alchemist-nrel 0.2.1__tar.gz → 0.3.0__tar.gz

alchemist_nrel-0.3.0/MANIFEST.in

@@ -0,0 +1,40 @@
+# MANIFEST.in - Include additional files in source distribution (sdist)
+
+# Include documentation
+include README.md
+include LICENSE
+include RELEASE_BUILD_GUIDE.md
+include RELEASE_NOTES_*.md
+
+# Include build hook
+include build_hooks.py
+
+# Include frontend source (for building from sdist) - but NOT node_modules or build artifacts
+recursive-include alchemist-web/src *
+recursive-include alchemist-web/public *
+include alchemist-web/package.json
+include alchemist-web/package-lock.json
+include alchemist-web/tsconfig.json
+include alchemist-web/tsconfig.*.json
+include alchemist-web/vite.config.ts
+include alchemist-web/tailwind.config.js
+include alchemist-web/postcss.config.js
+include alchemist-web/eslint.config.js
+include alchemist-web/index.html
+
+# Include run scripts
+include run_api.py
+include main.py
+
+# Exclude unnecessary files from sdist
+global-exclude __pycache__
+global-exclude *.py[co]
+global-exclude .DS_Store
+global-exclude node_modules
+recursive-exclude tests *
+recursive-exclude docs *
+recursive-exclude memory *
+recursive-exclude .github *
+recursive-exclude alchemist-web/node_modules *
+recursive-exclude alchemist-web/dist *
+recursive-exclude alchemist-web/.vite *

{alchemist_nrel-0.2.1 → alchemist_nrel-0.3.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: alchemist-nrel
-Version: 0.2.1
+Version: 0.3.0
 Summary: Active learning and optimization toolkit for chemical and materials research
 Author-email: Caleb Coatney <caleb.coatney@nrel.gov>
 License: BSD-3-Clause
@@ -42,6 +42,7 @@ Requires-Dist: fastapi>=0.109.0
 Requires-Dist: uvicorn[standard]>=0.27.0
 Requires-Dist: pydantic>=2.5.0
 Requires-Dist: python-multipart>=0.0.6
+Requires-Dist: requests
 Provides-Extra: test
 Requires-Dist: pytest>=8.0.0; extra == "test"
 Requires-Dist: pytest-cov>=4.0.0; extra == "test"
@@ -56,7 +57,7 @@ Requires-Dist: httpx>=0.25.0; extra == "dev"
 Requires-Dist: requests>=2.31.0; extra == "dev"
 Dynamic: license-file
 
-<img src="docs/assets/logo.png" alt="ALchemist" width="50%" />
+<img src="docs/assets/NEW_LOGO_LIGHT.png" alt="ALchemist" width="50%" />
 
 **ALchemist: Active Learning Toolkit for Chemical and Materials Research**
 
@@ -81,75 +82,91 @@ ALchemist accelerates discovery and optimization by combining:
 - **Probabilistic surrogate modeling:** Gaussian process regression via BoTorch or scikit-optimize backends.
 - **Advanced acquisition strategies:** Efficient sampling using qEI, qPI, qUCB, and qNegIntegratedPosteriorVariance.
 - **Modern web interface:** React-based UI with FastAPI backend for seamless active learning workflows.
+- **Autonomous optimization:** Human-out-of-the-loop optimization for real-time process control.
 - **Experiment tracking:** CSV logging, reproducible random seeds, and error tracking.
 - **Extensibility:** Abstract interfaces for models and acquisition functions enable future backend and workflow expansion.
 
+### Use Cases
+
+- **Interactive Optimization**: Desktop GUI or web UI for manual experiment design
+- **Programmatic Workflows**: Python Session API for scripts and notebooks
+- **Autonomous Operation**: REST API for real-time process control (reactors, synthesis, etc.)
+- **Remote Collaboration**: Web-based interface accessible from any device
+
 ---
 
 ## 🧭 Quick Start
 
-### Web Application (Recommended)
+### Installation
 
-**Development Mode:**
-```bash
-# Option 1: Manual start
-python run_api.py              # Terminal 1: Backend (port 8000)
-cd alchemist-web && npm run dev  # Terminal 2: Frontend (port 5173)
+**Requirements:** Python 3.11 or higher
 
-# Option 2: Automated start
-scripts\dev_start.bat    # Windows
-./scripts/dev_start.sh   # Linux/Mac
-```
+We recommend using [Anaconda](https://www.anaconda.com/products/distribution) to manage your Python environments.
 
