Giter Club home page Giter Club logo

openfreeenergy.github.io's Introduction

Website for OpenFreeEnergy

To build the website locally, you'll create a conda environment and install the website's bundle within that. Once you have conda installed, and this repo cloned, the commands to run (from within the root directory of this repo) are:

conda env create --file environment.yml
conda activate ofe-website
bundle install

From there you can launch a local web server with

bundle exec jekyll serve

or, if you want to have the website automatically update as you make changes:

bundle exec jekyll serve --watch

Contents:

Adding news items

News items are stored in the _posts/ directory. Each item is a file. That file must be named in the format YYYY-MM-DD-TITLE where YYYY-MM-DD gives the year month and day for the post. With this, it is possible to backdate posts.

The file will is Markdown format with YAML frontmatter. The YAML frontmatter should include the following:

  • layout: post: News items should use the post layout.
  • title: The title of the post.
  • categories: space-separated list of categories. Categories we encourage are names of specific software packages (e.g., gufe, openfe, lomap) and types of news item (e.g., releases, presentations, hirings).

Adding new team members

Each team member has a file that is just a markdown file with YAML frontmatter. Only the frontmatter is filled in. The frontmatter includes the following fields:

  • name: Full name as you want it on the website
  • position: Title at OpenFreeEnergy
  • image_path: URL or path to an image. We frequently use our GitHub avatars (in which case this should be the whole https URI). If using a file, place it in the assets/images/team/ directory. In that case, note that the image_path should have a preceding slash (i.e., /assets/images/team/image.jpg)
  • github: You GitHub username
  • scholar [optional]: A link to your Google Scholar profile. Should include everything that comes after https://scholar.google.com/ in your profile's URL. Leave this blank if you don't want to include your Google Scholar link.
  • blurb: A brief paragraph describing yourself.

You can copy _team/_defaults.md to get a template. You can see the rendered versions at https://openfree.energy/team/.

Adding new packages to our projects page

The details for these are in files in _projects/. Make a copy of _defaults.md. Note that these are markdown files with YAML frontmatter (although all you do is fill in the YAML). Fill in each of the fields. role can be one of flagship, developers, maintainers. Within each role, projects are listed alphabetically by filename.

Tracking upstream changes

It turns out this theme is poorly designed for customization. So I'm keeping in here our overrides along with the diff of the original, which will hopefully make future maintenance updates a little easier.

When creating a diff, it should always be

diff installed_file our_file > _file.diff

This way, we can check whether updated versions of the theme made changes to the files that we have changed -- if that diff is exactly the saved diff, then no changes have been made upstream.

You can find the location of the installed file with:

bundle info --path jekyll-theme-hydra

openfreeenergy.github.io's People

Contributors

dwhswenson avatar richardjgowers avatar jameseastwood avatar riesben avatar mikemhenry avatar diegoonolasco avatar ialibay avatar hannahbaumann avatar yoshanuikabundi avatar

Stargazers

 avatar

Watchers

 avatar  avatar

openfreeenergy.github.io's Issues

Add backdated news items

This isn't necessary for first launch, but keep in mind that we can backdate "news" ("blog") posts -- so we can write them for things like hire dates or previous releases. This can help us fill out some content in the short term.

Change URL for news items?

Right now, our URLs for news items include the "categories" (which we're actually treating as unordered tags). Example, a URL with categories lomap and release gives:

https://openfree.energy/lomap/release/2022/03/15/lomap-conda-forge/

Since we don't have a defined ordering on these, this could just as easily have been release/lomap/2022/03/15/lomap-conda-forge/. I think we should change this. Two ways to change (both about equally easy):

  1. Distinguish between actual categories and tags. Each post must have 1 category. Possible categories include:

    • releases
    • hirings
    • presentations
    • science
    • misc

    We aren't locked into any set; we can always add more categories later as needed. This could be nice from a URL standpoint because we could have openfree.energy/releases/ as an index with all releases, and then within it openfree.energy/releases/2022/03/15/lomap-conda-forge/ .

  2. Completely remove these labels from the URL. In this case, I'd probably want to add news/ as a level, and the URL would be openfree.energy/news/2022/03/15/lomap-conda-forge/

Either solution should be easy to implement (probably took me longer to write this issue).

Note that changing the URLs will break any existing links to them... but I highly doubt we have many incoming links to our 2 little news items.

Adding an Emeriti Page/Section

This is something that came up, during some discussions.

I think it would be really nice to have an Emeriti Section on the team page. (we could also add a Emeriti page, but I think that's to much Pages in the end. ;) )

1.0 release post-publication

Couple of things post-publication:

  1. Is there a missing picture?
  2. Bullet points are missing

i.e. "Relative Binding/Hydration Free Energy Calculations using the Hybrid Topology approach, including the capability of charge changing transformations Absolute Hydration Free Energy Calculations “Vanilla” Molecular Dynamics (MD) simulations Automated setup approaches for the calculations Automated analysis of results" should have bullet points.

