Aim 1.5: Documentation Website

[pauladkisson]

• Add Logo
• Set up Sphinx documentation generation
• Host documentation on ReadTheDocs
• Create step-by-step tutorials for new users
• Develop focused how-to guides for specific tasks and common use cases
• Generate technical reference documentation with complete API docs
• Auto-generate API documentation from docstrings
• Write in-depth user guide explaining key concepts and implementation details
• Create contributor guidelines (code style, testing requirements, PR process)
• Develop comprehensive troubleshooting section
• Base troubleshooting on user feedback and support tickets
• Tutorial of how to load and work with the HDF5 output data for custom plots #254

[h-mayorquin]

This is what I have on mind:

Documentation plan for GuPPy v2

GuPPy v2 has no hosted documentation. The GitHub Wiki covers v1.3.0 workflows but is not being updated for v2, and there is no API reference or conceptual background for new users. This issue tracks the full documentation effort using the Diataxis framework (Tutorials, How-to, Explanation, Reference) on a Read the Docs site built with Sphinx and MyST-Parser. The site is divided into user documentation and a contributing guide so that developer-facing content does not clutter the user experience.

User documentation

Tutorials

• Infrastructure: Sphinx + pydata-sphinx-theme + MyST-Parser + Read the Docs config (Add documentation site with Sphinx and a first tutorial #264)
• First tutorial: end-to-end GUI walkthrough using stubbed CSV data (Add documentation site with Sphinx and a first tutorial #264)
• Add screenshots to the first tutorial (Add content to first tutorial #303)

Explanation

• Z-score normalization (Add z-score normalization explanation page #308)
• Cross-correlation (Add cross-correlation explanation page #307)
• Fiber photometry (Add fiber photometry explainer #319)
• PSTH (Add PSTH explanation page #315)
• Isosbestic correction (Add isosbestic explainer #324)
• Transient detection (Add transient detection explainer #332)
• Artifacts orientation page (Add artifacts explainer #334)
• Manual artifact removal

How-to guides

• How to use TDT data
• How to use Doric data
• How to use Neurophotometrics (NPM) data
• How to remove artifacts
• How to run group analysis

Reference

• Parameter reference Documentation. Add parameters reference #341

Contributing guide

• How to set up a development environment
• How to run the test suite
• How to contribute a new recording format
• Pipeline architecture (HDF5 intermediates, subprocess model, frontend/backend split)
• Design decisions and extension points

Infrastructure

• Connect the Read the Docs project to the repository (requires repo admin access)

[DRZ-cloud]

It would be really helpful to add a section on cross-correlation, how it is calculated, and background of the measure.

[h-mayorquin]

It would be really helpful to add a section on cross-correlation, how it is calculated, and background of the measure.

#307

It can be read here:
https://guppy--307.org.readthedocs.build/explanation/cross_correlation.html

[DRZ-cloud]

Thank you, this is extremely helpful!