Feature/beartype exceptions2

[97gamjak]

All function that the end-user should `use are now implemented with customized runtime type checking.

Additionally, all raise and warns are substituted by corresponding logger calls.

[github-actions]

PYLINT REPORT

Your code has been rated at 9.85/10 (previous run: 9.86/10, -0.00)

Full report

Raw metrics

type	number	%	previous	difference
code	7609	39.85	7509	+100.00
docstring	8423	44.11	8413	+10.00
comment	262	1.37	265	-3.00
empty	2800	14.66	2788	+12.00

Duplication

	now	previous	difference
nb duplicated lines	0	0	0
percent duplicated lines	0.000	0.000	=

Messages by category

type	number	previous	difference
convention	2	2	2
refactor	51	49	49
warning	12	13	13
error	0	0	0

Messages

message id	occurrences
too-many-arguments	18
fixme	11
too-many-instance-attributes	10
inconsistent-return-statements	9
too-many-locals	3
too-complex	3
duplicate-code	3
too-many-branches	2
unused-argument	1
trailing-newlines	1
too-many-statements	1
too-many-return-statements	1
too-many-public-methods	1
too-many-lines	1

[codecov]

Codecov Report

Attention: Patch coverage is 83.96226% with 17 lines in your changes are missing coverage. Please review.

Project coverage is 80.29%. Comparing base (cf8c754) to head (271c968).
Report is 1 commits behind head on dev.

Additional details and impacted files

@@            Coverage Diff             @@
##              dev      #52      +/-   ##
==========================================
+ Coverage   80.02%   80.29%   +0.26%     
==========================================
  Files         122      122              
  Lines        4755     4825      +70     
==========================================
+ Hits         3805     3874      +69     
- Misses        950      951       +1     

Flag	Coverage Δ
unittests	80.29% <83.96%> (+0.26%)	⬆️

Files	Coverage Δ
PQAnalysis/__init__.py	82.14% <100.00%> (ø)
PQAnalysis/core/atom/atom.py	98.27% <ø> (ø)
PQAnalysis/physical_data/energy.py	100.00% <100.00%> (ø)
PQAnalysis/tools/traj_to_com_traj.py	100.00% <100.00%> (ø)
PQAnalysis/topology/api.py	63.15% <100.00%> (+6.90%)	⬆️
PQAnalysis/topology/bonded_topology/angle.py	100.00% <100.00%> (ø)
PQAnalysis/topology/bonded_topology/bond.py	100.00% <100.00%> (ø)
...alysis/topology/bonded_topology/bonded_topology.py	100.00% <100.00%> (ø)
PQAnalysis/topology/bonded_topology/dihedral.py	100.00% <100.00%> (ø)
PQAnalysis/topology/shake_topology.py	100.00% <100.00%> (ø)
... and 6 more