-**Production Mode:**
+**1. Create a new environment:**
 ```bash
-# Build and run
-scripts\build_production.bat    # Windows
-./scripts/build_production.sh   # Linux/Mac
+conda create -n alchemist-env python=3.11
+conda activate alchemist-env
+```
 
-# Start production server
-python run_api.py --production
+**2. Install ALchemist:**
 
-# Access at: http://localhost:8000
+*Option A: From PyPI (recommended):*
+```bash
+pip install alchemist-nrel
 ```
 
-**Docker Deployment:**
+*Option B: From GitHub:*
 ```bash
-# Build frontend first
-cd alchemist-web && npm run build && cd ..
+pip install git+https://github.com/NREL/ALchemist.git
+```
 
-# Run with Docker Compose
-cd docker
-docker-compose up --build
+*Option C: Development install (for contributors):*
+```bash
+git clone https://github.com/NREL/ALchemist.git
+cd ALchemist
+pip install -e .
 ```
 
-### Python Package Installation
+All dependencies are specified in `pyproject.toml` and will be installed automatically.
 
-Requirements: Python 3.9 or higher
+**Note:** The web UI is pre-built and included in the package. You do **not** need Node.js/npm to use ALchemist unless you're developing the frontend.
 
-We recommend using [Anaconda](https://www.anaconda.com/products/distribution) to manage your Python environments.
+### Running ALchemist
 
-**1. Create a new environment:**
+**Web Application (Recommended):**
 ```bash
-conda create -n alchemist-env python=3.12
-conda activate alchemist-env
+alchemist-web
+# Opens at http://localhost:8000
 ```
 
-**2. Install ALchemist:**
-
-*Option A: Install directly from GitHub:*
+**Desktop Application:**
 ```bash
-python -m pip install git+https://github.com/NREL/ALchemist.git
+alchemist
+# Launches CustomTkinter GUI
 ```
 
-*Option B: Clone and install (recommended for development):*
+**Development Mode (Frontend Developers):**
 ```bash
-git clone https://github.com/NREL/ALchemist.git
-cd ALchemist
-python -m pip install -e .
+# Terminal 1: Backend with hot-reload
+python run_api.py
+
+# Terminal 2: Frontend with hot-reload
+cd alchemist-web
+npm install  # First time only
+npm run dev
+# Opens at http://localhost:5173
 ```
 
-All dependencies are specified in `pyproject.toml` and will be installed automatically.
+**Docker Deployment:**
+```bash
+docker pull ghcr.io/nrel/alchemist:latest
+docker run -p 8000:8000 ghcr.io/nrel/alchemist:latest
+
+# Or build from source:
+cd docker
+docker-compose up --build
+```
 
 For step-by-step instructions, see the [Getting Started](https://nrel.github.io/ALchemist/) section of the documentation.
 

{alchemist_nrel-0.2.1 → alchemist_nrel-0.3.0}/README.md

@@ -1,4 +1,4 @@
-<img src="docs/assets/logo.png" alt="ALchemist" width="50%" />
+<img src="docs/assets/NEW_LOGO_LIGHT.png" alt="ALchemist" width="50%" />
 
 **ALchemist: Active Learning Toolkit for Chemical and Materials Research**
 
@@ -23,75 +23,91 @@ ALchemist accelerates discovery and optimization by combining:
 - **Probabilistic surrogate modeling:** Gaussian process regression via BoTorch or scikit-optimize backends.
 - **Advanced acquisition strategies:** Efficient sampling using qEI, qPI, qUCB, and qNegIntegratedPosteriorVariance.
 - **Modern web interface:** React-based UI with FastAPI backend for seamless active learning workflows.
+- **Autonomous optimization:** Human-out-of-the-loop optimization for real-time process control.
 - **Experiment tracking:** CSV logging, reproducible random seeds, and error tracking.
 - **Extensibility:** Abstract interfaces for models and acquisition functions enable future backend and workflow expansion.
 
+### Use Cases
+
+- **Interactive Optimization**: Desktop GUI or web UI for manual experiment design
+- **Programmatic Workflows**: Python Session API for scripts and notebooks
+- **Autonomous Operation**: REST API for real-time process control (reactors, synthesis, etc.)
+- **Remote Collaboration**: Web-based interface accessible from any device
+
 ---
 
 ## 🧭 Quick Start
 
-### Web Application (Recommended)
+### Installation
 
-**Development Mode:**
-```bash
-# Option 1: Manual start
-python run_api.py              # Terminal 1: Backend (port 8000)
-cd alchemist-web && npm run dev  # Terminal 2: Frontend (port 5173)
+**Requirements:** Python 3.11 or higher
 
-# Option 2: Automated start
-scripts\dev_start.bat    # Windows
-./scripts/dev_start.sh   # Linux/Mac
-```
+We recommend using [Anaconda](https://www.anaconda.com/products/distribution) to manage your Python environments.
 