Would you be able to update this accordingly @jameseastwood ?

Better team pictures?

For future consideration: We might get different pics (at least, some of us). They're a little blurry (especially noticeable on Mike), and Irfan looks... very different in real life.

GA Shows Up in Website

I am not sure how GA is showing up.
This bit seems to indicate that we have to have a site key set for it to add the script: https://github.com/OpenFreeEnergy/openfreeenergy.github.io/blob/main/_layouts/default.html#L14-L21

But it seems to be putting the script in anyway (viewing page source)

<script>
	window.ga=window.ga||function(){(ga.q=ga.q||[]).push(arguments)};ga.l=+new Date;
	ga('create', '', 'auto');
	ga('send', 'pageview');
</script>
<script async src='[https://www.google-analytics.com/analytics.js](view-source:https://www.google-analytics.com/analytics.js)'></script>

I wonder if instead of having our key set like this

google_analytics_key:

If it needs to be

google_analytics_key:''

or something

Improve "About" section

The target audience for this should be people who might fund OpenFE, and want to know more about what we're doing.

Add landing page images

  • Image for "Open Source"
  • Image for "Binding free energy"
  • Image for "Drug design and discovery"

First thoughts are:

  • Open source: that cheesy low-f image of a screen of code (maybe try to make it Python code, not HTML like everyone else does 😂)
  • BFE: Maybe a thermodynamic cycle similar fig 2 in the livecoms best practices
  • Drug design and discovery: Maybe one of our atom mapping visualizations for something interesting-looking?

CSS Issues

I'm using this issue to collect a few things that where we should eventually tweak the CSS to look better. This isn't high priority stuff, but if someone feels like taking a break from real coding to play with CSS for an hour or so, you can probably get some of these fixed.

Slightly important issues:

  • Hover transition on Read More links (News page): Until hover, the buttons use our color scheme. On hover, the transition reverts it to the old base theme color (solved in #24)
  • Links (in other-blue) are insufficiently distinct from the text. I tried increasing line weight; it seemed like overkill. Maybe a dashed underline would do it?

Very minor issues:

  • index page, OMSF banner: link is an unofficial color (but we might have to select something from outside the official set)
  • footer: links are unofficial color
  • Team page: GitHub icons aren't styled to match the link color
  • Team page: Names aren't styled according to our color scheme. Our names should be in badass-blue (obviously!)
  • Team page: blurb should probably have some spacing before it starts
  • News page Blog post h3 titles in li use the wrong font (this is a bug in the original theme)
  • Tags for news items: not using official colors. At least background should be either sandy Sergio or Sergio's cousin
  • Tags for news items: Forcing first-letter upper is wrong. These should be all-lower (this is a theme layout issue).

None of these should be considered blockers. They're just relatively low-hanging fruit that we can deal with whenever we have time.

Add Hannah to the website

@hannahbaumann : As part of your onboarding, we also usually ask you to add yourself to the team page of the website!

There are instructions in the README of this repo, you can see the recent PR where James added himself in #59, and you can see all of our individual pages in the _team/ directory. The results, after merged, will show up at https://openfree.energy/team/

For a picture, you can either use an existing online image (several of us use our GitHub avatars), or you can upload a picture as part of your PR.

Recommend Projects

  • React photo React

    A declarative, efficient, and flexible JavaScript library for building user interfaces.

  • Vue.js photo Vue.js

    🖖 Vue.js is a progressive, incrementally-adoptable JavaScript framework for building UI on the web.

  • Typescript photo Typescript

    TypeScript is a superset of JavaScript that compiles to clean JavaScript output.

  • TensorFlow photo TensorFlow

    An Open Source Machine Learning Framework for Everyone

  • Django photo Django

    The Web framework for perfectionists with deadlines.

  • D3 photo D3

    Bring data to life with SVG, Canvas and HTML. 📊📈🎉

Recommend Topics

  • javascript

    JavaScript (JS) is a lightweight interpreted programming language with first-class functions.

  • web

    Some thing interesting about web. New door for the world.

  • server

    A server is a program made to process requests and deliver data to clients.

  • Machine learning

    Machine learning is a way of modeling and interpreting data that allows a piece of software to respond intelligently.

  • Game

    Some thing interesting about game, make everyone happy.

Recommend Org

  • Facebook photo Facebook

    We are working to build community through open source technology. NB: members must have two-factor auth.

  • Microsoft photo Microsoft

    Open source projects and samples from Microsoft.

  • Google photo Google

    Google ❤️ Open Source for everyone.

  • D3 photo D3

    Data-Driven Documents codes.