manubot / manubot.org

Source code for https://manubot.org

manubot.org webpage source code

Acknowledgements

Cross-browser tested with:

manubot.org's Issues

Update philosophy section with Manufesto

We should update the Philosophy Section to include a mention / link to https://manubot.github.io/manufesto/. Currently, the section reads:

manubot.org/index.html

Lines 242 to 284 in 5dce1aa

	<section id="our-philosophy">
	<h3>
	Our Philosophy
	</h3>
	<div class="row">
	<p>
	Manuscripts are the primary basis of scholarly communication, yet the
	process of creating them has not kept in step with the advancement of
	technology or the evolving best-practices of science.
	</p>
	<p>
	Traditionally, authoring of manuscripts takes place in a closed manner.
	While most scientific material is eventually distributed to some kind of
	public medium, the process of developing and reviewing the material is
	usually done in private, contained to a handful of individuals. The tools
	used are often outmoded, restrictive, and overall poorly-suited for the
	task of collaborative, scientific writing. The time it takes to review and
	publish can be
	<a
	href="https://www.nature.com/news/does-it-take-too-long-to-publish-research-1.19320"
	>unreasonably long</a
	>.
	</p>
	<p>
	We believe that this process is antiquated and must be reformed. Good
	science depends upon many things that the conventional approach doesn't
	provide: A diversity of input and perspectives. Spontaneous and
	cross-discipline contributions. Organic and wide-spread discovery and
	dissemination of knowledge. The fostering of a free, global information
	commons. A method of real-time, continuous science, performed entirely in
	the open.
	</p>
	<p>
	Current technology easily affords huge advantages over the old way of
	doing things, both in convenience and in the quality of the result.
	Manubot is a solution to the past and a push towards a future ideal, where
	scientific writing is transparent, reproducible, immediate,
	permissionless, versioned, automated, collaborative, open, linked,
	provenanced, decentralized, hackable, interactive, annotated, and free of
	charge.
	</p>
	</div>
	</section>

@vincerubinetti do you have a preferred implementation of how we should mention the Manufesto?

Add steering committee

In addition to adding the current steering committee members to manubot.org, we might also discuss long term plans about governance, diversity, etc.

"tagline"

Would be good to have a standardized "tagline" for Manubot. @dhimmel @slochower @agitter Suggestions would be nice. We should have a short one -- 4 to 5 words -- that can fit in the document title/tab, and we can also have a longer one -- 10 to 20 words -- that will appear underneath the logo right up front.

Here are some of my off-the-cuff ideas:

• The future of scholarly publishing
• Automated publishing for the future
• Academic publishing for the new age

Ideally something that captures the main purpose/point of manubot existing, as well as some of its more essential features. Naturally it'll be impossible to capture everything it does, so just the most important stuff up front.

Site down?

https://manubot.org and https://het.io/ seem to be down. No outages reported at GitHub Status, and my many other gh-pages sites seem to be fine, including those hosted at a custom domain. I see a deploy was made a few days ago, but the gh-pages branch looks relatively normal. There's at least an index.html, so something should be showing up. Did something change with the management of the domains?

@dhimmel

Enable right-click options to work on cycling images

New website at https://manubot.org looks great. The cycling images are a nice feature. However, I am having trouble saving / opening in a new tab images that are not first in the rotation. Is it possible to make it so right-click open image in new tab will open the currently displayed image rather than the first image in the rotation?

Rebuild manubot.org/catalog when upstream catalog updates

https://manubot.org/catalog/ is generated here from the catalog.json file created by https://github.com/manubot/catalog. When a commit is made to the master branch of manubot/catalog, then catalog.json is generated by CI and deployed to https://manubot.github.io/catalog/catalog.json. However, this repository doesn't then automatically rebuild. Until this repository is rebuilt, the updated catalog data won't display at https://manubot.org/catalog/.

I've enabled a Travis cron job to run CI once a day:

Therefore, updates to manubot/catalog should deploy to the website within a day.

However, we could also consider whether the manubot/catalog CI deployment should trigger a manubot.org build, as discussed here.

Add Matomo analytics tracking

I realized we haven't set up analytics for this website, which is kind of a bummer cause I would have liked to see how the publication increased traffic. Better late than never.

