[Biopython-dev] Experimenting with migrating wiki to GitHub pages

[Peter Cock]

Dear all,

Those of you who have contributed to the Biopython wiki
in the past, and who have a GitHub account, might have
spotted this new repository:

https://github.com/peterjc/peterjc.github.io

I am experimenting with migrating the MediaWiki content
on biopython.org into MarkDown files (using pandoc, and
saving each wiki revision as a git commit), for display as
a webpage via GitHub Pages using Jekyll.

https://github.com/peterjc/mediawiki_to_git_md

The mapping from wiki user accounts to GitHub accounts
was done by hand. Please email me directly if I made a
mistake with your contributions. If I continue this effort I
will be re-running the migration script in future.

This conversion may not prove practical, and is not yet pretty
or even functional, but potentially could one day ofter an
alternative approach - and means we (the OBF) wouldn't
need to maintain a server running MediaWiki and Apache.

Note I'm not going to make any sudden changes to the
current biopython.org site without any warning or discussion.

Regards,

Peter

[Vincent Davis]

I think this I great! If I can help let me know.

Post by Peter Cock
Dear all,
Those of you who have contributed to the Biopython wiki
in the past, and who have a GitHub account, might have
https://github.com/peterjc/peterjc.github.io
I am experimenting with migrating the MediaWiki content
on biopython.org into MarkDown files (using pandoc, and
saving each wiki revision as a git commit), for display as
a webpage via GitHub Pages using Jekyll.
https://github.com/peterjc/mediawiki_to_git_md
The mapping from wiki user accounts to GitHub accounts
was done by hand. Please email me directly if I made a
mistake with your contributions. If I continue this effort I
will be re-running the migration script in future.
This conversion may not prove practical, and is not yet pretty
or even functional, but potentially could one day ofter an
alternative approach - and means we (the OBF) wouldn't
need to maintain a server running MediaWiki and Apache.
Note I'm not going to make any sudden changes to the
current biopython.org site without any warning or discussion.
Regards,
Peter
_______________________________________________
Biopython-dev mailing list
http://mailman.open-bio.org/mailman/listinfo/biopython-dev

[Peter Cock]

Post by Vincent Davis
I think this I great! If I can help let me know.

Thanks!

I made some good progress tonight, first off to get tables to work
just required asking pandoc to produce GitHub Flavour Markdown:
https://github.com/peterjc/mediawiki_to_git_md/commit/4a0271a3a86d9b0fa8fcc4c2feb9aa54e77034d6

Getting the python snippets to display nicely on GitHub both in
mediawiki format at markdown was surprisingly simple:
https://github.com/peterjc/mediawiki_to_git_md/commit/0a94c8fc9206cfb1cb2c366dc6a69a4f07feb098

The good news is this means most of the pages now look pretty
when browsing my latest test branch on GitHub :)

There are still plenty of things which might be desirable, first
amongst them is getting the URLs to work (ideally preserving
the old wiki page URL patterns to make server migration
easier).

Peter

[João Rodrigues]

Hi Peter, all,

I've used Jekyll + Github to create our lab webpage
<http://www.bonvinlab.org>. Turns out to be an amazingly simple solution
and very collaborative as well. Nice thought of moving the wiki to such a
system.

A quick question: why not make a page from "scratch" ? Using a template and
converting the HTML to markdown seems pretty simple, it's just a matter of
agreeing on a layout.

Maybe I'm missing the point and you're doing this already..

Cheers,

João

[Peter Cock]

On Wed, Mar 4, 2015 at 4:22 PM, João Rodrigues

Post by João Rodrigues
Hi Peter, all,
I've used Jekyll + Github to create our lab webpage. Turns out to be an
amazingly simple solution and very collaborative as well. Nice thought of
moving the wiki to such a system.
A quick question: why not make a page from "scratch" ? Using a template and
converting the HTML to markdown seems pretty simple, it's just a matter of
agreeing on a layout.
Maybe I'm missing the point and you're doing this already..
Cheers,
João

I've got the basic wiki content converted in markdown and showing nicely
(while preserving the wiki revisions and most of the contributors). Adding
a theme for a pretty layout is a finishing touch. First, all the links and files
need doing - definitely possible.

A key question is will it be as easy for people to edit as the wiki is/was?

Peter

[João Rodrigues]

We've been using our site as a "blog". It's extremely easy. Each commit is
a change to the website, e.g. a new page, new content, changing an image,
etc. Hosting on GitHub also makes it easy for everybody to make changes:
fork, change, pull request.

