CLI: xyz2rst tool added

[galjos]

Closes #117

[codecov]

Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 85.62%. Comparing base (1b191f8) to head (e7ee687).
Report is 18 commits behind head on dev.

Additional details and impacted files

@@            Coverage Diff             @@
##              dev     #118      +/-   ##
==========================================
+ Coverage   85.43%   85.62%   +0.18%     
==========================================
  Files         125      126       +1     
  Lines        5034     5092      +58     
==========================================
+ Hits         4301     4360      +59     
+ Misses        733      732       -1     

Flag	Coverage Δ
unittests	85.62% <100.00%> (+0.18%)	⬆️

Files with missing lines	Coverage Δ
PQAnalysis/atomic_system/atomic_system.py	97.72% <100.00%> (+0.06%)	⬆️
PQAnalysis/cli/main.py	65.51% <100.00%> (+1.23%)	⬆️
PQAnalysis/cli/xyz2rst.py	100.00% <100.00%> (ø)
PQAnalysis/io/__init__.py	100.00% <100.00%> (ø)
PQAnalysis/io/conversion_api.py	88.88% <100.00%> (+2.52%)	⬆️
PQAnalysis/io/restart_file/api.py	100.00% <100.00%> (ø)
PQAnalysis/io/restart_file/restart_writer.py	100.00% <100.00%> (ø)

... and 1 file with indirect coverage changes

[github-actions]

PYLINT REPORT

Your code has been rated at 9.79/10 (previous run: 9.79/10, -0.00)

Full report

Raw metrics

type	number	%	previous	difference
code	8039	40.11	7910	+129.00
docstring	8770	43.76	8668	+102.00
comment	268	1.34	268	=
empty	2963	14.79	2935	+28.00

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	71	69	69
warning	12	11	11
error	3	3	3

% errors / warnings by module

module	error	warning	refactor	convention
PQAnalysis.type_checking	66.67	0.00	0.00	0.00
PQAnalysis	33.33	0.00	0.00	0.00
PQAnalysis.atomic_system.atomic_system	0.00	16.67	12.68	0.00
PQAnalysis.topology.init	0.00	16.67	0.00	0.00
PQAnalysis.tools.traj_to_com_traj	0.00	16.67	0.00	0.00
PQAnalysis.io.moldescriptor_reader	0.00	16.67	0.00	0.00
PQAnalysis.tools.add_molecule	0.00	8.33	8.45	0.00
PQAnalysis.io.conversion_api	0.00	8.33	2.82	0.00
PQAnalysis.utils.custom_logging	0.00	8.33	0.00	0.00
PQAnalysis.io.write_api	0.00	8.33	0.00	0.00
PQAnalysis.io.nep.nep_writer	0.00	0.00	15.49	50.00
PQAnalysis.io.traj_file.trajectory_reader	0.00	0.00	8.45	0.00
PQAnalysis.analysis.rdf.rdf	0.00	0.00	7.04	0.00
PQAnalysis.topology.topology	0.00	0.00	4.23	0.00
PQAnalysis.topology.bonded_topology.dihedral	0.00	0.00	4.23	0.00
PQAnalysis.io.virial.virial_reader	0.00	0.00	4.23	0.00
PQAnalysis.core.residue	0.00	0.00	4.23	0.00
PQAnalysis.topology.bonded_topology.bonded_topology	0.00	0.00	2.82	0.00
PQAnalysis.topology.bonded_topology.bond	0.00	0.00	2.82	0.00
PQAnalysis.topology.bonded_topology.angle	0.00	0.00	2.82	0.00
PQAnalysis.io.traj_file.frame_reader	0.00	0.00	2.82	0.00
PQAnalysis.core.cell.cell	0.00	0.00	2.82	0.00
PQAnalysis.atomic_system._standard_properties	0.00	0.00	2.82	0.00
PQAnalysis.traj.formats	0.00	0.00	1.41	0.00
PQAnalysis.topology.selection	0.00	0.00	1.41	0.00
PQAnalysis.io.restart_file.restart_reader	0.00	0.00	1.41	0.00
PQAnalysis.io.input_file_reader.pq_analysis._parse	0.00	0.00	1.41	0.00
PQAnalysis.io.input_file_reader.pq.pq_input_file_reader	0.00	0.00	1.41	0.00
PQAnalysis.io.input_file_reader.input_file_parser	0.00	0.00	1.41	0.00
PQAnalysis.io.info_file_reader	0.00	0.00	1.41	0.00
PQAnalysis.io.formats	0.00	0.00	1.41	0.00
PQAnalysis.analysis.rdf.rdf_input_file_reader	0.00	0.00	0.00	50.00

Messages

message id	occurrences
too-many-positional-arguments	19
too-many-arguments	19
too-many-instance-attributes	10
inconsistent-return-statements	9
fixme	9
too-many-locals	3
too-complex	3
duplicate-code	3
too-many-branches	2
missing-kwoa	2
unused-import	1
too-many-statements	1
too-many-return-statements	1
too-many-public-methods	1
too-many-lines	1
possibly-used-before-assignment	1
missing-param-doc	1
invalid-name	1
arguments-differ	1