install external code on travis for complete analysis testing?

[orbeckst]

Testing on travis currently skips a number of tests that call external tools. Apart from the fact that it reduces our coverage it also simply not good to have code that only gets tested occasionally if one of the @MDAnalysis/coredevs feels like doing it locally.

Should we try to install external packages on travis in order to run these tests?

From the top of my head

• analysis.hole: HOLE (see installation instructions in the comments for 707b02b)
• analysis.align: clustal (there might even an Ubuntu package for installation)
• analysis.x3dna: x3dna – not easily accessible, not free, so that won't get done any time soon (see install external code on travis for complete analysis testing? #898 (comment))

HOLE and clustalx (or clustalw) should be pretty easy, x3dna I am not sure.

UPDATE: #906 proposes to make analysis.x3dna a legacy module.

[richardjgowers]

Yeah I'm in favour, more coverage helps reduce headaches down the road

[hainm]

you can build conda packages for external ones, so the travis builds are trivial.

[orbeckst]

True, although HOLE is not free, only available as binary, and I doubt that the license allows repackaging. Otherwise it would be very helpful to have it on Conda.

Oliver Beckstein
email: orbeckst@gmail.com

Am Jul 17, 2016 um 17:34 schrieb Hai Nguyen notifications@github.com:

you can build conda packages for external ones, so the travis builds are trivial.

[orbeckst]

Just FYI: the HOLE END USER LICENCE AGREEMENT NOT-FOR-PROFIT VERSION (attached) explicitly forbids making copies, e.g. for conda packages:

You may not:

• permit other individuals to use the Software except under the terms listed below;
• modify, translate, reverse engineer, decompile, disassemble (except to the extent applicable laws specifically prohibit such restriction), or create derivative works based on the Software;
• copy the Software (except for back-up purposes);
• rent, lease, transfer, or otherwise transfer rights to, the Software;
• remove any proprietary notices or labels on the Software.

Thus I cannot add it to a conda channel, even though I'd love to do it.

[hainm]

copy the Software (except for back-up purposes);

according to this, you can't not even copy/build it on travis.

[orbeckst]

On travis we download the software every single time from the original download location. Because this is not-for-profit and academic use as described in the license agreement I believe this falls under permitted use.

But yes, it's an awful license.

However, in the ion channel field, HOLE is the de-facto standard for measuring cavities so everybody wants to use it. (There are some alternative packages but I can't find any obvious links at the moment.)

[orbeckst]

PR #901 is pretty much complete for HOLE and clustalw. I am lacking the expertise (and currently the time) to do anything with x3dna. Furthermore, downloading x3dna requires user registration and "command-line tools such as wget and curl are blocked on purpose" and it is not open source as far as I can tell. I cannot even find a license on the site.

I don't have a big need for x3dna myself at the moment so I am just going to skip this and when the time comes, we can mark the x3dna module as legacy, as discussed in #743 and mandated for Tests of MDAnalysis.analysis.

[orbeckst]

Closed by #901.