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MolarVerse / PQAnalysis

PQAnalysis is a API/CLI python package for the analysis of MD simulations
https://molarverse.github.io/PQAnalysis/
MIT License
4 stars 2 forks source link

Feat: add topology comments when merging topologies #93

Closed 97gamjak closed 1 month ago

97gamjak commented 1 month ago

NEW Keep topologies data line comments when merging topologies

REFACTOR New output format for topology files - now with fixed length of indices... to have a nicer formatted output

Internal REFACTOR ShakeTopologyGenerator does not use anymore its own writing routine, but uses TopologyWriter internally

codecov[bot] commented 1 month ago

Codecov Report

Attention: Patch coverage is 92.15686% with 8 lines in your changes are missing coverage. Please review.

Project coverage is 85.76%. Comparing base (5de1575) to head (65891fa). Report is 1 commits behind head on dev.

Additional details and impacted files ```diff @@ Coverage Diff @@ ## dev #93 +/- ## ========================================== + Coverage 84.85% 85.76% +0.91% ========================================== Files 123 125 +2 Lines 4931 5001 +70 ========================================== + Hits 4184 4289 +105 + Misses 747 712 -35 ``` | [Flag](https://app.codecov.io/gh/MolarVerse/PQAnalysis/pull/93/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/93/flags?src=pr&el=flag&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=MolarVerse) | `85.76% <92.15%> (+0.91%)` | :arrow_up: | | [Files](https://app.codecov.io/gh/MolarVerse/PQAnalysis/pull/93?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/io/base.py](https://app.codecov.io/gh/MolarVerse/PQAnalysis/pull/93?src=pr&el=tree&filepath=PQAnalysis%2Fio%2Fbase.py&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=MolarVerse#diff-UFFBbmFseXNpcy9pby9iYXNlLnB5) | `100.00% <100.00%> (ø)` | | | [PQAnalysis/io/topology\_file/\_\_init\_\_.py](https://app.codecov.io/gh/MolarVerse/PQAnalysis/pull/93?src=pr&el=tree&filepath=PQAnalysis%2Fio%2Ftopology_file%2F__init__.py&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=MolarVerse#diff-UFFBbmFseXNpcy9pby90b3BvbG9neV9maWxlL19faW5pdF9fLnB5) | `100.00% <100.00%> (ø)` | | | [...QAnalysis/io/topology\_file/topology\_file\_writer.py](https://app.codecov.io/gh/MolarVerse/PQAnalysis/pull/93?src=pr&el=tree&filepath=PQAnalysis%2Fio%2Ftopology_file%2Ftopology_file_writer.py&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=MolarVerse#diff-UFFBbmFseXNpcy9pby90b3BvbG9neV9maWxlL3RvcG9sb2d5X2ZpbGVfd3JpdGVyLnB5) | `90.44% <100.00%> (+35.82%)` | :arrow_up: | | [PQAnalysis/topology/bonded\_topology/\_\_init\_\_.py](https://app.codecov.io/gh/MolarVerse/PQAnalysis/pull/93?src=pr&el=tree&filepath=PQAnalysis%2Ftopology%2Fbonded_topology%2F__init__.py&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=MolarVerse#diff-UFFBbmFseXNpcy90b3BvbG9neS9ib25kZWRfdG9wb2xvZ3kvX19pbml0X18ucHk=) | `100.00% <100.00%> (ø)` | | | [PQAnalysis/topology/bonded\_topology/angle.py](https://app.codecov.io/gh/MolarVerse/PQAnalysis/pull/93?src=pr&el=tree&filepath=PQAnalysis%2Ftopology%2Fbonded_topology%2Fangle.py&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=MolarVerse#diff-UFFBbmFseXNpcy90b3BvbG9neS9ib25kZWRfdG9wb2xvZ3kvYW5nbGUucHk=) | `100.00% <100.00%> (ø)` | | | [PQAnalysis/topology/bonded\_topology/bond.py](https://app.codecov.io/gh/MolarVerse/PQAnalysis/pull/93?src=pr&el=tree&filepath=PQAnalysis%2Ftopology%2Fbonded_topology%2Fbond.py&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=MolarVerse#diff-UFFBbmFseXNpcy90b3BvbG9neS9ib25kZWRfdG9wb2xvZ3kvYm9uZC5weQ==) | `100.00% <100.00%> (ø)` | | | [...alysis/topology/bonded\_topology/bonded\_topology.py](https://app.codecov.io/gh/MolarVerse/PQAnalysis/pull/93?src=pr&el=tree&filepath=PQAnalysis%2Ftopology%2Fbonded_topology%2Fbonded_topology.py&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=MolarVerse#diff-UFFBbmFseXNpcy90b3BvbG9neS9ib25kZWRfdG9wb2xvZ3kvYm9uZGVkX3RvcG9sb2d5LnB5) | `100.00% <ø> (ø)` | | | [PQAnalysis/topology/bonded\_topology/dihedral.py](https://app.codecov.io/gh/MolarVerse/PQAnalysis/pull/93?src=pr&el=tree&filepath=PQAnalysis%2Ftopology%2Fbonded_topology%2Fdihedral.py&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=MolarVerse#diff-UFFBbmFseXNpcy90b3BvbG9neS9ib25kZWRfdG9wb2xvZ3kvZGloZWRyYWwucHk=) | `100.00% <100.00%> (ø)` | | | [PQAnalysis/topology/shake\_topology.py](https://app.codecov.io/gh/MolarVerse/PQAnalysis/pull/93?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==) | `98.78% <100.00%> (+0.06%)` | :arrow_up: | | [PQAnalysis/types.py](https://app.codecov.io/gh/MolarVerse/PQAnalysis/pull/93?src=pr&el=tree&filepath=PQAnalysis%2Ftypes.py&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=MolarVerse#diff-UFFBbmFseXNpcy90eXBlcy5weQ==) | `100.00% <ø> (ø)` | | | ... and [2 more](https://app.codecov.io/gh/MolarVerse/PQAnalysis/pull/93?src=pr&el=tree-more&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=MolarVerse) | |
github-actions[bot] commented 1 month ago

