set up CI

[orbeckst]

Once we have a tests infrastructure in place #23, we need

• Travis CI
• coverage
• add test and coverage badges to README

[orbeckst]

For most of the tests we need to install Gromacs as well. This should be possible through aptitude on the containerized Travis infrastructure.

• Gromacs 4.6.5 is available as trusty (14.04 LTS): gromacs (4.6.5-1build1) [universe]
• Gromacs 5.0.x: wily: gromacs (5.0.6-1) [universe]
• Gromacs 5.1.x: Xenial: gromacs (5.1.2-1ubuntu1) [universe]

I don't know if it's possible to pull in newer packages into a 14.04 machine. Gromacs 4.6.5 will be easy, all the other... we will see. It would be great, though, to have a test matrix with different Gromacs installations.

[dotsdl]

We can use conda. There are builds provided by acellera: https://anaconda.org/acellera/gromacs

[orbeckst]

@dotsdl can you add the travis stuff from MDPOW? This seems to be almost working.

[dotsdl]

Yes. I'll convene with @ianmkenney and we'll slay this one. :D

[dotsdl]

We now have working CI, but some of the tests are failing. Haven't dug into fixing these yet; check the test output for starting points: https://travis-ci.org/Becksteinlab/GromacsWrapper

Coverage reads at 88%. Not bad, but I guess we cheat a bit since we generate many classes dynamically.

[orbeckst]

@dotsdl : I don't see the coverage at https://codecov.io/gh/Becksteinlab/GromacsWrapper — is this because codecov is only ran when the tests pass?

And the output from travis seems to indicate that the 88% coverage are the coverage in the test files, not in the code itself.

I added the badges to the README but until coverage shows up in codecov I will leave this issue open.

[dotsdl]

@orbeckst ah sorry, didn't look closely enough at what was included in coverage. I'll fix this.

[dotsdl]

K...now with better accounting, coverage looks like about 30%. I think codecov doesn't pick up failed builds, either, so we have to get these passing before that is fixed, too.

[orbeckst]

I can close this issue when I get coverage on travis but for this to happen, all current tests must pass, i.e., #61 must be fixed.

[orbeckst]

@ianmkenney got Gromacs working with PR Becksteinlab/MDPOW#44 (see Becksteinlab/MDPOW#41).

[orbeckst]

Tests passing and coverage properly reported.