Investigating external dataset usage.

[drewoldag]

Creating two new notebooks as well as a model and dataset class that showcase how to create and utilize modules that are defined outside of Hyrax.

[review-notebook-app]

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[drewoldag]

The unit test is failing because the environment that is being created to run the tests is using the latest version of Hyrax from PyPI (whcih is quite old). In testing locally against the main branch of Hyrax there are no failure notices about not implementing a __get_item__ method.

[codecov]

Codecov Report

❌ Patch coverage is 14.28571% with 6 lines in your changes missing coverage. Please review.
✅ Project coverage is 25.00%. Comparing base (ec8c269) to head (c8c64b5).
⚠️ Report is 9 commits behind head on main.

Files with missing lines	Patch %	Lines
src/external_hyrax_example/models/vgg11.py	14.28%	6 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##             main       #6      +/-   ##
==========================================
- Coverage   26.08%   25.00%   -1.09%     
==========================================
  Files           2        2              
  Lines          69       72       +3     
==========================================
  Hits           18       18              
- Misses         51       54       +3     

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[Copilot]

Pull request overview

This WIP PR explores using externally-defined datasets and models with Hyrax/HyraxQL by adding a minimal external dataset implementation (Galaxy10), expanding default config to include dataset settings, and adding a worked example notebook demonstrating training both HyraxCNN and a locally-defined VGG11 on the external dataset.

Changes:

• Updated VGG11 to infer channel dimensions from a batched image sample and renamed the input-prep helper to prepare_inputs.
• Added a new Galaxy10Dataset (HyraxDataset subclass) plus default config entries for its options.
• Added documentation assets: a new pre-executed notebook and a results plot image; removed the old intro notebook and cleared the notebooks toctree.

Reviewed changes

Copilot reviewed 7 out of 9 changed files in this pull request and generated 6 comments.

Show a summary per file

File	Description
src/external_hyrax_example/models/vgg11.py	Adjusts input shape inference and updates the model’s input-prep helper method.
src/external_hyrax_example/default_config.toml	Adds dataset config section and updates runtime “libpath” comments.
src/external_hyrax_example/datasets/galaxy10_dataset.py	Introduces an external HDF5-backed dataset implementation for Galaxy10.
pyproject.toml	Adds h5py to optional dev dependencies to support the notebook/dataset example.
docs/pre_executed/external_dataset_and_model_training_example.ipynb	New end-to-end example notebook for external dataset + model training.
docs/notebooks/intro_notebook.ipynb	Removes the old Sphinx notebook intro.
docs/notebooks.rst	Removes the notebook link(s), leaving an empty toctree.
docs/_static/HyraxCNN_vs_VGG11.png	Adds a plot image used by the new notebook.

Comments suppressed due to low confidence (1)

docs/notebooks.rst:5

• docs/notebooks.rst now contains an empty .. toctree:: with no entries, so the rendered “Notebooks” page will be blank (and can trigger Sphinx toctree warnings). Add links for the notebook(s) you want published (e.g., the new pre_executed/external_dataset_and_model_training_example notebook, and/or other notebooks).

Notebooks
========================================================================================

.. toctree::

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