-**Production Mode:**
+**1. Create a new environment:**
 ```bash
-# Build and run
-scripts\build_production.bat    # Windows
-./scripts/build_production.sh   # Linux/Mac
+conda create -n alchemist-env python=3.11
+conda activate alchemist-env
+```
 
-# Start production server
-python run_api.py --production
+**2. Install ALchemist:**
 
-# Access at: http://localhost:8000
+*Option A: From PyPI (recommended):*
+```bash
+pip install alchemist-nrel
 ```
 
-**Docker Deployment:**
+*Option B: From GitHub:*
 ```bash
-# Build frontend first
-cd alchemist-web && npm run build && cd ..
+pip install git+https://github.com/NREL/ALchemist.git
+```
 
-# Run with Docker Compose
-cd docker
-docker-compose up --build
+*Option C: Development install (for contributors):*
+```bash
+git clone https://github.com/NREL/ALchemist.git
+cd ALchemist
+pip install -e .
 ```
 
-### Python Package Installation
+All dependencies are specified in `pyproject.toml` and will be installed automatically.
 
-Requirements: Python 3.9 or higher
+**Note:** The web UI is pre-built and included in the package. You do **not** need Node.js/npm to use ALchemist unless you're developing the frontend.
 
-We recommend using [Anaconda](https://www.anaconda.com/products/distribution) to manage your Python environments.
+### Running ALchemist
 
-**1. Create a new environment:**
+**Web Application (Recommended):**
 ```bash
-conda create -n alchemist-env python=3.12
-conda activate alchemist-env
+alchemist-web
+# Opens at http://localhost:8000
 ```
 
-**2. Install ALchemist:**
-
-*Option A: Install directly from GitHub:*
+**Desktop Application:**
 ```bash
-python -m pip install git+https://github.com/NREL/ALchemist.git
+alchemist
+# Launches CustomTkinter GUI
 ```
 
-*Option B: Clone and install (recommended for development):*
+**Development Mode (Frontend Developers):**
 ```bash
-git clone https://github.com/NREL/ALchemist.git
-cd ALchemist
-python -m pip install -e .
+# Terminal 1: Backend with hot-reload
+python run_api.py
+
+# Terminal 2: Frontend with hot-reload
+cd alchemist-web
+npm install  # First time only
+npm run dev
+# Opens at http://localhost:5173
 ```
 
-All dependencies are specified in `pyproject.toml` and will be installed automatically.
+**Docker Deployment:**
+```bash
+docker pull ghcr.io/nrel/alchemist:latest
+docker run -p 8000:8000 ghcr.io/nrel/alchemist:latest
+
+# Or build from source:
+cd docker
+docker-compose up --build
+```
 
 For step-by-step instructions, see the [Getting Started](https://nrel.github.io/ALchemist/) section of the documentation.
 

