Feature/shake gen comments

[97gamjak]

Added possibility to complement shake topology generation with line comments for each shaked bond.

This includes two main approach:

1) add comments to function generate_equivalents for each distinct shake bond

2) add_comment function to explicitly add line comments for each of the shaked bonds

closes #71

[github-actions[bot]]

PYLINT REPORT

Your code has been rated at 9.52/10 (previous run: 9.85/10, -0.33)

Full report

Raw metrics =========== |type |number |% |previous |difference | |----------|-------|------|---------|-----------| |code |7738 |39.97 |7616 |+122.00 | |docstring |8506 |43.94 |8423 |+83.00 | |comment |264 |1.36 |261 |+3.00 | |empty |2852 |14.73 |2800 |+52.00 | 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 |2 |2 | |refactor |51 |51 |51 | |warning |10 |12 |12 | |error |31 |0 |0 | % errors / warnings by module ============================= |module |error |warning |refactor |convention | |--------------------------------------------------------|------|--------|---------|-----------| |PQAnalysis.io.topology_file.topology_file_reader |67.74 |0.00 |0.00 |0.00 | |PQAnalysis.io.nep.nep_writer |12.90 |0.00 |15.69 |100.00 | |PQAnalysis.io.traj_file.frame_reader |6.45 |0.00 |3.92 |0.00 | |PQAnalysis |3.23 |10.00 |0.00 |0.00 | |PQAnalysis.io.input_file_reader.input_file_parser |3.23 |0.00 |1.96 |0.00 | |PQAnalysis.io.traj_file.api |3.23 |0.00 |0.00 |0.00 | |PQAnalysis.io.gen_file.gen_file_reader |3.23 |0.00 |0.00 |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.atomic_system.atomic_system |0.00 |10.00 |11.76 |0.00 | |PQAnalysis.io.write_api |0.00 |10.00 |0.00 |0.00 | |PQAnalysis.core.api |0.00 |10.00 |0.00 |0.00 | |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.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.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 | |--------------------------------|------------| |possibly-used-before-assignment |30 | |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 | |unused-argument |1 | |too-many-statements |1 | |too-many-return-statements |1 | |too-many-public-methods |1 | |too-many-lines |1 | |no-member |1 |

[codecov[bot]]

Codecov Report

Attention: Patch coverage is 96.29630% with 1 lines in your changes are missing coverage. Please review.

Project coverage is 80.65%. Comparing base (caeddba) to head (8bc5c18).

Additional details and impacted files

```diff @@ Coverage Diff @@ ## dev #72 +/- ## ========================================== + Coverage 80.57% 80.65% +0.08% ========================================== Files 122 122 Lines 4901 4927 +26 ========================================== + Hits 3949 3974 +25 - Misses 952 953 +1 ``` | [Flag](https://app.codecov.io/gh/MolarVerse/PQAnalysis/pull/72/flags?src=pr&el=flags&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=MolarVerse) | Coverage Δ | | |---|---|---| | [unittests](https://app.codecov.io/gh/MolarVerse/PQAnalysis/pull/72/flags?src=pr&el=flag&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=MolarVerse) | `80.65% <96.29%> (+0.08%)` | :arrow_up: | | [Files](https://app.codecov.io/gh/MolarVerse/PQAnalysis/pull/72?dropdown=coverage&src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=MolarVerse) | Coverage Δ | | |---|---|---| | [PQAnalysis/topology/shake\_topology.py](https://app.codecov.io/gh/MolarVerse/PQAnalysis/pull/72?src=pr&el=tree&filepath=PQAnalysis%2Ftopology%2Fshake_topology.py&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=MolarVerse#diff-UFFBbmFseXNpcy90b3BvbG9neS9zaGFrZV90b3BvbG9neS5weQ==) | `98.71% <96.29%> (-1.29%)` | :arrow_down: |