feat: add provgigapath model

[vojtech-cifka]

Adds the config for running the provgigapath using the new SDK.

Summary by CodeRabbit

Chores

• Added preprocessing configuration support for the prov-gigapath model.

[coderabbitai]

📝 Walkthrough

Walkthrough

A new YAML configuration file for preprocessing embeddings is added to the experiment configuration directory. The file defines the prov-gigapath model with global package scope and Hydra-style defaults that map the dataset path to /data.

Changes

Prov-GigaPath Embedding Configuration

Layer / File(s)	Summary
Embedding configuration file configs/experiment/preprocessing/embeddings_prov_gigapath_05mpp.yaml	New YAML configuration declares global package scope, sets Hydra defaults to resolve dataset paths under /data, and specifies model: prov-gigapath.

Estimated code review effort

🎯 1 (Trivial) | ⏱️ ~2 minutes

Poem

A config takes shape, seven lines strong,
With prov-gigapath paths all along,
Hydra defaults guide the way,
New embeddings come to play. 🐇✨

🚥 Pre-merge checks | ✅ 5

✅ Passed checks (5 passed)

Check name	Status	Explanation
Description Check	✅ Passed	Check skipped - CodeRabbit’s high-level summary is enabled.
Title check	✅ Passed	The title 'feat: add provgigapath model' clearly and concisely describes the main change—adding configuration for the prov-gigapath model, which aligns with the pull request's objective.
Docstring Coverage	✅ Passed	No functions found in the changed files to evaluate docstring coverage. Skipping docstring coverage check.
Linked Issues check	✅ Passed	Check skipped because no linked issues were found for this pull request.
Out of Scope Changes check	✅ Passed	Check skipped because no linked issues were found for this pull request.

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✨ Finishing Touches

🧪 Generate unit tests (beta)

• Create PR with unit tests
• Commit unit tests in branch feature/embeddings-prov-gigapath

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[gemini-code-assist]

Code Review

This pull request introduces a new configuration file for preprocessing embeddings using the prov-gigapath model. Feedback was provided regarding a naming inconsistency between the model identifier and the filename, as well as a missing trailing newline in the configuration file.

[coderabbitai]

🧹 Nitpick comments (1)

configs/experiment/preprocessing/embeddings_prov_gigapath_05mpp.yaml (1)

1-7: 💤 Low value

Consider adding explicit resolution parameter for consistency with other preprocessing configs.

The filename includes 05mpp (0.5 microns per pixel), but this resolution is not explicitly set in the configuration. While other preprocessing configs (tiling_05mpp.yaml, tissue_masks_mpp2.yaml, etc.) explicitly define mpp parameters, the embedding configs use only the model name. Adding an explicit mpp: 0.5 would improve clarity and maintain consistency across preprocessing configurations.

🤖 Prompt for AI Agents

Verify each finding against current code. Fix only still-valid issues, skip the
rest with a brief reason, keep changes minimal, and validate.

In `@configs/experiment/preprocessing/embeddings_prov_gigapath_05mpp.yaml` around
lines 1 - 7, The config is missing an explicit resolution setting; update the
YAML by adding an mpp: 0.5 entry to this preprocessing config so it matches
other files that declare microns-per-pixel explicitly (e.g., alongside the
existing defaults block or near model: prov-gigapath) to make resolution
unambiguous and consistent with tiling_05mpp and related configs.

🤖 Prompt for all review comments with AI agents

Verify each finding against current code. Fix only still-valid issues, skip the
rest with a brief reason, keep changes minimal, and validate.

Nitpick comments:
In `@configs/experiment/preprocessing/embeddings_prov_gigapath_05mpp.yaml`:
- Around line 1-7: The config is missing an explicit resolution setting; update
the YAML by adding an mpp: 0.5 entry to this preprocessing config so it matches
other files that declare microns-per-pixel explicitly (e.g., alongside the
existing defaults block or near model: prov-gigapath) to make resolution
unambiguous and consistent with tiling_05mpp and related configs.

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ℹ️ Review info

⚙️ Run configuration

Configuration used: defaults

Review profile: CHILL

Plan: Pro

Run ID: 824c3782-6424-4b0e-b5e9-ff01245c1de7

📥 Commits

Reviewing files that changed from the base of the PR and between 727aba5 and 1f15e03.

📒 Files selected for processing (1)

• configs/experiment/preprocessing/embeddings_prov_gigapath_05mpp.yaml