Documentation updates

README.md

@@ -56,6 +56,7 @@ Students and researchers face significant barriers when working with different s
 - **Reproducibility issues** – Sharing and reproducing experiments is frequently cumbersome and error-prone.
 - **Scaling friction** – Moving from a local prototype to a cloud environment or dedicated compute cluster can be slow and difficult.
 
+
 ## The Solution
 
 Fluidize provides a standardized wrapper that turns complex scientific software into modular components. This makes it possible to:
@@ -66,12 +67,14 @@ Fluidize provides a standardized wrapper that turns complex scientific software
 
 All of this works with **minimal or no changes** to the existing codebase, allowing our framework to scale effortlessly to any repository.
 
+
 ## Architecture
 
 At Fluidize, we believe strong organization leads to better reproducibility and scalability.
 
 We treat each simulation pipeline as an individual project. Within projects, each pipeline is treated as a DAG (directed acyclic graph), where nodes represent individual pieces of scientific software (e.g. inputs, solvers, visualization tools, etc.) and edges represent data flow between nodes.
 
+
 ### Nodes
 Nodes are the foundational building blocks of simulation pipelines. Each node represents a computational unit with:
 
@@ -90,6 +93,7 @@ Nodes are the foundational building blocks of simulation pipelines. Each node re
 - No source code modification required
 - Automated node generation support (Public launch soon)
 
+
 ### Projects
 
 Projects store a simple data layer for managing individual modules within a pipeline.
@@ -99,10 +103,12 @@ Projects store a simple data layer for managing individual modules within a pipe
 | `graph.json` | Node (scientific software) and edge (data flow) definitions |
 | `metadata.yaml` | Project description and configuration |
 
+
 ### Runs
 
 Pipelines can be executed both locally and on the cloud. Local execution is handled by Docker engine. Cloud execution is routed through our API, and uses the Kubernetes engine with Argo Workflow Manager.
 
+
 ## Documentation
 
 Comprehensive documentation is available at [https://Fluidize-Inc.github.io/fluidize-python/](https://Fluidize-Inc.github.io/fluidize-python/)
@@ -112,12 +118,14 @@ Comprehensive documentation is available at [https://Fluidize-Inc.github.io/flui
 - [Project Orchestration](https://Fluidize-Inc.github.io/fluidize-python/projects)
 - [API Reference](https://Fluidize-Inc.github.io/fluidize-python/api)
 
+
 ## Contributing
 
 We would love to collaborate with you! Please see our [Contributing Guide](CONTRIBUTING.md) for details.
 
 Also - we would love to help streamline your pipeline! Please reach out to us at [founders@fluidize.ai](mailto:founders@fluidize.ai).
 
+
 ## Vision and Roadmap
 
 This is just the beginning of what we believe will be a really exciting new era for how we conduct research and make discoveries in science.
@@ -127,6 +135,7 @@ By standardizing tools, we hope to significantly increase the effectiveness of A
 - **Auto-Fluidize**: Automatically convert any scientific software to run anywhere with our framework.
 - **Fluidize AI Playground**: Explore and build simulation pipelines with natural language.
 
+
 ## License
 
 This project is licensed under the MIT License - see the [LICENSE](LICENSE) file for details.

docs/getting-started/client.md → docs/core-modules/client.md

@@ -6,22 +6,24 @@ The Fluidize Client is the primary interface to create and edit projects. There
 
 - **API Mode**: Runs on Fluidize API to manage projects and workflows in the cloud.
 
