chore: release v1.5.0

[galjos]

Summary

• document stable fields, scientific symbols, units, and definitions for analysis output columns
• preserve existing native output filenames and numeric layouts
• add native, CSV, TSV, and xmgrace-ready XVG output across tabular analysis CLIs
• support lossless conversion in every direction and multiple outputs per run
• refuse existing output paths by default before writing any requested file
• prepare the v1.5.0 minor release

Includes #163 and #165.

Validation

• current dev workflows passed: Test Coverage, Pylint, Docs
• release candidate pqanalysis-1.5.0.tar.gz passed twine check
• candidate metadata reports PQAnalysis 1.5.0 and contains the new codec, converter, documentation, and tests
• clean virtual-environment install built successfully and reports version 1.5.0
• installed CLI smoke test converted a PQAnalysis XVG table to CSV without data loss

[github-actions]

PYLINT REPORT

Your code has been rated at 9.78/10

Full report

Raw metrics

type	number	%	previous	difference
code	14399	44.48	NC	NC
docstring	12699	39.23	NC	NC
comment	455	1.41	NC	NC
empty	4821	14.89	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	8	NC	NC
refactor	129	NC	NC
warning	19	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	10.53	6.98	0.00
PQAnalysis.analysis.vibrational.vibrational_analysis	20.00	0.00	7.75	0.00
PQAnalysis	20.00	0.00	0.00	0.00
PQAnalysis.analysis.vacf._vacf_kernel_py	0.00	10.53	1.55	0.00
PQAnalysis.topology.init	0.00	10.53	0.00	0.00
PQAnalysis.tools.traj_to_com_traj	0.00	10.53	0.00	0.00
PQAnalysis.io.traj_file._process_lines_py	0.00	10.53	0.00	0.00
PQAnalysis.io.moldescriptor_reader	0.00	10.53	0.00	0.00
PQAnalysis.tools.add_molecule	0.00	5.26	4.65	0.00
PQAnalysis.analysis.rdf._rdf_kernel_py	0.00	5.26	2.33	0.00
PQAnalysis.analysis.msd._msd_kernel_py	0.00	5.26	2.33	0.00
PQAnalysis.io.conversion_api	0.00	5.26	1.55	0.00
PQAnalysis.version	0.00	5.26	0.00	0.00
PQAnalysis.utils.custom_logging	0.00	5.26	0.00	0.00
PQAnalysis.io.write_api	0.00	5.26	0.00	0.00
PQAnalysis.traj.api	0.00	0.00	11.63	0.00
PQAnalysis.analysis.rdf.rdf	0.00	0.00	7.75	12.50
PQAnalysis.analysis.msd.msd	0.00	0.00	6.20	0.00
PQAnalysis.io.nep.nep_writer	0.00	0.00	5.43	12.50
PQAnalysis.analysis.vacf.vacf	0.00	0.00	4.65	0.00
PQAnalysis.analysis.vacf.spectrum	0.00	0.00	3.88	0.00
PQAnalysis.io.traj_file.trajectory_reader	0.00	0.00	3.10	0.00
PQAnalysis.topology.bonded_topology.dihedral	0.00	0.00	2.33	0.00
PQAnalysis.io.traj_file._slab_parser_py	0.00	0.00	2.33	0.00
PQAnalysis.core.residue	0.00	0.00	2.33	0.00
PQAnalysis.topology.bonded_topology.bonded_topology	0.00	0.00	1.55	0.00
PQAnalysis.topology.bonded_topology.bond	0.00	0.00	1.55	0.00
PQAnalysis.topology.bonded_topology.angle	0.00	0.00	1.55	0.00
PQAnalysis.io.traj_file.raw_frame_reader	0.00	0.00	1.55	0.00
PQAnalysis.core.cell.cell	0.00	0.00	1.55	0.00
PQAnalysis.atomic_system._standard_properties	0.00	0.00	1.55	0.00
PQAnalysis.analysis.vacf.api	0.00	0.00	1.55	0.00
PQAnalysis.analysis.spectrum_broadening.api	0.00	0.00	1.55	0.00
PQAnalysis.analysis.momentum.api	0.00	0.00	1.55	0.00
PQAnalysis.analysis.vibrational.vibrational_input_file_reader	0.00	0.00	0.78	12.50
PQAnalysis.traj.formats	0.00	0.00	0.78	0.00
PQAnalysis.topology.topology	0.00	0.00	0.78	0.00
PQAnalysis.topology.selection	0.00	0.00	0.78	0.00
PQAnalysis.io.traj_file.frame_reader	0.00	0.00	0.78	0.00
PQAnalysis.io.restart_file.restart_reader	0.00	0.00	0.78	0.00
PQAnalysis.io.input_file_reader.pq_analysis._parse	0.00	0.00	0.78	0.00
PQAnalysis.io.input_file_reader.pq.pq_input_file_reader	0.00	0.00	0.78	0.00
PQAnalysis.io.input_file_reader.input_file_parser	0.00	0.00	0.78	0.00
PQAnalysis.io.info_file_reader	0.00	0.00	0.78	0.00
PQAnalysis.io.formats	0.00	0.00	0.78	0.00
PQAnalysis.analysis.momentum.momentum	0.00	0.00	0.78	0.00
PQAnalysis.core.atom.element	0.00	0.00	0.00	25.00
PQAnalysis.analysis.vacf.vacf_input_file_reader	0.00	0.00	0.00	12.50
PQAnalysis.analysis.rdf.rdf_input_file_reader	0.00	0.00	0.00	12.50
PQAnalysis.analysis.msd.msd_input_file_reader	0.00	0.00	0.00	12.50

