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43 add example notebooks #46

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Pepe-Marquez
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@Pepe-Marquez Pepe-Marquez commented Jan 13, 2025 •
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Summary by Sourcery

Add example notebooks demonstrating how to use the perovskite database and predict bandgap using CrabNet.

New Features:

  • Add example Jupyter notebooks for perovskite database usage and bandgap prediction with CrabNet.

Tests:

  • Added interactive prediction widget for testing different chemical formulas and comparing with dataset values.

@Pepe-Marquez Pepe-Marquez linked an issue Jan 13, 2025 that may be closed by this pull request
Add example notebooks #43
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sourcery-ai bot commented Jan 13, 2025 •
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Reviewer's Guide by Sourcery

This pull request adds example notebooks demonstrating how to use the perovskite solar cell database. It includes a notebook for predicting the band gap of perovskites using CrabNet and data from the Perovskite Database in NOMAD. The notebook covers data retrieval, cleaning, model building, evaluation, and prediction. It also adds example uploads for the ions database.

Flow diagram of the CrabNet perovskite bandgap prediction workflow

graph TD
    A[Data Retrieval] -->|NOMAD API| B[Data Processing]
    B --> C[Data Cleaning]
    C --> D[Split Data]
    D -->|80%| E[Training Set]
    D -->|10%| F[Validation Set]
    D -->|10%| G[Test Set]
    E --> H[Train CrabNet Model]
    F --> I[Validate Model]
    G --> J[Test Model]
    H --> K[Final Model]
    K --> L[Predict Individual Formulas]

    subgraph Data Cleaning
    M[Remove NaNs] --> N[Group Repeated Formulas]
    N --> O[Check Element Prevalence]
    end
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File-Level Changes

Change Details Files
Added example notebook for perovskite band gap prediction using CrabNet.
  • Fetched data from NOMAD API.
  • Cleaned and preprocessed the data.
  • Built and trained a CrabNet model.
  • Evaluated the model performance.
  • Added functionality for predicting band gap from individual formulas.
 src/perovskite_solar_cell_database/example_uploads/perovskite_database/crabnet-perovskite-bandgap-prediction.ipynb
Added example uploads for the ions database.
  • Added entry point for ions database examples.
  • Included example XYZ files for ions.
 src/perovskite_solar_cell_database/example_uploads/__init__.py
src/perovskite_solar_cell_database/example_uploads/ions_database/C2NH7S.xyz
src/perovskite_solar_cell_database/example_uploads/ions_database/CNH6.xyz
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sourcery-ai bot reviewed Jan 13, 2025
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Hey @Pepe-Marquez - I've reviewed your changes and they look great!

Here's what I looked at during the review
  • 🟢 General issues: all looks good
  • 🟢 Security: all looks good
  • 🟢 Testing: all looks good
  • 🟢 Complexity: all looks good
  • 🟢 Documentation: all looks good
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@Pepe-Marquez
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Pepe-Marquez commented Jan 13, 2025 •
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@hampusnasstrom, the first two notebooks are going in. @siamakn was doing some cleaning of the perovskite database, so let's make sure we include him as a contributor in the PR. The pipelines are not passing at the moment because there are empty notebooks.

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@Pepe-Marquez ideally you would have added siamak as a co-author of the commit where you added the notebook but I can try to add him to the PR itself later. Just don't forget it before me merge.

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@hampusnasstrom hampusnasstrom Awaiting requested review from hampusnasstrom

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Add example notebooks
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