From dd46f0353ae74e1675ff973ac815b369d02e1c07 Mon Sep 17 00:00:00 2001
From: jamin9902 <48889500+jamin9902@users.noreply.github.com>
Date: Sat, 16 Aug 2025 12:11:34 -0700
Subject: [PATCH 1/2] Documentation update and initial simulation manager

---
 docs/core-modules/client.md                   |  8 ++--
 docs/core-modules/graph.md                    | 12 +++---
 docs/core-modules/index.md                    | 43 +++++++++++++++++++
 docs/core-modules/node.md                     |  7 +++
 docs/core-modules/projects.md                 |  6 +--
 docs/core-modules/run.md                      | 10 ++---
 fluidize/core/modules/run/node/node_runner.py | 14 ++++++
 .../core/types/file_models/file_model_base.py |  4 +-
 fluidize/managers/node.py                     | 14 +++---
 fluidize/managers/simulations.py              | 29 +++++++++++++
 mkdocs.yml                                    |  2 +
 11 files changed, 117 insertions(+), 32 deletions(-)
 create mode 100644 docs/core-modules/index.md
 create mode 100644 docs/core-modules/node.md
 create mode 100644 fluidize/managers/simulations.py

diff --git a/docs/core-modules/client.md b/docs/core-modules/client.md
index 2c9bf16..b4411ae 100644
--- a/docs/core-modules/client.md
+++ b/docs/core-modules/client.md
@@ -1,4 +1,4 @@
-# Fluidize Client
+# Client Module
 
 The Fluidize Client is the primary interface to create and edit projects. There are two interfaces for this, with more on the way.
 
@@ -10,8 +10,7 @@ The Fluidize Client is the primary interface to create and edit projects. There
     options:
       show_source: false
       heading_level: 3
-      extra:
-        show_root_heading: true
+      show_root_heading: true
       members:
         - mode
         - adapters
@@ -22,8 +21,7 @@ The Fluidize Client is the primary interface to create and edit projects. There
     options:
       show_source: false
       heading_level: 3
-      extra:
-        show_root_heading: true
+      show_root_heading: true
       members:
         - is_local_mode
         - is_api_mode
diff --git a/docs/core-modules/graph.md b/docs/core-modules/graph.md
index a7d26d0..0919c44 100644
--- a/docs/core-modules/graph.md
+++ b/docs/core-modules/graph.md
@@ -5,8 +5,7 @@
     options:
       show_source: false
       heading_level: 3
-      extra:
-        show_root_heading: true
+      show_root_heading: true
       members:
         - get
         - add_node
@@ -20,30 +19,29 @@
     options:
       show_source: false
       heading_level: 3
-      extra:
-        show_root_heading: true
+      show_root_heading: true
 
 ## Graph Types
 
 ::: fluidize.core.types.graph.GraphData
     options:
       heading_level: 3
+      show_root_heading: true
       extra:
         show_attributes: true
-        show_root_heading: true
 
 
 ::: fluidize.core.types.graph.GraphNode
     options:
       heading_level: 3
+      show_root_heading: true
       extra:
         show_attributes: true
-        show_root_heading: true
 