alchemist_nrel-0.3.0/RELEASE_NOTES_v0.3.0.md

@@ -0,0 +1,154 @@
+# Release Notes - ALchemist v0.3.0
+
+**Release Date:** November 24, 2025  
+**Type:** Production Release  
+**Status:** Stable
+
+## 🎉 Highlights
+
+ALchemist v0.3.0 is now **production-ready** and fully deployable! This release marks a significant milestone with complete packaging, Docker support, and simplified installation for end users.
+
+## ✨ New Features
+
+### Production-Ready Packaging
+- **Pre-built Web UI**: Web interface is now bundled in the Python wheel - no Node.js required for end users!
+- **Single-command Installation**: `pip install alchemist-nrel` now includes everything needed to run both desktop and web apps
+- **Entry Points**: Two command-line tools after installation:
+  - `alchemist` - Launch desktop GUI (CustomTkinter)
+  - `alchemist-web` - Launch web application (React + FastAPI)
+
+### Docker Support
+- **Production-ready Dockerfile**: Optimized multi-stage build
+- **Docker Compose configuration**: One-command deployment
+- **Health checks**: Automated container health monitoring
+- **Volume mounting**: Persistent data for logs and cache
+
+### Enhanced Web UI
+- **Production mode**: Optimized build with minification and code splitting
+- **Static file serving**: FastAPI now serves React build artifacts efficiently
+- **Development mode preserved**: Hot-reload still available for frontend developers
+
+## 🔧 Technical Improvements
+
+### Build System
+- **Custom build hooks**: Automatic React UI compilation during `python -m build`
+- **Smart static file handling**: Supports both development and production workflows
+- **Clean git history**: Build artifacts excluded from repository
+
+### API Improvements
+- **Flexible CORS**: Environment variable configuration for production domains
+- **Static file priority**: Checks `api/static/` first (production), falls back to `alchemist-web/dist/` (development)
+- **Better logging**: Informative messages about static file serving
+
+### Configuration
+- **Version synchronization**: v0.3.0 across all components (pyproject.toml, package.json, API)
+- **Simplified MANIFEST.in**: Excludes node_modules from source distributions
+- **Production flags**: `--production` mode for optimized serving
+
+## 📦 Installation & Deployment
+
+### For End Users (No Node.js Required!)
+
+```bash
+# Install from PyPI (coming soon)
+pip install alchemist-nrel
+
+# Or install from GitHub
+pip install git+https://github.com/NREL/ALchemist.git
+
+# Run the web application
+alchemist-web
+
+# Or run the desktop application
+alchemist
+```
+
+### For NREL Server Deployment
+
+**Option 1: Docker (Recommended)**
+```bash
+docker pull ghcr.io/nrel/alchemist:v0.3.0
+docker run -p 8000:8000 ghcr.io/nrel/alchemist:v0.3.0
+```
+
+**Option 2: Docker Compose**
+```bash
+cd docker
+docker-compose up -d
+```
+
+**Option 3: Direct Python**
+```bash
+pip install alchemist-nrel
+alchemist-web --production
+```
+
+### For Developers
+
+```bash
+# Clone and install in editable mode
+git clone https://github.com/NREL/ALchemist.git
+cd ALchemist
+pip install -e .
+
+# Frontend development with hot-reload
+cd alchemist-web
+npm install
+npm run dev  # Terminal 1
+
+# Backend with auto-reload  
+python run_api.py  # Terminal 2
+```
+
+## 🐛 Bug Fixes
+
+- Fixed static file serving to use correct path for pip-installed packages
+- Corrected CORS configuration to include localhost:8000 for production mode
+- Fixed MANIFEST.in to exclude node_modules from source distributions
+- Resolved Dockerfile CMD to use entry point instead of direct uvicorn call
+
+## 🔄 Breaking Changes
+
+None! This release is fully backward compatible with v0.2.x.
+
+## 📝 Migration Guide
+
+If upgrading from v0.2.x:
+1. Uninstall old version: `pip uninstall alchemist-nrel`
+2. Install new version: `pip install alchemist-nrel`
+3. (Optional) Update your Docker images to use v0.3.0 tag
+
+## 🚀 What's Next
+
+### Planned for v0.3.1
+- PyPI publishing automation
+- Additional acquisition strategies
+- Enhanced documentation
+
+### Future Releases
+- Multi-objective optimization
+- Advanced DoE methods
+- PySide6 desktop UI migration
+
+## 🙏 Acknowledgments
+
+This work is supported by the U.S. Department of Energy's Bioenergy Technologies Office (BETO) through the ChemCatBio Consortium.
+
+## 📄 License
+
+BSD 3-Clause License
+
+## 🔗 Links
+
+- **GitHub**: https://github.com/NREL/ALchemist
+- **Documentation**: https://nrel.github.io/ALchemist/
+- **Issues**: https://github.com/NREL/ALchemist/issues
+- **NREL Software Record**: SWR-25-102
+
+---
+
+For detailed installation and deployment instructions, see:
+- `README.md` - General overview and quick start
+- `memory/RELEASE_BUILD_GUIDE.md` - Build system details
+- `memory/DOCKER.md` - Docker deployment guide
+- `memory/PRODUCTION_DEPLOYMENT.md` - Production configuration

alchemist_nrel-0.3.0/alchemist-web/eslint.config.js

@@ -0,0 +1,23 @@
+import js from '@eslint/js'
+import globals from 'globals'
+import reactHooks from 'eslint-plugin-react-hooks'
+import reactRefresh from 'eslint-plugin-react-refresh'
+import tseslint from 'typescript-eslint'
+import { defineConfig, globalIgnores } from 'eslint/config'
+
+export default defineConfig([
+  globalIgnores(['dist']),
+  {
+    files: ['**/*.{ts,tsx}'],
+    extends: [
+      js.configs.recommended,
+      tseslint.configs.recommended,
+      reactHooks.configs['recommended-latest'],
+      reactRefresh.configs.vite,
+    ],
+    languageOptions: {
+      ecmaVersion: 2020,
+      globals: globals.browser,
+    },
+  },
+])

alchemist_nrel-0.3.0/alchemist-web/index.html

@@ -0,0 +1,13 @@
+<!doctype html>
+<html lang="en" class="dark">
+  <head>
+    <meta charset="UTF-8" />
+    <link rel="icon" type="image/svg+xml" href="/NEW_ICON.png" />
+    <meta name="viewport" content="width=device-width, initial-scale=1.0" />
+    <title>ALchemist - Active Learning Toolkit</title>
+  </head>
+  <body>
+    <div id="root"></div>
+    <script type="module" src="/src/main.tsx"></script>
+  </body>
+</html>