ac13b31e13
* 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
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Developer convenience methods
Makefile
Documentation for the Makefile targets in the project root directory.
Build commands
builds source code
build - builds whole app client and server
build-cli - makes build dir and moves python and client files
build-client - runs webpack build
build-for-server-dev - builds client and copies output directly into source tree (only for server devlopment)
Clean commands
deletes generated files
clean - cleans everything including node modules (means build with take a while
clean-lite - cleans built directories
clean-server - cleans source tree
Dist commands
creates distribution for python module to upload to pypi
pydist - builds code and then builds sdist
Release commands
see release_process.md
Env commands
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
Installs cellxgene from different locations
install - installs from local build directory
install-dev - installs from local source tree
install-release-test - installs from test pypi
install-release - installs from pypi
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.
Runner scripts
start-frontend
About Serve the current client javascript independently from the server code.
Requires
- The server to be running. Best way to do this is with
make backend-dev make cito install the necessary node modules
Usage make start-frontend
backend-dev
About This script enables FE developers to run the REST API necessary to back the development server for the front end. It is intended to ensure that the FE developer gets the current version of the backend with a single command and no knowledge of python necessary. It creates and activates a virtual environment and installs cellxgene from the current branch.
Requires Python3.6 - virtual-env, pip
Usage make backend-dev. Optionally, you can then launch the node development server to serve the current state of
the FE with make start-frontend. You can also select a specific dataset using DATASET=<dataset path> make backend-dev.
You can also use CXG_OPTIONS to pass options to the cellxgene launch command, as in
CXG_OPTIONS='--experimental-annotations --experimental-annotations-file annotations.csv' make backend-dev.
Tips Developers will probably want to run this in parallel with the node dev server. You can either do this by running each in a separate termanial window or by running backend-dev in the background (add an & at the end of the command to run in the background: DATASET=<dataset> make backend-dev &).
Breakdown
| command | purpose |
|---|---|
| python3.6 -m venv cellxgene | creates cellxgene virtual environment |
| source cellxgene/bin/activate | activates virtual environment |
| yes | pip uninstall cellxgene || true | uninstalls cellxgene (if installed) |
| pip install -e . | installs current local version of cellxgene |
| cellxgene launch | launches cellxgene (must supply dataset as last parameter) |
Test scripts
test
About Run test locally. In order for this command to succeed you will need to give it a specific unit test to run. It won't pass if you run all tests as may be expected. This is because the unit tests and end to end (e2e) tests require different testing environments.
Usage make test
unit-test
About Runs all unit tests. It excludes any tests in the e2e folder. This is used by travis to run unit tests.
Usage make unit-test
smoke-test
About Starts backend development server and runs end to end tests. This is what travis runs. It depends on the e2e and the backend-dev targets. One starts the server, the other runs the tests. If developing a front-end feature and just checking if tests pass, this is probabaly the one you want to run.
Usage make smoke-test
e2e
About Runs backend tests without starting the server. You will need to start the rest api separately with the pbmc3k.h5ad file. Note you can use the JEST_ENV environment variable to change how JEST runs in the browser.
Usage make e2e