Feature/beartype exceptions

[97gamjak]

Introduced runtime-checking for core and atomicSystem module.

Now tests work with pytest.sh for RELEASE and DEBUG version (including or excluding beartype)

Furthermore, now every PQAnalysis internal exception has to inherit from PQException

[github-actions]

PYLINT REPORT

Your code has been rated at 9.86/10 (previous run: 9.88/10, -0.02)

Full report

Raw metrics

type	number	%	previous	difference
code	6789	39.18	6651	+138.00
docstring	7921	45.71	7881	+40.00
comment	269	1.55	265	+4.00
empty	2349	13.56	2320	+29.00

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	0	0	0
refactor	43	42	42
warning	16	9	9
error	0	0	0

Messages

message id	occurrences
too-many-arguments	18
too-many-instance-attributes	10
fixme	10
duplicate-code	4
too-many-locals	3
too-complex	3
unused-argument	2
too-many-branches	2
protected-access	2
unused-import	1
too-many-statements	1
too-many-return-statements	1
too-many-public-methods	1
broad-exception-raised	1

[codecov]

Codecov Report

Attention: Patch coverage is 95.90164% with 5 lines in your changes are missing coverage. Please review.

Project coverage is 80.23%. Comparing base (55bad1f) to head (84cb3a9).
Report is 2 commits behind head on dev.

Additional details and impacted files

@@            Coverage Diff             @@
##              dev      #48      +/-   ##
==========================================
+ Coverage   78.58%   80.23%   +1.64%     
==========================================
  Files         119      119              
  Lines        4334     4411      +77     
==========================================
+ Hits         3406     3539     +133     
+ Misses        928      872      -56     

Flag	Coverage Δ
unittests	80.23% <95.90%> (+1.64%)	⬆️

Files	Coverage Δ
PQAnalysis/analysis/rdf/rdf.py	77.24% <ø> (ø)
PQAnalysis/atomic_system/_decorators.py	100.00% <100.00%> (ø)
PQAnalysis/atomic_system/_positions.py	100.00% <100.00%> (ø)
PQAnalysis/atomic_system/_properties.py	100.00% <100.00%> (+2.12%)	⬆️
PQAnalysis/atomic_system/_standard_properties.py	100.00% <100.00%> (ø)
PQAnalysis/atomic_system/atomic_system.py	67.85% <100.00%> (+1.69%)	⬆️
PQAnalysis/atomic_system/exceptions.py	100.00% <100.00%> (ø)
PQAnalysis/core/api.py	100.00% <100.00%> (ø)
PQAnalysis/core/atom/atom.py	100.00% <100.00%> (+1.88%)	⬆️
PQAnalysis/core/atom/element.py	100.00% <100.00%> (ø)
... and 10 more

... and 30 files with indirect coverage changes