alchemist-nrel 0.2.1__tar.gz → 0.3.1__tar.gz

alchemist_nrel-0.3.1/MANIFEST.in

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+# MANIFEST.in - Include additional files in source distribution (sdist)
+
+# Include documentation
+include README.md
+include LICENSE
+include RELEASE_BUILD_GUIDE.md
+
+# Include build tools
+include build_tools/build_hooks.py
+include build_tools/setup.py
+include build_tools/__init__.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 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-0.3.1/PKG-INFO

@@ -0,0 +1,185 @@
+Metadata-Version: 2.4
+Name: alchemist-nrel
+Version: 0.3.1
+Summary: Active learning and optimization toolkit for chemical and materials research
+Author-email: Caleb Coatney <caleb.coatney@nrel.gov>
+License: BSD-3-Clause
+Project-URL: Homepage, https://github.com/NREL/ALchemist
+Project-URL: Documentation, https://nrel.github.io/ALchemist/
+Project-URL: Source, https://github.com/NREL/ALchemist
+Project-URL: Bug Tracker, https://github.com/NREL/ALchemist/issues
+Project-URL: Changelog, https://github.com/NREL/ALchemist/releases
+Keywords: active learning,bayesian optimization,gaussian processes,materials science,chemistry
+Classifier: Development Status :: 4 - Beta
+Classifier: Intended Audience :: Science/Research
+Classifier: License :: OSI Approved :: BSD License
+Classifier: Operating System :: OS Independent
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Topic :: Scientific/Engineering
+Classifier: Topic :: Scientific/Engineering :: Chemistry
+Requires-Python: >=3.11
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: numpy
+Requires-Dist: pandas
+Requires-Dist: scipy
+Requires-Dist: matplotlib
+Requires-Dist: mplcursors
+Requires-Dist: scikit-learn
+Requires-Dist: scikit-optimize
+Requires-Dist: botorch
+Requires-Dist: torch
+Requires-Dist: gpytorch
+Requires-Dist: ax-platform
+Requires-Dist: customtkinter
+Requires-Dist: tksheet
+Requires-Dist: tabulate
+Requires-Dist: ctkmessagebox
+Requires-Dist: joblib
+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"
+Requires-Dist: pytest-anyio>=0.0.0; extra == "test"
+Requires-Dist: httpx>=0.25.0; extra == "test"
+Requires-Dist: requests>=2.31.0; extra == "test"
+Provides-Extra: dev
+Requires-Dist: pytest>=8.0.0; extra == "dev"
+Requires-Dist: pytest-cov>=4.0.0; extra == "dev"
+Requires-Dist: pytest-anyio>=0.0.0; extra == "dev"
+Requires-Dist: httpx>=0.25.0; extra == "dev"
+Requires-Dist: requests>=2.31.0; extra == "dev"
+Dynamic: license-file
+
+<img src="docs/assets/NEW_LOGO_LIGHT.png" alt="ALchemist" width="50%" />
+
+**ALchemist: Active Learning Toolkit for Chemical and Materials Research**
+
+ALchemist is a modular Python toolkit that brings active learning and Bayesian optimization to experimental design in chemical and materials research. It is designed for scientists and engineers who want to efficiently explore or optimize high-dimensional variable spaces—using intuitive graphical interfaces, programmatic APIs, or autonomous optimization workflows.
+
+**NLR Software Record:** SWR-25-102
+
+---
+
+## Documentation
+
+Full user guide and documentation:  
+[https://nrel.github.io/ALchemist/](https://nrel.github.io/ALchemist/)
+
+---
+
+## Overview
+
+**Key Features:**
+
+- **Flexible variable space definition**: Real, integer, and categorical variables with bounds or discrete values
+- **Probabilistic surrogate modeling**: Gaussian process regression via BoTorch or scikit-learn 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
+- **Desktop GUI**: CustomTkinter desktop application for offline optimization
+- **Session management**: Save/load optimization sessions with audit logs for reproducibility