 
 ::: fluidize.core.types.graph.GraphEdge
     options:
       heading_level: 3
+      show_root_heading: true
       extra:
         show_attributes: true
-        show_root_heading: true
diff --git a/docs/core-modules/index.md b/docs/core-modules/index.md
new file mode 100644
index 0000000..f75ba97
--- /dev/null
+++ b/docs/core-modules/index.md
@@ -0,0 +1,43 @@
+# Core Modules
+
+The Fluidize library is composed of a set of core modules that provide a high-level interface for managing Fluidize resources. These modules are designed to be used together to build and execute scientific computing pipelines.
+
+## [Client](client.md)
+
+The **Fluidize Client** provides a unified, high-level interface for managing Fluidize resources in both local and cloud API modes. It serves as the primary entry point for creating and running pipelines across these environments.
+
+## [Projects](projects.md)
+
+The **Projects** module provides tools for managing project lifecycles:
+
+- [**Registry Manager**](projects.md#fluidize.managers.registry.RegistryManager):
+  Handles the user’s complete project registry, with functionality to create, edit, and delete projects.
+
+- [**Project Manager**](projects.md#fluidize.managers.project.ProjectManager):
+  Focuses on individual projects, managing the project graph, nodes, and runs, and supporting execution of project-specific workflows.
+
+## [Graph](graph.md)
+
+The **Graph** module provides tools for managing the project graph, which is a representation of the simulation pipeline.
+
+In a Fluidize project, pipelines are represented as a directed acyclic graph (DAG) where each node represents a module simulation and each edge represents the flow of data between nodes:
+
+- [**Graph Manager**](graph.md#fluidize.managers.graph.GraphManager):
+  Manages the project graph, and provides high level functionality to create, edit, and delete nodes and edges.
+
+- [**Graph Processor**](graph.md#fluidize.managers.graph.graph_processor.GraphProcessor):
+  Manages specific operations on the graph data structure within the local filesystem.
+
+## [Node](node.md)
+
+The **Node** module provides tools for managing the metadata, properties, and parameters of individual nodes within a project.
+
+## [Run](run.md)
+
+The **Run** module provides tools for managing simulation pipeline runs within a project:
+
+- [**Runs Manager**](run.md#fluidize.managers.run.RunsManager):
+  Manages the high level execution of runs and retrieving run status.
+
+- [**Project Runner**](run.md#fluidize.core.modules.run.project.ProjectRunner):
+  Manages the specific execution details of a project pipeline, including environment preparation and node execution order.
diff --git a/docs/core-modules/node.md b/docs/core-modules/node.md
new file mode 100644
index 0000000..88d11a1
--- /dev/null
+++ b/docs/core-modules/node.md
@@ -0,0 +1,7 @@
+# Node Module
+
+::: fluidize.managers.node.NodeManager
+    options:
+      show_source: false
+      heading_level: 3
+      show_root_heading: true
diff --git a/docs/core-modules/projects.md b/docs/core-modules/projects.md
index e51384c..6e8c8ff 100644
--- a/docs/core-modules/projects.md
+++ b/docs/core-modules/projects.md
@@ -5,13 +5,11 @@
     options:
       show_source: false
       heading_level: 3
-      extra:
-        show_root_heading: true
+      show_root_heading: true
 
 ## Project
 ::: fluidize.managers.project.ProjectManager
     options:
       show_source: false
       heading_level: 3
-      extra:
-        show_root_heading: true
+      show_root_heading: true
diff --git a/docs/core-modules/run.md b/docs/core-modules/run.md
index c21122f..dc6be19 100644
--- a/docs/core-modules/run.md
+++ b/docs/core-modules/run.md
@@ -6,8 +6,7 @@
     options:
       show_source: false
       heading_level: 3
-      extra:
-        show_root_heading: true
+      show_root_heading: true
       members:
         - run_flow
         - list
@@ -19,12 +18,11 @@
     options:
       show_source: false
       heading_level: 3
-      extra:
-        show_root_heading: true
+      show_signature: false
+      show_root_heading: true
 
 ::: fluidize.core.modules.run.project.ProjectRunner
     options:
       show_source: false
       heading_level: 3
-      extra:
-        show_root_heading: true
+      show_root_heading: true
diff --git a/fluidize/core/modules/run/node/node_runner.py b/fluidize/core/modules/run/node/node_runner.py
index a35668e..2684371 100644
--- a/fluidize/core/modules/run/node/node_runner.py
+++ b/fluidize/core/modules/run/node/node_runner.py
@@ -8,6 +8,10 @@
 
 # RunJob now uses a strategy instance to dynamically choose behavior.
 class RunJob:
+    """
+    A job that runs for a single node.
+    """
+
     def __init__(
         self,
         project: ProjectSummary,
@@ -18,6 +22,16 @@ def __init__(
         run_id: Optional[str] = None,
         run_metadata: Optional[object] = None,  # Add run metadata
     ):
+        """
+        Args:
+            project: The project this node belongs to
+            strategyClass: The strategy class to use for execution
+            nodeProperties_simulation: The node properties to run
+            prev_nodeProperties_simulation: The previous node properties (optional)
+            mlflow_tracker: The MLflow tracker (optional)
+            run_id: The run ID (optional)
+            run_metadata: The run metadata (optional)
+        """
         self.project = project
         self.nodeProperties_simulation = nodeProperties_simulation
         self.prev_nodeProperties_simulation = prev_nodeProperties_simulation
diff --git a/fluidize/core/types/file_models/file_model_base.py b/fluidize/core/types/file_models/file_model_base.py
index 3dc25f1..f037ad7 100644
--- a/fluidize/core/types/file_models/file_model_base.py
+++ b/fluidize/core/types/file_models/file_model_base.py
@@ -1,6 +1,6 @@
 from __future__ import annotations
 
-from typing import Any, TypeVar, Union
+from typing import Any, Optional, TypeVar, Union
 
 from pydantic import BaseModel, ConfigDict, PrivateAttr, ValidationError
 from upath import UPath
@@ -49,7 +49,7 @@ def from_file(cls: type[T], directory: Union[str, UPath]) -> T:
             return instance
 
