AntObi commented 1 week ago

Fixing the documentation

Description

This PR fixes the paths in the documentation for the notebooks. It also introduces featurisers as optional dependencies

Type of change

[x] Bug fix (non-breaking change which fixes an issue)
[x] New feature (non-breaking change which adds functionality)
[x] Breaking change (fix or feature that would cause existing functionality to not work as expected)
[x] This change requires a documentation update

How Has This Been Tested?

Test Configuration:

Python version: 3.10
Operating System: macOS

Reviewers

N/A

Checklist

[x] My code follows the style guidelines of this project
[x] I have performed a self-review of my own code
[x] I have commented my code, particularly in hard-to-understand areas
[x] I have made corresponding changes to the documentation
[x] My changes generate no new warnings
[x] I have added tests that prove my fix is effective or that my feature works
[x] New and existing unit tests pass locally with my changes
[x] Any dependent changes have been merged and published in downstream modules
[x] I have checked my code and corrected any misspellings

Summary by CodeRabbit

New Features
- Updated documentation version to 2.8.0.
- Introduced a new optional dependency group for featurisers in the project configuration, enhancing material science capabilities.
Improvements
- Enhanced clarity and functionality in multiple Jupyter notebooks, including improved installation commands and updated metadata.
- Refined examples for generating and analysing chemical compositions, ensuring users have the necessary tools and context.
Bug Fixes
- Adjusted data paths and outputs in notebooks to reflect updated repository structures and improve user experience.

coderabbitai[bot] commented 1 week ago

Walkthrough

The pull request introduces updates to the Sphinx documentation configuration and several Jupyter notebooks within the SMACT project. Key changes include incrementing version numbers in docs/conf.py, enhancing tutorial content and installation commands in various notebooks, and updating kernel specifications. Additionally, a new optional dependency group is added to pyproject.toml. These changes collectively aim to improve documentation clarity, functionality, and user experience.

Changes

File Path	Change Summary
`docs/conf.py`	Updated `version` from "2.7" to "2.8", `release` from "2.7.0" to "2.8.0", and `repository_branch` from "docs_updates" to "master".
`docs/examples/oxidation_states.ipynb`	Updated import statement to include `Lattice`, refined species list, clarified print statements, changed structure creation method, and updated kernel specification and Python version.
`docs/tutorials/crystal_space.ipynb`	Enhanced tutorial content, updated package installation command, and modified kernel specification.
`docs/tutorials/crystal_space_visualisation.ipynb`	Streamlined package installation command and updated kernel specification.
`docs/tutorials/smact_generation_of_solar_oxides.ipynb`	Changed installation command to specify a branch and optional features; no changes to core functionality.
`docs/tutorials/smact_validity_of_GNoMe.ipynb`	Enhanced content, modified installation command, adjusted worker count for `pandarallel`, updated data path, and changed kernel specification and Python version.
`pyproject.toml`	Added new optional dependency group `featurisers` with dependencies `["matminer", "ElementEmbeddings"]`.

Possibly related PRs

308: The changes in this PR include updates to the docs/conf.py file, specifically incrementing the version from "2.6" to "2.7" and the release from "2.6.0" to "2.7.0", which directly relates to the versioning updates made in the main PR.

Suggested labels

bug, enhancement, docs, dependencies

Poem

In the garden where knowledge blooms,
The docs and notebooks shed their glooms.
With versions fresh and examples bright,
We hop along, in pure delight!
Dependencies added, oh what a treat,
For every learner, a joyful feat! 🐰✨

📜 Recent review details

**Configuration used: CodeRabbit UI** **Review profile: CHILL**

📥 Commits

Reviewing files that changed from the base of the PR and between 347f2ad50aa2347280a80ae53000132d862188eb and 8434325b2ac33d227ad0462074d5a1531e282b0d.

📒 Files selected for processing (1)

* `pyproject.toml` (1 hunks)

🚧 Files skipped from review as they are similar to previous changes (1)

* pyproject.toml

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codecov[bot] commented 1 week ago

Codecov Report

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

Project coverage is 76.46%. Comparing base (1bac2b1) to head (8434325). Report is 13 commits behind head on master.

Additional details and impacted files

```diff @@ Coverage Diff @@ ## master #333 +/- ## ========================================== + Coverage 73.74% 76.46% +2.72% ========================================== Files 31 31 Lines 2544 2545 +1 ========================================== + Hits 1876 1946 +70 + Misses 668 599 -69 ```

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

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WMD-group / SMACT

Fix the documentation #333

Fixing the documentation

Description

Type of change

How Has This Been Tested?

Reviewers

Checklist

Summary by CodeRabbit

Walkthrough

Changes

Possibly related PRs

308: The changes in this PR include updates to the `docs/conf.py` file, specifically incrementing the version from "2.6" to "2.7" and the release from "2.6.0" to "2.7.0", which directly relates to the versioning updates made in the main PR.

Suggested labels

Poem

Codecov Report

WMD-group / SMACT

Fix the documentation #333

Fixing the documentation

Description

Type of change

How Has This Been Tested?

Reviewers

Checklist

Summary by CodeRabbit

Walkthrough

Changes

Possibly related PRs

308: The changes in this PR include updates to the docs/conf.py file, specifically incrementing the version from "2.6" to "2.7" and the release from "2.6.0" to "2.7.0", which directly relates to the versioning updates made in the main PR.

Suggested labels

Poem

Codecov Report

308: The changes in this PR include updates to the `docs/conf.py` file, specifically incrementing the version from "2.6" to "2.7" and the release from "2.6.0" to "2.7.0", which directly relates to the versioning updates made in the main PR.