mdmodels 0.2.4__tar.gz → 0.3.1__tar.gz

mdmodels-0.3.1/.github/scripts/start_ollama.sh

@@ -0,0 +1,16 @@
+#!/bin/bash
+
+# Start Ollama in the background.
+/bin/ollama serve &
+# Record Process ID.
+pid=$!
+
+# Pause for Ollama to start.
+sleep 5
+
+echo "🔴 Retrieve GEMMA2 model..."
+ollama pull gemma2:2b
+echo "🟢 Done!"
+
+# Wait for Ollama process to finish.
+wait $pid

mdmodels-0.3.1/.github/workflows/lint.yml

@@ -0,0 +1,24 @@
+name: Ruff
+
+on:
+  push:
+    paths:
+      - "mdmodels/**"
+      - "tests/**"
+      - "pyproject.toml"
+  pull_request:
+    paths:
+      - "mdmodels/**"
+      - "tests/**"
+      - "pyproject.toml"
+
+jobs:
+  ruff:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - uses: astral-sh/ruff-action@v2
+        with:
+          src: >-
+            mdmodels/
+            tests/

mdmodels-0.3.1/.github/workflows/publish.yml

@@ -0,0 +1,23 @@
+name: Build and publish
+
+on:
+  release:
+    types: [released]
+
+jobs:
+  deploy:
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v5
+
+      - name: Install uv
+        uses: astral-sh/setup-uv@v6
+
+      - name: Build and publish to PyPi
+        env:
+          UV_PUBLISH_TOKEN: ${{ secrets.PYPI_TOKEN }}
+        run: |
+          uv build
+          uv publish

mdmodels-0.3.1/.github/workflows/test-publish.yml

@@ -0,0 +1,25 @@
+name: Publish to TestPyPi
+
+on: workflow_dispatch
+
+jobs:
+  deploy:
+    runs-on: ubuntu-latest
+
+    steps:
+      - uses: actions/checkout@v2
+
+      - name: Set up Python
+        uses: actions/setup-python@v4
+        with:
+          python-version: "3.11"
+
+      - name: Install uv
+        uses: astral-sh/setup-uv@v6
+
+      - name: Publish Package
+        env:
+          UV_PUBLISH_TOKEN: ${{ secrets.TEST_PYPI_TOKEN }}
+        run: |
+          uv build
+          uv publish --index testpypi

mdmodels-0.3.1/.github/workflows/test.yml

@@ -0,0 +1,69 @@
+name: Library Tests
+
+on:
+  push:
+    paths:
+      - "mdmodels/**"
+      - "tests/**"
+      - "pyproject.toml"
+  pull_request:
+    paths:
+      - "mdmodels/**"
+      - "tests/**"
+      - "pyproject.toml"
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    strategy:
+      max-parallel: 4
+      matrix:
+        python-version: ["3.11", "3.12", "3.13"]
+    steps:
+      - name: "Checkout"
+        uses: "actions/checkout@v4"
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v4
+        with:
+          python-version: ${{ matrix.python-version }}
+      - name: Pull Ollama model
+        run: |
+          curl http://localhost:11434/api/pull -d '{
+            "model": "gemma2:2b"
+          }'
+
+      - name: Install uv
+        uses: astral-sh/setup-uv@v6
+      - name: Install dependencies
+        run: |
+          python3 -m pip install --upgrade pip
+          uv sync --all-extras --group dev --python ${{ matrix.python-version }}
+      - name: Wait for Neo4j service to be ready
+        run: |
+          until curl -s http://localhost:7474; do
+            echo "Waiting for Neo4j service to be ready..."
+            sleep 5
+          done
+      - name: Test with pytest
+        env:
+          NEO4J_USER: neo4j
+          NEO4J_PASSWORD: your_password
+          NEO4J_HOST: localhost
+          NEO4J_PORT: 7687
+          OLLAMA_HOST: "http://localhost:11434/v1"
+          OLLAMA_MODEL: "gemma2:2b"
+        run: |
+          uv run pytest -v
+
+    services:
+      neo4j:
+        image: neo4j:latest
+        ports:
+          - 7474:7474
+          - 7687:7687
+        env:
+          NEO4J_AUTH: neo4j/your_password
+      ollama:
+        image: ollama/ollama:latest
+        ports:
+          - 11434:11434

