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developer_guidelines.md

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Developer guidelines

Requirements

  • npm
  • Python 3.10+
  • Chrome

See dev section of README

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

Environment

For all make commands, common.mk automatically checks whether required environment variables are set and, if they are not set, assigns them default values from environment.default.json.

You can set these environment variables manually with the export shell command, as in export JEST_ENV=debug, or you can just pass the variables as part of the command. E.g., HEADFUL=true make e2e or JEST_ENV=debug npm run e2e

Running test suite

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

Unit tests

Steps to run the all unit tests:

  1. Start in the project root directory
  2. make dev-env
  3. make unit-test

To run unit tests for the client code only:

  1. Start in the project root directory
  2. cd client
  3. make unit-test

End to end tests

To run E2E tests, run cd client and make smoke-test

Flags

  1. JEST_ENV: This enables the following E2E test options. You can find their corresponding configs in jest-puppeteer.config.js:

    • dev - opens window, runs tests with minimal slowdown, close on exit.
    • debug - opens window, runs tests with 100ms slowdown, dev tools open, chrome stays open on exit.
    • prod[default] - run headless with no slowdown, window will not open.

  2. HEADFUL: Default is false. When set to true, it will launch the Chrome window for visual inspection. E.g., HEADFUL=true npm run e2e

  3. HEADLESS: Default is true. When set to false, it will launch the Chrome window for visual inspection. E.g., HEADLESS=false npm run e2e

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 e2e from the client directory

  4. To debug a failing test, add debugger in any line of JS code as breakpoint, and launch the test again with ndb. E.g., ndb make e2e or ndb npm run e2e.

    1. Please make sure to install ndb via npm install -g ndb

    2. Check out Debugging Tips for more ideas!

To run end to end tests exactly as they will be run on CI use the following command

JEST_ENV=prod make pydist install-dist dev-env smoke-test

Server dev

Install

To install from the source tree

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

To install from a candidate python distribution

  • Make the distribution: make pydist
  • Install it: make install-dist

Launch

  • cellxgene launch [options] <datafile> or make start-server

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 python and black for auto-formatting.

To auto-format code run make fmt. To run lint checks on the code run make lint.

Test

If you would like to run the server tests individually, follow the steps below

  1. Install development requirements make dev-env
  2. Run make unit-test in the server directory or make unit-test-server in the root directory.

Tips

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

Client dev

Install

  1. Install prereqs for client: make dev-env
  2. Install cellxgene server as described in the server install instructions above.

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 to source files.

  1. Launch server (the client relies on the REST API being available): cellxgene launch --debug [other_options] <datafile> or make start-server
  2. Launch client: in client/ directory run make start-frontend
  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

If you would like to run the client tests individually, follow the steps below in the client directory

  1. For unit tests run make unit-test
  2. For the smoke test run make smoke-test for the standard smoke test suite and make smoke-test-annotations for the annotations test suite.

If you would like to run the smoke tests against a hot-reloaded version of the client:

  1. Start the hot-reloading servers as described in the Client dev section. If you plan to run the standard test suite (without annotations), you'll have to start the backend server with annotations disabled (e.g. CXG_OPTIONS='--debug --disable-annotations' make start-server).
  2. From the project root, cd client
  3. Run either the standard E2E test suite with npm run e2e or the annotations test suite with npm run e2e-annotations

Tips

  • You can also install/launch the server side code from npm scrips (requires python3.10 with virtualenv) with the scripts/backend_dev script.

  • Check out e2e Tests for more details