     @classmethod
-    def from_dict_and_path(cls: type[T], data: dict, path: UPath) -> T:
+    def from_dict_and_path(cls: type[T], data: Any, path: Optional[UPath]) -> T:
         """Creates a model instance from a dictionary and a path, without reading the file again."""
         if not data:
             raise ValueError()
diff --git a/fluidize/managers/node.py b/fluidize/managers/node.py
index cef596e..41619d5 100644
--- a/fluidize/managers/node.py
+++ b/fluidize/managers/node.py
@@ -24,8 +24,6 @@ class NodeManager:
 
     def __init__(self, adapter: Any, project: ProjectSummary, node_id: str) -> None:
         """
-        Initialize node-scoped manager.
-
         Args:
             adapter: adapter adapter (FluidizeSDK or Localadapter)
             project: The project this node belongs to
@@ -268,13 +266,13 @@ def update_parameter(self, parameter: Parameter) -> Parameter:
 
     def set_parameters(self, parameters: list[Parameter]) -> list[Parameter]:
         """
-                Replace all parameters with the provided list.
+        Replace all parameters with the provided list.
+
+        Args:
+            parameters: List of parameters to set
 
-                Args:
-                    parameters: List of parameters to set
-        W
-                Returns:
-                    The list of parameters that were set
+        Returns:
+            The list of parameters that were set
         """
         parameters_model = self.get_parameters_model()
         parameters_model.parameters = parameters
diff --git a/fluidize/managers/simulations.py b/fluidize/managers/simulations.py
new file mode 100644
index 0000000..3c05141
--- /dev/null
+++ b/fluidize/managers/simulations.py
@@ -0,0 +1,29 @@
+from typing import Any
+
+from fluidize_sdk import FluidizeSDK
+
+from fluidize.core.types.node import nodeMetadata_simulation
+
+
+class SimulationsManager:
+    """
+    Simulations manager that provides access to the Fluidize simulation library.
+    """
+
+    def __init__(self, adapter: Any) -> None:
+        """
+        Args:
+            adapter: adapter (FluidizeSDK or LocalAdapter)
+        """
+        self._adapter = adapter
+        self.fluidize_sdk = FluidizeSDK()
+
+    def list_simulations(self) -> list[Any]:
+        """
+        List all simulations available in the Fluidize simulation library.
+
+        Returns:
+            List of simulation metadata
+        """
+        simulations = self.fluidize_sdk.graph.list_simulations(sim_global=True)
+        return [nodeMetadata_simulation.from_dict_and_path(data=simulation, path=None) for simulation in simulations]
diff --git a/mkdocs.yml b/mkdocs.yml
index ba159d6..b561f73 100644
--- a/mkdocs.yml
+++ b/mkdocs.yml
@@ -13,9 +13,11 @@ nav:
       - Quickstart: getting-started/quickstart.md
       - Examples: getting-started/examples.md
   - Core Modules:
+      - core-modules/index.md
       - Client: core-modules/client.md
       - Projects: core-modules/projects.md
       - Graph: core-modules/graph.md
+      - Node: core-modules/node.md
       - Run: core-modules/run.md
 plugins:
   - search

From a5146358e62f20a000c897f3c6d34473272e2497 Mon Sep 17 00:00:00 2001
From: jamin9902 <48889500+jamin9902@users.noreply.github.com>
Date: Sat, 16 Aug 2025 16:50:51 -0700
Subject: [PATCH 2/2] Working simulation manager and testing

---
 fluidize/managers/simulations.py              | 10 ++-
 pyproject.toml                                |  2 +-
 tests/integration/test_simulations_manager.py | 40 +++++++++
 tests/unit/managers/test_simulation.py        | 87 +++++++++++++++++++
 uv.lock                                       |  8 +-
 5 files changed, 139 insertions(+), 8 deletions(-)
 create mode 100644 tests/integration/test_simulations_manager.py
 create mode 100644 tests/unit/managers/test_simulation.py

diff --git a/fluidize/managers/simulations.py b/fluidize/managers/simulations.py
index 3c05141..e6f3ed5 100644
--- a/fluidize/managers/simulations.py
+++ b/fluidize/managers/simulations.py
@@ -16,7 +16,8 @@ def __init__(self, adapter: Any) -> None:
             adapter: adapter (FluidizeSDK or LocalAdapter)
         """
         self._adapter = adapter
-        self.fluidize_sdk = FluidizeSDK()
+        # TODO: Fix hardcoding of api_token and remove type ignore
+        self.fluidize_sdk = FluidizeSDK(api_token="placeholder")  # noqa: S106
 
