fix: keep the constructor topology in TrajectoryReader.read

[galjos]

read() overwrote the constructor-supplied topology with its own default None, so read_trajectory with a topology silently ignored it. The parameter is now only assigned when given.

The added test asserts atoms and residue ids from the constructor topology survive both reader.read() and read_trajectory(file, topology=...).

Fixes #186.

[codecov]

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 93.94%. Comparing base (0961625) to head (b0524e9).

Additional details and impacted files

@@           Coverage Diff           @@
##              dev     #187   +/-   ##
=======================================
  Coverage   93.94%   93.94%           
=======================================
  Files         177      177           
  Lines        9227     9228    +1     
=======================================
+ Hits         8668     8669    +1     
  Misses        559      559           

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

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

🚀 New features to boost your workflow:

• ❄️ Test Analytics: Detect flaky tests, report on failures, and find test suite problems.

[github-actions]

PYLINT REPORT

Your code has been rated at 9.78/10

Full report

Raw metrics

type	number	%	previous	difference
code	15655	45.61	NC	NC
docstring	13049	38.02	NC	NC
comment	463	1.35	NC	NC
empty	5156	15.02	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