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Update Dockerfile
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Upload folder using huggingface_hub
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Delete bioflow/__init__.py with huggingface_hub
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Rename Dockerfile.hf to Dockerfile
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Track more binary files with LFS
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Track large files with LFS
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Fix API response handling: extract molecules/proteins arrays from wrapped response
yassinekolsi550eaf1 -
Fix Next.js 16 build: disable cacheComponents, add force-dynamic to all API routes and pages with server fetches
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Add NEXT_PUBLIC_API_URL env pointing to HF Space backend
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Fix all TypeScript errors: remove unused imports, delete orphan reactflow components
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Fix explorer service argument mismatch and hardcoded URL, duplicate param type fixes
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Fix Next.js 15 breaking change: await params in API routes
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Add vercel.json for Next.js deployment
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Deployment setup: HuggingFace Spaces + Vercel config
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Deploy to HuggingFace Spaces
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fix: PR review fixes - dockerfile, encoders, orchestrator, paths
yassinekolsi- dockerfile: use conda run for pip installs, remove hardcoded proxy, add COPY, fix ENV PATH syntax - orchestrator: remove duplicate Optional import, fix retriever API (modality param), safe getattr - encoders: batch_encode honors pooling setting in protein/text encoders - qdrant_retriever: safe modality mapping for legacy values - plugins/__init__: replace print with logging - run_summary.json: convert absolute paths to relative (5 files) - BIOFLOW_README: fix license badge (Apache->MIT) - USE_POLICY: fix spelling (sperate->separate) - model_customization.ipynb: fix config path - enhanced_search: sort by score after MMR, qdrant API fallback - UI: database filter state management, result display improvements5770d80
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Bring Rami utility scripts and configs
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Merge Rami into main-merge-rami (manual conflict resolution)
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Fix explorer/ingestion UI and 3D endpoints
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Merge pull request #6 from hamzasammoud11-dotcom/merged-final
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docs: remove orchestrator from naming and update structure
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feat: enhance visualization with mock data fallback and update readme
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fix: remove /dashboard prefix, fix theme toggle position, fix 3D viewer, remove langflow
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feat: merge Rami's bioflow architecture with core-progress fixes
yassinekolsiMerged from origin/Rami: - Full bioflow/ package with agents, orchestrator, plugins - open_biomed/ integration for advanced models - Professional UI dashboard architecture - Docker support and batch scripts - Examples and workflow configs Kept from core-progress (our fixes): - Simplified theme toggle (single click, not dropdown) - 3Dmol viewer backgroundColor crash fix - Original server/api.py, config.py, ingest_qdrant.py - TECHNICAL_REPORT.md documentation - Original data/ and runs/ with prediction results - README.md Combined: Both DeepPurpose and OpenBioMed implementations2b2f173 -
feat: Complete Phase 4 UI/UX Polish with 3D visualization and workflow builder
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Merge pull request #5 from hamzasammoud11-dotcom/core-progress
yassinekolsiUnverified signaturefix: resolve 3Dmol viewer background color crash559ce8e -
fix: resolve 3Dmol viewer background color crash
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Merge pull request #4 from hamzasammoud11-dotcom/core-progress
yassinekolsiUnverified signaturefeat: add protein 2D/3D visualization component5fe718d -
fix: restructure dashboard pages and fix 404 errors
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fix: move theme toggle to status section and reduce visualization spacing
yassinekolsi- Move theme toggle next to Status label in sidebar - Make theme toggle a simple click toggle (light/dark) - Add ThemeProvider wrapper for proper dark mode support - Reduce gap and padding in visualization pages (gap-4 p-4)10283cc -
feat: add complete visualization system from feat/raed-ui
RaedAddala +1: RaedAddala- Add dashboard layout with sidebar navigation - Add molecules 2D page with SMILES visualization (smiles-drawer) - Add molecules 3D page with 3Dmol.js viewer - Add proteins 3D page with PDB structure viewer - Add API routes for molecules and proteins (mock data) - Add scroll-area and alert UI components - Add theme toggle component - Update sidebar with visualization menu items - Update routes to use /dashboard prefix Co-authored-by: RaedAddala <raed.addala@example.com>af68ace -
Merge branch 'feat/raed-ui' of https://github.com/hamzasammoud11-dotcom/lacoste001 into feat/raed-ui
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Phase 1: FastAPI integration with DeepPurpose DTI predictor
- Added bioflow/api/ with FastAPI server (port 8000) - Integrated DeepPurposePredictor from deeppurpose002.py logic - Updated Next.js API routes to call FastAPI backend - Created launch_bioflow_full.bat for dual-server startup - Merged OpenBioMed core + lacoste001 Next.js UIadecc9b -
feat: add protein 2D/3D visualization components
- Add Smiles2DViewer for 2D molecule visualization using smiles-drawer - Add ProteinViewer for 3D protein visualization using 3Dmol.js - Add visualization-api.ts for fetching molecule/protein data - Add visualization-types.ts for type definitions - Install smiles-drawer and 3dmol dependencies Co-authored-by: RaedAddala <addala.raed@gmail.com>3a0ae3e -
Merge pull request #3 from hamzasammoud11-dotcom/core-progress
yassinekolsiUnverified signaturefix: Replace batch runner with Python script and ensure Lucide icons …3642a9c
