chore: Bump pharmsol to 0.24#251
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TODO: Provide wrappers to interact with the cache in |
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Pull request overview
Updates the codebase to work with newer pharmsol (and ndarray) APIs, primarily by migrating error-model types and replacing faer-ext ndarray conversion helpers with explicit conversions / faer-native operations.
Changes:
- Bump dependencies:
pharmsolto0.23.0andndarrayto0.17.2. - Replace
ErrorModels/ErrorModelwithAssayErrorModels/AssayErrorModelacross routines and algorithms. - Remove
faer-ext-based ndarray conversions and compute Psi/Theta/W transformations using directfaerindexing and operations.
Reviewed changes
Copilot reviewed 10 out of 10 changed files in this pull request and generated 4 comments.
Show a summary per file
| File | Description |
|---|---|
src/structs/psi.rs |
Switch Psi calculation to log_likelihood_matrix + exp, remove ndarray/faer-ext conversions, and update tests to compare via faer matrix access. |
src/routines/settings.rs |
Migrate settings/builder/test code to AssayErrorModels and AssayErrorModel. |
src/routines/output/mod.rs |
Replace ndarray conversion helpers with explicit Array2::from_shape_fn conversions; simplify weight extraction. |
src/bestdose/posterior.rs |
Update function signatures to accept AssayErrorModels. |
src/bestdose/mod.rs |
Update posterior-density helper signature to accept AssayErrorModels. |
src/algorithms/postprob.rs |
Update stored error model type to AssayErrorModels. |
src/algorithms/npod.rs |
Update error model types and move Psi/weight computations to faer-native operations; revise Psi validation accordingly. |
src/algorithms/npag.rs |
Update error model types to AssayErrorModels / AssayErrorModel. |
src/algorithms/mod.rs |
Update Psi validation to iterate faer matrices directly (no ndarray conversions). |
Cargo.toml |
Bump ndarray and pharmsol versions. |
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| error_models: &ErrorModels, | ||
| error_models: &AssayErrorModels, | ||
| progress: bool, | ||
| cache: bool, |
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| // Check dimensions | ||
| assert_eq!(psi.nspp(), 2); | ||
| assert_eq!(psi.nsub(), 3); | ||
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| // First coerce all NaN and infinite in psi to 0.0 | ||
| for i in 0..psi.nrows() { | ||
| for j in 0..self.psi().matrix().ncols() { | ||
| let val = psi.get((i, j)).unwrap(); | ||
| for j in 0..psi.ncols() { | ||
| let val = psi[(i, j)]; | ||
| if val.is_nan() { |
Contributor
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Bencher Report| Branch | pharmsol-023 |
| Testbed | mhovd-pgx |
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| Benchmark | Latency | milliseconds (ms) |
|---|---|---|
| bimodal_ke_npag | 📈 view plot | 5,133.20 ms |
| bimodal_ke_npod | 📈 view plot | 1,470.90 ms |
| bimodal_ke_postprob | 📈 view plot | 271.10 ms |
Siel
approved these changes
Mar 24, 2026
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