gui/main.py
mv cellxgene.spec cellxgene-osx.spec
.PHONY: gui-spec-windows
gui-spec-windows: clean-lite dev-env
pip install -e .[gui]
pyi-makespec -D -w --additional-hooks-dir server/gui/ -n cellxgene --add-data server/app/web/templates;server/app/web/templates --add-data server/app/web/static;server/app/web/static --icon server/gui/images/icon.ico server/gui/main.py
mv cellxgene.spec cellxgene-windows.spec
.PHONY: gui-build-osx
gui-build-osx: clean-lite
pyinstaller --clean cellxgene-osx.spec
.PHONY: gui-build-windows
gui-build-windows: clean-lite
pyinstaller --clean cellxgene-windows.spec