Contributing

Quilt is an open source project, and we welcome contributions from the community.

Contributors must adhere to the Code of Conduct.

Reporting issues

Unsure about something? To get support, check out our Slack channel.

Found a bug? File it in our GitHub issues.

Cloning

To work on quilt you will first need to clone the repository.

$ git clone https://github.com/quiltdata/quilt

You can then set up your own branch version of the code, and work on your changes for a pull request from there.

$ cd quilt
$ git checkout -B new-branch-name

Local package development

Environment

Use pip to install quilt locally (including development dependencies):

$ cd api/python
$ pip install -e .[extra]

This will create an editable install of quilt, allowing you to modify the code and test your changes right away.

Testing

All new code contributions are expected to have complete unit test coverage, and to pass all preexisting tests.

Use pytest to test your changes during normal development. To run pytest on the entire codebase:

$ cd api/python/tests
$ pytest

Local catalog development

Note that, at the current time, it is only possible to run a local catalog if you already have a catalog deployed to AWS, because the catalog relies on certain services (namely, AWS Lambda and the AWS Elasticsearch Service) which cannot be run locally.

Environment

Use npm to install the catalog (quilt-navigator) dependencies locally:

$ cd catalog
$ npm install

There is one known issue with installation. At time of writing, the quilt-navigator package depends on iltorb@1.3.10, which may lack prebuilt binaries for your platform and may fall back on building from source using node-gyp. node-gyp depends on Python 2; if you only have Python 3 in your install environment it will fail.

To fix this, point npm to a Python 2 path on your machine. For example on macOS:

$ npm config set python /usr/bin/python
$ npm install

Next, you need to create a config.json and federation.json file in the catalog/static subdirectory. For federation.json use the following template:

{
   "buckets": [{
         "name":"quilt-example",
         "title":"Title here",
         "icon":"placeholder icon here",
         "description":"placeholder description here",
         "searchEndpoint":"$SEARCH_ENDPOINT",
         "apiGatewayEndpoint": "$PREVIEW_ENDPOINT",
         "region":"us-east-1"
      }
   ]
}

For config.json use the following template:

{
   "federations": [
      "/federation.json"
   ],
   "suggestedBuckets": [
   ],
   "apiGatewayEndpoint": "$PREVIEW_ENDPOINT",
   "sentryDSN": "",
   "alwaysRequiresAuth": false,
   "defaultBucket": "quilt-staging",
   "disableSignUp": true,
   "guestCredentials": {
      "accessKeyId": "$ACCESS_KEY_ID",
      "secretAccessKey": "$SECRET_ACCESS_KEY"
   },
   "intercomAppId": "",
   "mixpanelToken": "",
   "registryUrl": "$REGISTRY_ENDPOINT",
   "signInRedirect": "/",
   "signOutRedirect": "/"
}

Build

To build a static code bundle, as would be necessary in order to serve the catalog:

$ npm run build

To run the catalog in developer mode:

$ npm start

This uses webpack under the hood to compile code changes on the fly and provide live reloading, useful when developing.

Make sure that any images you check into the repository are optimized at check-in time.

Testing

To run the catalog unit tests:

npm run test

Creating a release

1. Once you are ready to cut a new release, you update the version in

   VERSION

   file and create a new git tag with git tag $VERSION, e.g. git tag 3.1.8.

2. Once you push the tag to GitHub with git push --tags a new CircleCI build is triggered.

3. Merge the new PR into master so the setup.py reflects the latest package.

Updating documentation

Documentation is served via GitBook, and is based on the docs/ folder in the master branch of the quilt repository.

Documentation changes go live at pull request merge time. There is currently no way to preview documentation updates except locally.

Updating the API Reference

The API Reference section of the documentation is served by processing the docstrings in the codebase using a script. We use our own fork of the pydoc-markdown package to do the necessary work.

To modify the API Reference, modify the docstring associated with a method of interest.

Then, run the following to install the latest version of our docstring parser:

pip install git+git://github.com/quiltdata/pydoc-markdown.git@quilt

Then navigate to the gendocs directory and execute python build.py.

The resulting files will land in docs/ and will be ready to be checked in.

Updating everything else

All other pages in the documentation are served from corresponding Markdown pages in the docs directory. To edit the page, edit the Markdown file. Then check that file in.

License

Quilt is open source under the Apache License, Version 2.0.