ENM Base class

[stratixs]

Logical changes

• Adds a base class ENM that handles common logic across GNM and ANM (specifically constructor, covariance calculation, calls to NMA). The goal is to reduce code duplications.
• The covariance is calculated with np.linalg.pinv. Internally this method uses np.linalg.eigh to calculate the eigenvalues/-vectors and constructs the pseudo-inverse using the reciprocal eigenvalues. This change makes this calculation explicitly and stores the eigenvalues/-vectors in the process so that they can be easily reused for NMA calculations without recalculation.
• Instead of relying on fixed number of trivial nodes the number of zero eigenvalues can be centrally calculated and returned alongside when calling the ENM.eigen() function.
• Optimize NMA calculations to reduce complexity for maintainers. These changes are also a result from the common attributes introduced by the ENM base class.

Bug fixes

• Use direct evaluation of coord difference between atoms instead of calling struc.displacement as the latter one forces float32 precision but float64 is desired.

Housekeeping

• Switches to hatch build system (the same as the biotite parent project)
• Extends/corrects docstrings to adhere to numpydoc standard (uses the same numpydoc lint rules as the parent project)
• Adds type information to attributes and return values so that users can utilize IDE's static analyzers when calling the functions
• Switches from .pdb to .cif files for tests because RCSB will phase out the old format.
• Boost test coverage from

Name                             Stmts   Miss Branch BrPart  Cover
------------------------------------------------------------------
src/springcraft/__init__.py          8      0      0      0   100%
src/springcraft/anm.py              79     18     24      4    73%
src/springcraft/forcefield.py      249     25     64     17    86%
src/springcraft/gnm.py              70     17     24      4    71%
src/springcraft/interaction.py      61      3     18      3    92%
src/springcraft/nma.py             151     44     58     10    66%
------------------------------------------------------------------
TOTAL                              618    107    188     38    78%

to

Name                             Stmts   Miss Branch BrPart  Cover
------------------------------------------------------------------
src/springcraft/__init__.py          8      0      0      0   100%
src/springcraft/anm.py              61      2      8      0    97%
src/springcraft/enm.py             112      5     28      2    95%
src/springcraft/forcefield.py      276     18     64     10    91%
src/springcraft/gnm.py              51      0      8      0   100%
src/springcraft/interaction.py      62      3     18      3    92%
src/springcraft/nma.py             109     35     42      7    62%
------------------------------------------------------------------
TOTAL                              679     63    168     22    88%