Feature cache cleaning

.devcontainer/Dockerfile

@@ -0,0 +1,17 @@
+FROM ghcr.io/astral-sh/uv:python3.12-bookworm
+
+# Install just and other system dependencies
+RUN apt-get update && apt-get install -y \
+    sudo \
+    curl \
+    && curl --proto '=https' --tlsv1.2 -sSf https://just.systems/install.sh | bash -s -- --to /usr/local/bin \
+    && apt-get clean \
+    && rm -rf /var/lib/apt/lists/*
+
+# Create non-root user with UID/GID typically used by VS Code (1000:1000)
+RUN useradd -ms /bin/bash -u 1000 vscode \
+    && apt-get update && apt-get install -y sudo \
+    && echo "vscode ALL=(ALL) NOPASSWD:ALL" >> /etc/sudoers
+
+USER vscode
+WORKDIR /workspaces

.devcontainer/devcontainer.json

@@ -0,0 +1,29 @@
+{
+  "name": "ai-agent-dev",
+  "build": {
+    "dockerfile": "Dockerfile"
+  },
+
+  // This is where your repo will be mounted inside the container
+  "remoteUser": "vscode",
+  "workspaceFolder": "/workspaces/${localWorkspaceFolderBasename}",
+
+  "customizations": {
+    "vscode": {
+    "settings": {
+      "python.defaultInterpreterPath": "${workspaceFolder}/.venv/bin/python",
+      "python.envFile": "${workspaceFolder}/.env"
+    },
+      "extensions": [
+        "ms-python.python",
+        "ms-python.vscode-pylance",
+        "tamasfe.even-better-toml"
+      ]
+    }
+  },
+
+  "forwardPorts": [7860],
+
+  // Install project in editable mode after the container is built  
+  "postCreateCommand": "rm -rf .venv && uv venv && uv pip install -e . && echo '. $PWD/.venv/bin/activate' >> /home/vscode/.bashrc"
+}

.env.dist

@@ -1,14 +1,14 @@
 OPENAI_API_KEY=sk-xxxx
 # Optional model overrides (defaults work):
-OPENAI_VLM_MODEL=gpt-4o
-OPENAI_MODEL=gpt-4o-mini
+OPENAI_MODEL=gpt-4o
 
 # Software catalog
 SOFTWARE_CATALOG=path/to/your/catalog.jsonl
 
 # Pipeline configuration
 TOP_K=8                # Number of candidates to retrieve
 NUM_CHOICES=3          # Number of tools to recommend
+USE_AGENT=1            # Use pydantic-ai agent (1) or standard pipeline (0)
 
