* Cleanup the backend-dev convenience method
* Add the frontend_dev convenience method
frontend_dev is a soup-to-nuts convenience method for setting up the FE
development environment with node running a the client code on port 3000
with the a separate cellxgene package serving the API over port 5005 in
the background.
The script can be run from Finder.
* Update the developer scripts documentation
* Remove the 'test' make target in the client Makefile
Rationale:
* Given how long the smoke tests take to run, it is unlikely that
developers will want to run all tests together.
* It is unlikely that developers will have set up the backend server
properly for the tests to pass.
* Available commands should be safe-ish and not lend themselves to
confusing errors.
* You can still group tests by concatenating them in a make command, as
in `make unit-test smoke-test`.
* This target isn't used in any of our CI pipelines -- KISS.
* Some version of python3...
* Minor typos in docs
* Respond to feedback from @bkmartinjr
* Make adjustments so that DATASET path is predictable
* Simplify environment defaults a bit
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.
* Add smoke test for annotations features
* Do not save during annotations tests
* Fix botched rebase in dev guidelines
* Revert "Do not save during annotations tests"
This reverts commit f0bd970bb2.
* Respond to feedback from @bkmartinjr
* Collect all env vars in one, easy-to-find place
Past state:
* Default environement variables were stored in both client/package.json
and client/__tests__/e2e/config.js
* Constants that should have been linked--like the cellxgene server port
during testing--were repeated.
With this commit:
* All environment variables are parameterized
* All environment variables are packaged in default env files
* Move npm scripts to client Makefile
* Respond to feedback from @seve and @bkmartinjr
