Conversation
Contributor
There was a problem hiding this comment.
Pull request overview
This pull request prepares the pharmsol repository for submission to the Journal of Open Source Software (JOSS). The submission includes the addition of a JOSS paper describing the library, new benchmarks demonstrating performance gains, comprehensive testing for stochastic differential equation (SDE) features, and various code quality improvements.
Key Changes:
- Added JOSS paper (
paper.md) and bibliography (paper.bib) documenting the library's purpose, features, and performance characteristics - Added comprehensive benchmarks comparing analytical vs ODE implementations across multiple compartmental models
- Added particle filter (SDE) test to validate stochastic differential equation likelihood estimation
- Minor code quality improvements (idiomatic Rust patterns in likelihood module)
- Updated README with improved installation instructions and examples
- Cleaned up repository by removing example files and test data
Reviewed changes
Copilot reviewed 11 out of 12 changed files in this pull request and generated 5 comments.
Show a summary per file
| File | Description |
|---|---|
| paper.md | JOSS submission paper documenting pharmsol's features, architecture, and use cases |
| paper.bib | Bibliography with citations for referenced pharmacometric software and libraries |
| tests/test_pf.rs | New test validating particle filter likelihood estimation with stochastic variability |
| benches/analytical_vs_ode.rs | Comprehensive benchmark comparing analytical vs ODE solutions for 1 and 2-compartment models |
| src/simulator/likelihood/mod.rs | Minor refactoring to use more idiomatic Rust patterns |
| README.md | Updated with clearer installation instructions and simplified examples |
| .github/workflows/render.yml | New CI workflow for rendering JOSS paper PDF |
| Cargo.toml | Added benchmark configuration for analytical_vs_ode |
| .gitignore | Added paper build artifacts to ignore list |
| examples/sde.rs | Removed (cleanup for JOSS submission) |
| examples/pf.rs | Removed (cleanup for JOSS submission) |
| test.csv | Removed (cleanup for JOSS submission) |
💡 Add Copilot custom instructions for smarter, more guided reviews. Learn how to get started.
To include Walter and Michael
Moved paper and references to a separate folder.
* Clarify summary and future work for 'pharmsol' library Updated the summary and conclusion sections to clarify the purpose of the 'pharmsol' library and its future development plans. * Clarify future development focus in conclusion Updated the conclusion section to specify 'non-compartmental analyses' instead of 'NCA analyses'. * Fix wording in conclusion section Corrected 'non-compartmental analyses' to 'non-compartmental analysis' for consistency.
Siel
approved these changes
Jan 3, 2026
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
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
3 participants
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.
No description provided.