add patient level features modelling support

[EzicStar]

• Add modeling support for patient-level features.
• Update docs.
• Fix encoding __init__.py unable to parse excel slide table #88 .
• Add PRISM.
• Add training and dataloading hyperparameters in a separate section of config.yaml file.

[Copilot]

Pull Request Overview

This PR adds full support for patient-level feature modeling by automatically detecting feature types, providing new patient-level data loaders and dataset classes, and introducing an MLP-based Lightning module for training and deployment.

• Detect feature type (tile or patient) and branch training, deployment, and cross-validation pipelines accordingly
• Introduce PatientFeatureDataset, patient_feature_dataloader, and load_patient_level_data in the data module
• Add LitMLPClassifier, update train_categorical_model_, deploy_categorical_model_, and cross-validation to use patient-level logic and tests

Reviewed Changes

Copilot reviewed 20 out of 21 changed files in this pull request and generated 2 comments.

Show a summary per file

File	Description
src/stamp/modeling/data.py	Add detect_feature_type, PatientFeatureDataset, patient_feature_dataloader, and patient-level data loading logic
src/stamp/modeling/train.py	Branch training on feature type, wire up patient-level loader and MLP classifier
src/stamp/modeling/mlp_classifier.py	New MLPClassifier and LitMLPClassifier for patient-level features
src/stamp/modeling/deploy.py	Update deployment to detect feature type and handle patient-level predictions
tests/random_data.py	Add helpers for creating patient-level feature files and datasets
tests/*	Update existing tests and add new integration/unit tests for patient-level modeling

Comments suppressed due to low confidence (1)

src/stamp/modeling/deploy.py:156

• [nitpick] In the dict comprehension, using pd for the loop variable shadows the common pandas alias. Consider renaming it to patient_data or similar to improve clarity.

        }

[s1787956]

I dont hate it, only other option is a useless slide-table again. Maybe we could make the slide table optional and take it if its there otherwise use this approach..

[EzicStar]

Yeah I thought about it but the idea of adding one more table type, even if I add it as an optional file, will confuse people even more.