mdmodels 0.1.0__tar.gz

mdmodels-0.1.0/PKG-INFO

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+Metadata-Version: 2.1
+Name: mdmodels
+Version: 0.1.0
+Summary: Python package for the MDModels Rust crate
+Author: Jan Range
+Author-email: range.jan@web.de
+Requires-Python: >=3.10,<4.0
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Programming Language :: Python :: 3.13
+Requires-Dist: astropy (>=6,<7)
+Requires-Dist: bigtree (>=0.21.1,<0.22.0)
+Requires-Dist: dotted-dict (>=1.1.3,<2.0.0)
+Requires-Dist: httpx (>=0.28,<0.29)
+Requires-Dist: mdmodels-core (>=0.1.7,<0.2.0)
+Requires-Dist: nest-asyncio (>=1.6.0,<2.0.0)
+Requires-Dist: pandas (>=2.2.3,<3.0.0)
+Requires-Dist: pydantic-xml (>=2.12.1,<3.0.0)
+Requires-Dist: python-forge (>=18.6.0,<19.0.0)
+Requires-Dist: python-jsonpath (>=1.2.0,<2.0.0)
+Requires-Dist: rich (>=13.9.4,<14.0.0)
+Requires-Dist: validators (>=0.34.0,<0.35.0)
+Description-Content-Type: text/markdown
+
+# pyMDModels
+
+This is the Python package for the MDModels Rust crate and hosts a set of tools to work with metadata models defined in markdown.
+
+**Whats in the bag?**
+
+- **Core** - The core functionality to work with MDModels
+- **PyDantic** - Generate Pydantic models (on steroids) from MDModels
+- **LLM tools** - Use LLMs to extract, transform and explore data
+- **SQL tools** - Create SQL databases and query them with SQLAlchemy
+- **Graph tools** - Create graph databases and query them with SPARQL
+
+One note before you start: This package is work in progress and the API will likely change in the future. Issues and contributions are very welcome!
+
+## Installation
+
+To install the package, you can use the following command:
+
+```bash
+pip install mdmodels
+
+# LLM tools
+pip install mdmodels[chat]
+
+# Graph tools
+pip install mdmodels[graph]
+
+# SQL tools
+pip install mdmodels[sql]
+
+# All tools
+pip install mdmodels[all]
+```
+
+## Examples
+
+To get you started, have a look at the [examples](./examples) folder, featuring notebooks that showcase the usage of the package. This is what is available right now:
+
+- [Core](./examples/basic)
+    - [Basic](./examples/basic) - Basic usage of the core functionality
+- [LLM tools](./examples/llm)
+    - [Question Answering](./examples/llm/answering) - Use LLMs to answer questions about the data
+    - [Metadata Extraction](./examples/llm/extraction) - Use LLMs to extract metadata from text and to databases
+    - [Metadata Mapping](./examples/llm/mapping) - Use LLMs to map metadata from one format to another
+    - [Similarity Search](./examples/llm/embedding) - Use LLMs to find similar items in a database
+- [SQL tools](./examples/sql)
+    - [Basic](./examples/sql/basic) - Create a SQL database and interact with it
+- [Graph tools](./examples/graph)
+    - [Basic](./examples/graph/basic) - Create a graph database and interact with it

mdmodels-0.1.0/README.md

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+# pyMDModels
+
+This is the Python package for the MDModels Rust crate and hosts a set of tools to work with metadata models defined in markdown.
+
+**Whats in the bag?**
+
+- **Core** - The core functionality to work with MDModels
+- **PyDantic** - Generate Pydantic models (on steroids) from MDModels
+- **LLM tools** - Use LLMs to extract, transform and explore data
+- **SQL tools** - Create SQL databases and query them with SQLAlchemy
+- **Graph tools** - Create graph databases and query them with SPARQL
+
+One note before you start: This package is work in progress and the API will likely change in the future. Issues and contributions are very welcome!
+
+## Installation
+
+To install the package, you can use the following command:
+
+```bash
+pip install mdmodels
+
+# LLM tools
+pip install mdmodels[chat]
+
+# Graph tools
+pip install mdmodels[graph]
+
+# SQL tools
+pip install mdmodels[sql]
+
+# All tools
+pip install mdmodels[all]
+```
+
+## Examples
+
+To get you started, have a look at the [examples](./examples) folder, featuring notebooks that showcase the usage of the package. This is what is available right now:
+
+- [Core](./examples/basic)
+    - [Basic](./examples/basic) - Basic usage of the core functionality
+- [LLM tools](./examples/llm)
+    - [Question Answering](./examples/llm/answering) - Use LLMs to answer questions about the data
+    - [Metadata Extraction](./examples/llm/extraction) - Use LLMs to extract metadata from text and to databases
+    - [Metadata Mapping](./examples/llm/mapping) - Use LLMs to map metadata from one format to another
+    - [Similarity Search](./examples/llm/embedding) - Use LLMs to find similar items in a database
+- [SQL tools](./examples/sql)
+    - [Basic](./examples/sql/basic) - Create a SQL database and interact with it
+- [Graph tools](./examples/graph)
+    - [Basic](./examples/graph/basic) - Create a graph database and interact with it