On Wed, Mar 4, 2015 at 4:22 PM, João Rodrigues

Post by João Rodrigues
Hi Peter, all,
I've used Jekyll + Github to create our lab webpage. Turns out to be an
amazingly simple solution and very collaborative as well. Nice thought of
moving the wiki to such a system.
A quick question: why not make a page from "scratch" ? Using a template

and

Post by João Rodrigues
converting the HTML to markdown seems pretty simple, it's just a matter

of

Post by João Rodrigues
agreeing on a layout.
Maybe I'm missing the point and you're doing this already..
Cheers,
João

I've got the basic wiki content converted in markdown and showing nicely
(while preserving the wiki revisions and most of the contributors). Adding
a theme for a pretty layout is a finishing touch. First, all the links and files
need doing - definitely possible.
A key question is will it be as easy for people to edit as the wiki is/was?
Peter

[Peter Cock]

On Wed, Mar 4, 2015 at 4:48 PM, João Rodrigues

We've been using our site as a "blog". It's extremely easy. Each commit is a
change to the website, e.g. a new page, new content, changing an image, etc.
Hosting on GitHub also makes it easy for everybody to make changes: fork,
change, pull request.

I'm glad to hear positive experiences about using GitHub Pages for
a group blog :)

I'm also thing about using this approach instead of WordPress
for the OBF blog, http://news.open-bio.org/ - ideally having first
extracted all the old posts with any images.

Peter

[Peter Cock]

Dear Biopythoneers,

In reference to my earlier email, the website migration has become more
urgent as the main biopython.org website is down until the AWS server
can be rebuilt:

http://lists.open-bio.org/pipermail/biopython/2016-April/015909.html
http://lists.open-bio.org/pipermail/biopython-dev/2016-April/021308.html

BioPerl has already got a potential replacement home page up and
running using GitHub Pages, but this did not preserve the contribution
history:

http://bioperl.github.io
https://github.com/bioperl/bioperl.github.io

You may recall last year I started work on a migration from MediaWiki
to markdown using GitHub Pages?

https://github.com/peterjc/mediawiki_to_git_md [migration tool]

Andreas and the BioJava team started with my migration tool, and have
already raced ahead with adding styling on top to make something
quite impressive:

http://biojava.github.io/wiki/Main_Page [pretty]
https://github.com/biojava/biojava.github.io

In comparison right now the Biopython migration is currently very
plain:

http://biopython.github.io/wiki/Biopython
https://github.com/biopython/biopython.github.io

I was hoping to fix some of the remaining issues in the conversion, in
particular the categories, but perhaps it is good enough already for the
Biopython wiki? (Some of these limitations would have been/are more
of a problem for the BioPerl wiki with many templates, and the main
OBF wiki with many wiki pages using subfolder slashes in their names):

https://github.com/peterjc/mediawiki_to_git_md/issues

Right now there are various things to do, including switching to the
kramdown markup engine and other tweaks for Jekyll 3.0 (which
Andreas has already done for BioJava):

https://github.com/blog/2100-github-pages-now-faster-and-simpler-with-jekyll-3-0

After than I think it would be sensible to start adopting much of the
styling work pioneered by Andreas for the BioJava team?

Do we have any GitHub pages experts in the community?

In general, please have a look at the trial migration wiki pages
and if you see any glitches, please report them via:

https://github.com/biopython/biopython.github.io/issues
and/or https://github.com/peterjc/mediawiki_to_git_md/issues

Thank you,

Peter

Post by Peter Cock
I've got the basic wiki content converted in markdown and showing nicely
(while preserving the wiki revisions and most of the contributors). Adding
a theme for a pretty layout is a finishing touch. First, all the links and files
need doing - definitely possible.
A key question is will it be as easy for people to edit as the wiki is/was?
Peter
On Wed, Mar 4, 2015 at 4:22 PM, João Rodrigues

Post by João Rodrigues
Hi Peter, all,
I've used Jekyll + Github to create our lab webpage. Turns out to be an
amazingly simple solution and very collaborative as well. Nice thought of
moving the wiki to such a system.
A quick question: why not make a page from "scratch" ? Using a template and
converting the HTML to markdown seems pretty simple, it's just a matter of
agreeing on a layout.
Maybe I'm missing the point and you're doing this already..
Cheers,
João

[Peter Cock]

Hi all,

A short update on the MediaWiki to Markdown / GitHub pages work.

