diff --git a/.github/workflows/pr-e2e-tests.yaml b/.github/workflows/pr-e2e-tests.yaml index bd50770d..18e8608c 100644 --- a/.github/workflows/pr-e2e-tests.yaml +++ b/.github/workflows/pr-e2e-tests.yaml @@ -49,8 +49,6 @@ jobs: - 6333:6333 steps: - - name: Install graphviz package - run: sudo apt install graphviz graphviz-dev - name: Check out repository code uses: actions/checkout@v4 - name: Docker Prune diff --git a/.github/workflows/pr.yaml b/.github/workflows/pr.yaml index 19c92be0..91fbea6a 100644 --- a/.github/workflows/pr.yaml +++ b/.github/workflows/pr.yaml @@ -8,8 +8,6 @@ jobs: matrix: python-version: [ '3.9', '3.10', '3.11', '3.12' ] steps: - - name: Install graphviz package - run: sudo apt install graphviz graphviz-dev - name: Check out repository code uses: actions/checkout@v4 - name: Set up Python ${{ matrix.python-version }} diff --git a/.github/workflows/scheduled-e2e-tests.yaml b/.github/workflows/scheduled-e2e-tests.yaml index 16b061ce..0d8822fc 100644 --- a/.github/workflows/scheduled-e2e-tests.yaml +++ b/.github/workflows/scheduled-e2e-tests.yaml @@ -57,8 +57,6 @@ jobs: - 6333:6333 steps: - - name: Install graphviz package - run: sudo apt install graphviz graphviz-dev - name: Check out repository code uses: actions/checkout@v4 - name: Docker Prune diff --git a/CHANGELOG.md b/CHANGELOG.md index 3aaf3660..b149f2d4 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -13,6 +13,9 @@ ### Changed - Improved log output readability in Retrievers and GraphRAG and added embedded vector to retriever result metadata for debugging. +- Switched from pygraphviz to neo4j-viz + - Renders interactive graph now on HTML instead of PNG + - Removed `get_pygraphviz_graph` method ### Fixed diff --git a/README.md b/README.md index 3c2634d9..60677256 100644 --- a/README.md +++ b/README.md @@ -59,7 +59,6 @@ the extra dependencies described below: - **pinecone**: store vectors in Pinecone - **qdrant**: store vectors in Qdrant - **experimental**: experimental features mainly related to the Knowledge Graph creation pipelines. - - Warning: this dependency group requires `pygraphviz`. See below for installation instructions. Install package with optional dependencies with (for instance): @@ -68,11 +67,6 @@ Install package with optional dependencies with (for instance): pip install "neo4j-graphrag[openai]" ``` -#### pygraphviz - -`pygraphviz` is used for visualizing pipelines. -Installation instructions can be found [here](https://pygraphviz.github.io/documentation/stable/install.html). - ## 💻 Example Usage The scripts below demonstrate how to get started with the package and make use of its key features. diff --git a/docs/source/index.rst b/docs/source/index.rst index 52fb68dd..d6700ef5 100644 --- a/docs/source/index.rst +++ b/docs/source/index.rst @@ -98,7 +98,6 @@ List of extra dependencies: - **pinecone**: store vectors in Pinecone - **qdrant**: store vectors in Qdrant - **experimental**: experimental features mainly from the Knowledge Graph creation pipelines. - - Warning: this requires `pygraphviz`. Installation instructions can be found `here `_. - nlp: - **spaCy**: load spaCy trained models for nlp pipelines, used by `SpaCySemanticMatchResolver` component from the Knowledge Graph creation pipelines. - fuzzy-matching: diff --git a/docs/source/user_guide_pipeline.rst b/docs/source/user_guide_pipeline.rst index 703e48ab..297db2a8 100644 --- a/docs/source/user_guide_pipeline.rst +++ b/docs/source/user_guide_pipeline.rst @@ -111,25 +111,26 @@ Pipelines can be visualized using the `draw` method: pipe = Pipeline() # ... define components and connections - pipe.draw("pipeline.png") + pipe.draw("pipeline.html") -Here is an example pipeline rendering: +Here is an example pipeline rendering as an interactive HTML visualization: -.. image:: images/pipeline_no_unused_outputs.png - :alt: Pipeline visualisation with hidden outputs if unused +.. code:: python + # To view the visualization in a browser + import webbrowser + webbrowser.open("pipeline.html") By default, output fields which are not mapped to any component are hidden. They -can be added to the canvas by setting `hide_unused_outputs` to `False`: +can be added to the visualization by setting `hide_unused_outputs` to `False`: .. code:: python - pipe.draw("pipeline.png", hide_unused_outputs=False) - -Here is an example of final result: - -.. image:: images/pipeline_full.png - :alt: Pipeline visualisation + pipe.draw("pipeline_full.html", hide_unused_outputs=False) + + # To view the full visualization in a browser + import webbrowser + webbrowser.open("pipeline_full.html") ************************ diff --git a/examples/customize/build_graph/pipeline/visualization.py b/examples/customize/build_graph/pipeline/visualization.py index 6445f780..b0add6c1 100644 --- a/examples/customize/build_graph/pipeline/visualization.py +++ b/examples/customize/build_graph/pipeline/visualization.py @@ -54,5 +54,5 @@ async def run(self, number: IntDataModel) -> IntDataModel: pipe.connect("times_two", "addition", {"a": "times_two.value"}) pipe.connect("times_ten", "addition", {"b": "times_ten.value"}) pipe.connect("addition", "save", {"number": "addition"}) - pipe.draw("graph.png") - pipe.draw("graph_full.png", hide_unused_outputs=False) + pipe.draw("graph.html") + pipe.draw("graph_full.html", hide_unused_outputs=False) diff --git a/poetry.lock b/poetry.lock index 7cdddabe..f7a66df5 100644 --- a/poetry.lock +++ b/poetry.lock @@ -1,4 +1,4 @@ -# This file is automatically @generated by Poetry 1.8.4 and should not be changed by hand. +# This file is automatically @generated by Poetry 1.8.2 and should not be changed by hand. 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width of unicode strings in a terminal" +optional = false +python-versions = "*" +files = [ + {file = "wcwidth-0.2.13-py2.py3-none-any.whl", hash = "sha256:3da69048e4540d84af32131829ff948f1e022c1c6bdb8d6102117aac784f6859"}, + {file = "wcwidth-0.2.13.tar.gz", hash = "sha256:72ea0c06399eb286d978fdedb6923a9eb47e1c486ce63e9b4e64fc18303972b5"}, +] + [[package]] name = "weasel" version = "0.4.1" @@ -6283,13 +6556,13 @@ wasabi = ">=0.9.1,<1.2.0" [[package]] name = "weaviate-client" -version = "4.11.1" +version = "4.12.0" description = "A python native Weaviate client" optional = true python-versions = ">=3.9" files = [ - {file = "weaviate_client-4.11.1-py3-none-any.whl", hash = "sha256:5fa117dd2f3fa18a3fe683ba80ac6936936eb8d03ff037e984f1e4ad0a50e7b9"}, - {file = "weaviate_client-4.11.1.tar.gz", hash = "sha256:1a2062cd76d7c7047c29efc3468ec9117223f321c424a685ec3ecf09f6421d61"}, + {file = "weaviate_client-4.12.0-py3-none-any.whl", hash = "sha256:72299b18edca40a97d44917ecf1a488949e71a82cab6e19e93d2408bcdcb1eea"}, + {file = "weaviate_client-4.12.0.tar.gz", hash = "sha256:4bbccecd87a17d612a52394825fea696569def2faf37d1e268b4a23c4f91748a"}, ] [package.dependencies] @@ -6634,10 +6907,10 @@ cffi = ["cffi (>=1.11)"] anthropic = ["anthropic"] cohere = ["cohere"] examples = [] -experimental = ["langchain-text-splitters", "llama-index", "pygraphviz", "pygraphviz"] +experimental = ["langchain-text-splitters", "llama-index", "neo4j-viz"] fuzzy-matching = ["rapidfuzz"] google = ["google-cloud-aiplatform"] -kg-creation-tools = ["pygraphviz", "pygraphviz"] +kg-creation-tools = ["neo4j-viz"] mistralai = ["mistralai"] nlp = ["spacy"] ollama = ["ollama"] @@ -6650,4 +6923,4 @@ weaviate = ["weaviate-client"] [metadata] lock-version = "2.0" python-versions = ">=3.9.0,<3.13" -content-hash = "db268ee432426e9d8609ebacdf59ed9546fc9135d8dcd6a4b2eff6df89f2ef00" +content-hash = "4f373456b1c2ff708850be549f8629cd27502fabc4d5ba3f8fdc2cd5ddc7919e" diff --git a/pyproject.toml b/pyproject.toml index 563bdadc..a3eb90c3 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -38,10 +38,7 @@ pyyaml = "^6.0.2" types-pyyaml = "^6.0.12.20240917" # optional deps langchain-text-splitters = {version = "^0.3.0", optional = true } -pygraphviz = [ - {version = "^1.13.0", python = ">=3.10,<4.0.0", optional = true}, - {version = "^1.0.0", python = "<3.10", optional = true} -] +neo4j-viz = {version = "^0.2.2", optional = true } weaviate-client = {version = "^4.6.1", optional = true } pinecone-client = {version = "^4.1.0", optional = true } google-cloud-aiplatform = {version = "^1.66.0", optional = true } @@ -68,6 +65,7 @@ sphinx = { version = "^7.2.6", python = "^3.9" } langchain-openai = {version = "^0.2.2", optional = true } langchain-huggingface = {version = "^0.1.0", optional = true } enum-tools = {extras = ["sphinx"], version = "^0.12.0"} +neo4j-viz = "^0.2.2" [tool.poetry.extras] weaviate = ["weaviate-client"] @@ -79,9 +77,9 @@ ollama = ["ollama"] openai = ["openai"] mistralai = ["mistralai"] qdrant = ["qdrant-client"] -kg_creation_tools = ["pygraphviz"] +kg_creation_tools = ["neo4j-viz"] sentence-transformers = ["sentence-transformers"] -experimental = ["langchain-text-splitters", "pygraphviz", "llama-index"] +experimental = ["langchain-text-splitters", "neo4j-viz", "llama-index"] examples = ["langchain-openai", "langchain-huggingface"] nlp = ["spacy"] fuzzy-matching = ["rapidfuzz"] diff --git a/src/neo4j_graphrag/experimental/pipeline/neo4j_viz.pyi b/src/neo4j_graphrag/experimental/pipeline/neo4j_viz.pyi new file mode 100644 index 00000000..1bfb8415 --- /dev/null +++ b/src/neo4j_graphrag/experimental/pipeline/neo4j_viz.pyi @@ -0,0 +1,54 @@ +# Copyright (c) "Neo4j" +# Neo4j Sweden AB [https://neo4j.com] +# # +# Licensed under the Apache License, Version 2.0 (the "License"); +# you may not use this file except in compliance with the License. +# You may obtain a copy of the License at +# # +# https://www.apache.org/licenses/LICENSE-2.0 +# # +# Unless required by applicable law or agreed to in writing, software +# distributed under the License is distributed on an "AS IS" BASIS, +# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +# See the License for the specific language governing permissions and +# limitations under the License. + +from typing import Any, Dict, List, Optional, Union + +class Node: + id: Union[str, int] + caption: Optional[str] = None + size: Optional[float] = None + properties: Optional[Dict[str, Any]] = None + + def __init__( + self, + id: Union[str, int], + caption: Optional[str] = None, + size: Optional[float] = None, + properties: Optional[Dict[str, Any]] = None, + **kwargs: Any, + ) -> None: ... + +class Relationship: + source: Union[str, int] + target: Union[str, int] + caption: Optional[str] = None + properties: Optional[Dict[str, Any]] = None + + def __init__( + self, + source: Union[str, int], + target: Union[str, int], + caption: Optional[str] = None, + properties: Optional[Dict[str, Any]] = None, + **kwargs: Any, + ) -> None: ... + +class VisualizationGraph: + nodes: List[Node] + relationships: List[Relationship] + + def __init__( + self, nodes: List[Node], relationships: List[Relationship] + ) -> None: ... diff --git