From abab41c0fef482f27c13037a372c55bf21381e74 Mon Sep 17 00:00:00 2001
From: Markus Hovd <markushh@uio.no>
Date: Tue, 18 Feb 2025 14:22:53 +0100
Subject: [PATCH] Refactor project structure (#80)

* Project structure

Routines is now under /src, and not /src/algorithms. Cleaned up mod-files and lib.rs

* Update README.md

* Simplify prelude
---
 README.md                                     |  4 +--
 examples/bimodal_ke/main.rs                   |  1 -
 examples/debug.rs                             |  5 +++-
 examples/drusano/main.rs                      |  5 +++-
 examples/meta/main.rs                         |  1 -
 examples/theophylline/main.rs                 |  5 +++-
 examples/toml.rs                              |  2 +-
 examples/two_eq_lag/main.rs                   |  6 +----
 meta_rust.csv                                 |  2 --
 src/algorithms/mod.rs                         |  8 +++---
 src/algorithms/npag.rs                        | 19 +++++++------
 src/algorithms/npod.rs                        | 10 +++----
 src/algorithms/postprob.rs                    |  8 ++++--
 src/algorithms/routines/mod.rs                | 27 -------------------
 src/algorithms/routines/optimization/optim.rs | 22 ---------------
 src/lib.rs                                    | 18 ++++++-------
 .../prune.rs => routines/condensation/mod.rs} |  0
 .../routines/evaluation/ipm.rs                |  0
 .../routines/evaluation/ipm_faer.rs           |  0
 src/routines/evaluation/mod.rs                |  2 ++
 .../routines/evaluation/qr.rs                 |  0
 .../routines/expansion/adaptative_grid.rs     |  2 +-
 src/routines/expansion/mod.rs                 |  1 +
 .../routines/initialization/latin.rs          |  0
 .../routines/initialization/mod.rs            |  2 +-
 .../routines/initialization/sobol.rs          | 16 ++++++++---
 src/{ => routines}/logger.rs                  |  4 +--
 src/routines/mod.rs                           | 16 +++++++++++
 .../optimization/mod.rs}                      |  0
 src/{algorithms => }/routines/output.rs       |  2 +-
 src/{algorithms => }/routines/settings.rs     |  0
 31 files changed, 85 insertions(+), 103 deletions(-)
 delete mode 100644 meta_rust.csv
 delete mode 100644 src/algorithms/routines/mod.rs
 delete mode 100644 src/algorithms/routines/optimization/optim.rs
 rename src/{algorithms/routines/condensation/prune.rs => routines/condensation/mod.rs} (100%)
 rename src/{algorithms => }/routines/evaluation/ipm.rs (100%)
 rename src/{algorithms => }/routines/evaluation/ipm_faer.rs (100%)
 create mode 100644 src/routines/evaluation/mod.rs
 rename src/{algorithms => }/routines/evaluation/qr.rs (100%)
 rename src/{algorithms => }/routines/expansion/adaptative_grid.rs (98%)
 create mode 100644 src/routines/expansion/mod.rs
 rename src/{algorithms => }/routines/initialization/latin.rs (100%)
 rename src/{algorithms => }/routines/initialization/mod.rs (98%)
 rename src/{algorithms => }/routines/initialization/sobol.rs (90%)
 rename src/{ => routines}/logger.rs (96%)
 create mode 100644 src/routines/mod.rs
 rename src/{algorithms/routines/optimization/d_optimizer.rs => routines/optimization/mod.rs} (100%)
 rename src/{algorithms => }/routines/output.rs (99%)
 rename src/{algorithms => }/routines/settings.rs (100%)

