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Modified main index.rst & created User Guide index.rst
To keep the user_guide table of contents easy to modify, I created a seperate user_guide folder with it's own index.rst, the file shows the sections covering basic RPE usage. As a starting point files for each section are located within the same user_guide folder, they will be moved to their own directories with respective index.rst files once subsections are finalized.
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docs/source/index.rst

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Welcome to Rapid Power Estimator's Documentation!
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Introduction
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Overview
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============
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Power and thermal specifications are critical considerations in the early stages of designing SoCs and FPGAs. Determining accurate power requirements and cooling solutions is essential to avoid over-designing or under-designing your product's power and thermal systems. It is a valuable tool in this process.
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RPE allows you to estimate power consumption at various stages of your design cycle. It simplifies the input of design information through intuitive wizards and delivers comprehensive power and thermal data analysis.
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GUI Design and Technology Choices
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=================================
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Contents
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========
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.. toctree::
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:maxdepth: 2
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:caption: Contents:
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user_guide/index
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.. toctree::
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:maxdepth: 1
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installation
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usage
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api_reference
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Indices and tables

docs/source/usage.rst

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docs/source/user_guide/FPGA.rst

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FPGA Input
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=============
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This section will document FPGA inpout for Rapid Power Estimator.

docs/source/user_guide/SoC.rst

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SoC Input
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=============
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This section will document SoC input for Rapid Power Estimator.

docs/source/user_guide/index.rst

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User Guide
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=====
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.. toctree::
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:maxdepth: 2
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:caption: Table of Contents
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introduction
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launch
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FPGA
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SoC
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peripherals
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memory
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results
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Introduction to Rapid Power Estimator
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=============
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This section will document the Introduction of Rapid Power Estimator.

docs/source/user_guide/launch.rst

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Launching Rapid Power Estimator
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=============
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This section will document launching of Rapid Power Estimator.

docs/source/user_guide/memory.rst

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Memory Usage
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This section will document memory on Rapid Power Estimator.
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Peripheral Usage
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=============
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This section will document peripherals on Rapid Power Estimator.

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