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nlesc-nano / auto-FOX

A library for analyzing potential energy surfaces (PESs) and using the resulting PES descriptors for constructing forcefield parameters.
GNU Lesser General Public License v3.0
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ENH: Add the TOPContainer class for managing .top files #296

Closed BvB93 closed 1 year ago

BvB93 commented 1 year ago

xref https://github.com/nlesc-nano/auto-FOX/issues/293

Adds the new FOX.TOPContainer class and use it as intermediate for managing GROMACS .top files in the create_top recipe.

A notable change is that FOX.recipes.create_top now returns a TOPContainer, rather than directly creating a .top file.

codecov[bot] commented 1 year ago

Codecov Report

Merging #296 (db5900a) into master (f53d10d) will increase coverage by 3.53%. The diff coverage is 79.51%.

@@            Coverage Diff             @@
##           master     #296      +/-   ##
==========================================
+ Coverage   71.32%   74.85%   +3.53%     
==========================================
  Files          69       70       +1     
  Lines        7560     7923     +363     
  Branches     1376     1678     +302     
==========================================
+ Hits         5392     5931     +539     
+ Misses       1793     1570     -223     
- Partials      375      422      +47
Impacted Files Coverage Δ
FOX/__init__.py 100.00% <ø> (ø)
FOX/io/read_prm.py 63.94% <73.07%> (+0.63%) :arrow_up:
FOX/io/_read_rtf.py 78.96% <79.31%> (-1.04%) :arrow_down:
FOX/io/_read_top.py 79.66% <79.66%> (ø)
FOX/recipes/top.py 74.54% <80.64%> (+64.83%) :arrow_up:
FOX/io/__init__.py 100.00% <100.00%> (ø)

... and 12 files with indirect coverage changes