mdmodels-0.3.1/.gitignore

@@ -0,0 +1,172 @@
+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+*.so
+*.pyc
+
+# Distribution / packaging
+.Python
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+share/python-wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+MANIFEST
+
+# PyInstaller
+#  Usually these files are written by a python script from a template
+#  before PyInstaller builds the exe, so as to inject date/other infos into it.
+*.manifest
+*.spec
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.nox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+*.py,cover
+.hypothesis/
+.pytest_cache/
+cover/
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+db.sqlite3
+db.sqlite3-journal
+
+# Flask stuff:
+instance/
+.webassets-cache
+
+# Scrapy stuff:
+.scrapy
+
+# Sphinx documentation
+docs/_build/
+
+# PyBuilder
+.pybuilder/
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# IPython
+profile_default/
+ipython_config.py
+
+# pyenv
+#   For a data_model or package, you might want to ignore these files since the code is
+#   intended to run in multiple environments; otherwise, check them in:
+# .python-version
+
+# pipenv
+#   According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
+#   However, in case of collaboration, if having platform-specific dependencies or dependencies
+#   having no cross-platform support, pipenv may install dependencies that don't work, or not
+#   install all needed dependencies.
+#Pipfile.lock
+
+# poetry
+#   Similar to Pipfile.lock, it is generally recommended to include poetry.lock in version control.
+#   This is especially recommended for binary packages to ensure reproducibility, and is more
+#   commonly ignored for libraries.
+#   https://python-poetry.org/docs/basic-usage/#commit-your-poetrylock-file-to-version-control
+#poetry.lock
+
+# pdm
+#   Similar to Pipfile.lock, it is generally recommended to include pdm.lock in version control.
+#pdm.lock
+#   pdm stores project-wide configurations in .pdm.toml, but it is recommended to not include it
+#   in version control.
+#   https://pdm.fming.dev/latest/usage/project/#working-with-version-control
+.pdm.toml
+.pdm-python
+.pdm-build/
+
+# PEP 582; used by e.g. github.com/David-OConnor/pyflow and github.com/pdm-project/pdm
+__pypackages__/
+
+# Celery stuff
+celerybeat-schedule
+celerybeat.pid
+
+# SageMath parsed files
+*.sage.py
+
+# Environments
+.env
+.venv
+env/
+venv/
+ENV/
+env.bak/
+venv.bak/
+
+# Spyder project settings
+.spyderproject
+.spyproject
+
+# Rope project settings
+.ropeproject
+
+# mkdocs documentation
+/site
+
+# mypy
+.mypy_cache/
+.dmypy.json
+dmypy.json
+
+# Pyre type checker
+.pyre/
+
+# pytype static type analyzer
+.pytype/
+
+# Cython debug symbols
+cython_debug/
+
+# PyCharm
+#  JetBrains specific template is maintained in a separate JetBrains.gitignore that can
+#  be found at https://github.com/github/gitignore/blob/main/Global/JetBrains.gitignore
+#  and can be added to the global gitignore or merged into this file.  For a more nuclear
+#  option (not recommended) you can uncomment the following to ignore the entire idea folder.
+.idea/
+
+# MacOs
+.DS_Store
+**/.DS_Store
+
+.ruff_cache/
+.vscode/
+app.py
+poetry.lock

mdmodels-0.3.1/Dockerfile

@@ -0,0 +1,23 @@
+ARG PYTHON_VERSION=3.11
+FROM python:${PYTHON_VERSION}-slim
+
+ENV PYTHONDONTWRITEBYTECODE=1 \
+    PYTHONUNBUFFERED=1 \
+    PIP_NO_CACHE_DIR=1
+
+WORKDIR /app
+
+RUN apt-get update && \
+    apt-get install -y --no-install-recommends build-essential pkg-config && \
+    rm -rf /var/lib/apt/lists/*
+
+COPY pyproject.toml README.md /app/
+COPY mdmodels /app/mdmodels
+COPY tests /app/tests
+
+RUN python3 -m pip install --upgrade pip && \
+    python3 -m pip install uv && \
+    uv sync --all-extras --group dev --python ${PYTHON_VERSION}
+
+# Run tests by default.
+CMD ["uv", "run", "pytest", "-v", "-m", "not expensive"]

