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fix: register -n and --n-molecules as separate option strings - #207

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fix: register -n and --n-molecules as separate option strings#207
galjos wants to merge 1 commit into
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fix/add-molecules-flag

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@galjos

@galjos galjos commented Aug 24, 2026

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The option was added as one string "-n, --n-molecules" instead of two, so the advertised long flag was rejected as unrecognized. Split into two option strings.

The added tests pin the option strings, both flags, and the default.

Fixes #206.

The -n and --n-molecules aliases were passed to add_argument as a
single comma-joined string, so argparse registered one malformed
option. The help text advertised --n-molecules, but using it failed
with unrecognized arguments and only -n worked via prefix matching.
Splitting the aliases into separate option strings makes both work.
@galjos
galjos requested a review from 97gamjak August 24, 2026 07:29
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PYLINT REPORT

Your code has been rated at 9.78/10

Full report

Raw metrics

type number % previous difference
code 15654 45.61 NC NC
docstring 13050 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

@codecov

codecov Bot commented Aug 24, 2026

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Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 93.94%. Comparing base (0961625) to head (514ed60).

Additional details and impacted files
@@           Coverage Diff           @@
##              dev     #207   +/-   ##
=======================================
  Coverage   93.94%   93.94%           
=======================================
  Files         177      177           
  Lines        9227     9227           
=======================================
  Hits         8668     8668           
  Misses        559      559           
Flag Coverage Δ
unittests 93.94% <ø> (ø)
Files with missing lines Coverage Δ
PQAnalysis/cli/add_molecules.py 100.00% <ø> (ø)
🚀 New features to boost your workflow:
  • ❄️ Test Analytics: Detect flaky tests, report on failures, and find test suite problems.

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