     def list_simulations(self) -> list[Any]:
         """
@@ -25,5 +26,8 @@ def list_simulations(self) -> list[Any]:
         Returns:
             List of simulation metadata
         """
-        simulations = self.fluidize_sdk.graph.list_simulations(sim_global=True)
-        return [nodeMetadata_simulation.from_dict_and_path(data=simulation, path=None) for simulation in simulations]
+        simulations = self.fluidize_sdk.simulation.list_simulations(sim_global=True)
+        return [
+            nodeMetadata_simulation.from_dict_and_path(data=simulation.model_dump(), path=None)
+            for simulation in simulations
+        ]
diff --git a/pyproject.toml b/pyproject.toml
index f6b43ce..f0844da 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -20,7 +20,7 @@ classifiers = [
 dependencies = [
     "asciitree>=0.3.3",
     "docker>=7.1.0",
-    "fluidize-sdk>=0.4.0",
+    "fluidize-sdk>=0.6.0",
     "jinja2>=3.1.6",
     "mlflow>=3.1.4",
     "networkx>=3.2.1",
diff --git a/tests/integration/test_simulations_manager.py b/tests/integration/test_simulations_manager.py
new file mode 100644
index 0000000..43ef738
--- /dev/null
+++ b/tests/integration/test_simulations_manager.py
@@ -0,0 +1,40 @@
+"""Integration tests for SimulationsManager - tests real API connectivity."""
+
+import pytest
+
+from fluidize.managers.simulations import SimulationsManager
+
+
+class TestSimulationsManagerIntegration:
+    """Integration test suite for SimulationsManager class."""
+
+    @pytest.fixture
+    def mock_adapter(self):
+        """Create a mock adapter for testing."""
+        from unittest.mock import Mock
+
+        adapter = Mock()
+        return adapter
+
+    def test_list_simulations_integration(self, mock_adapter):
+        """Integration test that actually calls the API and prints output."""
+
+        # Create manager without mocking SDK
+        manager = SimulationsManager(mock_adapter)
+
+        # Act - make real API call
+        result = manager.list_simulations()
+
+        # Assert basic functionality
+        assert isinstance(result, list)
+
+        # Print results for manual verification
+        print("\n=== Integration Test Results ===")
+        print(f"Number of simulations found: {len(result)}")
+        for sim in result:
+            print("Simulation details:")
+            print(f"  Name: {sim.name}")
+            print(f"  ID: {sim.id}")
+            print(f"  Description: {sim.description}")
+            print(f"  Version: {sim.version}")
+            print("\n")
diff --git a/tests/unit/managers/test_simulation.py b/tests/unit/managers/test_simulation.py
new file mode 100644
index 0000000..7137e98
--- /dev/null
+++ b/tests/unit/managers/test_simulation.py
@@ -0,0 +1,87 @@
+"""Unit tests for Simulations Manager - high-level simulation library interface."""
+
+from unittest.mock import Mock, patch
+
+import pytest
+
+from fluidize.managers.simulations import SimulationsManager
+
+
+class TestSimulationsManager:
+    """Test suite for SimulationsManager class."""
+
+    @pytest.fixture
+    def mock_adapter(self):
+        """Create a mock adapter for testing."""
+        adapter = Mock()
+        return adapter
+
+    @pytest.fixture
+    def simulations_manager(self, mock_adapter):
+        """Create a SimulationsManager instance for testing."""
+        with patch("fluidize.managers.simulations.FluidizeSDK"):
+            return SimulationsManager(mock_adapter)
+
+    @patch("fluidize.managers.simulations.FluidizeSDK")
+    def test_init(self, mock_sdk_class, mock_adapter):
+        """Test SimulationsManager initialization."""
+        manager = SimulationsManager(mock_adapter)
+
+        assert manager._adapter is mock_adapter
+        assert manager.fluidize_sdk is not None
+        mock_sdk_class.assert_called_once()
+
+    @patch("fluidize.managers.simulations.FluidizeSDK")
+    def test_list_simulations_returns_list(self, mock_sdk_class, simulations_manager):
+        """Test that list_simulations returns a list."""
+        # Arrange
+        mock_sdk_instance = mock_sdk_class.return_value
+        simulations_manager.fluidize_sdk = mock_sdk_instance
+        # Create a mock simulation object with model_dump method
+        mock_simulation = Mock()
+        mock_simulation.model_dump.return_value = {
+            "name": "Test Simulation",
+            "id": "sim_001",
+            "description": "A test simulation",
+            "date": "2024-01-01",
+            "version": "1.0.0",
+            "authors": [],
+            "tags": [],
+        }
+        mock_sdk_instance.simulation.list_simulations.return_value = [mock_simulation]
+
+        # Act
+        result = simulations_manager.list_simulations()
+
+        # Assert
+        assert isinstance(result, list)
+        mock_sdk_instance.simulation.list_simulations.assert_called_once_with(sim_global=True)
+
+    @patch("fluidize.managers.simulations.FluidizeSDK")
+    def test_list_simulations_empty_list(self, mock_sdk_class, simulations_manager):
+        """Test that list_simulations handles empty results."""
+        # Arrange
+        mock_sdk_instance = mock_sdk_class.return_value
+        simulations_manager.fluidize_sdk = mock_sdk_instance
+        mock_sdk_instance.simulation.list_simulations.return_value = []
+
+        # Act
+        result = simulations_manager.list_simulations()
+
+        # Assert
+        assert result == []
+        mock_sdk_instance.simulation.list_simulations.assert_called_once_with(sim_global=True)
+
+    @patch("fluidize.managers.simulations.FluidizeSDK")
+    def test_list_simulations_sdk_delegation(self, mock_sdk_class, simulations_manager):
+        """Test that list_simulations properly delegates to SDK."""
+        # Arrange
+        mock_sdk_instance = mock_sdk_class.return_value
+        simulations_manager.fluidize_sdk = mock_sdk_instance
+        mock_sdk_instance.simulation.list_simulations.return_value = []
+
+        # Act
+        simulations_manager.list_simulations()
+
+        # Assert
+        mock_sdk_instance.simulation.list_simulations.assert_called_once_with(sim_global=True)
diff --git a/uv.lock b/uv.lock
index b5e98e6..e1f8dcf 100644
--- a/uv.lock
+++ b/uv.lock
@@ -759,7 +759,7 @@ dev = [
 requires-dist = [
     { name = "asciitree", specifier = ">=0.3.3" },
     { name = "docker", specifier = ">=7.1.0" },
-    { name = "fluidize-sdk", specifier = ">=0.4.0" },
+    { name = "fluidize-sdk", specifier = ">=0.6.0" },
     { name = "jinja2", specifier = ">=3.1.6" },
     { name = "mlflow", specifier = ">=3.1.4" },
     { name = "networkx", specifier = ">=3.2.1" },
@@ -786,7 +786,7 @@ dev = [
 
