Websites: where do we go from here?

[thibautjombart]

The old adegenet website is getting a bit outdated: http://adegenet.r-forge.r-project.org/

The project is now a lot more the product of a community than my own work. A devel page makes sense, and I'm starting to use the wiki here. I think eventually the old adegenet website needs to go, or at least be relocated.

Questions:

• Shall we have 2 separate websites for the devel and stable version?
• If so, shall we move the old website to github pages?

Thoughts anyone?

[romunov]

I'm a big fan of the KISS principle. I think a github page (README) with devel and stable sections would be sufficient.

[thibautjombart]

I see your point and agree when it comes to finding information. From a communication point of view though, I am afraid the rather raw project page on github will put some people off.

On Thu, Jun 25, 2015 at 12:06 PM, Roman Luštrik [email protected] wrote:

I'm a big fan of the KISS principle. I think a github page (README) with devel and stable sections would be sufficient.

— Reply to this email directly or view it on GitHub https://github.com/thibautjombart/adegenet/issues/66#issuecomment-115211613 .

[KlausVigo]

Just for inspiration. Hadley Wickham just twittered this: If there was a prize for best #rstats package website, I'm sure http://rich-iannone.github.io/DiagrammeR/ would win it

[thibautjombart]

Nice! Looks indeed fancier.. Any idea how it's done? On 25 Jun 2015 13:18, "klash" [email protected] wrote:

Just for inspiration. Hadley Wickham just twittered this: If there was a prize for best #rstats package website, I'm sure http://rich-iannone.github.io/DiagrammeR/ would win it

— Reply to this email directly or view it on GitHub https://github.com/thibautjombart/adegenet/issues/66#issuecomment-115254705 .

[KlausVigo]

If I would know my phangorn page would look like it. Seems they use a lot of bootstrap.

[psolymos]

I've just spent some time on exploring github pages + jekyll + bootstrap/bootswatch/jQuery + MathJax + highlighter + remark.js and the results is this: http://datacloning.org/ Feel free to fork it, I can help and explain, there are many undocumented features and all this is in a bit of a flux: http://datacloning.org/

A one-paged theme (similar to that of DiagrammeR's) was used for my personal website: http://peter.solymos.org https://github.com/psolymos/psolymos.github.io

[thibautjombart]

This is waaaay cooler than the current adegenet website :) Will definitely check it out - thanks!

[KlausVigo]

That looks great, I think phangorn needs something like this too.

[psolymos]

You can change the look & feel in the _config.yml by changing these lines:

# Bootswatch theme
theme: flatly
# fancy fonts on/off
fancyfonts: true
# navbar style: inverse, transparent
navbar: inverse

See all the themes here: http://bootswatch.com/

[thibautjombart]

This is really cool. How long did it take you to master the beast?

[psolymos]

It kind of fall into my lap because of a website templating project (http://species.abmi.ca/) where the premise was: we want content for 2000 species up the web and don't care about design. But everyone kept telling me: good, good, but could be nicer. I recall the first streak taking roughly 2 days. A good place to start is the jekyll site: http://jekyllrb.com/ .

[psolymos]

It fell into my lap because of a website templating project (http://species.abmi.ca/) where the premise was: we want content for 2000 species up the web and don't care about design. But everyone kept telling me: good, good, but could be nicer. I recall the first streak taking roughly 2 days. A good place to start is the jekyll site: http://jekyllrb.com/ .

[romunov]

I thought http://pillow.readthedocs.org/ was nice along side the fact that it resides on github and appears to be rendered from there.

[thibautjombart]

Yes, this is nice too! I must prepare the next adegenet teaching week, but will investigate soon.

[romunov]

If we want to go something like "documentation website", docster would be a nice choice. http://jekyllthemes.org/themes/docster/

There is also http://idratherbewriting.com/documentation-theme-jekyll/mydoc/home.html which appears promising (but visually docster takes the cake).

[thibautjombart]

Looks nice! I have admittedly little time to look into changes for a website at the moment, but good to have this on the issue ;)

[romunov]

Once we settle on what should go on the website, I can try and get this in motion. The only thing that isn't yet clear to me is how to have documentation generated from .Rd files or even roxygen2 documented .R files. I'll ask around.

[thibautjombart]

If we want to go down that road, we'd have to generate pages from the Rd files. adegenet only partially uses roxygen2 (the pain of reforming an old package...).

Thanks for the offer, that sounds great. I'll try and have a look at options so far today.

Dr Thibaut Jombart Lecturer, Department of Infectious Disease Epidemiology Imperial College London https://sites.google.com/site/thibautjombart/ https://github.com/thibautjombart Twitter: @TeebzR https://twitter.com/TeebzR

On 15 February 2016 at 11:07, Roman Luštrik [email protected] wrote:

Once we settle on what should go on the website, I can try and get this in motion. The only thing that isn't yet clear to me is how to have documentation generated from .Rd files or even roxygen2 documented .R files. I'll ask around.

— Reply to this email directly or view it on GitHub https://github.com/thibautjombart/adegenet/issues/66#issuecomment-184168238 .

[thibautjombart]

I remember having headaches trying to get jekyll to work on my linux system (ruby deps etc). So I'd be keen on not relying on it.

So I think so far, my favourites are:

• http://species.abmi.ca/ by @psolymos
• http://thibautjombart.github.io/adegenet/

I had forgotten about the latter, but that may be the easiest course of action as it is generated by github.

I think this one http://rich-iannone.github.io/DiagrammeR/ looks very fancy but not that good in terms of accessing the info easily.

What do you guys think?

[romunov]

While looking at some docs of docs.ggplot2.org I clicked on the "Built by staticdocs..." at the bottom which links to Hadley's repo that drumroll generates html pages from Rd files. Add a fancy bootstrap theme et voila.

[thibautjombart]

Yes, but this is not exactly what I want. This would be a website replicating Rd files content. What I am looking for is more general - a proper website (i.e. content of the current website). In fact, I'm looking much more for a revamp of the old website than for new technical content (though it is welcome). New content, yes, but probably not so much technical e.g. a 'contributors' section with pics + short description of the current devel team, etc.

[romunov]

I've clicked through the demos over the weekend and some of the themes are lovely to say the least. The current github website you set up is only missing a few tabs and it's good to go to be filled with contents. And now I'll shut up and give time to other to express their opinion. :)

[zkamvar]

This might be of interest: https://github.com/hrbrmstr/markdowntemplates

[plantarum]

Hi there,

I understand updating the website is a big project, and probably not a priority for anyone. One small change I would suggest is to remove the circular referencing between github and R-forge. That is, the first line on the R-forge page (http://adegenet.r-forge.r-project.org/) currently directs users to the github wiki. The first link in the github wiki directs users to the R-forge website. I think at this point the wiki is more up-to-date, so perhaps the link back to R-forge could be removed to clarify where we ought to look for info?

Best,

Tyler