diff --git a/README.md b/README.md
index 0e9c8e284..a9ffc4237 100644
--- a/README.md
+++ b/README.md
@@ -1,7 +1,7 @@
 # PMcore
-![Build](https://github.com/LAPKB/PMcore/actions/workflows/rust.yml/badge.svg)
+[![Build](https://github.com/LAPKB/PMcore/actions/workflows/rust.yml/badge.svg)](https://github.com/LAPKB/PMcore/actions/workflows/rust.yml)
 [![Documentation](https://github.com/LAPKB/PMcore/actions/workflows/docs.yml/badge.svg)](https://lapkb.github.io/PMcore/pmcore/)
-![Security Audit](https://github.com/LAPKB/PMcore/actions/workflows/security_audit.yml/badge.svg)
+[![Security Audit](https://github.com/LAPKB/PMcore/actions/workflows/security_audit.yml/badge.svg)](https://github.com/LAPKB/PMcore/actions/workflows/security_audit.yml)
 [![crates.io](https://img.shields.io/crates/v/pmcore.svg)](https://crates.io/crates/pmcore)
 
 
diff --git a/examples/bimodal_ke/main.rs b/examples/bimodal_ke/main.rs
index 640e44adf..83dc14b4c 100644
--- a/examples/bimodal_ke/main.rs
+++ b/examples/bimodal_ke/main.rs
@@ -1,4 +1,3 @@
-use logger::setup_log;
 use pmcore::prelude::*;
 fn main() {
     let eq = equation::ODE::new(
diff --git a/examples/debug.rs b/examples/debug.rs
index 842e9146c..b9cd1c13b 100644
--- a/examples/debug.rs
+++ b/examples/debug.rs
@@ -1,7 +1,10 @@
 use algorithms::{npag::NPAG, Algorithm};
 use ipm::burke;
 use logger::setup_log;
-use pmcore::prelude::*;
+use pmcore::{
+    prelude::*,
+    routines::{evaluation::ipm, logger, settings},
+};
 fn main() {
     let ode = equation::ODE::new(
         |x, p, _t, dx, rateiv, _cov| {
diff --git a/examples/drusano/main.rs b/examples/drusano/main.rs
index 21440ab5c..dde98e671 100644
--- a/examples/drusano/main.rs
+++ b/examples/drusano/main.rs
@@ -4,7 +4,10 @@ use argmin::{
     solver::neldermead::NelderMead,
 };
 use logger::setup_log;
-use pmcore::prelude::*;
+use pmcore::{
+    prelude::*,
+    routines::{logger, settings},
+};
 use std::process::exit;
 #[allow(unused_variables)]
 fn main() {
diff --git a/examples/meta/main.rs b/examples/meta/main.rs
index 834827fdd..db4f26632 100644
--- a/examples/meta/main.rs
+++ b/examples/meta/main.rs
@@ -2,7 +2,6 @@
 #![allow(unused_variables)]
 #![allow(unused_imports)]
 
-use logger::setup_log;
 use pmcore::prelude::*;
 
 fn main() {
diff --git a/examples/theophylline/main.rs b/examples/theophylline/main.rs
index 576e9d289..8ebbca786 100644
--- a/examples/theophylline/main.rs
+++ b/examples/theophylline/main.rs
@@ -1,4 +1,7 @@
-use pmcore::prelude::{models::one_compartment_with_absorption, *};
+use pmcore::{
+    prelude::{models::one_compartment_with_absorption, *},
+    routines::settings,
+};
 
 fn main() {
     // let eq = Equation::new_ode(
diff --git a/examples/toml.rs b/examples/toml.rs
index f51b0347e..49fbc10c2 100644
--- a/examples/toml.rs
+++ b/examples/toml.rs
@@ -1,4 +1,4 @@
-use pmcore::prelude::*;
+use pmcore::routines::settings;
 
 fn main() {
     let path = "examples/bimodal_ke/config.toml".to_string();
diff --git a/examples/two_eq_lag/main.rs b/examples/two_eq_lag/main.rs
index 197a2043e..c82b54895 100644
--- a/examples/two_eq_lag/main.rs
+++ b/examples/two_eq_lag/main.rs
@@ -1,12 +1,8 @@
 #![allow(dead_code)]
 #![allow(unused_variables)]
 #![allow(unused_imports)]
-use std::path::Path;
 