I have just updated the migration at:

https://github.com/biopython/biopython.github.io
http://biopython.github.io/wiki/Biopython

This required minor changes to the settings and conversion due to
GitHub's updates, e.g.

https://github.com/biopython/biopython.github.io/commit/88c2e291d2fbb94a004a47aeb0548659148d20d4
https://github.com/peterjc/mediawiki_to_git_md/commit/e7a94e1f7f42490ed31e15de1d48f41fb7ea5732

I also filled in a few more mappings from the old MediaWiki usernames
to GitHub email addresses - hopefully these are all correct?

https://github.com/biopython/biopython.github.io/graphs/contributors

Likewise if anyone claims one of the following (number of edits, old username),
please email me:

1 - Amitjoshi
1 - Daniel P.
1 - Dj winter
3 - Einar
1 - Emeryl
1 - Hugog
1 - James Estevez
1 - Jbbrown
1 - Jflatow
1 - Jtriley
1 - Kian.ho
1 - Kmcallenberg
1 - Konrad
2 - Krishna
1 - Marc Juul
3 - MatatTHC
2 - Matsen
1 - Mys 721tx
2 - Mzapala
2 - NeilenMarais
3 - Newacct
2 - Nfdelane
1 - Nuin
1 - Robschia
1 - Zach Stednick

In other news, BioJava are hoping to switch over to their GitHub Pages
website shortly...

Peter

Post by Peter Cock
Dear Biopythoneers,
In reference to my earlier email, the website migration has become more
urgent as the main biopython.org website is down until the AWS server
http://lists.open-bio.org/pipermail/biopython/2016-April/015909.html
http://lists.open-bio.org/pipermail/biopython-dev/2016-April/021308.html
BioPerl has already got a potential replacement home page up and
running using GitHub Pages, but this did not preserve the contribution
http://bioperl.github.io
https://github.com/bioperl/bioperl.github.io
You may recall last year I started work on a migration from MediaWiki
to markdown using GitHub Pages?
https://github.com/peterjc/mediawiki_to_git_md [migration tool]
Andreas and the BioJava team started with my migration tool, and have
already raced ahead with adding styling on top to make something
http://biojava.github.io/wiki/Main_Page [pretty]
https://github.com/biojava/biojava.github.io
In comparison right now the Biopython migration is currently very
http://biopython.github.io/wiki/Biopython
https://github.com/biopython/biopython.github.io
I was hoping to fix some of the remaining issues in the conversion, in
particular the categories, but perhaps it is good enough already for the
Biopython wiki? (Some of these limitations would have been/are more
of a problem for the BioPerl wiki with many templates, and the main
https://github.com/peterjc/mediawiki_to_git_md/issues
Right now there are various things to do, including switching to the
kramdown markup engine and other tweaks for Jekyll 3.0 (which
https://github.com/blog/2100-github-pages-now-faster-and-simpler-with-jekyll-3-0
After than I think it would be sensible to start adopting much of the
styling work pioneered by Andreas for the BioJava team?
Do we have any GitHub pages experts in the community?
In general, please have a look at the trial migration wiki pages
https://github.com/biopython/biopython.github.io/issues
and/or https://github.com/peterjc/mediawiki_to_git_md/issues
Thank you,
Peter

Post by Peter Cock
I've got the basic wiki content converted in markdown and showing nicely
(while preserving the wiki revisions and most of the contributors). Adding
a theme for a pretty layout is a finishing touch. First, all the links and files
need doing - definitely possible.
A key question is will it be as easy for people to edit as the wiki is/was?
Peter
On Wed, Mar 4, 2015 at 4:22 PM, João Rodrigues

Post by João Rodrigues
Hi Peter, all,
I've used Jekyll + Github to create our lab webpage. Turns out to be an
amazingly simple solution and very collaborative as well. Nice thought of
moving the wiki to such a system.
A quick question: why not make a page from "scratch" ? Using a template and
converting the HTML to markdown seems pretty simple, it's just a matter of
agreeing on a layout.
Maybe I'm missing the point and you're doing this already..
Cheers,
João

[Tiago Rodrigues Antao]

Post by Peter Cock
In other news, BioJava are hoping to switch over to their GitHub Pages
website shortly...

I am all for moving sooner rather than later.
While there might be problems, the truth is that the existing
infrastructure has its own very serious problems.

