cellxgene/dev_docs/developer_guidelines.md

Developer guidelines

Requirements

• npm
• Python 3.6+
• Chrome

See dev section of README

All instructions are expected to be run from the top level cellxgene directory unless otherwise specified.

Server dev

Install

• Build the client and put static files in place: make build-for-server-dev
• Install from local files: make install-dev

Launch

• cellxgene launch [options] <datafile>

Reloading

If you install cellxgene using make install-dev the server will be restarted every time you make changes on the server code. If changes affects the client, the browser must be reloaded.

Linter

We use flake8 to lint code. Travis CI runs flake8 server.

Test

1. Install development requirements pip install -r server/requirements-dev.txt
2. Run tests pytest server/test

Tips

• Install in a virtualenv
• May need to rebuild/reinstall when you make client changes

Client dev

Install

1. Install prereqs for client: npm install --prefix client/ client
2. Install cellxgene server: pip install -e . Caveat: this will not build the production client package - you must use the server install instructions above to serve web assets.

Launch

To launch with hot reloading you need to launch the server and the client separately. Node's hot reloading starts the client on its own node server and auto-refreshes when changes are made.

1. Launch server (the client relies on the REST API being available): cellxgene launch [options] <datafile>
2. Launch client: in client/ directory run npm run start
3. Client will be served on localhost:3000

Build

To build only the client: make build-client

Linter

We use eslint to lint the code and prettier as our code formatter.

Test

In client/ directory run npm run unit-test

Tips

• You can also install/launch the server side code from npm scrips (requires python3.6 with virtualenv) in client/ directory run npm run backend-dev

Running tests

Client and server tests run on Travis CI for every push, PR, and commit to master on github. End to end tests run nightly on master only.

Server unit tests

Install development requirements pip install -r server/requirements-dev.txt Run tests pytest server/test

Client unit tests

In client/ directory run npm run unit-test

End to end tests

End to end tests use two env variables:

• JEST_ENV - environment to run end to end tests. Default dev
  • prod - run headless with no slowdown, chromium will not open.
  • dev - opens chromimum, runs tests with minimal slowdown, close on exit.
  • debug - opens chromium, runs tests with 100ms slowdown, dev tools open, chrome stays open on exit.
• JEST_CXG_PORT - port that end to end tests are being run on. Default 3000 (client hosted port).

On CI the end to end tests are run with JEST_ENV set to prod using the smoke-test npm script

To run end to end tests as they will be run on CI

1. cellxgene should be built and installed as specified in server dev
2. export JEST_ENV='prod'
3. export JEST_CXG_PORT='5000'
4. Run npm run --prefix client/ smoke-test

Run end to end tests interactively during development

1. cellxgene should be installed as specified in client dev
2. Follow launch instructions for client dev with dataset example-dataset/pbmc3k
3. Run npm run --prefix client/ e2e
4. To debug a failing test export JEST_ENV='debug' and re-run.