Fix filename bug

[mimischi]

Fixes #53.

Changes made in this pull request:

• Change the way we handle filenames.

PR Checklist

• Added unit tests
• Added changelog fragment in ./changelog/ (more information)?
• Issue raised/referenced?

[codecov]

Codecov Report

Merging #54 into master will decrease coverage by 0.21%.
The diff coverage is 90.47%.

@@            Coverage Diff             @@
##           master      #54      +/-   ##
==========================================
- Coverage   87.27%   87.06%   -0.22%     
==========================================
  Files          11       11              
  Lines         448      456       +8     
==========================================
+ Hits          391      397       +6     
- Misses         57       59       +2

Impacted Files	Coverage Δ
mdbenchmark/generate.py	95.83% <100%> (ø)	⬆️
mdbenchmark/mdengines/gromacs.py	100% <100%> (ø)	⬆️
mdbenchmark/mdengines/namd.py	97.53% <71.42%> (-2.47%)	⬇️

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[kain88-de]

name isn't used anymore and it must have been defined.

[mimischi]

I cannot wrap my head around that. My local tests fail at this line, while Travis-CI does not seem to have any problems. I've cleared all caches already using make clean.

[mimischi]

Just realized what is causing the problem: for testing purposes I created md.namd, md.psf and md.pdb inside my mdbenchmark folder. Somehow pytest picks these up during testing and errors out. Deleting those resolves the issues.

Is something is wrong with our pytest setup?

[mimischi]

@kain88-de This is finished. I'd like to finish #49 before we release a new version.

[kain88-de]

Somehow pytest picks these up during testing and errors out. Deleting those resolves the issues.

I don't know what files you had exactly so I can't say. To my knowledge, there isn't anything wrong. Also, test files should best be generated in a folder outside of the source code.

[kain88-de]

better 'Fixed edge-case in input filename parsing.'

It's not like it wasn't parsed correctly before. We just missed a specific edge case.

[mimischi]

I don't know what files you had exactly so I can't say. To my knowledge, there isn't anything wrong. Also, test files should best be generated in a folder outside of the source code.

touch md.namd, touch md.psf and touch md.pdb inside the root folder. Then run pytest inside of that.

[kain88-de]

you invoke the CLI interface from the folder where you call pytest. To avoid this behavior you need to ensure that the cli invocation happens in a temporary folder. It might be time to refactor the CLI testing functions.