Matomo suggests the following code:

<!-- Matomo -->
<script type="text/javascript">
  var _paq = window._paq || [];
  /* tracker methods like "setCustomDimension" should be called before "trackPageView" */
  _paq.push(['trackPageView']);
  _paq.push(['enableLinkTracking']);
  (function() {
    var u="https://piwik.dhimmel.com/";
    _paq.push(['setTrackerUrl', u+'matomo.php']);
    _paq.push(['setSiteId', '9']);
    var d=document, g=d.createElement('script'), s=d.getElementsByTagName('script')[0];
    g.type='text/javascript'; g.async=true; g.defer=true; g.src=u+'matomo.js'; s.parentNode.insertBefore(g,s);
  })();
</script>
<noscript><p><img src="https://piwik.dhimmel.com/matomo.php?idsite=9&amp;rec=1" style="border:0;" alt="" /></p></noscript>
<!-- End Matomo Code -->

@vincerubinetti do you want to integrate this to the right place in the jekyll?

GitHub pages doesn't support custom Jekyll plugins

The only way to load the catalog from an external .json file is to write a custom plugin. There is this old plugin that can fetch external data, but it is unmaintained and doesn't seem to work, even locally.

I took that old plugin's code and modified it to at least work locally, as follows:

require 'open-uri'

module Fetch_Catalog
  class Generator < Jekyll::Generator
    def generate(site)
      site.data['catalog'] = JSON.load(open('https://manubot.github.io/catalog/catalog.json'))
    end
  end
end

Basically it uses a Ruby-built-in open function to get the external resource, then parses it as JSON, and adds it to the global variable site.data.catalog, which any page/template can access and then display.

However after much troubleshooting, I found that GitHub pages does not support these types of plugins. It seems like this is the old way to do it, with a plain .rb ruby script file, and the new preferred way is to have it as a gem package, which I guess is more easy to maintain and more secure? But making it a package like this is more involved and I'm not familiar enough with Ruby to do it in a timely manner. Also, even if I was able to make it, it seems GitHub pages might only support a small white-list of gem packages, too, though that is still unclear to me.

So, we'll have to set up a CI for this instead to get it to work.

Move catalog thumbnails to their respective repositories

Just made this issue about thumbnails being stored in the manuscript repo itself:
manubot/rootstock#267

As such, we should eventually move the thumbnails that are right now stored in this repo to their respective repos. This will also be a good excuse to update the rootstock theme for all those manuscripts, because I see that some of the papers are using old CSS with glitches.

For the papers that we don't directly control, I can even submit PRs for.

Once we do this, we can change the catalog script to fetch the thumbnails from the repos instead (hopefully that is easy).

"Why use Manubot" or testimonials section

Copying from #6 (comment)

What if we add a "Why use Manubot?" section with 3-4 hypothetical users after the "The best parts section?"

Jenny loves reproducibility. She keeps versioned code, figures, and summary statistics in a GitHub repository and uses Manubot to automatically update figures and data in her manuscript.

Rodrigo wants to improve his work based on feedback from his scientific peers. He uses Manubot to write his paper in private. When a complete draft is ready, he makes it public and revises it based on pull requests, issues, and comments from the community.

In #6 we also discussed using real testimonials instead once we have a broad enough user base.

Made with Manubot

@dhimmel @agitter @slochower Please suggest some manuscripts that we can include in the "Made With Manubot" section. In this issue I'd like to come up with an in-order list of 5 to 10 manuscripts to feature.

Then I'll go a pull some nice screenshots from them as well as some metadata to show on hover or something.

update logos from resources

I recently updated manubot/resources/brand, tweaking the logos slightly and adding hopefully all the formats/sizes of it people might want.

Need to update the manubot.org favicon metadata to just point to that repo, I think. Also need to make the catalog use the logo with the red background from resources/brand as well, instead of the grayed-out version of the logo it is now.

Add images to website

Currently the website, which is available at http://staging.manubot.org, has placeholders for images.

This issue is for proposing and discussing image ideas.

Site down?

Duplicate of #39

update catalog thumbnails to be in line with guidelines

update catalog thumbnails to be in line with the new thumbnail guidelines (soon-to-be) in manubot/catalog readme.