-use data::read_pmetrics;
-use logger::setup_log;
-use ndarray::Array2;
-use pmcore::prelude::{models::one_compartment_with_absorption, simulator::Equation, *};
+use pmcore::prelude::*;
 
 fn main() {
     let eq = equation::ODE::new(
diff --git a/meta_rust.csv b/meta_rust.csv
deleted file mode 100644
index 12159aaec..000000000
--- a/meta_rust.csv
+++ /dev/null
@@ -1,2 +0,0 @@
-converged,ncycles
-true,110
diff --git a/src/algorithms/mod.rs b/src/algorithms/mod.rs
index 1436d39ca..281b05d55 100644
--- a/src/algorithms/mod.rs
+++ b/src/algorithms/mod.rs
@@ -1,23 +1,21 @@
 use std::fs;
 use std::path::Path;
 
-use crate::prelude::{self, settings::Settings};
-
+use crate::routines::output::NPResult;
+use crate::routines::settings::Settings;
 use anyhow::{bail, Result};
 use anyhow::{Context, Error};
 use ndarray::Array2;
 use npag::*;
 use npod::NPOD;
-use output::NPResult;
 use pharmsol::prelude::{data::Data, simulator::Equation};
 use postprob::POSTPROB;
-use prelude::*;
+
 // use self::{data::Subject, simulator::Equation};
 
 pub mod npag;
 pub mod npod;
 pub mod postprob;
-pub mod routines;
 
 pub trait Algorithm<E: Equation> {
     fn new(config: Settings, equation: E, data: Data) -> Result<Box<Self>, Error>
diff --git a/src/algorithms/npag.rs b/src/algorithms/npag.rs
index a02361d30..21e931bb1 100644
--- a/src/algorithms/npag.rs
+++ b/src/algorithms/npag.rs
@@ -1,10 +1,11 @@
-use crate::prelude::{
-    algorithms::Algorithm,
-    ipm::burke,
-    output::{CycleLog, NPCycle, NPResult},
-    qr,
-    settings::Settings,
-};
+use crate::prelude::algorithms::Algorithm;
+
+pub use crate::routines::evaluation::ipm::burke;
+pub use crate::routines::evaluation::qr;
+use crate::routines::settings::Settings;
+
+use crate::routines::output::{CycleLog, NPCycle, NPResult};
+
 use anyhow::Error;
 use anyhow::Result;
 use pharmsol::{
@@ -15,10 +16,12 @@ use pharmsol::{
     Subject,
 };
 
+use crate::routines::initialization;
+
 use ndarray::{Array, Array1, Array2, ArrayBase, Axis, Dim, OwnedRepr};
 use ndarray_stats::{DeviationExt, QuantileExt};
 
-use super::{adaptative_grid::adaptative_grid, initialization};
+use crate::routines::expansion::adaptative_grid::adaptative_grid;
 
 const THETA_E: f64 = 1e-4; // Convergence criteria
 const THETA_G: f64 = 1e-4; // Objective function convergence criteria
diff --git a/src/algorithms/npod.rs b/src/algorithms/npod.rs
index 4d2e1c15b..2138858c5 100644
--- a/src/algorithms/npod.rs
+++ b/src/algorithms/npod.rs
@@ -1,9 +1,9 @@
 use crate::prelude::{
     algorithms::Algorithm,
-    ipm::burke,
-    output::{CycleLog, NPCycle, NPResult},
-    qr,
-    settings::Settings,
+    routines::evaluation::ipm::burke,
+    routines::evaluation::qr,
+    routines::output::{CycleLog, NPCycle, NPResult},
+    routines::settings::Settings,
 };
 use anyhow::Error;
 use anyhow::Result;
@@ -21,7 +21,7 @@ use ndarray::{
 };
 use ndarray_stats::{DeviationExt, QuantileExt};
 
