feat: Use pharmsol 0.25

[mhovd]

No description provided.

[Copilot]

Pull request overview

This PR updates PMcore to use pharmsol 0.25 and adapts the codebase to the upstream caching API changes by removing PMcore’s Settings-level cache configuration and enabling default equation caching at equation construction sites.

Changes:

• Bump dependency to pharmsol = "=0.25".
• Remove Config.cache / Settings::set_cache and update tests/examples accordingly.
• Adjust debug logging to materialize prediction states via to_vec().

Reviewed changes

Copilot reviewed 20 out of 20 changed files in this pull request and generated 1 comment.

Show a summary per file

File	Description
Cargo.toml	Updates pharmsol version requirement to 0.25.
src/routines/settings.rs	Removes cache configuration from Settings/Config and updates defaults/tests accordingly.
src/algorithms/mod.rs	Changes prediction state capture from cloning a reference to allocating an owned Vec.
tests/settings_tests.rs	Removes assertions related to the removed cache setting.
tests/onecomp.rs	Enables default equation caching via .with_default_cache().
tests/bestdose_tests.rs	Enables default equation caching via .with_default_cache() across multiple tests.
examples/*	Updates examples to use .with_default_cache() and removes settings.set_cache(...) calls.

Comments suppressed due to low confidence (1)

src/routines/settings.rs:151

• Removing Config.cache while keeping #[serde(deny_unknown_fields)] makes previously serialized settings (e.g., settings.json) that still contain a cache field fail to deserialize. If backward compatibility matters, consider keeping a deprecated cache field (e.g., Option<bool> with #[serde(default)]/#[serde(skip_serializing)]) or otherwise allowing/handling the legacy field during deserialization.

/// General configuration settings
#[derive(Debug, Deserialize, Clone, Serialize)]
#[serde(deny_unknown_fields, default)]
pub struct Config {
    /// Maximum number of cycles to run
    pub cycles: usize,
    /// Denotes the algorithm to use
    pub algorithm: Algorithm,
    /// Should a progress bar be displayed for the first cycle
    ///
    /// The progress bar is not written to logs, but is written to stdout. It incurs a minor performance penalty.
    pub progress: bool,
}

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[github-actions]

Bencher Report

Branch	pharmsol-0.25
Testbed	mhovd-pgx

Click to view all benchmark results

Benchmark	Latency	Benchmark Result milliseconds (ms) (Result Δ%)	Upper Boundary milliseconds (ms) (Limit %)
bimodal_ke_npag	📈 view plot 🚷 view threshold	4,957.70 ms (+1.16%) Baseline: 4,900.86 ms	5,048.30 ms (98.21%)
bimodal_ke_npod	📈 view plot 🚷 view threshold	1,259.60 ms (-11.35%) Baseline: 1,420.84 ms	1,614.39 ms (78.02%)
bimodal_ke_postprob	📈 view plot 🚷 view threshold	58.84 ms (-85.37%) Baseline: 402.20 ms	588.37 ms (10.00%)

🐰 View full continuous benchmarking report in Bencher