 # Logging configuration
 LOGLEVEL_CONSOLE=WARNING

.github/copilot-instructions.md

@@ -0,0 +1,130 @@
+# AI Agent — Copilot Instructions
+
+This is a **RAG + VLM imaging tool recommender** that helps users find the right imaging software for their images and tasks. Users drop an image, describe their task, and get ranked software recommendations with demo links.
+
+## Architecture Overview
+
+The system follows a two-stage pipeline:
+
+1. **Retrieval Stage** (`retriever/`, `api/pipeline.py`): Fast text search using BGE-M3 embeddings + CrossEncoder reranker. No LLM calls. Returns top-K candidates.
+
+2. **Selection Stage** (`generator/`): Single VLM call (OpenAI GPT-4o/mini) that sees the image + candidates + metadata and returns ranked recommendations with accuracy scores.
+
+### Key Components
+
+- **`api/pipeline.RAGImagingPipeline`**: Main orchestrator. Handles file validation, metadata extraction, retrieval, and VLM selection.
+- **`retriever/embedders.py`**: FAISS vector index with BGE-M3 + CrossEncoder reranker for candidate retrieval.
+- **`generator/generator.VLMToolSelector`**: Vision-language model that selects best tools from candidates.
+- **`utils/image_meta.py`**: Robust metadata extraction for DICOM, NIfTI, TIFF stacks with medical imaging focus.
+- **`utils/tags.py`**: Control tags system for query refinement (`[EXCLUDE:tool1|tool2]`, `[NO_RERANK]`, `[REFINE]`).
+
+## Data Flow Patterns
+
+### Input Processing
+- Files validated via `utils/file_validator.py` (size limits, format checks)
+- Images converted to PNG previews for VLM via `utils/previews.py`
+- Metadata extracted preserving original format info (critical for format compatibility matching)
+- Format tokens added to retrieval query (e.g. `format:DICOM format:NIfTI`)
+
+### Retrieval Query Construction
+```python
+# Clean task text + format tokens from uploaded files
+query = f"{clean_task} format:{ext_tokens}"  # e.g. "segment lungs format:DICOM"
+```
+
+### VLM Selection Input
+The VLM receives:
+- **Text**: User task + candidate table + original file metadata
+- **Image**: PNG preview (converted from any format) 
+- **Metadata**: Original extension, dimensions, file info (crucial for IO compatibility)
+
+## Critical Patterns
+
+### Error Handling
+- **Graceful degradation**: If image conversion fails, continue text-only
+- **Robust metadata**: All metadata extraction wrapped in try/catch with sensible defaults
+- **File validation**: Early validation prevents downstream errors
+
+### Control Tags System
+Users can control behavior via tags in their queries:
+- `[EXCLUDE:toolname1|toolname2]` - Exclude specific tools from results
+- `[NO_RERANK]` - Skip CrossEncoder reranker (faster, less accurate)
+- `[REFINE]` - Force clarification turn for alternatives
+
+### Conversation Flow
+- **Complete**: Normal success with tool recommendations
+- **Needs Clarification**: VLM asks followup questions when task is ambiguous
+- **Terminal No-Tool**: No suitable tools found with explanation
+
+## Development Workflows
+
+### Running the App
+```bash
+# Install with pip using pyproject.toml
+pip install -e ".[dev]"
+
+# Configure .env with OPENAI_API_KEY and SOFTWARE_CATALOG path
+ai_agent ui  # Launches Gradio on port 7860
+```
+
+### Testing
+- **`tests/full_test.py`**: End-to-end pipeline tests driven by `tests/data/test_data.json`
+- Uses test doubles for VLM calls to avoid API costs
+- Run with: `pytest tests/`
+
+### Change Documentation
+- **`CHANGELOG.md`**: Follow [Keep a Changelog](https://keepachangelog.com/) format
+- Use semantic versioning with sections: Added, Changed, Deprecated, Removed, Fixed, Security
+- Update CHANGELOG.md for ALL user-facing changes before merging PRs
+- Format: `### Added\n- New feature description` under version heading
+- Version entries: `## [x.y.z] - YYYY-MM-DD`
+
+### Environment Management
+- **uv**: Fast Python package manager used in `tools/image/Dockerfile`
+- Creates isolated `.venv` environments for reproducible builds
+- Dockerfile uses `uv venv && uv pip install -e .` pattern for container builds
+
+### Logging & Debugging
+- Set `LOG_PROMPTS=1` to save VLM prompts + images to `logs/`
+- File logs in `logs/app_YYYYMMDD.log` with structured JSON events
+- Console/file log levels configurable via `.env`
+
+## Project Conventions
+
+### Schema Patterns
+- **Pydantic models** in `generator/schema.py` with robust field validation and aliasing for catalog compatibility
+- **Enum-based** conversation states and tool reasons for type safety
+- **Field normalization**: Dimensions (2D/3D/4D), modalities (CT/MRI/XR), file formats via validators
+
+### Catalog Integration
+- Software catalog in JSONL format following schema.org SoftwareSourceCode structure
+- **Runnable examples**: Links to HuggingFace Spaces, notebooks, web demos
+- **Supporting data**: Format compatibility info used for matching
+
+### Module Boundaries
+- `api/`: Pipeline orchestration, no UI dependencies
+- `generator/`: Pure VLM logic, no retrieval dependencies  
+- `retriever/`: Pure vector search, no generation dependencies
+- `utils/`: Shared utilities, no business logic
+- `ui/`: Gradio interface only
+
+### Configuration
+- Environment-based config via `.env` (API keys, model names, catalog paths)
+- Sensible defaults for all settings
+- No hardcoded paths or credentials
+
+## Medical Imaging Context
+
+This tool specializes in medical/scientific imaging:
+- **Modalities**: CT, MRI, X-ray, Ultrasound, PET, SPECT, Microscopy
+- **Formats**: DICOM, NIfTI, TIFF stacks, standard images
+- **Dimensions**: 2D images, 3D volumes, 4D timeseries
+- **Tasks**: Segmentation, registration, analysis, visualization
+
+The VLM selection considers format compatibility as a primary factor - tools supporting the user's input format are strongly preferred.
+
+## Security Notes
+- Only makes external calls to OpenAI VLM API (with user image preview)
+- Never uploads user data to third-party tool demos
+- Returns links only; user chooses whether to visit demos
+- Prompt logging is optional and local-only