-use super::{condensation::prune::prune, initialization, optimization::d_optimizer::SppOptimizer};
+use crate::routines::{condensation::prune, initialization, optimization::SppOptimizer};
 
 const THETA_F: f64 = 1e-2;
 const THETA_D: f64 = 1e-4;
diff --git a/src/algorithms/postprob.rs b/src/algorithms/postprob.rs
index 50e33b9bc..d8dde26ec 100644
--- a/src/algorithms/postprob.rs
+++ b/src/algorithms/postprob.rs
@@ -1,4 +1,4 @@
-use crate::prelude::{algorithms::Algorithm, ipm::burke, output::NPResult, settings::Settings};
+use crate::prelude::algorithms::Algorithm;
 use anyhow::{Error, Result};
 use pharmsol::prelude::{
     data::{Data, ErrorModel, ErrorType},
@@ -7,7 +7,11 @@ use pharmsol::prelude::{
 
 use ndarray::{Array1, Array2};
 
-use super::{initialization, output::CycleLog};
+use crate::routines::evaluation::ipm::burke;
+use crate::routines::initialization;
+use crate::routines::output::CycleLog;
+use crate::routines::output::NPResult;
+use crate::routines::settings::Settings;
 
 /// Posterior probability algorithm
 /// Reweights the prior probabilities to the observed data and error model
diff --git a/src/algorithms/routines/mod.rs b/src/algorithms/routines/mod.rs
deleted file mode 100644
index 138982aac..000000000
--- a/src/algorithms/routines/mod.rs
+++ /dev/null
@@ -1,27 +0,0 @@
-/// Routines for initializing the grid
-pub mod initialization;
-pub mod optimization {
-    pub mod d_optimizer;
-    pub mod optim;
-}
-
-/// Routines for writing results to file, such as predicted values
-pub mod output;
-/// Routines for condensing grids
-pub mod condensation {
-    pub mod prune;
-}
-/// Routines for expanding grids
-pub mod expansion {
-    pub mod adaptative_grid;
-}
-
-/// Provides routines for reading and parsing settings
-pub mod settings;
-pub mod evaluation {
-
-    /// Interior point method for solving the optimization problem
-    pub mod ipm;
-    pub mod ipm_faer;
-    pub mod qr;
-}
diff --git a/src/algorithms/routines/optimization/optim.rs b/src/algorithms/routines/optimization/optim.rs
deleted file mode 100644
index d75f13a7d..000000000
--- a/src/algorithms/routines/optimization/optim.rs
+++ /dev/null
@@ -1,22 +0,0 @@
-// use crate::prelude::*;
-// use argmin::core::CostFunction;
-// use datafile::Scenario;
-// use ndarray::{Array1, Array2};
-// use sigma::ErrorModel;
-
-// use self::simulator::likelihood::SubjectPredictions;
-
-// struct GamLam<'a> {
-//     prediction: &'a SubjectPredictions,
-//     scenarios: &'a Vec<Scenario>,
-//     ep: ErrorModel<'a>,
-// }
-
-// impl<'a> CostFunction for GamLam<'a> {
-//     type Param = f64;
-//     type Output = f64;
-//     fn cost(&self, _param: &Self::Param) -> Result<Self::Output, argmin::core::Error> {
-//         let prob = self.prediction.likelihood(&self.ep);
-//         Ok(prob.sum())
-//     }
-// }
diff --git a/src/lib.rs b/src/lib.rs
index 9a5e884de..1909698e3 100644
--- a/src/lib.rs
+++ b/src/lib.rs
@@ -50,8 +50,9 @@
 /// Provides the various algorithms used within the framework
 // pub mod algorithms;
 pub mod algorithms;
-/// Logger functionality for the framework using [tracing]
-pub mod logger;
+
+/// Routines
+pub mod routines;
 