+- **Multiple interfaces**: No-code GUI, Python Session API, or REST API for different use cases
+- **Autonomous optimization**: Human-out-of-the-loop operation for real-time process control
+- **Experiment tracking**: CSV logging, reproducible random seeds, and comprehensive audit trails
+- **Extensibility**: Abstract interfaces for models and acquisition functions enable future backend and workflow expansion
+**Architecture:**
+
+ALchemist is built on a clean, modular architecture:
+
+- **Core Session API**: Headless Bayesian optimization engine (`alchemist_core`) that powers all interfaces
+- **Desktop Application**: CustomTkinter GUI using the Core Session API, designed for human-in-the-loop and offline optimization
+- **REST API**: FastAPI server providing a thin wrapper around the Core Session API for remote access
+- **Web Application**: React UI consuming the REST API, supporting both interactive and autonomous optimization workflows
+
+Session files (JSON format) are fully interoperable between desktop and web applications, enabling seamless workflow transitions.
+
+---
+
+## Use Cases
+
+- **Interactive Optimization**: Use desktop or web GUI for manual experiment design and human-in-the-loop optimization
+- **Programmatic Workflows**: Import the Session API in Python scripts or Jupyter notebooks for batch processing
+- **Autonomous Optimization**: Use the REST API to integrate ALchemist with automated laboratory equipment for real-time process control
+- **Remote Monitoring**: Web dashboard provides read-only monitoring mode when ALchemist is being remote-controlled
+
+For detailed application examples, see [Use Cases](https://nrel.github.io/ALchemist/use_cases/) in the documentation.
+
+---
+
+## Installation
+
+**Requirements:** Python 3.11 or higher
+
+**Recommended (Optional):** We recommend using [Anaconda](https://www.anaconda.com/products/distribution) to manage Python environments:
+
+```bash
+conda create -n alchemist-env python=3.11
+conda activate alchemist-env
+```
+
+**Basic Installation:**
+
+```bash
+pip install alchemist-nrel
+```
+
+**From GitHub:**
+> *Note: This installs the latest unreleased version. The web application is not pre-built with this method because static build files are not included in the repository.*
+
+```bash
+pip install git+https://github.com/NREL/ALchemist.git
+```
+
+For advanced installation options, Docker deployment, and development setup, see the [Advanced Installation Guide](https://nrel.github.io/ALchemist/#advanced-installation) in the documentation.
+
+---
+
+## Running ALchemist
+
+**Web Application:**
+```bash
+alchemist-web
+```
+Opens at [http://localhost:8000/app](http://localhost:8000/app)
+
+**Desktop Application:**
+```bash
+alchemist
+```
+
+For detailed usage instructions, see [Getting Started](https://nrel.github.io/ALchemist/) in the documentation.
+
+---
+
+## Development Status
+
+ALchemist is under active development at NLR as part of the DataHub project within the ChemCatBio consortium.
+
+---
+
+## Issues & Troubleshooting
+
+If you encounter any issues or have questions, please [open an issue on GitHub](https://github.com/NREL/ALchemist/issues) or contact ccoatney@nrel.gov.
+
+For the latest known issues and troubleshooting tips, see the [Issues & Troubleshooting Log](docs/ISSUES_LOG.md).
+
+We appreciate your feedback and bug reports to help improve ALchemist!
+
+---
+
+## License
+
+This project is licensed under the BSD 3-Clause License. See the [LICENSE](LICENSE) file for details.
+
+---
+
+## Repository
+
+[https://github.com/NREL/ALchemist](https://github.com/NREL/ALchemist)
+

