Source code for the anvi'o community web page served at https://anvio.org

After getting a copy of it, you can run this web page on your local using the following command:

bundle exec jekyll serve --incremental

Once you run a copy of the web page, visit http://localhost:4000/web-tips/ to find some useful tips for content developers.

If you get an error like this:

/var/lib/gems/3.0.0/gems/jekyll-4.2.1/lib/jekyll/commands/serve/servlet.rb:3:in `require': cannot load such file -- webrick (LoadError).

You can just run this command to install Webrick toolkit:

bundle add webrick

After Webrick succesfully installed, you can run this web page on your local using the following command:

bundle exec jekyll serve --incremental --trace

Contributing

If you have any questions regarding anything below, please get in touch with us on the anvi'o Slack channel (an up-to-date link is at the top of the front page of https://anvio.org).

Update / add new anvi'o resources defined in the main page

Please edit the relevant file under _data/resources/ in this repository. To add a new resource, you don't need to do anything in the anvi'o codebase, unless the author of the resource is not defined in _data/people.yaml. If that is the case, you will first have to take care of it by adding them into DEVELOPERS.yaml or CONTRIBUTORS.yaml. If you'd like to do it yourself, please read the section below on how to 'update people data'. If you don't want to deal with that, please reach out to an anvi'o developer.

Updating the resouces file should be easy. But please note that the order of items in that file should have a logical order from basic to more advanced things within each section. Follow an example for variables and language, and try to use existing tags unless there is certainly a need to define a new one.

Contribute a blog post or tutorial to be hosted on anvio.org

If you would like to write a blog post or tutorial for the anvi'o web page, anvio.org would be more than happy to host you!

Upkeeping

A lot of the components of this web page is dynamic, but others require some hands-on upkeeping (at least for now). You can update EVERYTHING all at once by running this command:

_scripts/update-all.sh

Please remember: Everything above and below assumes that you are tracking the development branch of anvi'o, and you are working with an up-to-date repository, unless otherwise is stated. Please don't forget to double-check git status to make sure you know what you're about to commit.

The following sections clarify individual updates that are run by update-all.sh script. If you run that, you don't need to run any of the ones below, but they're here for posterity.

Update people data

To update the list of anvi'o authors and contributors, run this (assuming your anvi'o code directory is at ~/github/anvio):

_scripts/update-people-data.sh

If there is a new name to be mentioned in _data/resources.yaml, their GitHub username must be first mentioned in _data/people.yaml. If they are not in there, please first add their information to either DEVELOPERS.yaml or CONTRIBUTORS.yaml in the anvi'o repository following the style of the previous entries, and then run _scripts/update-people-data.sh from the root directory of the anvio.org repository. Yes, it is tedious, but also very important to keep track of people in both repositories.

Please see this README file in the anvi'o repository to see how you can improve the accurate tracking of anvi'o indivdiuals.

Update help pages

Help pages are served at, https://anvio.org/help/main or (http://localhost:4000/help/main if you are running the web page on your local) for the active development branch. Others can be found under help/7 or help/7.1 (which will be consolidated into a single help/stable folder in the future).

Never edit the help pages manually or in the anvio.org repository. They are meant to be updated in the anvi'o main repository under anvio/docs. What is rendered on the web page is automatically generated by anvi'o (because that's how cool anvi'o is).

To update the help pages on the web with the latest changes in anvi'o main repository, run this command:

anvi-script-gen-help-pages -o help/main

But please do not update help/7 or help/7.1 and contact Meren if there is something wrong with any of the files under them.

Triple check git status to make sure you know what you're about to commit.

Update the anvi'o programs and concepts network

The anvi'o network is served at https://anvio.org/network or at http://localhost:4000/network if you are running the web page on your local.

To update the help pages with the latest changes in anvi'o main repository, run this command:

anvi-script-gen-programs-network -o network/network.json