 // Re-export commonly used items
 pub use anyhow::Result;
@@ -63,14 +64,11 @@ pub mod prelude {
     pub use super::Result;
     pub use crate::algorithms;
     pub use crate::algorithms::dispatch_algorithm;
-    pub use crate::algorithms::routines::condensation;
-    pub use crate::algorithms::routines::expansion::*;
-    pub use crate::algorithms::routines::initialization::*;
-    pub use crate::algorithms::routines::optimization;
-    pub use crate::logger;
-    pub use crate::prelude::evaluation::*;
-    // pub use crate::algorithms::routines::settings::*;
-    pub use crate::algorithms::routines::*;
+    pub use crate::routines;
+    pub use crate::routines::logger;
+    pub use crate::routines::logger::setup_log;
+    pub use crate::routines::settings;
+
     //Alma re-exports
     pub mod simulator {
         pub use pharmsol::prelude::simulator::*;
diff --git a/src/algorithms/routines/condensation/prune.rs b/src/routines/condensation/mod.rs
similarity index 100%
rename from src/algorithms/routines/condensation/prune.rs
rename to src/routines/condensation/mod.rs
diff --git a/src/algorithms/routines/evaluation/ipm.rs b/src/routines/evaluation/ipm.rs
similarity index 100%
rename from src/algorithms/routines/evaluation/ipm.rs
rename to src/routines/evaluation/ipm.rs
diff --git a/src/algorithms/routines/evaluation/ipm_faer.rs b/src/routines/evaluation/ipm_faer.rs
similarity index 100%
rename from src/algorithms/routines/evaluation/ipm_faer.rs
rename to src/routines/evaluation/ipm_faer.rs
diff --git a/src/routines/evaluation/mod.rs b/src/routines/evaluation/mod.rs
new file mode 100644
index 000000000..b9ad757e7
--- /dev/null
+++ b/src/routines/evaluation/mod.rs
@@ -0,0 +1,2 @@
+pub mod ipm;
+pub mod qr;
diff --git a/src/algorithms/routines/evaluation/qr.rs b/src/routines/evaluation/qr.rs
similarity index 100%
rename from src/algorithms/routines/evaluation/qr.rs
rename to src/routines/evaluation/qr.rs
diff --git a/src/algorithms/routines/expansion/adaptative_grid.rs b/src/routines/expansion/adaptative_grid.rs
similarity index 98%
rename from src/algorithms/routines/expansion/adaptative_grid.rs
rename to src/routines/expansion/adaptative_grid.rs
index 35ccb048c..8d14d7dfd 100644
--- a/src/algorithms/routines/expansion/adaptative_grid.rs
+++ b/src/routines/expansion/adaptative_grid.rs
@@ -1,6 +1,6 @@
 use ndarray::{Array, Array2};
 
-use crate::algorithms::routines::condensation::prune::prune;
+use crate::routines::condensation::prune;
 
 /// Implements the adaptive grid algorithm for support point expansion.
 ///
diff --git a/src/routines/expansion/mod.rs b/src/routines/expansion/mod.rs
new file mode 100644
index 000000000..a84c84fad
--- /dev/null
+++ b/src/routines/expansion/mod.rs
@@ -0,0 +1 @@
+pub mod adaptative_grid;
diff --git a/src/algorithms/routines/initialization/latin.rs b/src/routines/initialization/latin.rs
similarity index 100%
rename from src/algorithms/routines/initialization/latin.rs
rename to src/routines/initialization/latin.rs
diff --git a/src/algorithms/routines/initialization/mod.rs b/src/routines/initialization/mod.rs
similarity index 98%
rename from src/algorithms/routines/initialization/mod.rs
rename to src/routines/initialization/mod.rs
index c36bb9425..91459f2d5 100644
--- a/src/algorithms/routines/initialization/mod.rs
+++ b/src/routines/initialization/mod.rs
@@ -6,7 +6,7 @@ use anyhow::{bail, Context, Result};
 use ndarray::{Array1, Array2};
 use pharmsol::prelude::EstimateTheta;
 