mdmodels-0.3.1/PKG-INFO

@@ -0,0 +1,162 @@
+Metadata-Version: 2.4
+Name: mdmodels
+Version: 0.3.1
+Summary: Python package for the MDModels Rust crate
+Author-email: Jan Range <range.jan@web.de>
+License-Expression: MIT
+Requires-Python: >=3.11
+Requires-Dist: astropy>=6.1.7
+Requires-Dist: bigtree<0.22,>=0.21.1
+Requires-Dist: dotenv>=0.9.9
+Requires-Dist: dotted-dict<2,>=1.1.3
+Requires-Dist: fastexcel>=0.19.0
+Requires-Dist: httpx<0.29,>=0.28
+Requires-Dist: mdmodels-core<0.3,>=0.2.9
+Requires-Dist: nest-asyncio<2,>=1.6.0
+Requires-Dist: pandas>=2.2.3
+Requires-Dist: polars>=1.39.3
+Requires-Dist: pydantic-xml<3,>=2.12.1
+Requires-Dist: python-forge<19,>=18.6.0
+Requires-Dist: python-jsonpath<2,>=1.2.0
+Requires-Dist: rich<14,>=13.9.4
+Requires-Dist: toml>=0.10.2
+Requires-Dist: typer>=0.20.0
+Requires-Dist: validators<0.35,>=0.34.0
+Provides-Extra: chat
+Requires-Dist: openai<2,>=1.57.0; extra == 'chat'
+Requires-Dist: tabulate<0.10,>=0.9.0; extra == 'chat'
+Provides-Extra: graph
+Requires-Dist: neomodel<6,>=5.4.0; extra == 'graph'
+Provides-Extra: graphql
+Requires-Dist: strawberry-graphql>=0.296.0; extra == 'graphql'
+Requires-Dist: uvicorn>=0.38.0; extra == 'graphql'
+Provides-Extra: mcp
+Requires-Dist: fastmcp[apps]>=3.2.0; extra == 'mcp'
+Requires-Dist: toon-format==0.9.0b1; extra == 'mcp'
+Provides-Extra: mysql
+Requires-Dist: pymysql>=1.1.2; extra == 'mysql'
+Requires-Dist: sqlmodel>=0.0.22; extra == 'mysql'
+Provides-Extra: pgvector
+Requires-Dist: fastembed>=0.7.3; extra == 'pgvector'
+Requires-Dist: pgvector>=0.4.1; extra == 'pgvector'
+Requires-Dist: psycopg2-binary>=2.9.11; extra == 'pgvector'
+Requires-Dist: sentence-transformers<3,>=2.2.2; extra == 'pgvector'
+Requires-Dist: sqlmodel<0.0.23,>=0.0.22; extra == 'pgvector'
+Provides-Extra: postgres
+Requires-Dist: psycopg2-binary>=2.9.11; extra == 'postgres'
+Requires-Dist: sqlmodel<0.0.23,>=0.0.22; extra == 'postgres'
+Provides-Extra: rest
+Requires-Dist: fastapi>=0.123.8; extra == 'rest'
+Requires-Dist: pyyaml>=6.0.3; extra == 'rest'
+Requires-Dist: uvicorn>=0.38.0; extra == 'rest'
+Provides-Extra: sqlserver
+Requires-Dist: pyodbc>=5.3.0; extra == 'sqlserver'
+Requires-Dist: sqlmodel>=0.0.22; extra == 'sqlserver'
+Description-Content-Type: text/markdown
+
+# Python MD-Models
+
+![Tests](https://github.com/FairCHemistry/py-mdmodels/actions/workflows/test.yml/badge.svg)
+![PyPI - Version](https://img.shields.io/pypi/v/mdmodels)
+![PyPI - Python Version](https://img.shields.io/pypi/pyversions/mdmodels)
+
