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Update all docstrings and exceptions to be used for documentation (neo4j#55)
* Update docstrings, exceptions * Update src/neo4j_genai/retrievers/external/weaviate/weaviate.py Co-authored-by: Oskar Hane <oh@oskarhane.com> * Update src/neo4j_genai/retrievers/external/weaviate/weaviate.py Co-authored-by: Oskar Hane <oh@oskarhane.com> * Fixed tests * Included check whether e.message attribute exists * Add external vector index support for Pinecone (neo4j#52) * Added pinecone-client to poetry * Copied weaviate populate_dbs.py to pinecone_e2e * Updated tests/e2e/pinecone_e2e/populate_dbs.py to work with Pinecone * Copied the Weaviate retriever to use as a base for the Pinecone retriever * Added first draft of PineconeNeo4jRetriever * Added input validation to PineconeNeo4jRetriever * Renamed PineconeModel to PineconeClientModel * Added Pinecone retriever unit tests * Added E2E tests for pinecone retriever * Updated pinecone retriever to work with new return types * Updated E2E tests to work with new types * Added __init__.py to E2E tests * Update src/neo4j_genai/retrievers/external/pinecone/pinecone.py Co-authored-by: willtai <william.tai@neo4j.com> * Updated Pinecone retriever with new Exceptions * Added Pinecone example scripts * Moved Pinecone Pydantic types to their own file * Ran import organizer on examples/weaviate/text_search_local_embedder.py * Added docs for PineconeNeo4jRetriever * Pinecone E2E test fix * Pinecone E2E test update * Pincone E2E test fix * Moved populate_neo4j to its own file * Moved populate_neo4j to utils * Updated PineconeNeo4jRetriever import in test_pinecone_e2e.py * Removed copyright from Pinecone and Weaviate examples * Refactored E2E test utils * Small fix to tests/e2e/utils.py * Ran poetry lock --no-update * Small formatting changes * More formatting changes * Moved embedding_biology.py to the examples folder * mypy fixes * Removed unused imports * More mypy fixes * More mypy fixes * Added .venv to .gitignore * Fixed mypy pytest conflict --------- Co-authored-by: willtai <william.tai@neo4j.com> * Update docs build * Ruff formatting * Exclude docs in mypy check * Docstring for format_record_function in retrievers * Updated Text2CypherRetrievalError --------- Co-authored-by: Oskar Hane <oh@oskarhane.com> Co-authored-by: Alex Thomas <alexthomas93@users.noreply.github.com>
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‎README.md

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the UI, and any other changes can be made in your fork and committed to the PR branch.
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- As you update your PR and apply changes, mark each conversation as [resolved](https://docs.github.com/en/github/collaborating-with-issues-and-pull-requests/commenting-on-a-pull-request#resolving-conversations).
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- Update the `CHANGELOG.md` if you have made significant changes to the project, these include:
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- Major changes:
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- New features
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- Bug fixes with high impact
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- Breaking changes
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- Minor changes:
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- Documentation improvements
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- Code refactoring without functional impact
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- Minor bug fixes
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- Major changes:
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- New features
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- Bug fixes with high impact
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- Breaking changes
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- Minor changes:
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- Documentation improvements
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- Code refactoring without functional impact
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- Minor bug fixes
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- Keep `CHANGELOG.md` changes brief and focus on the most important changes.
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### Updating the `CHANGELOG.md`

‎docs/source/_templates/gentree.html

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{%- extends "layout.html" %}
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{% set title = _('Tree') %}
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{% block body %}
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<h1>{{ _('Tree') }}</h1>
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{{ toctree(includehidden=True, collapse=False, maxdepth=-1) }}
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{% endblock %}

‎docs/source/_templates/indexnav.html

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<div id="indexlinkbox">
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<h3 id="indexlinklabel">{{ _('Index') }}</h3>
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<div class="indexlinkwrapper nav-menu">
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<ul>
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<li class="toctree-l1">
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<a href="{{ pathto('genindex')|e }}" class="indexlink genindex">
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{{ _('Alphabetical') }}
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</a>
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</li>
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<li class="toctree-l1">
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<a href="{{ pathto('gentree')|e }}" class="indexlink gentree">
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{{ _('Tree') }}
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</a>
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</li>
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</ul>
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</div>
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</div>

‎docs/source/api.rst

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* :class:`neo4j_genai.exceptions.Neo4jVersionError`
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* :class:`neo4j_genai.exceptions.Text2CypherRetrievalError`
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* :class:`neo4j_genai.exceptions.SchemaFetchError`
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Neo4jGenAiError
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===============
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.. autoclass:: neo4j_genai.exceptions.Neo4jVersionError
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:show-inheritance:
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Text2CypherRetrievalError
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==========================
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.. autoclass:: neo4j_genai.exceptions.Text2CypherRetrievalError
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:show-inheritance:
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SchemaFetchError
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================
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.. autoclass:: neo4j_genai.exceptions.SchemaFetchError
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:show-inheritance:

‎docs/source/conf.py

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html_theme = "neo4j"
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html_theme_path = ["themes"]
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# 01-nav.js is a copy of a js file of the same name that is included in the
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# docs-ui bundle
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def setup(app):
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app.add_js_file("https://neo4j.com/docs/assets/js/site.js", loading_method="defer")
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app.add_js_file("js/12-fragment-jumper.js", loading_method="defer")
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# Additional templates that should be rendered to pages, maps page names to
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# template names.
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html_additional_pages = {"gentree": "gentree.html"}
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# The name of the Pygments (syntax highlighting) style to use.
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# pygments_style = "sphinx"
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pygments_style = "friendly"

‎docs/source/themes/neo4j/layout.html

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<header class="header">
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<nav class="navbar">
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<div class="navbar-brand">
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<a class="navbar-item" href="/docs/source/themes/themes/neo4j/static">
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<a class="navbar-item" href="https://neo4j.com/">
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<img class="navbar-logo" src="https://dist.neo4j.com/wp-content/uploads/20210422142941/neo4j-logo-2020.svg" alt="Neo4j Logo">
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</a>
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<a href="{{ pathto(root_doc)|e }}" class="navbar-item no-left-padding" aria-label="{{ html_title }}">

‎pyproject.toml

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ignore_missing_imports = true
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allow_subclassing_any = true
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disallow_untyped_calls = false
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exclude = ["docs"]
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[[tool.mypy.overrides]]
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module = [

‎src/neo4j_genai/exceptions.py

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def __init__(self) -> None:
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super().__init__("This package only supports Neo4j version 5.18.1 or greater")
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class Text2CypherRetrievalError(Neo4jGenAiError):
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"""Exception raised when text-to-cypher retrieval fails."""
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pass
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class SchemaFetchError(Neo4jGenAiError):
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"""Exception raised when a Neo4jSchema cannot be fetched."""
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pass

‎src/neo4j_genai/retrievers/base.py

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def get_result_formatter(self) -> Callable[[neo4j.Record], RetrieverResultItem]:
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"""
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Returns the function to use to transform a neo4j.Record to aRetrieverResultItem.
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Returns the function to use to transform a neo4j.Record to a RetrieverResultItem.
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"""
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if hasattr(self, "format_record_function"):
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return self.format_record_function or self.default_format_record

‎src/neo4j_genai/retrievers/external/pinecone/pinecone.py

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class PineconeNeo4jRetriever(ExternalRetriever):
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"""
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Provides retrieval method using vector search over embeddings with a Pinecone database.
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If an embedder is provided, it needs to have the required Embedder type.
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Example:
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.. code-block:: python
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from neo4j import GraphDatabase
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from neo4j_genai import PineconeNeo4jRetriever
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from pinecone import Pinecone
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with GraphDatabase.driver(NEO4J_URL, auth=NEO4J_AUTH) as neo4j_driver:
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pc_client = Pinecone(PC_API_KEY)
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embedder = HuggingFaceEmbeddings(model_name="all-MiniLM-L6-v2")
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retriever = PineconeNeo4jRetriever(
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driver=neo4j_driver,
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client=pc_client,
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index_name="jeopardy",
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id_property_neo4j="id",
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embedder=embedder, # type: ignore
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)
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result = retriever.search(query_text="biology", top_k=2)
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Args:
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driver (neo4j.Driver): The Neo4j Python driver.
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client (Pinecone): The Pinecone client object.
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collection (str): Name of a set of Weaviate objects that share the same data structure.
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id_property_external (str): The name of the Weaviate property that has the identifier that refers to a corresponding Neo4j node id property.
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id_property_neo4j (str): The name of the Neo4j node property that's used as the identifier for relating matches from Weaviate to Neo4j nodes.
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embedder (Optional[Embedder]): Embedder object to embed query text.
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return_properties (Optional[list[str]]): List of node properties to return.
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format_record_function (Optional[Callable[[Any], Any]]): Function to transform a neo4j.Record to a RetrieverResultItem.
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Raises:
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RetrieverInitializationError: If validation of the input arguments fail.
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"""
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driver: neo4j.Driver,
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from neo4j_genai import PineconeNeo4jRetriever
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id_property_neo4j="id"
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)
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embedding = ...
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biology_embedding = ...
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retriever.search(query_vector=biology_embedding, top_k=2)
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