Fix dead links on migrated website (Error 404 etc)

[peterjc]

We know about a few problem links e.g. #8 #13 #17, but should check this systematically. There are also some external links which no longer work.

Ideally we'd have a TravisCI configuration to run Jekyll and then spider the _site/ folder to spot any link breakage.

[JoaoRodrigues]

@peterjc We can try this approach. Seems to be exactly what we are looking for.

[peterjc]

Yes exactly :)

[JoaoRodrigues]

I can give it a try, but I guess I'd need access to TravisCI?

[peterjc]

You should be able to try this by forking this to JoaoRodrigues.github.io and using your personal TravisCI account, e.g. https://github.com/peterjc/peterjc.github.io/blob/pre_auto_import/.travis.yml (currently out of sync) would just install and run Jekyll?

[peterjc]

I've just turned on https://travis-ci.org/biopython/biopython.github.io/ which should read https://github.com/biopython/biopython.github.io/blob/master/.travis.yml next time we update the website.

Currently the Travis configuration just runs Jekyll (a useful test in itself).

[vincentdavis]

Attached are two link reports, Internal only and all dead links.
Where are the /DIST files hosted?

I will happily work on links.

All bad links v2 April 19 2016.csv.zip

Internal Bad links April 19 2016.csv.zip

[peterjc]

They're on a GitHub Pages "project" repository, see #7 and https://github.com/biopython/DIST (note gh-pages branch)

GitHub isn't ideal for what are mostly a collection of static files - and this is largely separate from the website so this seemed like a good idea. Long term I'd like us to host all our releases on PyPI (which currently doesn't cover Windows EXE/MSI files, but can do wheels).

[peterjc]

Many of the "internal" links Vincent flagged were inter-wiki links, mostly to BioPerl's wiki - see #17

[MarkusPiotrowski]

If I don't find a folder/file on https://github.com/biopython/DIST, e.g. http://biopython.org/DIST/docs/cluster/cluster.pdf, wasn't it transferred, did it go elsewhere or was is already missing before?

[peterjc]

@MarkusPiotrowski the DIST folder is being done as a GitHub Project Page, see https://github.com/biopython/DIST and earlier comments on this issue.

I had missed the cluster.pdf file, thanks for reporting that. I've committed that under @mdehoon's name under the publication date (July 2008): biopython/DIST@282fcb0

[MarkusPiotrowski]

Other files on DIST that I'm missing are ACMbiopy.pdf and ACMbiopy.html (Chapman & Chang 2000 Biopython paper), formerly on [http://biopython.org/DIST/docs/acm/]