PYLINT REPORT

Your code has been rated at 9.52/10 (previous run: 9.52/10, +0.01)

Full report Raw metrics =========== |type |number |% |previous |difference | |----------|-------|------|---------|-----------| |code |7876 |39.93 |7783 |+93.00 | |docstring |8660 |43.90 |8595 |+65.00 | |comment |268 |1.36 |269 |-1.00 | |empty |2921 |14.81 |2872 |+49.00 | 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 |14 |14 |14 | |error |31 |31 |31 | % 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 |7.14 |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.atomic_system.atomic_system |0.00 |14.29 |11.76 |0.00 | |PQAnalysis.topology.__init__ |0.00 |14.29 |0.00 |0.00 | |PQAnalysis.tools.traj_to_com_traj |0.00 |14.29 |0.00 |0.00 | |PQAnalysis.io.moldescriptor_reader |0.00 |14.29 |0.00 |0.00 | |PQAnalysis.utils.custom_logging |0.00 |7.14 |0.00 |0.00 | |PQAnalysis.io.write_api |0.00 |7.14 |0.00 |0.00 | |PQAnalysis.io.input_file_reader.pq.output_files |0.00 |7.14 |0.00 |0.00 | |PQAnalysis.core.api |0.00 |7.14 |0.00 |0.00 | |PQAnalysis.atomic_system._decorators |0.00 |7.14 |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 | |fixme |10 | |inconsistent-return-statements |9 | |too-many-locals |3 | |too-complex |3 | |duplicate-code |3 | |unused-import |2 | |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 | |arguments-differ |1 |
97gamjak commented 1 month ago

closes #93