+Build metadata-first Python apps from Markdown-defined models. `mdmodels` is the Python package for the [MDModels Rust crate](https://github.com/FairCHemistry/md-models), with batteries included for data modeling, AI workflows, SQL/graph backends, and API generation. 🚀
+
+## Why MD-Models?
+
+- 🧩 **Model once** in Markdown, then generate strongly typed Python models
+- 🤖 **Work with AI** for extraction, mapping, Q&A, and similarity search
+- 🗃️ **Persist and query** with SQL, vectors, and graph databases
+- 🌐 **Ship interfaces fast** via REST, GraphQL, and MCP helpers
+
+## What's in the bag? 🎒
+
+- 🧱 **Core model tooling** - Load, inspect, and work with metadata models
+- 🐍 **Pydantic generation** - Generate rich Python model classes from MD-Models
+- 🤖 **LLM workflows** - Extract, map, search, and answer questions over metadata
+- 🗄️ **SQL and vector search** - Build SQL-backed stores and pgvector-style embedding workflows
+- 🕸️ **Graph databases** - Build and query graph representations of your models
+- 🌐 **API generation** - Expose model-backed services through REST and GraphQL helpers
+- 🔌 **MCP integrations** - Create MCP-compatible interfaces for model and SQL workflows
+
+> **Note:** This package is actively evolving and APIs may change. Feedback and contributions are welcome. 🙌
+
+## Installation
+
+We recommend using `uv` for a fast, reproducible Python workflow.
+
+Install `uv` (if needed):
+
+```bash
+curl -LsSf https://astral.sh/uv/install.sh | sh
+```
+
+Install the base package:
+
+```bash
+uv pip install mdmodels
+```
+
+Install optional feature sets:
+
+```bash
+# LLM tools
+uv pip install "mdmodels[chat]"
+
+# Graph database tools
+uv pip install "mdmodels[graph]"
+
+# SQL backends
+uv pip install "mdmodels[postgres]"
+uv pip install "mdmodels[mysql]"
+uv pip install "mdmodels[sqlserver]"
+
+# Vector search (pgvector + embeddings)
+uv pip install "mdmodels[pgvector]"
+
+# API integrations
+uv pip install "mdmodels[rest]"
+uv pip install "mdmodels[graphql]"
+
+# MCP integration
+uv pip install "mdmodels[mcp]"
+```
+
+## Documentation 📚
+
+Guides, tutorials, and API usage:
+
+- [py-mdmodels.vercel.app](https://py-mdmodels.vercel.app/)
+
+## Development
+
+Run all tests:
+
+```bash
+uv run pytest
+```
+
+Run tests with coverage report:
+
+```bash
+uv run pytest --cov=mdmodels --cov-report=html
+```
+
+Run tests in Docker:
+
+```bash
+docker build --build-arg PYTHON_VERSION=3.12 -t mdmodels .
+docker run -v $(pwd):/app mdmodels
+```
+
+Use the helper script:
+
+```bash
+./run-tests.sh --python=3.12
+```
+
+Skip expensive tests:
+
+```bash
+uv run pytest -m "not expensive"
+```

