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Molara-Lab / Molara

Molara is a Python package for the visualization of chemical structures such as molecules or crystals. It provides a graphical user interface for importing structures from output files of popular computational chemistry software as well as for creating custom structures.
GNU General Public License v3.0
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Increase coverage #305

Closed adrianusler closed 3 months ago

adrianusler commented 4 months ago

Increase test coverage of crystal.py, importer.py, importer_crystal.py, molecule.py, structure.py

I need the [WIP] pull request to make sure that the tests are passing. My local pytest doesn't work at the moment.

Once finished, this closes #303.

Summary by CodeRabbit

codecov[bot] commented 4 months ago

Codecov Report

Attention: Patch coverage is 75.47170% with 13 lines in your changes are missing coverage. Please review.

Project coverage is 69.44%. Comparing base (bb3bb2a) to head (5790f8c).

Files Patch % Lines
src/molara/Structure/io/importer_crystal.py 75.00% 11 Missing :warning:
src/molara/Structure/structure.py 75.00% 2 Missing :warning:
Additional details and impacted files ```diff @@ Coverage Diff @@ ## main #305 +/- ## ========================================== + Coverage 68.20% 69.44% +1.24% ========================================== Files 38 38 Lines 3227 3198 -29 ========================================== + Hits 2201 2221 +20 + Misses 1026 977 -49 ```

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adrianusler commented 4 months ago

Codecov update on current improvements:

coderabbitai[bot] commented 3 months ago

Walkthrough

The recent updates to the codebase involve refining the structure and import functionalities within a scientific computing library, focusing on crystallography. Key changes include the removal of redundant methods, enhancements in object copying and atom manipulation, and improved file parsing flexibility. Tests have been expanded to ensure the new functionalities work as intended and to increase the overall code coverage, directly aligning with the project's goals of robustness and reliability.

Changes

Files Changes
.../crystal.py Removed re import; Deleted from_poscar method
.../importer_crystal.py Updated load method; Added parse_poscar method
.../structure.py Added coords attribute; Modified copy method; Added center_of_mass property; Updated add_atom and remove_atom methods
.../test_crystal.py Added and modified tests for POSCAR parsing and crystal object comparison; Implemented test_toggle_bonds
.../test_molecule.py Added tests for toggle_bonds, copy, compute_collision, and center_coordinates; Modified existing tests

Assessment against linked issues

Objective Addressed Explanation
Increase test coverage of crystal.py, importer.py, importer_crystal.py, molecule.py, structure.py (#303) ✅

🐇💻🌟
Changes abound, both big and small,
In code and tests, we've touched them all.
From crystals clear to molecules round,
New functionalities now abound.
So hop along on this code spree,
For better science, we all agree.
🌈🚀🐇

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Michel-Heinz commented 3 months ago

Is this ready?

adrianusler commented 3 months ago

Is this ready?

I would say yes. I guess I won't continue working on this any time soon, so we might just as well merge it now.