-## Client API
-
-### FluidizeClient
 ::: fluidize.client.FluidizeClient
     options:
       show_source: false
+      heading_level: 3
+      extra:
+        show_root_heading: true
       members:
         - mode
         - adapters
         - projects
         - runs
 
-### FluidizeConfig
 ::: fluidize.config.FluidizeConfig
     options:
       show_source: false
+      heading_level: 3
+      extra:
+        show_root_heading: true
       members:
         - is_local_mode
         - is_api_mode

docs/core-modules/graph.md

@@ -1,8 +1,12 @@
 # Graph Module
 
+## Graph Manager
 ::: fluidize.managers.graph.GraphManager
     options:
       show_source: false
+      heading_level: 3
+      extra:
+        show_root_heading: true
       members:
         - get
         - add_node
@@ -11,29 +15,35 @@
         - add_edge
         - delete_edge
 
+## Graph Processor
 ::: fluidize.core.modules.graph.GraphProcessor
     options:
       show_source: false
+      heading_level: 3
+      extra:
+        show_root_heading: true
 
 ## Graph Types
 
-### GraphData
-::: fluidize.core.types.GraphData
+::: fluidize.core.types.graph.GraphData
     options:
-      show_source: false
-      show_root_heading: true
       heading_level: 3
+      extra:
+        show_attributes: true
+        show_root_heading: true
+
 
-### GraphNode
-::: fluidize.core.types.GraphNode
+::: fluidize.core.types.graph.GraphNode
     options:
-      show_source: false
-      show_root_heading: true
       heading_level: 3
+      extra:
+        show_attributes: true
+        show_root_heading: true
+
 
-### GraphEdge
-::: fluidize.core.types.GraphEdge
+::: fluidize.core.types.graph.GraphEdge
     options:
-      show_source: false
-      show_root_heading: true
       heading_level: 3
+      extra:
+        show_attributes: true
+        show_root_heading: true

docs/core-modules/projects.md

@@ -4,12 +4,14 @@
 ::: fluidize.managers.registry.RegistryManager
     options:
       show_source: false
-      show_root_heading: true
       heading_level: 3
+      extra:
+        show_root_heading: true
 
 ## Project
 ::: fluidize.managers.project.ProjectManager
     options:
       show_source: false
-      show_root_heading: true
       heading_level: 3
+      extra:
+        show_root_heading: true

docs/core-modules/run.md

@@ -2,23 +2,29 @@
 
 ## Run Management
 
-### RunsManager
 ::: fluidize.managers.runs.RunsManager
     options:
       show_source: false
+      heading_level: 3
+      extra:
+        show_root_heading: true
       members:
         - run_flow
         - list
         - get_status
 
 ## Run Execution
 
-### RunJob
 ::: fluidize.core.modules.run.RunJob
     options:
       show_source: false
+      heading_level: 3
+      extra:
+        show_root_heading: true
 
-### ProjectRunner
-::: fluidize.core.modules.run.ProjectRunner
+::: fluidize.core.modules.run.project.ProjectRunner
     options:
       show_source: false
+      heading_level: 3
+      extra:
+        show_root_heading: true

docs/getting-started/quickstart.md

@@ -0,0 +1 @@
+# Getting Started

docs/index.md

@@ -1,8 +1,94 @@
-# fluidize-python
+# Fluidize
 
-[![Release](https://img.shields.io/github/v/release/Fluidize-Inc/fluidize-python)](https://img.shields.io/github/v/release/Fluidize-Inc/fluidize-python)
-[![Build status](https://img.shields.io/github/actions/workflow/status/Fluidize-Inc/fluidize-python/main.yml?branch=main)](https://github.com/Fluidize-Inc/fluidize-python/actions/workflows/main.yml?query=branch%3Amain)
-[![Commit activity](https://img.shields.io/github/commit-activity/m/Fluidize-Inc/fluidize-python)](https://img.shields.io/github/commit-activity/m/Fluidize-Inc/fluidize-python)
-[![License](https://img.shields.io/github/license/Fluidize-Inc/fluidize-python)](https://img.shields.io/github/license/Fluidize-Inc/fluidize-python)
+[![Python](https://img.shields.io/badge/python-3.9%2B-blue?style=for-the-badge&logo=python&logoColor=white)](https://python.org)
+[![PyPI](https://img.shields.io/pypi/v/fluidize?style=for-the-badge&logo=pypi&logoColor=white)](https://pypi.org/project/fluidize/)
+[![License](https://img.shields.io/github/license/Fluidize-Inc/fluidize-python?style=for-the-badge)](LICENSE)
+[![Documentation](https://img.shields.io/badge/docs-available-brightgreen?style=for-the-badge&logo=gitbook&logoColor=white)](https://Fluidize-Inc.github.io/fluidize-python/)
 
