[WIP] Add option to use pre-supplied embeddings within SMACT for the dopant_prediction module

AntObi commented 3 weeks ago

Description

Added cosine similarity of SkipSpecies embeddings to data directory of SMACT
Updated Doper in doper.py to accept using pre-loaded similarities

Type of change

[x] Bug fix (non-breaking change which fixes an issue)
[x] New feature (non-breaking change which adds functionality)
[x] This change requires a documentation update

How Has This Been Tested?

[ ] Test A
[ ] Test B

Test Configuration:

Python version: 3.10
Operating System: Windows 10

Reviewers

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
- Enhanced Doper class to support an additional embedding parameter and a use_probability flag for more flexible dopant predictions.
Documentation
- Added "tabulate" module to the list of imported modules in the documentation configuration.
Tests
- Renamed test class to DopantPredictionTest and added new test methods for dopant prediction and number formatting.

coderabbitai[bot] commented 3 weeks ago

[!WARNING]

Review failed

The pull request is closed.

Walkthrough

The Doper class in the smact library has been enhanced to include an embedding parameter and a use_probability flag, enabling more flexible and accurate dopant predictions. The get_dopants and to_table methods have been updated to reflect these changes, and a new method _calculate_species_sim_prob has been added. Additionally, the documentation configuration has been updated, and new tests have been introduced to ensure the reliability of the new features.

Changes

Files	Change Summary
`smact/dopant_prediction/doper.py`	Enhanced `Doper` class with `embedding` and `use_probability` parameters; updated methods accordingly
`docs/conf.py`	Added `"tabulate"` module to the list of imported modules
`smact/tests/test_doper.py`	Renamed test class, added file path handling, and introduced new test methods

Sequence Diagram(s) (Beta)

sequenceDiagram
    participant User
    participant Doper
    participant DataLoader
    participant SimilarityCalculator

    User->>Doper: Initialize with embedding and use_probability
    Doper->>DataLoader: Load embedding data
    Doper->>SimilarityCalculator: Calculate species similarity/probability
    User->>Doper: Call get_dopants
    Doper->>Doper: Check use_probability flag
    Doper->>SimilarityCalculator: Get similarity/probability scores
    Doper->>User: Return dopant predictions

Poem

In the land of code, where data's delight,
A rabbit hops with changes bright. 🐇
Embeddings and probabilities now in play,
Dopants predicted in a smarter way.
Tests and docs join the dance,
Ensuring all works at first glance.
Cheers to progress, in code we trust,
For in every byte, precision's a must!

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AntObi commented 3 weeks ago

@coderabbitai review

coderabbitai[bot] commented 3 weeks ago

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Review triggered. > Note: CodeRabbit is an incremental review system and does not re-review already reviewed commits. This command is applicable only when automatic reviews are paused.

codecov[bot] commented 3 weeks ago

Codecov Report

Attention: Patch coverage is 82.22222% with 8 lines in your changes missing coverage. Please review.

Project coverage is 74.18%. Comparing base (579e67c) to head (51bd29c).

:exclamation: Current head 51bd29c differs from pull request most recent head e58ef9b

Please upload reports for the commit e58ef9b to get more accurate results.

Files	Patch %	Lines
smact/dopant_prediction/doper.py	75.00%	7 Missing :warning:
smact/tests/test_doper.py	94.11%	1 Missing :warning:

Additional details and impacted files

```diff @@ Coverage Diff @@ ## develop #260 +/- ## =========================================== + Coverage 73.82% 74.18% +0.35% =========================================== Files 24 24 Lines 2048 2080 +32 =========================================== + Hits 1512 1543 +31 - Misses 536 537 +1 ```

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

AntObi commented 3 weeks ago

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coderabbitai[bot] commented 3 weeks ago

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Review triggered. > Note: CodeRabbit is an incremental review system and does not re-review already reviewed commits. This command is applicable only when automatic reviews are paused.

AntObi commented 3 weeks ago

@coderabbitai review

coderabbitai[bot] commented 3 weeks ago

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Review triggered. > Note: CodeRabbit is an incremental review system and does not re-review already reviewed commits. This command is applicable only when automatic reviews are paused.

WMD-group / SMACT