Tiago

[Fields, Christopher J]

Post by Tiago Rodrigues Antao

Post by Peter Cock
In other news, BioJava are hoping to switch over to their GitHub Pages
website shortly...

I am all for moving sooner rather than later.
While there might be problems, the truth is that the existing infrastructure has its own very serious problems.
Tiago

On the bioperl end we just decided to pull the trigger and set up the redirect to Github Pages, as Brian Osborne had already started us well along the way (though we don’t have the level of history detail that Peter has in his repo). So, the next step is to decide how much we want to try pulling from the old site or whether we will attempt something more refined as Peter has done.

chris

[Peter Cock]

On Fri, Apr 8, 2016 at 10:58 PM, Fields, Christopher J

Post by Fields, Christopher J

Post by Tiago Rodrigues Antao

Post by Peter Cock
In other news, BioJava are hoping to switch over to their GitHub Pages
website shortly...

I am all for moving sooner rather than later.
While there might be problems, the truth is that the existing
infrastructure has its own very serious problems.
Tiago

On the bioperl end we just decided to pull the trigger and set up
the redirect to Github Pages, as Brian Osborne had already
started us well along the way (though we don’t have the level
of history detail that Peter has in his repo). So, the next step
is to decide how much we want to try pulling from the old site
or whether we will attempt something more refined as Peter
has done.
chris

Yes - I'm also hoping to switch biopython.org to the GitHub
pages version ASAP (and we the OBF need to write a blog
post about this too):

https://github.com/biopython/biopython.github.io
http://biopython.github.io/wiki/Biopython

I made some progress on the migration, and will tackle the
category pages next, then "borrow" some of Andreas' styling
work as showcased on the (now live) http://biojava.org site.

Adding the static API docuemntation pages should be easy,
the old release might be more trouble if there are any hosting
or file size limits we might hit...

Peter

[Markus Piotrowski]

I made some progress on the migration, and will tackle the category
pages next, then "borrow" some of Andreas' styling work as showcased
on the (now live) http://biojava.org site. Adding the static API
docuemntation pages should be easy, the old release might be more
trouble if there are any hosting or file size limits we might hit...

BioJava looks great, it uses "Spectral" from HTML5 UP
(http://html5up.net/). Personally, I like "Strongly Typed"
(http://html5up.net/strongly-typed) more, maybe because it's easier for
me to imagine how the old site would like there ;-)
Is there any possibility to assist you? Let us know!

Markus

[Peter Cock]

On Sat, Apr 9, 2016 at 7:28 AM, Markus Piotrowski

I made some progress on the migration, and will tackle the category pages
next, then "borrow" some of Andreas' styling work as showcased on the (now
live) http://biojava.org site. Adding the static API docuemntation pages
should be easy, the old release might be more trouble if there are any
hosting or file size limits we might hit...

BioJava looks great, it uses "Spectral" from HTML5 UP (http://html5up.net/).
Personally, I like "Strongly Typed" (http://html5up.net/strongly-typed)
more, maybe because it's easier for me to imagine how the old site would
like there ;-)
Is there any possibility to assist you? Let us know!
Markus

Hi Markus,

It sounds like you know more about the Jekyll styles that I do,
so your advice and help would be welcome :)

I think people could fork the repository but should use their own
account name for the repository name - i.e. username.github.io in
order to get it rendered by GitHub, e.g. my username is peterjc:

https://github.com/peterjc/peterjc.github.io --> http://peterjc.github.io/

(At some point I will delete that now we have this under the
Biopython GitHub account, maybe one day I'll use that for
a personal homepage hosted by GitHub instead?)

Or, in theory you can work on the website look-and-feel using
a locally installed version of Jekyll 3.0.

If you can get something looking good and make a GitHub
pull request, that should work out nicely :)

If you (or anyone else) is mosre interested in the migration step,
I can send you the MediaWiki dump XML file off list and you can
then contribute to the converter tool at:
https://github.com/peterjc/mediawiki_to_git_md

Thanks!

Peter

[João Rodrigues]

Addendum: Don't forget to add the gh-pages gem or whatever it is to your
environment, to mimic as best as possible the github pages environment. Had
a few surprises already when deploying changes..

Post by Peter Cock
On Sat, Apr 9, 2016 at 7:28 AM, Markus Piotrowski

I made some progress on the migration, and will tackle the category

pages

next, then "borrow" some of Andreas' styling work as showcased on the

(now

live) http://biojava.org site. Adding the static API docuemntation

pages

should be easy, the old release might be more trouble if there are any
hosting or file size limits we might hit...

