test: stabilize linear MSD fit tolerance

[galjos]

Summary

• allow cross-platform floating-point noise in an exact linear MSD fit
• keep the tolerance below 1e-8 without changing production behavior

Verification

• focused MSD tests pass in both runtime modes
• full suite: 749 passed, 4 skipped in both runtime modes

Unblocks #157.

[github-actions]

PYLINT REPORT

Your code has been rated at 9.76/10

Full report

Raw metrics

type	number	%	previous	difference
code	13031	42.96	NC	NC
docstring	12355	40.73	NC	NC
comment	455	1.50	NC	NC
empty	4494	14.81	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	126	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	7.14	0.00
PQAnalysis.analysis.vibrational.vibrational_analysis	20.00	0.00	7.94	0.00
PQAnalysis	20.00	0.00	0.00	0.00
PQAnalysis.analysis.vacf._vacf_kernel_py	0.00	10.53	1.59	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	4.76	0.00
PQAnalysis.analysis.rdf._rdf_kernel_py	0.00	5.26	2.38	0.00
PQAnalysis.analysis.msd._msd_kernel_py	0.00	5.26	2.38	0.00
PQAnalysis.io.conversion_api	0.00	5.26	1.59	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.cli.init	0.00	0.00	11.11	0.00
PQAnalysis.analysis.rdf.rdf	0.00	0.00	6.35	12.50
PQAnalysis.analysis.msd.msd	0.00	0.00	6.35	0.00
PQAnalysis.io.nep.nep_writer	0.00	0.00	5.56	12.50
PQAnalysis.analysis.vacf.vacf	0.00	0.00	4.76	0.00
PQAnalysis.analysis.vacf.spectrum	0.00	0.00	3.97	0.00
PQAnalysis.io.traj_file.trajectory_reader	0.00	0.00	3.17	0.00
PQAnalysis.topology.bonded_topology.dihedral	0.00	0.00	2.38	0.00
PQAnalysis.io.traj_file._slab_parser_py	0.00	0.00	2.38	0.00
PQAnalysis.core.residue	0.00	0.00	2.38	0.00
PQAnalysis.topology.bonded_topology.bonded_topology	0.00	0.00	1.59	0.00
PQAnalysis.topology.bonded_topology.bond	0.00	0.00	1.59	0.00
PQAnalysis.topology.bonded_topology.angle	0.00	0.00	1.59	0.00
PQAnalysis.io.traj_file.raw_frame_reader	0.00	0.00	1.59	0.00
PQAnalysis.core.cell.cell	0.00	0.00	1.59	0.00
PQAnalysis.atomic_system._standard_properties	0.00	0.00	1.59	0.00
PQAnalysis.analysis.vacf.api	0.00	0.00	1.59	0.00
PQAnalysis.analysis.spectrum_broadening.api	0.00	0.00	1.59	0.00
PQAnalysis.analysis.momentum.api	0.00	0.00	1.59	0.00
PQAnalysis.analysis.vibrational.vibrational_input_file_reader	0.00	0.00	0.79	12.50
PQAnalysis.traj.formats	0.00	0.00	0.79	0.00
PQAnalysis.topology.topology	0.00	0.00	0.79	0.00
PQAnalysis.topology.selection	0.00	0.00	0.79	0.00
PQAnalysis.io.traj_file.frame_reader	0.00	0.00	0.79	0.00
PQAnalysis.io.restart_file.restart_reader	0.00	0.00	0.79	0.00
PQAnalysis.io.input_file_reader.pq_analysis._parse	0.00	0.00	0.79	0.00
PQAnalysis.io.input_file_reader.pq.pq_input_file_reader	0.00	0.00	0.79	0.00
PQAnalysis.io.input_file_reader.input_file_parser	0.00	0.00	0.79	0.00
PQAnalysis.io.info_file_reader	0.00	0.00	0.79	0.00
PQAnalysis.io.formats	0.00	0.00	0.79	0.00
PQAnalysis.analysis.momentum.momentum	0.00	0.00	0.79	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	28
too-many-arguments	28
too-many-locals	15
duplicate-code	14
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

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 93.18%. Comparing base (bd653f9) to head (dee66b4).
⚠️ Report is 5 commits behind head on dev.

Additional details and impacted files

@@           Coverage Diff           @@
##              dev     #158   +/-   ##
=======================================
  Coverage   93.18%   93.18%           
=======================================
  Files         170      170           
  Lines        7928     7928           
=======================================
  Hits         7388     7388           
  Misses        540      540           

Flag	Coverage Δ
unittests	93.18% <ø> (ø)

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