Merge master into develop branch

[AntObi]

Summary by CodeRabbit

Release Notes

• New Features

  • Introduced sorting option for species occurrences in the oxidation states filter.
  • Added a new tutorial on filtering ICSD oxidation states.

• Bug Fixes

  • Enhanced error handling in various functions to accommodate input lists of differing lengths.

• Documentation

  • Updated versioning in documentation files to reflect the latest release.
  • Improved clarity in tutorial content and examples.

• Tests

  • Adjusted tests to accommodate new parameters and improve robustness against varying input sizes.

[coderabbitai]

Caution

Review failed

The pull request is closed.

Walkthrough

The changes in this pull request encompass updates to the CI workflow, documentation, Jupyter notebooks, and various Python files. Key modifications include enhancements to dependency management in the CI configuration, version updates in documentation files, and improvements to several Jupyter notebooks for clarity and functionality. Additionally, updates to Python files involve changes to method signatures, the introduction of new parameters, and adjustments to error handling, particularly in relation to the handling of zipped sequences and the parsing of species data.

Changes

File Path	Change Summary
.github/workflows/ci.yml	Updated dependency installation command to include optional extras; added MP_API_KEY env variable for tests.
docs/conf.py	Version updated from "2.7" to "2.8"; release updated from "2.7.0" to "2.8.0"; branch reference changed to "master".
docs/examples/oxidation_states.ipynb	Updated imports, modified output of get_included_species, refined print statements, and changed structure loading method.
docs/requirements.txt	Updated tornado package version from 6.4.1 to 6.4.2.
docs/tutorials.rst	Reordered tutorial entries and added a new tutorial entry for filtering_icsd_oxidation_states.ipynb.
docs/tutorials/crystal_space.ipynb	Enhanced markdown content, updated Colab link, modified package installation command, and changed kernel specification.
docs/tutorials/crystal_space_visualisation.ipynb	Updated Colab link, consolidated installation commands, and modified kernel specification.
docs/tutorials/oxidation_states.ipynb	Updated hyperlink to point to the master branch; no changes to logic.
docs/tutorials/smact_generation_of_solar_oxides.ipynb	Updated Colab link, modified installation command, and changed kernel specification and Python version.
docs/tutorials/smact_validity_of_GNoMe.ipynb	Updated Colab link, modified data loading path, and changed kernel specification and Python version.
pyproject.toml	Updated project version to 2.8, relaxed pymatgen version constraints, added new optional dependencies, and updated tool configurations.
smact/__init__.py	Updated attribute name from oxidation_states_icsd to oxidation_states_icsd16.
smact/builder.py	Modified zip function calls in cubic_perovskite and wurtzite functions to include strict=False.
smact/data_loader.py	Updated dictionary construction in lookup_element_data to include strict=False in zip.
smact/dopant_prediction/doper.py	Added strict=False to zip in _merge_dicts method.
smact/screening.py	Updated zip calls in multiple functions to include strict=False; modified oxidation_states_set parameters.
smact/structure_prediction/mutation.py	Added Callable to imports and updated alpha parameter in methods for explicit type hinting.
smact/structure_prediction/structure.py	Added strict=False to zip calls in parsing methods and refined error handling in from_mp.
smact/structure_prediction/utilities.py	Updated parse_spec function with new logic and added _parse_spec_old for fallback parsing.
smact/tests/test_core.py	Updated test parameters for test_smact_validity to reflect new oxidation state definitions.
smact/tests/test_doper.py	Added strict=False to zip in test_dopant_prediction.
smact/tests/test_structure.py	Updated zip calls in tests to include strict=False for flexible iteration.
smact/tests/test_utils.py	Adjusted test conditions with pytest for improved error handling and added cleanup steps.
smact/utils/composition.py	Added strict=False to zip calls in comp_maker function and updated docstring.
smact/utils/crystal_space/generate_composition_with_smact.py	Added strict=False to zip calls in convert_formula and main function.
smact/utils/oxidation.py	Updated get_species_occurrences_df method to include sort_by_occurrences parameter.

Possibly related PRs

• Download crystal space optional dependencies in ci #331: Directly relates to CI workflow configuration updates in .github/workflows/ci.yml, specifically regarding the dependency installation command.
• Try MP_API_KEY in Github Actions #332: Modifies .github/workflows/ci.yml by adding the MP_API_KEY environment variable for the test job, relevant to the main PR.
• Fix documentation and tutorial notebooks ahead of new release #334: Includes updates to documentation and tutorial notebooks, which may relate to the enhancements in the testing process and environment configuration.

Suggested labels

dependencies, bug, enhancement, docs, feature

Poem

🐇 In the garden where changes bloom,
New paths are forged, dispelling gloom.
With dependencies spruced and docs refined,
Our code hops forward, well-aligned.
Let tests run free, with errors tamed,
In the world of SMACT, we’re unashamed! 🌼

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