BioJava looks great, it uses "Spectral" from HTML5 UP (

http://html5up.net/).

Personally, I like "Strongly Typed" (http://html5up.net/strongly-typed)
more, maybe because it's easier for me to imagine how the old site would
like there ;-)
Is there any possibility to assist you? Let us know!
Markus

Hi Markus,
It sounds like you know more about the Jekyll styles that I do,
so your advice and help would be welcome :)
I think people could fork the repository but should use their own
account name for the repository name - i.e. username.github.io in
https://github.com/peterjc/peterjc.github.io --> http://peterjc.github.io/
(At some point I will delete that now we have this under the
Biopython GitHub account, maybe one day I'll use that for
a personal homepage hosted by GitHub instead?)
Or, in theory you can work on the website look-and-feel using
a locally installed version of Jekyll 3.0.
If you can get something looking good and make a GitHub
pull request, that should work out nicely :)
If you (or anyone else) is mosre interested in the migration step,
I can send you the MediaWiki dump XML file off list and you can
https://github.com/peterjc/mediawiki_to_git_md
Thanks!
Peter
_______________________________________________
Biopython-dev mailing list
http://mailman.open-bio.org/mailman/listinfo/biopython-dev

[Peter Cock]

Both BioPerl.org and BioJava.org are now pointing at
GitHub Pages sites.

Post by Peter Cock
Yes - I'm also hoping to switch biopython.org to the GitHub
pages version ASAP (and we the OBF need to write a blog
https://github.com/biopython/biopython.github.io
http://biopython.github.io/wiki/Biopython
I made some progress on the migration, and will tackle the
category pages next,

That's working now, meaning most of the content is usable.
There are other minor issues, but as far as I can tell, nothing
we couldn't fix after making the switch to GitHub pages live.

https://github.com/biopython/biopython.github.io/issues

Please do have a look round the conversion to see if you
can spot any problems with it, relevant pages:

http://biopython.github.io/wiki/Biopython
http://biopython.github.io/wiki/Download
http://biopython.github.io/wiki/Mailing_lists
http://biopython.github.io/wiki/Documentation
http://biopython.github.io/wiki/Category:Cookbook
http://biopython.github.io/wiki/SourceCode
http://biopython.github.io/wiki/Participants
http://biopython.github.io/wiki/Scriptcentral

Post by Peter Cock
then "borrow" some of Andreas' styling
work as showcased on the (now live) http://biojava.org site.

This is where I am most hoping for help, tracking issue:
https://github.com/biopython/biopython.github.io/issues/3

Post by Peter Cock
Adding the static API documentation pages should be easy,
the old release might be more trouble if there are any hosting
or file size limits we might hit...

On a related point, I don't think there is much point having a
snapshot of the code under the /SRC/ folder - the only reason
I've used it have been for a simple HTTP link to test files or the
licence. I think we can put a place holder page up directing
people to GitHub instead?

Peter

[Fields, Christopher J]

Post by Peter Cock
then "borrow" some of Andreas' styling
work as showcased on the (now live) http://biojava.org<https://urldefense.proofpoint.com/v2/url?u=http-3A__biojava.org&d=BQMFaQ&c=8hUWFZcy2Z-Za5rBPlktOQ&r=fbHa8Njtvh9VmSnzJxiEUTW9NWDwMMwQAzhgZDO41GQ&m=PjdPbwyTIuTLaGHmCSHok46_6fQxYYt1ihdIDhxSewo&s=ujEimdzjZnPF7QHmHSLYNiDl2wYgZCp6fbIhVhuU5H0&e=> site.

Just to chime in on this: Of course you are welcome to do this. The design is based on this template:

http://html5up.net/spectral<https://urldefense.proofpoint.com/v2/url?u=http-3A__html5up.net_spectral&d=BQMFaQ&c=8hUWFZcy2Z-Za5rBPlktOQ&r=fbHa8Njtvh9VmSnzJxiEUTW9NWDwMMwQAzhgZDO41GQ&m=PjdPbwyTIuTLaGHmCSHok46_6fQxYYt1ihdIDhxSewo&s=wus6lqwyx7Aesd9GQIgmaLlP4EH1wtClDlDH-R9HiIw&e=>

If you check the html5up website, there are also others (all under CC-BY).

