MDAnalysis / pmda

Parallel algorithms for MDAnalysis

https://www.mdanalysis.org/pmda/

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Consolidate root-mean-square functions #107

Closed nawtrey closed 5 years ago

nawtrey commented 5 years ago

Moves all root-mean-square calculations (currently RMSD and RMSF) into their own module, updates documentation, tests, and .rst files to match new structure.

Fixes #103

Changes:

Create pmda/rms
Rename and move rms.py to pmda/rms.rmsd.py
Add example to RMSD documentation in /rms.rmsd.py
Move rmsf.py into /rms
Fix imports in tests and .rst files
Correct documentation example imports

PR Checklist

[x] Tests?
[x] Docs?
[x] CHANGELOG updated?
[x] Issue raised/referenced?

codecov[bot] commented 5 years ago

Codecov Report

Merging #107 into master will increase coverage by 0.01%. The diff coverage is 100%.

@@            Coverage Diff             @@
##           master     #107      +/-   ##
==========================================
+ Coverage    97.8%   97.81%   +0.01%     
==========================================
  Files          10       11       +1     
  Lines         637      642       +5     
  Branches       78       78              
==========================================
+ Hits          623      628       +5     
  Misses          8        8              
  Partials        6        6

Impacted Files	Coverage Δ
pmda/density.py	`100% <ø> (ø)`	:arrow_up:
pmda/rms/rmsd.py	`100% <100%> (ø)`
pmda/rms/__init__.py	`100% <100%> (ø)`
pmda/rms/rmsf.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 1e99541...d083361. Read the comment docs.

codecov[bot] commented 5 years ago

Codecov Report

Merging #107 into master will increase coverage by 0.01%. The diff coverage is 100%.

@@            Coverage Diff             @@
##           master     #107      +/-   ##
==========================================
+ Coverage    97.8%   97.81%   +0.01%     
==========================================
  Files          10       11       +1     
  Lines         637      642       +5     
  Branches       78       78              
==========================================
+ Hits          623      628       +5     
  Misses          8        8              
  Partials        6        6

Impacted Files	Coverage Δ
pmda/density.py	`100% <ø> (ø)`	:arrow_up:
pmda/rms/rmsd.py	`100% <100%> (ø)`
pmda/rms/__init__.py	`100% <100%> (ø)`
pmda/rms/rmsf.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 1e99541...d083361. Read the comment docs.

orbeckst commented 5 years ago

Sorry @nawtrey – totally fell off my radar.