-Python package for automatic generation of scientific computing software pipelines.
+## About
+
+ **fluidize-python** is a library for building modular, reproducible scientific computing pipelines. It provides a unified interface to a wide range of physical simulation tools, eliminating the need to navigate the inconsistent, incomplete instructions that often vary from tool to tool.
+
+This library marks our first step toward AI-orchestrated scientific computing. By standardizing tools and practices within our framework, AI agents can automatically build, configure, and execute computational pipelines across domains and simulation platforms.
+
+Our goal is to improve today’s simulation tools so AI can assist researchers and scientists in accelerating the pace of innovation and scientific discovery.
+
+## Installation
+
+### Prerequesites:
+
+- Python 3.9+
+- Docker Desktop (for local execution). Download and install Docker Desktop from https://docs.docker.com/desktop/.
+
+  After installation, verify with:
+  ```bash
+  docker --version
+  ```
+
+
+
+### From PyPI
+```bash
+pip install fluidize
+```
+
+### From Source
+```bash
+git clone https://github.com/Fluidize-Inc/fluidize-python.git
+cd fluidize-python
+make install
+```
+
+## Run Examples
+
+Example projects are located in this folder: [examples/](https://github.com/Fluidize-Inc/fluidize-python/tree/main/examples). There you can find an [Jupyter Notebook](https://github.com/Fluidize-Inc/fluidize-python/blob/main/examples/demo.ipynb) of a simple simulation
+
+## Architecture
+
+At Fluidize, we believe strong organization leads to better reproducibility and scalability.
+
+We treat each simulation pipeline as an individual project. Within projects, each pipeline is treated as a DAG (directed acyclic graph), where nodes represent individual pieces of scientific software (e.g. inputs, solvers, visualization tools, etc.) and edges represent data flow between nodes.
+
+
+### Nodes
+Nodes are the foundational building blocks of simulation pipelines. Each node represents a computational unit with:
+
+| File | Purpose |
+|------|---------|
+| `properties.yaml` | Container configuration, working directory, and output paths |
+| `metadata.yaml` | Node description, version, authors, and repository URL |
+| `Dockerfile` | Environment setup and dependency installation |
+| `parameters.json` | Tunable parameters for experiments |
+| `main.sh` | Execution script for the source code |
+| `source/` | Original scientific computing code |
+
+**Key Features:** <br>
+- Predictable input/output paths <br>
+- Modular and extensible design <br>
+- No source code modification required <br>
+- Automated node generation support (Public launch soon)
+
+
+### Projects
+
+Projects store a simple data layer for managing individual modules within a pipeline.
+
+| File | Purpose |
+|------|---------|
+| `graph.json` | Node (scientific software) and edge (data flow) definitions |
+| `metadata.yaml` | Project description and configuration |
+
+
+### Runs
+
+Pipelines can be executed both locally and on the cloud. Local execution is handled by Docker engine. Cloud execution is routed through our API, and uses the Kubernetes engine with Argo Workflow Manager.
+
+## Contributing
+
+We would love to collaborate with you! Please see our [Contributing Guide](https://github.com/Fluidize-Inc/fluidize-python/blob/main/CONTRIBUTING.md) for details.
+
+Also - we would love to help streamline your pipeline! Please reach out to us at [founders@fluidize.ai](mailto:founders@fluidize.ai).
+
+## License
+
+This project is licensed under the MIT License - see the [LICENSE](LICENSE) file for details.

examples/example-projects/MUJOCO/Mujoco-Simulation/parameters.json

@@ -8,9 +8,6 @@
       "name": "motor_strength",
       "latex": null,
       "location": [
-        "source/pinata_simulation.py",
-        "source/pinata_simulation.py",
-        "source/pinata_simulation.py",
         "source/pinata_simulation.py"
       ],
       "options": null,