perf: reduce CLI startup overhead

[galjos]

Changes

• Lazy-load package exports and unified CLI commands.
• Reuse the RDF input batch for cell setup and histogramming.
• Batch exact MSD calculations for changing orthorhombic cells.
• Preserve bounded-memory fallbacks and the public msd, rdf, and vacf exports.

Performance

Cold-process startup against dev (cc67f768):

Command	dev	PR	Speedup
Root help	287 ms	83 ms	3.47x
VACF help	469 ms	410 ms	1.15x
MSD help	385 ms	280 ms	1.38x
RDF help	322 ms	268 ms	1.20x
Momentum help	373 ms	303 ms	1.23x

Real-trajectory medians at b67b7fc; seven rotated rounds after one warmup, one fresh process per run, and legacy C compiled with -O2:

Analysis	Legacy C	PQAnalysis	Speedup
VACF	0.775 s	0.417 s	1.86x
MSD	2.183 s	0.448 s	4.87x
RDF	1.926 s	1.363 s	1.41x
Combined	4.885 s	2.228 s	2.19x

Correctness

• MSD is bitwise identical to exact streaming on the 75,000-frame changing-box trajectory.
• RDF is bitwise identical to legacy C on the 12,500-frame, 428-atom trajectory.
• Boundary coverage includes empty files, changing and unsupported cells, half-box ties, parser failures, memory limits, and one-atom self-selection.

Validation

• DEBUG: 948 passed, 4 skipped
• RELEASE: 948 passed, 4 skipped
• PQEnalyzer: 272 passed
• Pylint: 9.78/10
• Sphinx and all GitHub/Codecov checks passed

[codecov]

Codecov Report

❌ Patch coverage is 99.17355% with 2 lines in your changes missing coverage. Please review.
✅ Project coverage is 93.86%. Comparing base (cc67f76) to head (576eb98).

Files with missing lines	Patch %	Lines
PQAnalysis/__init__.py	0.00%	1 Missing ⚠️
PQAnalysis/_lazy_import.py	96.29%	1 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##              dev     #171      +/-   ##
==========================================
+ Coverage   93.82%   93.86%   +0.03%     
==========================================
  Files         176      177       +1     
  Lines        9108     9215     +107     
==========================================
+ Hits         8546     8650     +104     
- Misses        562      565       +3     

Flag	Coverage Δ
unittests	93.86% <99.17%> (+0.03%)	⬆️

Files with missing lines	Coverage Δ
PQAnalysis/analysis/__init__.py	100.00% <100.00%> (ø)
PQAnalysis/analysis/momentum/momentum.py	100.00% <100.00%> (ø)
PQAnalysis/analysis/msd/msd.py	99.38% <100.00%> (-0.02%)	⬇️
PQAnalysis/analysis/rdf/rdf.py	99.50% <100.00%> (+0.02%)	⬆️
PQAnalysis/analysis/vacf/vacf.py	99.59% <100.00%> (ø)
PQAnalysis/cli/_argument_parser.py	98.21% <100.00%> (+0.10%)	⬆️
PQAnalysis/cli/main.py	98.00% <100.00%> (+0.77%)	⬆️
PQAnalysis/core/__init__.py	100.00% <100.00%> (ø)
PQAnalysis/formats.py	100.00% <100.00%> (ø)
PQAnalysis/io/__init__.py	100.00% <100.00%> (ø)
... and 13 more

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[github-actions]

PYLINT REPORT

Your code has been rated at 9.78/10

Full report

Raw metrics

type	number	%	previous	difference
code	15638	45.62	NC	NC
docstring	13023	37.99	NC	NC
comment	463	1.35	NC	NC
empty	5152	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	134	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	6.72	0.00
PQAnalysis.analysis.vibrational.vibrational_analysis	20.00	0.00	7.46	0.00
PQAnalysis	20.00	0.00	0.00	0.00
PQAnalysis.analysis.vacf._vacf_kernel_py	0.00	11.76	1.49	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	4.48	0.00
PQAnalysis.analysis.rdf._rdf_kernel_py	0.00	5.88	2.24	0.00
PQAnalysis.analysis.msd._msd_kernel_py	0.00	5.88	2.24	0.00
PQAnalysis.io.conversion_api	0.00	5.88	1.49	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.core.atom.element	0.00	0.00	14.18	13.33
PQAnalysis.analysis.rdf.rdf	0.00	0.00	6.72	6.67
PQAnalysis.analysis.msd.msd	0.00	0.00	5.97	33.33
PQAnalysis.io.nep.nep_writer	0.00	0.00	5.22	6.67
PQAnalysis.analysis.vacf.vacf	0.00	0.00	4.48	13.33
PQAnalysis.io.traj_file._slab_parser_py	0.00	0.00	3.73	0.00
PQAnalysis.analysis.vacf.spectrum	0.00	0.00	3.73	0.00
PQAnalysis.io.traj_file.trajectory_reader	0.00	0.00	2.99	0.00
PQAnalysis.topology.bonded_topology.dihedral	0.00	0.00	2.24	0.00
PQAnalysis.core.residue	0.00	0.00	2.24	0.00
PQAnalysis.topology.bonded_topology.bonded_topology	0.00	0.00	1.49	0.00
PQAnalysis.topology.bonded_topology.bond	0.00	0.00	1.49	0.00
PQAnalysis.topology.bonded_topology.angle	0.00	0.00	1.49	0.00
PQAnalysis.io.traj_file.raw_frame_reader	0.00	0.00	1.49	0.00
PQAnalysis.core.cell.cell	0.00	0.00	1.49	0.00
PQAnalysis.atomic_system._standard_properties	0.00	0.00	1.49	0.00
PQAnalysis.analysis.vacf.api	0.00	0.00	1.49	0.00
PQAnalysis.analysis.spectrum_broadening.api	0.00	0.00	1.49	0.00
PQAnalysis.analysis.momentum.api	0.00	0.00	1.49	0.00
PQAnalysis.analysis.vibrational.vibrational_input_file_reader	0.00	0.00	0.75	6.67
PQAnalysis.traj.formats	0.00	0.00	0.75	0.00
PQAnalysis.topology.topology	0.00	0.00	0.75	0.00
PQAnalysis.topology.selection	0.00	0.00	0.75	0.00
PQAnalysis.io.traj_file.frame_reader	0.00	0.00	0.75	0.00
PQAnalysis.io.restart_file.restart_reader	0.00	0.00	0.75	0.00
PQAnalysis.io.input_file_reader.pq_analysis._parse	0.00	0.00	0.75	0.00
PQAnalysis.io.input_file_reader.pq.pq_input_file_reader	0.00	0.00	0.75	0.00
PQAnalysis.io.input_file_reader.input_file_parser	0.00	0.00	0.75	0.00
PQAnalysis.io.info_file_reader	0.00	0.00	0.75	0.00
PQAnalysis.io.formats	0.00	0.00	0.75	0.00
PQAnalysis.analysis.momentum.momentum	0.00	0.00	0.75	0.00
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	19
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