Preformance Improvement of traj reader via cython

[github-actions[bot]]

PYLINT REPORT

Your code has been rated at 9.85/10 (previous run: 9.52/10, +0.32)

Full report

Raw metrics =========== |type |number |% |previous |difference | |----------|-------|------|---------|-----------| |code |7901 |39.99 |7874 |+27.00 | |docstring |8660 |43.83 |8660 |= | |comment |267 |1.35 |270 |-3.00 | |empty |2930 |14.83 |2922 |+8.00 | Duplication =========== | |now |previous |difference | |-------------------------|------|---------|-----------| |nb duplicated lines |0 |0 |0 | |percent duplicated lines |0.000 |0.000 |= | Messages by category ==================== |type |number |previous |difference | |-----------|-------|---------|-----------| |convention |1 |1 |1 | |refactor |51 |51 |51 | |warning |10 |14 |14 | |error |2 |31 |31 | % errors / warnings by module ============================= |module |error |warning |refactor |convention | |--------------------------------------------------------|------|--------|---------|-----------| |PQAnalysis.io.traj_file.api |50.00 |0.00 |0.00 |0.00 | |PQAnalysis |50.00 |0.00 |0.00 |0.00 | |PQAnalysis.atomic_system.atomic_system |0.00 |20.00 |11.76 |0.00 | |PQAnalysis.topology.__init__ |0.00 |20.00 |0.00 |0.00 | |PQAnalysis.tools.traj_to_com_traj |0.00 |20.00 |0.00 |0.00 | |PQAnalysis.io.moldescriptor_reader |0.00 |20.00 |0.00 |0.00 | |PQAnalysis.utils.custom_logging |0.00 |10.00 |0.00 |0.00 | |PQAnalysis.io.write_api |0.00 |10.00 |0.00 |0.00 | |PQAnalysis.io.nep.nep_writer |0.00 |0.00 |15.69 |100.00 | |PQAnalysis.io.traj_file.trajectory_reader |0.00 |0.00 |9.80 |0.00 | |PQAnalysis.tools.add_molecule |0.00 |0.00 |7.84 |0.00 | |PQAnalysis.atomic_system._properties |0.00 |0.00 |5.88 |0.00 | |PQAnalysis.analysis.rdf.rdf |0.00 |0.00 |5.88 |0.00 | |PQAnalysis.topology.topology |0.00 |0.00 |3.92 |0.00 | |PQAnalysis.topology.bonded_topology.dihedral |0.00 |0.00 |3.92 |0.00 | |PQAnalysis.io.traj_file.frame_reader |0.00 |0.00 |3.92 |0.00 | |PQAnalysis.core.residue |0.00 |0.00 |3.92 |0.00 | |PQAnalysis.atomic_system._standard_properties |0.00 |0.00 |3.92 |0.00 | |PQAnalysis.traj.formats |0.00 |0.00 |1.96 |0.00 | |PQAnalysis.topology.selection |0.00 |0.00 |1.96 |0.00 | |PQAnalysis.topology.bonded_topology.bonded_topology |0.00 |0.00 |1.96 |0.00 | |PQAnalysis.topology.bonded_topology.bond |0.00 |0.00 |1.96 |0.00 | |PQAnalysis.topology.bonded_topology.angle |0.00 |0.00 |1.96 |0.00 | |PQAnalysis.io.restart_file.restart_reader |0.00 |0.00 |1.96 |0.00 | |PQAnalysis.io.input_file_reader.pq_analysis._parse |0.00 |0.00 |1.96 |0.00 | |PQAnalysis.io.input_file_reader.pq.pq_input_file_reader |0.00 |0.00 |1.96 |0.00 | |PQAnalysis.io.input_file_reader.input_file_parser |0.00 |0.00 |1.96 |0.00 | |PQAnalysis.io.info_file_reader |0.00 |0.00 |1.96 |0.00 | |PQAnalysis.io.formats |0.00 |0.00 |1.96 |0.00 | |PQAnalysis.core.cell.cell |0.00 |0.00 |1.96 |0.00 | Messages ======== |message id |occurrences | |--------------------------------|------------| |too-many-arguments |18 | |too-many-instance-attributes |10 | |inconsistent-return-statements |9 | |fixme |9 | |too-many-locals |3 | |too-complex |3 | |duplicate-code |3 | |too-many-branches |2 | |too-many-statements |1 | |too-many-return-statements |1 | |too-many-public-methods |1 | |too-many-lines |1 | |possibly-used-before-assignment |1 | |no-member |1 | |arguments-differ |1 |