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server refactor (#1140)

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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
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12
dev_docs/developer_scripts.md
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@@ -43,7 +43,6 @@ Installs requirements files
```
dev-env - installs requirements and requirments-dev (for building code)
gui-env - installs requirements and requirments-dev and requirments-gui (for building native app)
```
### install commands
@@ -59,17 +58,6 @@ install-dist - installs from local dist folder
uninstall - uninstalls cellxgene
```
### gui
Commands for building the native app
```
build-assets - builds the image and icon assets for the gui to pull from
gui-spec-osx - creates the initial spec file for osx, do not run unless you are starting from scratch, one time only
gui-spec-windows - creates the initial spec file for windows, do not run unless you are starting from scratch, one time only
gui-build-osx - builds the app from the osx spec file
gui-build-windows - builds the app from the windows spec file
```
## Client Makefile
The following phony `make` targets in `client/Makefile` are convenience methods for getting you up and developing.