Auspice

Auspice

  • Docs

›Contributing

Introduction

  • Overview
  • Install Auspice
  • How to Run Auspice

Advanced Functionality

  • Displaying multiple trees
  • View Settings
  • Adding extra metadata via CSV/TSV
  • Miscellaneous

Customising Auspice

  • Customising Auspice
  • Client Customisation API
  • Requests Made from the Client

Using a Custom Server

  • Auspice servers
  • Server API
  • Authentication

Narratives

  • Communicating Results Using Narratives
  • Writing a Narrative
  • Converting a narrative to PDF

Release Notes

  • Changelog
  • Auspice Version 2.0

Contributing

  • Contributing to Auspice development

Contributing to Auspice development

Thank you for helping us to improve Nextstrain!

To get started, please see the contributing guide for useful information about how to pick an issue, submit your contributions, and so on.

This project strictly adheres to the Contributor Covenant Code of Conduct.

Please see the project boards for currently available issues.

Contributing code

Code contributions are welcomed! Please see the main auspice docs for details on how to install and run auspice from source.

Please comment on an open issue if you are working on it. For changes unrelated to an open issue, please make an issue outlining what you would like to change/add.

Where possible, please rebase your work onto master rather than merging changes from master into your PR.

Make sure tests are passing

When you submit a pull request to the auspice repository, a variety of integration and unit tests will need to pass before it can be merged.

You will likely want to run these tests locally before submitting:

First, install the dependencies with npm i, then:

For unit tests:

Run npm test.

For linting:

Run npm run lint. If there are issues run npm run lint:fix.

For integration tests:

  1. Fetch the datasets with npm run get-data and npm run get-narratives.
  2. Ensure you are not currently running the site locally, then run npm run integration-test:ci.

For smoke tests:

  1. Fetch the datasets with npm run get-data and npm run get-narratives.
  2. Ensure you are not currently running the site locally, then run npm run smoke-test:ci.

Contributing to Documentation

Nextstrain documentation is available at nextstrain.github.io/auspice/.

This documentation is built from files contained within the Auspice GitHub repo -- see the docs-src/README within the docs-src directory for more details and instructions on how to contribute.

Note that currently the documentation must be rebuilt & pushed to GitHub after a new version is released in order for the changelog to correctly appear at nextstrain.github.io/auspice/releases/changelog.

Contributing to Internationalization and Localization (i18n/l18n)

If you can assist in efforts to translate the Auspice interface to more languages your assistance would be very much appreciated. The currently available languages are displayed via a drop-down at the bottom of the sidebar.

Adding a new language:

  1. Add the language to the getlanguageOptions function in this file
  2. If this is a new language, copy the folder (and the JSONs within it) src/locales/en and name it to match the language code for the new translation -- e.g. for Spanish this would be src/locales/es
  3. For each key-value in the JSONs, translate the english phrase to the new locale. (Do not modify the strings within {{...}} sections.)

For example, a spanish translation would change the English:

  "sampled between {{from}} and {{to}}": "sampled between {{from}} and {{to}}",
  "and comprising": "and comprising",

to

  "sampled between {{from}} and {{to}}": "aislados entre {{from}} y {{to}}",
  "and comprising": "y compuesto de",

Helper script to check what parts of a translation are out-of-date or missing:

Run npm run diff-lang -- X, where X is the language you wish to check, for instance es. This will display the strings which:

  • need to be added to the translation
  • are present but should be removed as they are no longer used
  • are present but are simply a copy of the English version & need to be translated

Running npm run diff-lang will check all available languages.

Improving an existing translation:

If a translation of a particular string is not yet available, then auspice will fall-back to the english version.

  1. Find the relevant key in the (EN) JSONs in this directory
  2. Add the key to the JSON with the same name, but in the directory corresponding to the language you are translating into (see above for an example).

Releases & versioning

New versions are released via the ./releaseNewVersion.sh script from an up-to-date master branch. It will prompt you for the version number increase, push changes to the release branch and, as long as Travis-CI is successful then a new version will be automatically published to npm.

Last updated on 24/03/2020
← Auspice Version 2.0
  • Contributing code
    • Make sure tests are passing
  • Contributing to Documentation
  • Contributing to Internationalization and Localization (i18n/l18n)
  • Releases & versioning
Auspice
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If you use auspice, please cite Hadfield et al., 2018
Copyright © 2014-2020 Richard Neher & Trevor Bedford