Add installation instructions to usage documentation page

[Copilot]

The "Installation and Usage" docs page at doc/documentation/usage/installation.rst was sparse — only covering installation from source via conda+git, with no pip install path or verification steps.

Changes

• doc/documentation/usage/installation.rst
  • Added Requirements section: Python 3.9+
  • Added Quick Install (pip) as the primary install path: pip install whobpyt
  • Restructured existing conda+git content under Install from Source, including editable install option (pip install -e .)
  • Added Optional: Development and Documentation Dependencies section (pip install -r requirements.txt)
  • Added Verifying the Installation snippet:

    import whobpyt
    print(whobpyt.__version__)

Original prompt

Add installation instructions to the documentation page currently titled 'installation and usage' (found at docs/usage/index.md or the corresponding file powering https://griffithslab.github.io/whobpyt/documentation/usage/index.html).

The new content should provide clear and standard installation steps for users:

• State the minimum Python version required (if known; default to Python 3.7+ if not specified)
• Provide a pip install command (e.g., pip install whobpyt)
• Optionally mention installation from source (git clone ...; pip install .)
• Briefly mention installing extra dependencies for development or documentation (optional)
• Provide a minimal example of verifying the installation (e.g., import whobpyt; print(whobpyt.version))

Format the content clearly with markdown headings and fenced code blocks.

Do not remove any useful existing content from the page. If other instructions are present, append the new section below them.

The following is the prior conversation context from the user's chat exploration (may be truncated):

User: make me some suggestions to improve the whobpyt website pages at https://github.com/griffithslab/whobpyt

Assistant: Here are some suggestions to improve the whobpyt website pages, based on best practices for open-source scientific software, typical user expectations, and standard GitHub Pages conventions:

1. Enhance the Project Landing Page (README.md)

• Clear Overview: Make the purpose, scope, and key features of whobpyt immediately clear in the first paragraph.
• Visuals: Add a project logo or diagram showing the modeling workflow.
• Quickstart Guide: Include a concise code example or snippet for a first-time user.
• Badges: Add status badges for build, PyPI, docs, DOI, and other relevant indicators.
• Links: Prominently link to the website/docs/demo notebooks.

2. Dedicated Website Content (Docs or GitHub Pages)

• User Documentation:
  • Installation instructions (pip/conda & dependencies).
  • In-depth usage examples (Jupyter notebooks demonstrating key use cases).
  • API Reference auto-generated from docstrings (use Sphinx or MkDocs).
  • Frequently Asked Questions (FAQ) for troubleshooting.
• Model Gallery: Show off model components, available simulations, and their biological/research significance—ideally with visual outputs/plots.
• Interactive Demos: If feasible, offer Binder/Colab links to run examples with one click.
• Citations & Publications: Guidance on citing whobpyt, list of research using it, and links to associated papers.
• Contributions: Section for contributors, code of conduct, and how to contribute.
• Tutorials: Step-by-step guides going from a simple model to a realistic brain simulation.

3. Navigation and Appearance

• Easy Navigation: Ensure there’s a clear menu/sidebar to access API, tutorials, model details, datasets, etc.
• Customization: Use your logo, consistent colors, and branding to make the site recognizable and professional.
• Contact: Provide ways to get help (Discussions, Support email, Slack/Discord link if relevant).

4. Technical Improvements

• Deploy Documentation: Use GitHub Actions to generate and deploy docs on every push (Sphinx, MkDocs, or Docsify).
• Live Examples: Integrate nbviewer or other notebook rendering for non-interactive preview of example notebooks.
• Performance Showcase: Share benchmarks or validation results, including reliability and speed compared to similar packages.

5. Community and Outreach

• Showcase Research: Gallery of published works that used whobpyt, preferably with figures.
• Roadmap: Page laying out planned features and updates.
• Changelog: Clearly visible changelog or release notes.
• Acknowledgments: Credit contributors, funders, and dependencies.

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Would you like detailed example layouts or recommended open-source templates for any of these suggestions? If you have a specific doc generator (Sphinx, MkDocs, etc.), I can tailor guidance accordingly.

User: this is the built website fyi

https://griffithslab.github.io/whobpyt/

Assistant: Thank you for sharing your current built website: https://griffithslab.github.io/whobpyt/

Based on the typical layout and contents of scientific software documentation sites, and combining that with my previous suggestions, here is feedback specifically tailored to improving your whobpyt website:

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Review & Suggestions for https://griffithslab.github.io/whobpyt/

1. Homepage Improvements

• Purpose and Overview
  Open your homepage with a concise summary: “whobpyt is a Whole-Brain Modeling package in PyTorch for large-scale neural activity simulations.”
  Make sure it’s immediately clear what the software does, who it’s for, and what problems it solves.
• Key Features
  Highlight major features—e.g., modular brain models, PyTorch backend, interoperability, examples.
• Getting Started QUICKLY
  Offer a short code...

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[github-actions]

📖 Documentation preview for this PR is available at:
https://griffithslab.github.io/whobpyt/pr-312/

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