Refactor common MD engine functions

[mimischi]

Changes made in this pull request:

• Consolidate write_bench function from mdengines.gromacs.write_bench and mdengines.namd.write_bench into mdengines.utils.write_benchmark.
• Add unit tests to mdengines.utils.write_benchmark. We now also check wheter all variables in the generated bench.job were replaced correctly.
• Consolidate cleanup_before_restart for both NAMD and GROMACS.
• Consolidate parse_ns_day, parse_ncores and analyze_run for both NAMD and GROMACS.

PR Checklist

• Added changelog fragment in ./changelog/ (more information)?
• [ ] Issue raised/referenced?

[codecov]

Codecov Report

Merging #57 into master will decrease coverage by 0.22%.
The diff coverage is 100%.

@@            Coverage Diff             @@
##           master      #57      +/-   ##
==========================================
- Coverage   89.35%   89.13%   -0.23%     
==========================================
  Files          11       12       +1     
  Lines         526      506      -20     
==========================================
- Hits          470      451      -19     
+ Misses         56       55       -1

Impacted Files	Coverage Δ
mdbenchmark/mdengines/namd.py	97.61% <100%> (+0.08%)	⬆️
mdbenchmark/mdengines/utils.py	100% <100%> (ø)
mdbenchmark/mdengines/__init__.py	100% <100%> (ø)	⬆️
mdbenchmark/mdengines/gromacs.py	100% <100%> (ø)	⬆️
mdbenchmark/analyze.py	43.67% <100%> (+0.65%)	⬆️
mdbenchmark/submit.py	97.67% <100%> (+0.11%)	⬆️
mdbenchmark/generate.py	100% <100%> (ø)	⬆️

---

Continue to review full report at Codecov.

Legend - Click here to learn more
Δ = absolute <relative> (impact), ø = not affected, ? = missing data
Powered by Codecov. Last update 3133526...44b37dd. Read the comment docs.

[mimischi]

Regarding 0446c91: I consolidated parse_ns_day into mdengines/utils.py, but still test the cases separately inside of tests/mdengines/test_namd.py and tests/mdengines/test_gromacs.py. I somewhat have the feeling we should do that testing inside of tests/mdengines/test_utils.py, but we could compromise here to have the tests engine specific.

[mimischi]

We now always pass the actual MD engine via engine (currently: mdengines/gromacs.py or mdengines/namd.py) in the code base. Subsequent functions now call engine.NAME internally, to access the NAME property, like @kain88-de suggested.

We could later think about rewriting parts of the MD engine to use classes, but this should be fine as a first step.

This is ready to be reviewed @MSiggel @kain88-de.

[MSiggel]

maybe top_directory?