feat/v1.1.0 (#28)

- Added `encode-slide`.
- Added `encode-patient`.
- `process` remains patch-only.
- Added built-in slide encoders: `titan`, `prism`, `moozy`.
- Added built-in patient encoder: `moozy`.
- Patch features remain in `patches/<stem>.h5` under `features/<patch_encoder>`.
- Slide embeddings are written to `slide_features/<slide_encoder>` inside the per-slide H5.
- Patient embeddings are written to `patient_features/<encoder>/<case_id>.h5`.
- `encode-slide` reuses existing slide H5 files and computes missing required patch features when needed.
- `encode-patient` reuses existing slide H5 files and computes missing required patch features when needed.
- Added optional install extras:
  - `atlas-patch[patch-encoders]`
  - `atlas-patch[titan]`
  - `atlas-patch[prism]`
  - `atlas-patch[moozy]`
  - `atlas-patch[slide-encoders]`
  - `atlas-patch[patient-encoders]`

Author: yousefkotp

.github/workflows/publish.yml

@@ -0,0 +1,44 @@
+name: publish
+
+on:
+  release:
+    types: [published]
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    permissions:
+      contents: read
+    steps:
+      - uses: actions/checkout@v4
+      - uses: actions/setup-python@v5
+        with:
+          python-version: "3.12"
+      - name: Install build tooling
+        run: python -m pip install --upgrade build twine
+      - name: Build distributions
+        run: python -m build
+      - name: Validate distributions
+        run: python -m twine check dist/*
+      - name: Upload distributions
+        uses: actions/upload-artifact@v4
+        with:
+          name: python-dist
+          path: dist/*
+
+  publish:
+    needs: build
+    runs-on: ubuntu-latest
+    environment: pypi
+    permissions:
+      id-token: write
+    steps:
+      - name: Download distributions
+        uses: actions/download-artifact@v4
+        with:
+          name: python-dist
+          path: dist
+      - name: Publish to PyPI
+        uses: pypa/gh-action-pypi-publish@release/v1
+        with:
+          packages-dir: dist

CHANGELOG.md

@@ -5,6 +5,21 @@ All notable changes to AtlasPatch will be documented in this file.
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.1.0/),
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
+## [1.1.0] - Unreleased
+
+### Added
+
+#### Slide and Patient Encoding
+- `encode-slide` command for slide embeddings appended into `slide_features/<encoder>` inside the canonical per-slide H5
+- `encode-patient` command for manifest-driven patient embeddings written under `patient_features/<encoder>/<case_id>.h5`
+- Slide encoder registry and built-in slide encoders: `titan`, `prism`, `moozy`
+- Patient encoder registry and built-in patient encoder: `moozy`
+
+#### Packaging and Release
+- Optional extras for slide and patient encoder stacks: `titan`, `prism`, `moozy`, `slide-encoders`, and `patient-encoders`
+- GitHub Release to PyPI trusted publishing workflow in `publish.yml`
+
+
 ## [1.0.0] - 2025-02-03
 
 ### Added