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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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Add periodic table data and color scheme information #362

Closed ab5424 closed 5 months ago

ab5424 commented 5 months ago

Closes #223

Summary by CodeRabbit

Summary by CodeRabbit

coderabbitai[bot] commented 5 months ago

Walkthrough

This update refines the handling of periodic table data in the Molara project. It involves adding new functionalities for data retrieval and storage, updating atom handling logic to accommodate hydrogen isotopes, adjusting testing accordingly, and optimizing the pre-commit configuration to exclude JSON files.

Changes

Files Change Summary
.pre-commit-config.yaml Added exclusion for JSON files in the check-yaml hook configuration.
data/periodic_table/get_json.py Retrieves periodic table data, saves it as JSON, includes licensing information.
src/molara/Structure/atom.py Updated to load data from a JSON file, modified handling for hydrogen isotopes.
src/molara/Structure/periodic_table_copyright.txt Added licensing information for periodic table data.
tests/molara/Structure/test_atom.py Modified tests to accommodate changes in the element_symbol_to_atomic_number function.
.github/workflows/lint.yml Updated dependency installation commands and added a new package types-requests.
develop/colors/get_colors.py Introduced a new file to fetch atom colors and generate a JSON file with color information.
develop/periodic_table/get_pd_data.py Added a new file to fetch periodic table data from pymatgen repository and save it to files.
src/molara/Structure/crystal.py Modified the calculation of molar_mass using atomic mass from _pt_data and updated imports.
src/molara/Structure/io/exporter.py Removed import elements and updated writing structure to an xyz-file.
src/molara/Structure/periodic_table_copyright Added a new file containing periodic table data sourced from pymatgen.
tests/molara/Structure/test_crystal.py Updated the calculation of molar mass in the crystal test.

Assessment against linked issues

Objective Addressed Explanation
Periodic table data (#223) ✅ The changes incorporate periodic table data from the pymatgen repository as planned.

Poem

🐰✨ In the garden of code, where the data trees bloom, A rabbit hopped by, with a brush and a broom. Sweeping the bugs, with a twirl and a swoop, Adding sparkles of JSON, in a joyful loop. "Hop, skip, and a jump," it cheerfully said, "Let’s make our code cleaner, before we head to bed!" 🌟🌙

Recent Review Details **Configuration used: CodeRabbit UI** **Review profile: CHILL**
Commits Files that changed from the base of the PR and between 01a741eae3b1f99e8582b6752cf59a58120ffca2 and 68737f8b6075d75d548b09de78d3b3b80857e2bb.
Files selected for processing (2) * .pre-commit-config.yaml (1 hunks) * develop/periodic_table/get_pd_data.py (1 hunks)
Files skipped from review as they are similar to previous changes (2) * .pre-commit-config.yaml * develop/periodic_table/get_pd_data.py
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codecov[bot] commented 5 months ago

Codecov Report

All modified and coverable lines are covered by tests :white_check_mark:

Project coverage is 71.83%. Comparing base (7431d46) to head (01a741e).

:exclamation: Current head 01a741e differs from pull request most recent head 68737f8. Consider uploading reports for the commit 68737f8 to get more accurate results

Additional details and impacted files ```diff @@ Coverage Diff @@ ## main #362 +/- ## ========================================== + Coverage 71.70% 71.83% +0.13% ========================================== Files 40 40 Lines 3463 3479 +16 ========================================== + Hits 2483 2499 +16 Misses 980 980 ```

:umbrella: View full report in Codecov by Sentry.
:loudspeaker: Have feedback on the report? Share it here.

ab5424 commented 5 months ago

Ready to merge. Next week, I will work on #211 so the user can select the color scheme in the new structure costumizer.

ab5424 commented 5 months ago

Btw, I deliberately didn't add the libraries used in the developer scripts to the requirements/pyproject. Realistically speaking, these scripts will be executed less than once a year.

Michel-Heinz commented 5 months ago

Works just fine for me and now we have a good source for the information! Does the MIT clash with our License?

ab5424 commented 5 months ago

I don't think so, MIT should be more liberal and I made sure that the licenses text is included in the releases

See also https://opensource.stackexchange.com/questions/13029/how-mixing-mit-licensed-code-with-gplv3-project-works