alchemist_nrel-0.3.1/README.md

@@ -0,0 +1,126 @@
+<img src="docs/assets/NEW_LOGO_LIGHT.png" alt="ALchemist" width="50%" />
+
+**ALchemist: Active Learning Toolkit for Chemical and Materials Research**
+
+ALchemist is a modular Python toolkit that brings active learning and Bayesian optimization to experimental design in chemical and materials research. It is designed for scientists and engineers who want to efficiently explore or optimize high-dimensional variable spaces—using intuitive graphical interfaces, programmatic APIs, or autonomous optimization workflows.
+
+**NLR Software Record:** SWR-25-102
+
+---
+
+## Documentation
+
+Full user guide and documentation:  
+[https://nrel.github.io/ALchemist/](https://nrel.github.io/ALchemist/)
+
+---
+
+## Overview
+
+**Key Features:**
+
+- **Flexible variable space definition**: Real, integer, and categorical variables with bounds or discrete values
+- **Probabilistic surrogate modeling**: Gaussian process regression via BoTorch or scikit-learn 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
+- **Desktop GUI**: CustomTkinter desktop application for offline optimization
+- **Session management**: Save/load optimization sessions with audit logs for reproducibility
+- **Multiple interfaces**: No-code GUI, Python Session API, or REST API for different use cases
+- **Autonomous optimization**: Human-out-of-the-loop operation for real-time process control
+- **Experiment tracking**: CSV logging, reproducible random seeds, and comprehensive audit trails
+- **Extensibility**: Abstract interfaces for models and acquisition functions enable future backend and workflow expansion
+**Architecture:**
+
+ALchemist is built on a clean, modular architecture:
+
+- **Core Session API**: Headless Bayesian optimization engine (`alchemist_core`) that powers all interfaces
+- **Desktop Application**: CustomTkinter GUI using the Core Session API, designed for human-in-the-loop and offline optimization
+- **REST API**: FastAPI server providing a thin wrapper around the Core Session API for remote access
+- **Web Application**: React UI consuming the REST API, supporting both interactive and autonomous optimization workflows
+
+Session files (JSON format) are fully interoperable between desktop and web applications, enabling seamless workflow transitions.
+
+---
+
+## Use Cases
+
+- **Interactive Optimization**: Use desktop or web GUI for manual experiment design and human-in-the-loop optimization
+- **Programmatic Workflows**: Import the Session API in Python scripts or Jupyter notebooks for batch processing
+- **Autonomous Optimization**: Use the REST API to integrate ALchemist with automated laboratory equipment for real-time process control
+- **Remote Monitoring**: Web dashboard provides read-only monitoring mode when ALchemist is being remote-controlled
+
+For detailed application examples, see [Use Cases](https://nrel.github.io/ALchemist/use_cases/) in the documentation.
+
+---
+
+## Installation
+
+**Requirements:** Python 3.11 or higher
+
+**Recommended (Optional):** We recommend using [Anaconda](https://www.anaconda.com/products/distribution) to manage Python environments:
+
+```bash
+conda create -n alchemist-env python=3.11
+conda activate alchemist-env
+```
+
+**Basic Installation:**
+
+```bash
+pip install alchemist-nrel
+```
+
+**From GitHub:**
+> *Note: This installs the latest unreleased version. The web application is not pre-built with this method because static build files are not included in the repository.*
+
+```bash
+pip install git+https://github.com/NREL/ALchemist.git
+```
+
+For advanced installation options, Docker deployment, and development setup, see the [Advanced Installation Guide](https://nrel.github.io/ALchemist/#advanced-installation) in the documentation.
+
+---
+
+## Running ALchemist
+
+**Web Application:**
+```bash
+alchemist-web
+```
+Opens at [http://localhost:8000/app](http://localhost:8000/app)
+
+**Desktop Application:**
+```bash
+alchemist
+```
+
+For detailed usage instructions, see [Getting Started](https://nrel.github.io/ALchemist/) in the documentation.
+
+---
+
+## Development Status
+
+ALchemist is under active development at NLR as part of the DataHub project within the ChemCatBio consortium.
+
+---
+
+## Issues & Troubleshooting
+
+If you encounter any issues or have questions, please [open an issue on GitHub](https://github.com/NREL/ALchemist/issues) or contact ccoatney@nrel.gov.
+
+For the latest known issues and troubleshooting tips, see the [Issues & Troubleshooting Log](docs/ISSUES_LOG.md).
+
+We appreciate your feedback and bug reports to help improve ALchemist!
+
+---
+
+## License
+
+This project is licensed under the BSD 3-Clause License. See the [LICENSE](LICENSE) file for details.
+
+---
+
+## Repository
+
+[https://github.com/NREL/ALchemist](https://github.com/NREL/ALchemist)
+

alchemist_nrel-0.3.1/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-0.3.1/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>