-use crate::prelude::settings::Settings;
+use crate::routines::settings::Settings;
 
 pub mod latin;
 pub mod sobol;
diff --git a/src/algorithms/routines/initialization/sobol.rs b/src/routines/initialization/sobol.rs
similarity index 90%
rename from src/algorithms/routines/initialization/sobol.rs
rename to src/routines/initialization/sobol.rs
index a3d2e47a0..8b0cba031 100644
--- a/src/algorithms/routines/initialization/sobol.rs
+++ b/src/routines/initialization/sobol.rs
@@ -45,12 +45,15 @@ pub fn generate(
 }
 
 #[cfg(test)]
-use crate::prelude::*;
-
 #[test]
 fn basic_sobol() {
     assert_eq!(
-        initialization::sobol::generate(5, &vec![(0., 1.), (0., 1.), (0., 1.)], 347).unwrap(),
+        crate::routines::initialization::sobol::generate(
+            5,
+            &vec![(0., 1.), (0., 1.), (0., 1.)],
+            347
+        )
+        .unwrap(),
         ndarray::array![
             [0.10731887817382813, 0.14647412300109863, 0.5851038694381714],
             [0.9840304851531982, 0.7633365392684937, 0.19097506999969482],
@@ -64,7 +67,12 @@ fn basic_sobol() {
 #[test]
 fn scaled_sobol() {
     assert_eq!(
-        initialization::sobol::generate(5, &vec![(0., 1.), (0., 2.), (-1., 1.)], 347).unwrap(),
+        crate::routines::initialization::sobol::generate(
+            5,
+            &vec![(0., 1.), (0., 2.), (-1., 1.)],
+            347
+        )
+        .unwrap(),
         ndarray::array![
             [
                 0.10731887817382813,
diff --git a/src/logger.rs b/src/routines/logger.rs
similarity index 96%
rename from src/logger.rs
rename to src/routines/logger.rs
index 3c73f6555..c2bfb8d3b 100644
--- a/src/logger.rs
+++ b/src/routines/logger.rs
@@ -1,7 +1,7 @@
 use std::time::Instant;
 
-use crate::algorithms::routines::settings::Settings;
-use crate::prelude::output::OutputFile;
+use crate::routines::output::OutputFile;
+use crate::routines::settings::Settings;
 use anyhow::Result;
 use tracing_subscriber::fmt::time::FormatTime;
 use tracing_subscriber::fmt::{self};
diff --git a/src/routines/mod.rs b/src/routines/mod.rs
new file mode 100644
index 000000000..25c311da3
--- /dev/null
+++ b/src/routines/mod.rs
@@ -0,0 +1,16 @@
+// Routines for condensation
+pub mod condensation;
+// Routines for evaluation
+pub mod evaluation;
+// Routines for expansion
+pub mod expansion;
+// Routines for initialization
+pub mod initialization;
+// Routines for logging
+pub mod logger;
+// Routines for optimization
+pub mod optimization;
+// Routines for output
+pub mod output;
+// Routines for settings
+pub mod settings;
diff --git a/src/algorithms/routines/optimization/d_optimizer.rs b/src/routines/optimization/mod.rs
similarity index 100%
rename from src/algorithms/routines/optimization/d_optimizer.rs
rename to src/routines/optimization/mod.rs
diff --git a/src/algorithms/routines/output.rs b/src/routines/output.rs
similarity index 99%
rename from src/algorithms/routines/output.rs
rename to src/routines/output.rs
index b5fb433ce..ec4534ccd 100644
--- a/src/algorithms/routines/output.rs
+++ b/src/routines/output.rs
@@ -7,7 +7,7 @@ use pharmsol::prelude::data::*;
 use pharmsol::prelude::simulator::Equation;
 use serde::Serialize;
 // use pharmsol::Cache;
-use settings::Settings;
+use crate::routines::settings::Settings;
 use std::fs::{create_dir_all, File, OpenOptions};
 use std::path::{Path, PathBuf};
 /// Defines the result objects from an NPAG run
diff --git a/src/algorithms/routines/settings.rs b/src/routines/settings.rs
similarity index 100%
rename from src/algorithms/routines/settings.rs
rename to src/routines/settings.rs