Messages

message id	occurrences
too-many-positional-arguments	29
too-many-arguments	29
too-many-locals	15
duplicate-code	15
too-many-instance-attributes	13
fixme	9
too-complex	8
inconsistent-return-statements	8
invalid-name	6
too-many-branches	5
missing-type-doc	4
too-many-return-statements	3
unused-import	2
too-many-statements	2
too-many-lines	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

❌ Patch coverage is 94.18758% with 44 lines in your changes missing coverage. Please review.
✅ Project coverage is 93.32%. Comparing base (ff24cc7) to head (570bb6c).
⚠️ Report is 2 commits behind head on main.

Files with missing lines	Patch %	Lines
PQAnalysis/analysis/output.py	92.50%	23 Missing ⚠️
PQAnalysis/analysis/_xvg.py	90.00%	20 Missing ⚠️
PQAnalysis/analysis/rdf/api.py	66.66%	1 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##             main     #166      +/-   ##
==========================================
+ Coverage   93.18%   93.32%   +0.14%     
==========================================
  Files         170      175       +5     
  Lines        7933     8588     +655     
==========================================
+ Hits         7392     8015     +623     
- Misses        541      573      +32     

Flag	Coverage Δ
unittests	93.32% <94.18%> (+0.14%)	⬆️

Files with missing lines	Coverage Δ
PQAnalysis/analysis/__init__.py	100.00% <100.00%> (ø)
PQAnalysis/analysis/_output_header.py	100.00% <100.00%> (ø)
PQAnalysis/analysis/_output_schemas.py	100.00% <100.00%> (ø)
PQAnalysis/analysis/momentum/api.py	100.00% <100.00%> (ø)
...s/analysis/momentum/momentum_output_file_writer.py	100.00% <100.00%> (ø)
PQAnalysis/analysis/msd/api.py	100.00% <100.00%> (ø)
PQAnalysis/analysis/msd/msd_input_file_reader.py	100.00% <ø> (ø)
PQAnalysis/analysis/msd/msd_output_file_writer.py	100.00% <100.00%> (ø)
PQAnalysis/analysis/rdf/rdf.py	99.25% <100.00%> (-0.01%)	⬇️
PQAnalysis/analysis/rdf/rdf_input_file_reader.py	100.00% <ø> (ø)
... and 21 more

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