a/src/neo4j_graphrag/experimental/pipeline/pipeline.py b/src/neo4j_graphrag/experimental/pipeline/pipeline.py index 4d12d8d8..91dab34e 100644 --- a/src/neo4j_graphrag/experimental/pipeline/pipeline.py +++ b/src/neo4j_graphrag/experimental/pipeline/pipeline.py @@ -24,9 +24,11 @@ from neo4j_graphrag.utils.logging import prettify try: - import pygraphviz as pgv + from neo4j_viz import Node, Relationship, VisualizationGraph + + neo4j_viz_available = True except ImportError: - pgv = None + neo4j_viz_available = False from pydantic import BaseModel @@ -198,53 +200,126 @@ def show_as_dict(self) -> dict[str, Any]: def draw( self, path: str, layout: str = "dot", hide_unused_outputs: bool = True ) -> Any: - G = self.get_pygraphviz_graph(hide_unused_outputs) - G.layout(layout) - G.draw(path) + """Render the pipeline graph to an HTML file at the specified path""" + G = self._get_neo4j_viz_graph(hide_unused_outputs) + + # Write the visualization to an HTML file + with open(path, "w") as f: + f.write(G.render().data) + + return G - def get_pygraphviz_graph(self, hide_unused_outputs: bool = True) -> pgv.AGraph: - if pgv is None: + def _get_neo4j_viz_graph( + self, hide_unused_outputs: bool = True + ) -> VisualizationGraph: + """Generate a neo4j-viz visualization of the pipeline graph""" + if not neo4j_viz_available: raise ImportError( - "Could not import pygraphviz. " - "Follow installation instruction in pygraphviz documentation " - "to get it up and running on your system." + "Could not import neo4j-viz. Install it with 'pip install \"neo4j-graphrag[experimental]\"'" ) + self.validate_parameter_mapping() - G = pgv.AGraph(strict=False, directed=True) - # create a node for each component - for n, node in self._nodes.items(): - comp_inputs = ",".join( + + nodes = [] + relationships = [] + node_ids = {} # Map node names to their numeric IDs + next_id = 0 + + # Create nodes for each component + for n, pipeline_node in self._nodes.items(): + comp_inputs = ", ".join( f"{i}: {d['annotation']}" - for i, d in node.component.component_inputs.items() + for i, d in pipeline_node.component.component_inputs.items() ) - G.add_node( - n, - node_type="component", - shape="rectangle", - label=f"{node.component.__class__.__name__}: {n}({comp_inputs})", + + node_ids[n] = next_id + label = f"{pipeline_node.component.__class__.__name__}: {n}({comp_inputs})" + + # Create Node with properties parameter + viz_node = Node( # type: ignore + id=next_id, + caption=label, + size=20, + properties={"node_type": "component"}, ) - # create a node for each output field and connect them it to its component - for o in node.component.component_outputs: + nodes.append(viz_node) + next_id += 1 + + # Create nodes for each output field + for o in pipeline_node.component.component_outputs: param_node_name = f"{n}.{o}" - G.add_node(param_node_name, label=o, node_type="output") - G.add_edge(n, param_node_name) - # then we create the edges between a component output - # and the component it gets added to + + # Skip if we're hiding unused outputs and it's not used + if hide_unused_outputs: + # Check if this output is used as a source in any parameter mapping + is_used = False + for params in self.param_mapping.values(): + for mapping in params.values(): + source_component = mapping["component"] + source_param_name = mapping.get("param") + if source_component == n and source_param_name == o: + is_used = True + break + if is_used: + break + + if not is_used: + continue + + node_ids[param_node_name] = next_id + # Create Node with properties parameter + output_node = Node( # type: ignore + id=next_id, + caption=o, + size=15, + properties={"node_type": "output"}, + ) + nodes.append(output_node) + + # Connect component to its output + # Connect component to its output + rel = Relationship( # type: ignore + source=node_ids[n], + target=node_ids[param_node_name], + properties={"type": "HAS_OUTPUT"}, + ) + relationships.append(rel) + next_id += 1 + + # Create edges between components based on parameter mapping for component_name, params in self.param_mapping.items(): for param, mapping in params.items(): source_component = mapping["component"] source_param_name = mapping.get("param") + if source_param_name: source_output_node = f"{source_component}.{source_param_name}" else: source_output_node = source_component - G.add_edge(source_output_node, component_name, label=param) - # remove outputs that are not mapped - if hide_unused_outputs: - for n in G.nodes(): - if n.attr["node_type"] == "output" and G.out_degree(n) == 0: # type: ignore - G.remove_node(n) - return G + + if source_output_node in node_ids and component_name in node_ids: + rel = Relationship( # type: ignore + source=node_ids[source_output_node], + target=node_ids[component_name], + caption=param, + properties={"type": "CONNECTS_TO"}, + ) + relationships.append(rel) + + # Create the visualization graph + viz_graph = VisualizationGraph(nodes=nodes, relationships=relationships) + return viz_graph + + def get_pygraphviz_graph(self, hide_unused_outputs: bool = True) -> Any: + """Legacy method for backward compatibility. + Uses neo4j-viz instead of pygraphviz. + """ + warnings.warn( + "get_pygraphviz_graph is deprecated, use draw instead", + DeprecationWarning, + stacklevel=2, + ) + return self._get_neo4j_viz_graph(hide_unused_outputs) def add_component(self, component: Component, name: str) -> None: """Add a new component. Components are uniquely identified diff --git a/tests/unit/experimental/pipeline/test_pipeline.py b/tests/unit/experimental/pipeline/test_pipeline.py index 868aaae8..d37fc65f 100644 --- a/tests/unit/experimental/pipeline/test_pipeline.py +++ b/tests/unit/experimental/pipeline/test_pipeline.py @@ -380,39 +380,39 @@ async def test_pipeline_async() -> None: assert pipeline_result[1].result == {"add": {"result": 12}} -def test_pipeline_to_pgv() -> None: +def test_pipeline_to_viz() -> None: pipe = Pipeline() component_a = ComponentAdd() component_b = ComponentMultiply() pipe.add_component(component_a, "a") pipe.add_component(component_b, "b") pipe.connect("a", "b", {"number1": "a.result"}) - g = pipe.get_pygraphviz_graph() + g = pipe._get_neo4j_viz_graph() # 3 nodes: # - 2 components 'a' and 'b' # - 1 output 'a.result' - assert len(g.nodes()) == 3 - g = pipe.get_pygraphviz_graph(hide_unused_outputs=False) + assert len(g.nodes) == 3 + g = pipe._get_neo4j_viz_graph(hide_unused_outputs=False) # 4 nodes: # - 2 components 'a' and 'b' # - 2 output 'a.result' and 'b.result' - assert len(g.nodes()) == 4 + assert len(g.nodes) == 4 def test_pipeline_draw() -> None: pipe = Pipeline() pipe.add_component(ComponentAdd(), "add") - t = tempfile.NamedTemporaryFile() + t = tempfile.NamedTemporaryFile(suffix=".html") pipe.draw(t.name) content = t.file.read() assert len(content) > 0 -@patch("neo4j_graphrag.experimental.pipeline.pipeline.pgv", None) -def test_pipeline_draw_missing_pygraphviz_dep() -> None: +@patch("neo4j_graphrag.experimental.pipeline.pipeline.neo4j_viz_available", False) +def test_pipeline_draw_missing_neo4j_viz_dep() -> None: pipe = Pipeline() pipe.add_component(ComponentAdd(), "add") - t = tempfile.NamedTemporaryFile() + t = tempfile.NamedTemporaryFile(suffix=".html") with pytest.raises(ImportError): pipe.draw(t.name)