mdmodels-0.1.0/mdmodels/__init__.py

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+#  -----------------------------------------------------------------------------
+#   Copyright (c) 2024 Jan Range
+#
+#   Permission is hereby granted, free of charge, to any person obtaining a copy
+#   of this software and associated documentation files (the "Software"), to deal
+#   in the Software without restriction, including without limitation the rights
+#   to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+#   copies of the Software, and to permit persons to whom the Software is
+#   furnished to do so, subject to the following conditions:
+#  #
+#   The above copyright notice and this permission notice shall be included in
+#   all copies or substantial portions of the Software.
+#  #
+#   THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+#   IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+#   FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+#   AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+#   LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+#   OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+#   THE SOFTWARE.
+#  -----------------------------------------------------------------------------
+import nest_asyncio
+from mdmodels_core import Templates  # noqa
+
+from .datamodel import DataModel
+
+
+def patch_nest_asyncio():
+    nest_asyncio.apply()
+
+
+__all__ = [
+    "DataModel",
+    "Templates",
+]

mdmodels-0.1.0/mdmodels/adder_method.py

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+#  -----------------------------------------------------------------------------
+#   Copyright (c) 2024 Jan Range
+#
+#   Permission is hereby granted, free of charge, to any person obtaining a copy
+#   of this software and associated documentation files (the "Software"), to deal
+#   in the Software without restriction, including without limitation the rights
+#   to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+#   copies of the Software, and to permit persons to whom the Software is
+#   furnished to do so, subject to the following conditions:
+#  #
+#   The above copyright notice and this permission notice shall be included in
+#   all copies or substantial portions of the Software.
+#  #
+#   THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+#   IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+#   FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+#   AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+#   LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+#   OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+#   THE SOFTWARE.
+#  -----------------------------------------------------------------------------
+import builtins
+from typing import Union, get_origin, get_args, Annotated
+import warnings
+
+import forge
+
+from forge import FParameter, sign, FSignature
+
+from mdmodels import DataModel
+from mdmodels.units.unit_definition import UnitDefinition, BaseUnit
+from mdmodels.utils import extract_dtype
+
+
+def apply_adder_methods(cls: type[DataModel]):
+    """
+    Apply adder methods to the given DataModel class.
+
+    Args:
+        cls (type[DataModel]): The DataModel class to which adder methods will be applied.
+    """
+    for name, field in cls.model_fields.items():
+        if get_origin(field.annotation) is not list:
+            continue
+
+        method_name = f"add_to_{name}"
+        underlying_type = get_args(field.annotation)
+
+        if len(underlying_type) != 1 or get_origin(underlying_type[0]) is Union:
+            warnings.warn(
+                f"Only one type is supported for adder methods. {cls.__name__}.{name} has multiple types. Skipping.",
+            )
+            continue
+        else:
+            underlying_type = underlying_type[0]
+
+        if underlying_type in [UnitDefinition, BaseUnit] or is_builtin_type(
+            underlying_type
+        ):
+            continue
+
+        add_method = _create_add_method(underlying_type, name)
+        setattr(cls, method_name, add_method)
+
+
+def is_builtin_type(obj):
+    """
+    Check if the given object is a built-in type.
+
+    Args:
+        obj: The object to check.
+
+    Returns:
+        bool: True if the object is a built-in type, False otherwise.
+    """
+    return obj.__name__ in dir(builtins)
+
+
+def _create_add_method(
+    coll_cls: type[DataModel],
+    field: str,
+):
+    """
+    Create an adder method for the given collection class and field.
+
+    Args:
+        coll_cls (type[DataModel]): The collection class for which the adder method is created.
+        field (str): The field to which the adder method will be applied.
+
+    Returns:
+        function: The created adder method.
+    """
+
+    @sign(*_create_signature(coll_cls))
+    def add_method(self, **kwargs):
+        coll = getattr(self, field)
+        coll.append(coll_cls(**kwargs))
+        return coll[-1]
+
+    return add_method
+
+
+def _create_signature(coll_cls: type[DataModel]):
+    """
+    Create a signature for the adder method.
+
+    Args:
+        coll_cls (type[DataModel]): The collection class for which the signature is created.
+
+    Returns:
+        FSignature: The created signature.
+    """
+    if get_origin(coll_cls) is Annotated:
+        coll_cls = extract_dtype(coll_cls)
+
+    annotations = coll_cls.__annotations__
+    parameters = [
+        FParameter(
+            kind=FParameter.KEYWORD_ONLY,
+            name=name,
+            type=annotations[name],
+            default=None if get_origin(annotations[name]) is not list else [],
+        )
+        for name in annotations
+        if name != "return"
+    ]
+
+    return FSignature(
+        [forge.self] + parameters,
+    )