fix: track written frames for traj2box step indices

[galjos]

The box writer derived the step offset from the current trajectory's length times the file counter, which is only correct when every input file has the same frame count. It now counts the frames actually written and uses that as the offset; reset_counter=True resets it.

The added test writes unequal trajectories and asserts the step sequence with and without the reset.

Fixes #194.

[github-actions]

PYLINT REPORT

Your code has been rated at 9.78/10

Full report

Raw metrics

type	number	%	previous	difference
code	15657	45.61	NC	NC
docstring	13049	38.01	NC	NC
comment	463	1.35	NC	NC
empty	5158	15.03	NC	NC

Duplication

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

Messages by category

type	number	previous	difference
convention	15	NC	NC
refactor	135	NC	NC
warning	17	NC	NC
error	5	NC	NC

% errors / warnings by module

module	error	warning	refactor	convention
PQAnalysis.type_checking	40.00	0.00	0.00	0.00
PQAnalysis.atomic_system.atomic_system	20.00	11.76	6.67	0.00
PQAnalysis.analysis.vibrational.vibrational_analysis	20.00	0.00	7.41	0.00
PQAnalysis	20.00	0.00	0.00	0.00
PQAnalysis.analysis.vacf._vacf_kernel_py	0.00	11.76	1.48	0.00
PQAnalysis.tools.traj_to_com_traj	0.00	11.76	0.00	0.00
PQAnalysis.io.traj_file._process_lines_py	0.00	11.76	0.00	0.00
PQAnalysis.io.moldescriptor_reader	0.00	11.76	0.00	0.00
PQAnalysis.tools.add_molecule	0.00	5.88	4.44	0.00
PQAnalysis.analysis.rdf._rdf_kernel_py	0.00	5.88	2.22	0.00
PQAnalysis.analysis.msd._msd_kernel_py	0.00	5.88	2.22	0.00
PQAnalysis.io.conversion_api	0.00	5.88	1.48	0.00
PQAnalysis.version	0.00	5.88	0.00	0.00
PQAnalysis.utils.custom_logging	0.00	5.88	0.00	0.00
PQAnalysis.io.write_api	0.00	5.88	0.00	0.00
PQAnalysis.io.restart_file.restart_writer	0.00	0.00	14.81	0.00
PQAnalysis.analysis.rdf.rdf	0.00	0.00	6.67	6.67
PQAnalysis.analysis.msd.msd	0.00	0.00	5.93	33.33
PQAnalysis.io.nep.nep_writer	0.00	0.00	5.19	6.67
PQAnalysis.analysis.vacf.vacf	0.00	0.00	4.44	13.33
PQAnalysis.io.traj_file._slab_parser_py	0.00	0.00	3.70	0.00
PQAnalysis.analysis.vacf.spectrum	0.00	0.00	3.70	0.00
PQAnalysis.io.traj_file.trajectory_reader	0.00	0.00	2.96	0.00
PQAnalysis.topology.bonded_topology.dihedral	0.00	0.00	2.22	0.00
PQAnalysis.core.residue	0.00	0.00	2.22	0.00
PQAnalysis.topology.bonded_topology.bonded_topology	0.00	0.00	1.48	0.00
PQAnalysis.topology.bonded_topology.bond	0.00	0.00	1.48	0.00
PQAnalysis.topology.bonded_topology.angle	0.00	0.00	1.48	0.00
PQAnalysis.io.traj_file.raw_frame_reader	0.00	0.00	1.48	0.00
PQAnalysis.core.cell.cell	0.00	0.00	1.48	0.00
PQAnalysis.atomic_system._standard_properties	0.00	0.00	1.48	0.00
PQAnalysis.analysis.vacf.api	0.00	0.00	1.48	0.00
PQAnalysis.analysis.spectrum_broadening.api	0.00	0.00	1.48	0.00
PQAnalysis.analysis.momentum.api	0.00	0.00	1.48	0.00
PQAnalysis.analysis.vibrational.vibrational_input_file_reader	0.00	0.00	0.74	6.67
PQAnalysis.traj.formats	0.00	0.00	0.74	0.00
PQAnalysis.topology.topology	0.00	0.00	0.74	0.00
PQAnalysis.topology.selection	0.00	0.00	0.74	0.00
PQAnalysis.io.traj_file.frame_reader	0.00	0.00	0.74	0.00
PQAnalysis.io.restart_file.restart_reader	0.00	0.00	0.74	0.00
PQAnalysis.io.input_file_reader.pq_analysis._parse	0.00	0.00	0.74	0.00
PQAnalysis.io.input_file_reader.pq.pq_input_file_reader	0.00	0.00	0.74	0.00
PQAnalysis.io.input_file_reader.input_file_parser	0.00	0.00	0.74	0.00
PQAnalysis.io.info_file_reader	0.00	0.00	0.74	0.00
PQAnalysis.io.formats	0.00	0.00	0.74	0.00
PQAnalysis.analysis.momentum.momentum	0.00	0.00	0.74	0.00
PQAnalysis.core.atom.element	0.00	0.00	0.00	13.33
PQAnalysis.analysis.vacf.vacf_input_file_reader	0.00	0.00	0.00	6.67
PQAnalysis.analysis.rdf.rdf_input_file_reader	0.00	0.00	0.00	6.67
PQAnalysis.analysis.msd.msd_input_file_reader	0.00	0.00	0.00	6.67

Messages

message id	occurrences
too-many-positional-arguments	29
too-many-arguments	29
duplicate-code	20
too-many-locals	15
too-many-instance-attributes	13
invalid-name	12
too-complex	9
inconsistent-return-statements	8
fixme	7
too-many-branches	5
missing-type-doc	4
too-many-return-statements	3
too-many-lines	3
unused-import	2
too-many-statements	2
redefined-builtin	2
missing-kwoa	2
use-set-for-membership	1
unexpected-keyword-arg	1
too-many-public-methods	1
possibly-used-before-assignment	1
no-member	1
missing-param-doc	1
arguments-differ	1

[codecov]

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 93.94%. Comparing base (0961625) to head (c094dfd).

Additional details and impacted files

@@           Coverage Diff           @@
##              dev     #195   +/-   ##
=======================================
  Coverage   93.94%   93.94%           
=======================================
  Files         177      177           
  Lines        9227     9230    +3     
=======================================
+ Hits         8668     8671    +3     
  Misses        559      559           

Flag	Coverage Δ
unittests	93.94% <100.00%> (+<0.01%)	⬆️

Files with missing lines	Coverage Δ
PQAnalysis/io/box_writer.py	100.00% <100.00%> (ø)

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