 [[package]]
 name = "fluidize-sdk"
-version = "0.4.0"
+version = "0.6.0"
 source = { registry = "https://pypi.org/simple" }
 dependencies = [
     { name = "anyio" },
@@ -796,9 +796,9 @@ dependencies = [
     { name = "sniffio" },
     { name = "typing-extensions" },
 ]
-sdist = { url = "https://files.pythonhosted.org/packages/90/ef/167f581b140afec073ee4961b18fe347c090477b3263a5276656539cf9af/fluidize_sdk-0.4.0.tar.gz", hash = "sha256:0b80ff0a561fadf01cf7da6a1c0b425bfec287af9d31a8596d6e3cd15e476381", size = 118050, upload-time = "2025-08-10T10:16:28.617Z" }
+sdist = { url = "https://files.pythonhosted.org/packages/f0/6d/41a511df1e9f2cfb6526a349162ea7032ef2ef3d4ced52b8ff81a036ca84/fluidize_sdk-0.6.0.tar.gz", hash = "sha256:cb4548e3ebac5c949b177a6f352edc91be5ffd82900dd0267159027ffb895633", size = 119144, upload-time = "2025-08-16T09:45:34.48Z" }
 wheels = [
-    { url = "https://files.pythonhosted.org/packages/cf/f4/8d1b1f630058a951bd5702f29069ea6f1bf1396d3649663a3752f7f4b699/fluidize_sdk-0.4.0-py3-none-any.whl", hash = "sha256:501e7093f998cecc171e95e57d4f4e9d207820859f13bdb8a0a45e1c72d9f21b", size = 120117, upload-time = "2025-08-10T10:16:27.245Z" },
+    { url = "https://files.pythonhosted.org/packages/e9/6e/25a81bd993b6dec0733e7f4f13f199a40e3500222907bfab54fc5e946eea/fluidize_sdk-0.6.0-py3-none-any.whl", hash = "sha256:22db9101b88bbf0adea113057f96ce9436985ce3b9e635fedcdb421fff399ab2", size = 121524, upload-time = "2025-08-16T09:45:32.874Z" },
 ]
 
 [[package]]