Andreas

That is pretty nice!

chris

[PD Dr. Markus Piotrowski]

On Sun, Apr 10, 2016 at 11:16 PM, Markus Piotrowski

- I also was to dumb to fork the biopython.github.io respository, I pulled
the contend to my github.io respository, so at the moment I don't now how to
make pull requests.

That's not the end of the world - I can manually grab your changes
as long as is is clear which files you altered.
If you can see how to make this easier for other people to contribute
to the website styling in future, that would be useful to know.

I think, the solution may be to fork first and then rename the
respository to username.github.io.
(as you suggested...) I will try this later.

I played around a little bit with the automatic page generator. I used one
of the standard designs of Github Pages - "Slate" - which is quite simple
and plain but gives the actual pages a nice view.
http://markuspiotrowski.github.io/wiki/Biopython

Simple and elegant - I'd like to get the logo in there somewhere,
but otherwise we could start with this.
https://twitter.com/biopython?lang=en-gb

I have put the logo into the header. Is someone around, who has a
transparent version of the logo?
I have made it transparent by using the "magic wand" tool of Photoshop,
but the result is not perfect. I will give it another try later.
The thin white glowing shadow may be removed, if we don't like it.
That's the recent version:

http://markuspiotrowski.github.io/wiki/Biopython

All I have done is to change the head and foot htmls in the _includes
folder, and of course it requires the images, javascripts and stylesheets
folders which where installed during the automatic page construction.
-Markus

May I try to import these changes, putting the commit under your name?
Peter

If you like it, yes!

Markus

[Markus Piotrowski]

Post by PD Dr. Markus Piotrowski
I have put the logo into the header. Is someone around, who has a
transparent version of the logo?
I have made it transparent by using the "magic wand" tool of
Photoshop, but the result is not perfect. I will give it another try
later.
The thin white glowing shadow may be removed, if we don't like it.
http://markuspiotrowski.github.io/wiki/Biopython

The Biopython logo is nicer now, and I have added the Twitter and GitHub
logo to the footer.

http://markuspiotrowski.github.io/wiki/Biopython
or:
http://markuspiotrowski.github.io

Be aware that I only worked on the style things, some links don't work
from my respository and some links may already be outdated.

Markus

[Peter Cock]

On Mon, Apr 11, 2016 at 4:49 PM, Markus Piotrowski

Post by Markus Piotrowski

Post by PD Dr. Markus Piotrowski
I have put the logo into the header. Is someone around, who has a
transparent version of the logo?
I have made it transparent by using the "magic wand" tool of Photoshop,
but the result is not perfect. I will give it another try later.
The thin white glowing shadow may be removed, if we don't like it. That's
http://markuspiotrowski.github.io/wiki/Biopython

The Biopython logo is nicer now, and I have added the Twitter and GitHub
logo to the footer.
http://markuspiotrowski.github.io/wiki/Biopython
http://markuspiotrowski.github.io
Be aware that I only worked on the style things, some links don't work from
my respository and some links may already be outdated.
Markus

Thanks Markus,

This looks good - and it is reassuringly straightforward to switch the
theme now that the content is converted (and mostly looks fine).

I agree the edge of the black background logo looks a little rough -
I don't know what Leighton did for the Twitter background image
but that might be a better starting point?

https://twitter.com/biopython

Also code syntax colouring isn't working - but don't spend long on that:

http://markuspiotrowski.github.io/wiki/SeqIO

Currently I'm trying the hyde theme out, which since it has a sidebar
is a bit more like the old MediaWiki layout, e.g.

http://biopython.github.io/wiki/SeqIO

Do you know enough CSS to get the Biopython logo into the sidebar?

Do you have any ideas for embedding an RSS/Atom news feed?

https://github.com/biopython/biopython.github.io/issues/4

Regardless of which theme we end up picking, I think we should
be able to switch to the GitHub pages site shortly - its much better
than no website, even if the downloads remain offline a bit longer.

Peter

P.S. I did find and fix a minor glitch with some of the cookbook
entries: https://github.com/biopython/biopython.github.io/issues/5

[Markus Piotrowski]

Post by Peter Cock
Thanks Markus,
This looks good - and it is reassuringly straightforward to switch the
theme now that the content is converted (and mostly looks fine).
I agree the edge of the black background logo looks a little rough -
I don't know what Leighton did for the Twitter background image
but that might be a better starting point?
https://twitter.com/biopython

That was easily repaired, just putting the syntax.css into the header.