.github/workflows/publish_image_in_GHCR.yaml

@@ -0,0 +1,167 @@
+name: Build and Publish Docker Images
+
+on:
+  push:
+    branches: [ "main", "develop" ]
+  pull_request:
+    branches: [ "main", "develop" ]
+
+jobs:
+  build-and-publish:
+    runs-on: ubuntu-latest
+    permissions:
+      contents: write # needed to create the release
+      packages: write # needed to publish the image
+
+    # Skip building images for draft PRs
+    if: |
+      github.event_name == 'push' || 
+      (github.event_name == 'pull_request' && 
+       github.event.pull_request.draft == false)
+
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v4
+
+      - name: Extract version from pyproject.toml
+        id: project_version
+        run: |
+          VERSION=$(grep 'version =' pyproject.toml | sed -E 's/version = "([^"]+)"/\1/')
+          echo "version=${VERSION}" >> $GITHUB_OUTPUT
+
+      - name: Extract changelog section for version
+        id: changelog
+        if: github.ref == 'refs/heads/main' && github.event_name == 'push'
+        run: |
+          VERSION="${{ steps.project_version.outputs.version }}"
+
+          # Extract the section for this version from CHANGELOG.md
+          # This awk script finds the section between [VERSION] and the next [VERSION] or end of file
+          CHANGELOG_SECTION=$(awk -v version="[$VERSION]" '
+            BEGIN { found=0; content="" }
+            $0 ~ "^## \\[" {
+              if (found) exit
+              if ($0 ~ version) {
+                found=1
+                content = $0 "\n"
+                next
+              }
+            }
+            found { content = content $0 "\n" }
+            END { print content }
+          ' CHANGELOG.md)
+
+          # If no section found, use a default message
+          if [ -z "$CHANGELOG_SECTION" ]; then
+            CHANGELOG_SECTION="## Release v${VERSION}\n\nNo changelog entry found for this version."
+          fi
+
+          # Save to file and output
+          echo "$CHANGELOG_SECTION" > release_notes.md
+          echo "changelog_file=release_notes.md" >> $GITHUB_OUTPUT
+
+          # Also output as multiline string for debugging
+          {
+            echo 'content<<EOF'
+            echo "$CHANGELOG_SECTION"
+            echo 'EOF'
+          } >> $GITHUB_OUTPUT
+
+      - name: Log in to GitHub Container Registry
+        uses: docker/login-action@v3
+        with:
+          registry: ghcr.io
+          username: ${{ github.actor }}
+          password: ${{ secrets.GITHUB_TOKEN }}
+
+      - name: Extract metadata for Docker
+        id: meta
+        uses: docker/metadata-action@v5
+        with:
+          images: ghcr.io/${{ github.repository }}
+          tags: |
+            # For main branch: latest and version tags
+            type=raw,value=latest,enable={{is_default_branch}}
+            type=raw,value=${{ steps.project_version.outputs.version }},enable={{is_default_branch}}
+            # For develop branch: develop tag
+            type=raw,value=develop,enable=${{ github.ref == 'refs/heads/develop' }}
+            # For PRs only: pr-{number} tag
+            type=ref,event=pr,prefix=pr-
+          labels: |
+            org.opencontainers.image.title=${{ github.repository }}
+            org.opencontainers.image.description=${{ github.event.repository.description }}
+            org.opencontainers.image.url=${{ github.event.repository.html_url }}
+            org.opencontainers.image.source=${{ github.event.repository.clone_url }}
+            org.opencontainers.image.revision=${{ github.sha }}
