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cellxgene/dev_docs/developer_guidelines.md
Matt Weiden f3015cb9df Makefile modularity, test targets, and auto-formatting (#1070) 
* Fix Makefile whitespace and .PHONY use

* Fix Makefile filename

* Modularize Makefile into client and server Makefiles

Part of the reason that the Makefile in the root directory is a bit
complicated is that it tries to handle tasks that can be handled
separately in the client and server modules.

This commit pushes some of the make logic specific to each module into
their own makefiles and calls out to those makefiles from that in the
project root.

* Add auto-formatting to client and server modules

One thing that can make linting faster is auto-formatting. This commit
adds the yapf auto-formatting tool to the server module and uses
eslint's "fix" functionality to speed up the linting/formatting process.

* Add yapf for automatic code formatting

* Add a root test target that calls sub-tests

* Apply yapf to python files

* Do not duplicate npm commands, simply pass through

* Update documentation

* Do not shadow reserved word len

* Add general test target

* Fix make call in dev-env

* Use black instead of yapf

* Run flake8 from the root directory

* Revert "Apply yapf to python files"

This reverts commit cdca128a01.

* Apply black to python code

* Resolve lint errors resulting from black format

* Add explanation of server unit tests in dev guidelines
2019-12-27 14:43:37 -08:00

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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.

Running test suite

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.

Unit tests

Steps to run the all unit tests:

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

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 make smoke-test
  4. To debug a failing test export JEST_ENV='debug' and re-run.

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 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: make install-dev 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

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

  1. For unit tests run npm run unit-test or make unit-test
  2. For the smoke test run npm run smoke-test or make smoke-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
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