[Peter Cock]

Hello all,

It might be time to retitle this thread: The experiment is going live!
At this point although still unfinished, it is much better than no website
(much the same thinking as with BioPerl and BioJava which made
the switch at the end of last week).

I appreciate this was a unilateral decision, and I hope no one objects.
(Insert joke about benevolent dictators here?)

I've added the magic CNAME file and asked Hilmar via our root-l
SysAdmin mailing list to make the DNS changes, so shortly using
biopython.org should take you to the GitHub Pages site.

Main announcement email here:

http://lists.open-bio.org/pipermail/biopython/2016-April/015919.html
http://lists.open-bio.org/pipermail/biopython-dev/2016-April/021333.html

Note that I split off the https://biopython.org/DIST/ content into a
separate repository which uses just a gh-pages branch as a
GitHub "Project" Page: https://github.com/biopython/DIST

I have attempted to populate this with all the original files with their
approximate date and authorship where appropriate. Note that for
things like the API documentation files and Tutorial, I just took the
latest version.

This has advantages in terms of repository size, and perhaps also
access control. It looks like it will work OK for hosting the Windows
installers etc, more on that in a follow up email.

Note that switching the website to GitHub pages need not be
permanent, but the OBF had been looking at reducing the
SysAdmin needs of our servers for some time, and at this point
the GitHub Pages route looks very practical.

Thanks,

Peter

[Peter Cock]

Post by Peter Cock
Both BioPerl.org and BioJava.org are now pointing at
GitHub Pages sites.

Post by Peter Cock
Yes - I'm also hoping to switch biopython.org to the GitHub
pages version ASAP (and we the OBF need to write a blog
https://github.com/biopython/biopython.github.io
http://biopython.github.io/wiki/Biopython
I made some progress on the migration, and will tackle the
category pages next,

That's working now, meaning most of the content is usable.
There are other minor issues, but as far as I can tell, nothing
we couldn't fix after making the switch to GitHub pages live.
https://github.com/biopython/biopython.github.io/issues
Please do have a look round the conversion to see if you
http://biopython.github.io/wiki/Biopython
http://biopython.github.io/wiki/Download
http://biopython.github.io/wiki/Mailing_lists
http://biopython.github.io/wiki/Documentation
http://biopython.github.io/wiki/Category:Cookbook
http://biopython.github.io/wiki/SourceCode
http://biopython.github.io/wiki/Participants
http://biopython.github.io/wiki/Scriptcentral

Post by Peter Cock
then "borrow" some of Andreas' styling
work as showcased on the (now live) http://biojava.org site.

https://github.com/biopython/biopython.github.io/issues/3

Markus has been working on this - thank you!

Post by Peter Cock

Post by Peter Cock
Adding the static API documentation pages should be easy,

Done, live at

http://biopython.github.io/DIST/docs/api/
https://github.com/biopython/biopython.github.io/tree/master/DIST/docs/api

Post by Peter Cock

Post by Peter Cock
the old release might be more trouble if there are any hosting
or file size limits we might hit...

I have imported the tutorial etc, under the docs folder:

http://biopython.github.io/DIST/docs/ (currently 404 error)
https://github.com/biopython/biopython.github.io/tree/master/DIST/docs

If you know the URL, you can link directly to existing files, e.g.
the BOSC 2003 talk which Brad gave featuring many of the other
candidate logos for Biopython:

https://biopython.github.io/DIST/docs/presentations/bosc_biopython.pdf
https://github.com/biopython/biopython.github.io/blob/master/DIST/docs/presentations/bosc_biopython.pdf

It ought to be simple to add file listings to these folder with Jekyll...

Post by Peter Cock
On a related point, I don't think there is much point having a
snapshot of the code under the /SRC/ folder - the only reason
I've used it have been for a simple HTTP link to test files or the
licence. I think we can put a place holder page up directing
people to GitHub instead?

Done:

https://github.com/biopython/biopython.github.io/tree/master/SRC
http://biopython.github.io/SRC/

Curiously GitHub Pages with Jekyll 3.0 hasn't automatically made
"naked" URLs into links - this looks like a regression from GitHub
switching to kramdown, simplest fix is wrapping the URL as <URL>
instead.

http://hakanu.net/markdown/2016/03/22/switched-to-redcarpet-instead-of-kramdown-as-markdown-renderer/

Peter