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:

rm -rf _site && bundle exec jekyll serve --incremental --trace

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).

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.

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!

A lot of the components of this web page are automatically generated and YOU SHOULD NOT MAKE ANY MANUAL CHANGES TO THE CONTENT UNLESS YOU ARE 100% SURE THAT YOU SHOULD :)

Luckily, you can update EVERYTHING all at once, and synchronize author and help pages to the latest in anvi'o codebase, by running this command in your local copy of the repository:

_scripts/update-all.sh

Please remember the following items before doing this:

• Every script update-all.sh runs will assumes that you are in the root directory of the web repository (such as ~/github/anvio.org/), so don't use absolute paths to run anything under _sripts directory from somewhere else.
• Every script will assume that you have an anvi'o git repository at ~/github/anvio -- please make sure it is the case, and make sure you have checked out the master branch with a clean git pull (so your repository is fully synced with the upstream).
• Every script will ALSO assume that you are in an anvi'o environemnt. I.e., when you run anvi-self-test --version you do not get a command not found error, and see the anvio-dev as the version (i.e., anvi'o is not installed on your system but you are set up to be tracking the active development repo).
• Make sure to run the update-all.sh (or any other script for that matter) while you are not running the Jekyll server. You should start your local Jekyll server to see how things are only after the scripts are successfully finished running. And you should always run the Jekyll locally to make sure you are not getting any weird errors during runtime and things are looking as you expect them to look :)

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.

To update the list of anvi'o authors and contributors, as well as their GitHub contributions, run this (everything below will assume that you have the up-to-date git repository for anvi'o at and you have checkedout the master branch):

_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.

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.

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