mdmodels-0.3.1/README.md

@@ -0,0 +1,106 @@
+# Python MD-Models
+
+![Tests](https://github.com/FairCHemistry/py-mdmodels/actions/workflows/test.yml/badge.svg)
+![PyPI - Version](https://img.shields.io/pypi/v/mdmodels)
+![PyPI - Python Version](https://img.shields.io/pypi/pyversions/mdmodels)
+
+Build metadata-first Python apps from Markdown-defined models. `mdmodels` is the Python package for the [MDModels Rust crate](https://github.com/FairCHemistry/md-models), with batteries included for data modeling, AI workflows, SQL/graph backends, and API generation. 🚀
+
+## Why MD-Models?
+
+- 🧩 **Model once** in Markdown, then generate strongly typed Python models
+- 🤖 **Work with AI** for extraction, mapping, Q&A, and similarity search
+- 🗃️ **Persist and query** with SQL, vectors, and graph databases
+- 🌐 **Ship interfaces fast** via REST, GraphQL, and MCP helpers
+
+## What's in the bag? 🎒
+
+- 🧱 **Core model tooling** - Load, inspect, and work with metadata models
+- 🐍 **Pydantic generation** - Generate rich Python model classes from MD-Models
+- 🤖 **LLM workflows** - Extract, map, search, and answer questions over metadata
+- 🗄️ **SQL and vector search** - Build SQL-backed stores and pgvector-style embedding workflows
+- 🕸️ **Graph databases** - Build and query graph representations of your models
+- 🌐 **API generation** - Expose model-backed services through REST and GraphQL helpers
+- 🔌 **MCP integrations** - Create MCP-compatible interfaces for model and SQL workflows
+
+> **Note:** This package is actively evolving and APIs may change. Feedback and contributions are welcome. 🙌
+
+## Installation
+
+We recommend using `uv` for a fast, reproducible Python workflow.
+
+Install `uv` (if needed):
+
+```bash
+curl -LsSf https://astral.sh/uv/install.sh | sh
+```
+
+Install the base package:
+
+```bash
+uv pip install mdmodels
+```
+
+Install optional feature sets:
+
+```bash
+# LLM tools
+uv pip install "mdmodels[chat]"
+
+# Graph database tools
+uv pip install "mdmodels[graph]"
+
+# SQL backends
+uv pip install "mdmodels[postgres]"
+uv pip install "mdmodels[mysql]"
+uv pip install "mdmodels[sqlserver]"
+
+# Vector search (pgvector + embeddings)
+uv pip install "mdmodels[pgvector]"
+
+# API integrations
+uv pip install "mdmodels[rest]"
+uv pip install "mdmodels[graphql]"
+
+# MCP integration
+uv pip install "mdmodels[mcp]"
+```
+
+## Documentation 📚
+
+Guides, tutorials, and API usage:
+
+- [py-mdmodels.vercel.app](https://py-mdmodels.vercel.app/)
+
+## Development
+
+Run all tests:
+
+```bash
+uv run pytest
+```
+
+Run tests with coverage report:
+
+```bash
+uv run pytest --cov=mdmodels --cov-report=html
+```
+
+Run tests in Docker:
+
+```bash
+docker build --build-arg PYTHON_VERSION=3.12 -t mdmodels .
+docker run -v $(pwd):/app mdmodels
+```
+
+Use the helper script:
+
+```bash
+./run-tests.sh --python=3.12
+```
+
+Skip expensive tests:
+
+```bash
+uv run pytest -m "not expensive"
+```

mdmodels-0.3.1/docs/.gitignore

@@ -0,0 +1,21 @@
+# build output
+dist/
+# generated types
+.astro/
+
+# dependencies
+node_modules/
+
+# logs
+npm-debug.log*
+yarn-debug.log*
+yarn-error.log*
+pnpm-debug.log*
+
+
+# environment variables
+.env
+.env.production
+
+# macOS-specific files
+.DS_Store

mdmodels-0.3.1/docs/README.md

@@ -0,0 +1,49 @@
+# Starlight Starter Kit: Basics
+
+[![Built with Starlight](https://astro.badg.es/v2/built-with-starlight/tiny.svg)](https://starlight.astro.build)
+
+```
+npm create astro@latest -- --template starlight
+```
+
+> 🧑‍🚀 **Seasoned astronaut?** Delete this file. Have fun!
+
+## 🚀 Project Structure
+
+Inside of your Astro + Starlight project, you'll see the following folders and files:
+
+```
+.
+├── public/
+├── src/
+│   ├── assets/
+│   ├── content/
+│   │   └── docs/
+│   └── content.config.ts
+├── astro.config.mjs
+├── package.json
+└── tsconfig.json
+```
+
+Starlight looks for `.md` or `.mdx` files in the `src/content/docs/` directory. Each file is exposed as a route based on its file name.
+
+Images can be added to `src/assets/` and embedded in Markdown with a relative link.
+
+Static assets, like favicons, can be placed in the `public/` directory.
+
+## 🧞 Commands
+
+All commands are run from the root of the project, from a terminal:
+
+| Command                   | Action                                           |
+| :------------------------ | :----------------------------------------------- |
+| `npm install`             | Installs dependencies                            |
+| `npm run dev`             | Starts local dev server at `localhost:4321`      |
+| `npm run build`           | Build your production site to `./dist/`          |
+| `npm run preview`         | Preview your build locally, before deploying     |
+| `npm run astro ...`       | Run CLI commands like `astro add`, `astro check` |
+| `npm run astro -- --help` | Get help using the Astro CLI                     |
+
+## 👀 Want to learn more?
+
+Check out [Starlight’s docs](https://starlight.astro.build/), read [the Astro documentation](https://docs.astro.build), or jump into the [Astro Discord server](https://astro.build/chat).