Merge master into develop branch

[!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

#331: Directly relates to CI workflow configuration updates in .github/workflows/ci.yml, specifically regarding the dependency installation command.
#332: Modifies .github/workflows/ci.yml by adding the MP_API_KEY environment variable for the test job, relevant to the main PR.
#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! 🌼

Thank you for using CodeRabbit. We offer it for free to the OSS community and would appreciate your support in helping us grow. If you find it useful, would you consider giving us a shout-out on your favorite social media?

❤️ Share

- [X](https://twitter.com/intent/tweet?text=I%20just%20used%20%40coderabbitai%20for%20my%20code%20review%2C%20and%20it%27s%20fantastic%21%20It%27s%20free%20for%20OSS%20and%20offers%20a%20free%20trial%20for%20the%20proprietary%20code.%20Check%20it%20out%3A&url=https%3A//coderabbit.ai) - [Mastodon](https://mastodon.social/share?text=I%20just%20used%20%40coderabbitai%20for%20my%20code%20review%2C%20and%20it%27s%20fantastic%21%20It%27s%20free%20for%20OSS%20and%20offers%20a%20free%20trial%20for%20the%20proprietary%20code.%20Check%20it%20out%3A%20https%3A%2F%2Fcoderabbit.ai) - [Reddit](https://www.reddit.com/submit?title=Great%20tool%20for%20code%20review%20-%20CodeRabbit&text=I%20just%20used%20CodeRabbit%20for%20my%20code%20review%2C%20and%20it%27s%20fantastic%21%20It%27s%20free%20for%20OSS%20and%20offers%20a%20free%20trial%20for%20proprietary%20code.%20Check%20it%20out%3A%20https%3A//coderabbit.ai) - [LinkedIn](https://www.linkedin.com/sharing/share-offsite/?url=https%3A%2F%2Fcoderabbit.ai&mini=true&title=Great%20tool%20for%20code%20review%20-%20CodeRabbit&summary=I%20just%20used%20CodeRabbit%20for%20my%20code%20review%2C%20and%20it%27s%20fantastic%21%20It%27s%20free%20for%20OSS%20and%20offers%20a%20free%20trial%20for%20proprietary%20code)

🪧 Tips

### Chat There are 3 ways to chat with [CodeRabbit](https://coderabbit.ai): - Review comments: Directly reply to a review comment made by CodeRabbit. Example: - `I pushed a fix in commit , please review it.` - `Generate unit testing code for this file.` - `Open a follow-up GitHub issue for this discussion.` - Files and specific lines of code (under the "Files changed" tab): Tag `@coderabbitai` in a new review comment at the desired location with your query. Examples: - `@coderabbitai generate unit testing code for this file.` - `@coderabbitai modularize this function.` - PR comments: Tag `@coderabbitai` in a new PR comment to ask questions about the PR branch. For the best results, please provide a very specific query, as very limited context is provided in this mode. Examples: - `@coderabbitai gather interesting stats about this repository and render them as a table. Additionally, render a pie chart showing the language distribution in the codebase.` - `@coderabbitai read src/utils.ts and generate unit testing code.` - `@coderabbitai read the files in the src/scheduler package and generate a class diagram using mermaid and a README in the markdown format.` - `@coderabbitai help me debug CodeRabbit configuration file.` Note: Be mindful of the bot's finite context window. It's strongly recommended to break down tasks such as reading entire modules into smaller chunks. For a focused discussion, use review comments to chat about specific files and their changes, instead of using the PR comments. ### CodeRabbit Commands (Invoked using PR comments) - `@coderabbitai pause` to pause the reviews on a PR. - `@coderabbitai resume` to resume the paused reviews. - `@coderabbitai review` to trigger an incremental review. This is useful when automatic reviews are disabled for the repository. - `@coderabbitai full review` to do a full review from scratch and review all the files again. - `@coderabbitai summary` to regenerate the summary of the PR. - `@coderabbitai resolve` resolve all the CodeRabbit review comments. - `@coderabbitai configuration` to show the current CodeRabbit configuration for the repository. - `@coderabbitai help` to get help. ### Other keywords and placeholders - Add `@coderabbitai ignore` anywhere in the PR description to prevent this PR from being reviewed. - Add `@coderabbitai summary` to generate the high-level summary at a specific location in the PR description. - Add `@coderabbitai` or `@coderabbitai title` anywhere in the PR title to generate the title automatically. ### CodeRabbit Configuration File (`.coderabbit.yaml`) - You can programmatically configure CodeRabbit by adding a `.coderabbit.yaml` file to the root of your repository. - Please see the [configuration documentation](https://docs.coderabbit.ai/guides/configure-coderabbit) for more information. - If your editor has YAML language server enabled, you can add the path at the top of this file to enable auto-completion and validation: `# yaml-language-server: $schema=https://coderabbit.ai/integrations/schema.v2.json` ### Documentation and Community - Visit our [Documentation](https://docs.coderabbit.ai) for detailed information on how to use CodeRabbit. - Join our [Discord Community](http://discord.gg/coderabbit) to get help, request features, and share feedback. - Follow us on [X/Twitter](https://twitter.com/coderabbitai) for updates and announcements.

WMD-group / SMACT