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* 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
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Developer convenience scripts
This document describes scripts for accelerating cellxgene development.
Paths are relative to the root project directory. If you need to know what
this is, run PROJECT_ROOT=$(git rev-parse --show-toplevel); echo $PROJECT_ROOT.
Project-level scripts
Build
Usage: from the $PROJECT_ROOT directory run:
make buildbuilds whole app client and servermake build-clientruns webpack buildmake build-for-server-devbuilds client and copies output directly into source tree (only for server devlopment)
Clean
Deletes generated files.
Usage: from the $PROJECT_ROOT directory run:
make cleancleans everything including node modules (means build with take a whilemake clean-litecleans built directoriesmake clean-servercleans source tree
Distribution
Creates distribution for python module to upload to pypi.
Usage: from the $PROJECT_ROOT directory run:
make pydistbuilds code and then builds sdist
Release
See release_process.md.
Development environment
Installs requirements files.
Usage: from the $PROJECT_ROOT directory run:
make dev-envinstalls requirements and requirments-dev (for building code)
Installing cellxgene packages
Usage: from the $PROJECT_ROOT directory:
install-dev- installs from local source treeinstall-release-test- installs from test pypiinstall-release- installs from pypiinstall-dist- installs from local dist folderuninstall- uninstalls cellxgene
Client-level scripts
Running the client
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 backend_dev.
make cito install the necessary node modules
Usage: from the $PROJECT_ROOT/client directory run 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: from the $PROJECT_ROOT directory run ./scripts/backend_dev
Options:
- In parallel, you can then launch the node development server to serve the
current state of the FE with
start-frontend, usually in a different terminal tab. - You can also select a specific dataset using
DATASET=<dataset path> ./scripts/backend_dev. - You can also use
CXG_OPTIONSto pass options to thecellxgene launchcommand, as inCXG_OPTIONS='--disable-annotations' ./scripts/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) |
Client test scripts
Methods used to test the client javascript code
Usage: from the $PROJECT_ROOT/client directory run:
make unit-testRuns all unit tests. It excludes any tests in the e2e folder. This is used by travis to run unit tests.make smoke-testStarts backend development server and runs end to end tests. This is what travis runs. It depends on thee2eand thebackend-devtargets. 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.make e2eRuns backend tests without starting the server. You will need to start the rest api separately with the pbmc3k.h5ad file. Note you can use theJEST_ENVenvironment variable to change how JEST runs in the browser.