+            org.opencontainers.image.licenses=${{ github.event.repository.license.spdx_id }}
+            # Add cleanup hint for PR images
+            io.github.pr-image=${{ github.event_name == 'pull_request' && 'true' || 'false' }}
+
+      - name: Build and push Docker image
+        uses: docker/build-push-action@v5
+        with:
+          context: .
+          file: tools/image/Dockerfile
+          platforms: linux/amd64
+          push: true
+          tags: ${{ steps.meta.outputs.tags }}
+          labels: ${{ steps.meta.outputs.labels }}
+
+      - name: Create GitHub Release
+        # Only create releases for main branch pushes
+        if: github.ref == 'refs/heads/main' && github.event_name == 'push'
+        uses: softprops/action-gh-release@v2
+        with:
+          tag_name: v${{ steps.project_version.outputs.version }}
+          name: Release v${{ steps.project_version.outputs.version }}
+          body_path: ${{ steps.changelog.outputs.changelog_file }}
+          fail_on_unmatched_files: false
+
+  # Clean up PR images when PR is closed
+  cleanup-pr-image:
+    runs-on: ubuntu-latest
+    if: github.event_name == 'pull_request' && github.event.action == 'closed'
+    permissions:
+      packages: write
+
+    steps:
+      - name: Delete PR image
+        uses: actions/github-script@v7
+        with:
+          github-token: ${{ secrets.GITHUB_TOKEN }}
+          script: |
+            const owner = context.repo.owner;
+            const repo = context.repo.repo;
+            const packageName = `${owner}/${repo}`;
+            const prNumber = context.payload.pull_request.number;
+            const prTag = `pr-${prNumber}`;
+
+            try {
+              // Get all package versions
+              const { data: versions } = await github.rest.packages.getAllPackageVersionsForPackageOwnedByOrg({
+                package_type: 'container',
+                package_name: packageName,
+                org: owner,
+                per_page: 100
+              });
+
+              // Find the PR image version
+              const prVersion = versions.find(version => 
+                version.metadata.container.tags.includes(prTag)
+              );
+
+              if (prVersion) {
+                console.log(`Deleting PR image: ${prTag} (version ID: ${prVersion.id})`);
+                await github.rest.packages.deletePackageVersionForOrg({
+                  package_type: 'container',
+                  package_name: packageName,
+                  org: owner,
+                  package_version_id: prVersion.id
+                });
+                console.log(`Successfully deleted PR image: ${prTag}`);
+              } else {
+                console.log(`No image found for PR: ${prTag}`);
+              }
+            } catch (error) {
+              console.log(`Error cleaning up PR image (this is normal if no image was built): ${error.message}`);
+            }

CHANGELOG.md

@@ -0,0 +1,20 @@
+# Changelog
+
+All notable changes to this project will be documented in this file.
+
+## [0.1.2] - 2025-10-07
+
+### Added
+- Pydantic AI pipeline working with a few tools
+- Better handling of the runnable example link and reranker
+
+## [0.1.1] - 2025-10-02
+
+### Added
+- Experimental Pydantic AI agent skeleton with tool-based retrieval (feature flag `USE_AGENT=1`).
+- Multimodal agent pathway (image preview + candidates) producing structured `ToolSelection` output.
+
+## [0.1.0] - 2025-09-30
+
+### Added
+- Chat functionality