Docs update #75
Merged
Docs update #75
Conversation
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Added an example for fitting inhomogeneous Poisson process models in docs/examples/Inhomogeneous.jl, including custom intensity functions and model comparison. Extended fit methods in src/poisson/inhomogeneous/fit.jl to support unmarked processes and piecewise constant intensity with custom breakpoints. Added test_fix.jl for basic fitting tests. Updated docs/Project.toml with additional dependencies required for examples and documentation.
Enhanced the negative_loglikelihood_ipp function to check for finite and positive intensity values and log-sums, returning Inf for invalid cases. Also updated documentation dependencies and added explanatory comments in the inhomogeneous example.
Integrates Literate.jl to automatically convert example scripts to markdown for documentation, dynamically builds the documentation pages list to include processed examples, and adds a server.jl script using LiveServer for local documentation development. Also adds a new example markdown page and minor cleanup in the Inhomogeneous.jl example.
Enhances the Basics example and documentation by adding a realistic event time dataset, visualizations (raster plot, binned counts, waiting time histogram, QQ plot), and formal statistical tests (KS test) to assess the fit of a homogeneous Poisson process. Also adds HypothesisTests and StatsBase as documentation dependencies. Improves clarity and depth of the tutorial for users learning about point process modeling and inference.
Appended '# hide' to print statements and output lines in Inhomogeneous.jl and Inhomogeneous.md to suppress their display in documentation outputs. Also added 'nothing #hide' in Basics.md to prevent output display, improving the clarity of rendered examples.
Added an active development warning to the index documentation and annotated example output lines in Inhomogeneous.md with '# hide' for improved clarity in rendered examples.
![github-actions[bot]](https://avatars.githubusercontent.com/in/15368?s=60&v=4){kind=small}
Codecov Report❌ Patch coverage is
📢 Thoughts on this report? Let us know! |
There was a problem hiding this comment.
Pull request overview
This PR updates documentation for an upcoming version bump and includes a critical bug fix for inhomogeneous Poisson process fitting. The documentation improvements add comprehensive tutorials with examples, automate example processing via Literate.jl, and provide a local development server setup.
Key Changes
- Bug fix: Enhanced intensity function validation to check for finite values and prevent optimizer failures when fitting polynomial intensity with log link
- Tutorial additions: Two complete example tutorials demonstrating basic point process modeling and inhomogeneous Poisson process fitting with custom intensity functions
- Documentation automation: Integrated Literate.jl to automatically process Julia example files into markdown documentation pages
Reviewed changes
Copilot reviewed 10 out of 10 changed files in this pull request and generated 19 comments.
Show a summary per file
| File | Description |
|---|---|
src/poisson/inhomogeneous/fit.jl |
Adds finite value checks to intensity validation and new fit methods for unmarked and piecewise constant processes |
docs/src/index.md |
Comprehensive rewrite with quick start examples, model overview table, and improved getting started section |
docs/examples/Basics.jl |
Tutorial introducing point process fundamentals, simulation, and inference with homogeneous Poisson processes |
docs/examples/Inhomogeneous.jl |
Advanced tutorial on fitting inhomogeneous models and creating custom intensity functions |
docs/src/examples/Basics.md |
Generated markdown from Basics.jl example |
docs/src/examples/Inhomogeneous.md |
Generated markdown from Inhomogeneous.jl example |
docs/make.jl |
Integrates Literate.jl to dynamically process examples and build documentation navigation |
docs/server.jl |
New utility script for local documentation preview using LiveServer |
docs/Project.toml |
Adds dependencies for plotting, statistics, and documentation generation |
test_fix.jl |
Test script demonstrating the intensity validation bug fix |
💡 Add Copilot custom instructions for smarter, more guided reviews. Learn how to get started.
Collaborator
Author
|
This should be good to go modulo one uncovered line contingent on a positive review |
JoseKling
approved these changes
Dec 23, 2025
Owner
JoseKling
left a comment
JoseKling
left a comment
There was a problem hiding this comment.
Looks good. Merging for version bump.
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
PR of the current status of the docs in anticipation of a version bump so that these docs will correspond with the tagged release. These are mostly non-code edits except for a bug fix where I add a barrier to the log likelihood of IPPs to ensure the intensity function remains finite.
Documentation Examples and Tutorials
Basics.jl(intro to point process modeling and inference) andInhomogeneous.jl(fitting and customizing inhomogeneous Poisson process models), with code, plots, and explanations. [1] [2]Documentation Build and Workflow Automation
docs/exampleswith Literate.jl, converting them to markdown pages in the documentation and dynamically adding them to the docs navigation.server.jl) using LiveServer for easy live preview during development.Dependency Management
docs/Project.tomlto include new documentation and plotting dependencies:Distributions,HypothesisTests,Literate,LiveServer,Plots,SpecialFunctions,StableRNGs,StatsAPI,StatsBase, enabling rich examples and smooth doc builds.