Update on constraint module; Add generalized constraint class

[skim0119]

Dev Note

Related to #54 , the current constraint component does not pass the indices to the class methods. As a result, it is difficult to implement constraint or boundary conditions at the middle of the rod. I talked to @tp5uiuc, and this is definitely not intended behavior.

To fix the issue and improve future functionality, I'm exposing system(rod), position indices, and director indices to the constraining/BC class. This should make BC implementation more flexible.

In addition, I refactored @nmnaughton 's implementation on more general BC: FixedRodBC and FixedNodeBC (#54). I added an example script on how to use new constraint FixedConstraint. The PR also includes test codes.

How to use FixedConstraint

Update

• ConstraintBase abstract class is added to provide template for all constraint classes.
  • People who inherited FreeRod should not get errors, but a deprecation warning should appear.
• Properties for system, position_indices, and director_indices are added.
• FreeRod and OneEndFixedRod are refactored to FreeBC and OneEndFixedBC. I made an alias and deprecation note so that people have time to notice the change and convert their code.
• Boundary condition FixedConstraint with documentation.
• Test code for FixedConstraint is added and tested.
• Test code for the ConstraintBase class is added and tested.
• Documentation is added for new classes.

resolve #55

[codecov-commenter]

Codecov Report

Merging #56 (c629a78) into update-0.2.2 (1c008ba) will increase coverage by 0.43%.
The diff coverage is 96.63%.

@@               Coverage Diff                @@
##           update-0.2.2      #56      +/-   ##
================================================
+ Coverage         81.26%   81.70%   +0.43%     
================================================
  Files                40       40              
  Lines              2552     2645      +93     
  Branches            357      372      +15     
================================================
+ Hits               2074     2161      +87     
- Misses              453      458       +5     
- Partials             25       26       +1     

Impacted Files	Coverage Δ
elastica/boundary_conditions.py	95.36% <96.46%> (-2.97%)	⬇️
elastica/wrappers/constraints.py	100.00% <100.00%> (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 1c008ba...c629a78. Read the comment docs.

[armantekinalp]

I think everything looks good. I have some questions, could you please address them @skim0119

[armantekinalp]

LGTM, one small documentation comment.