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

@@ -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)
 
 

examples/bimodal_ke/main.rs

@@ -1,4 +1,3 @@
-use logger::setup_log;
 use pmcore::prelude::*;
 fn main() {
     let eq = equation::ODE::new(

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| {

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() {

examples/meta/main.rs

@@ -2,7 +2,6 @@
 #![allow(unused_variables)]
 #![allow(unused_imports)]
 
-use logger::setup_log;
 use pmcore::prelude::*;
 
 fn main() {

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(

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();

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(

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>

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

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;

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

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::*;

src/routines/evaluation/mod.rs

@@ -0,0 +1,2 @@
+pub mod ipm;
+pub mod qr;

src/algorithms/routines/expansion/adaptative_grid.rs → 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.
 ///

src/routines/expansion/mod.rs

@@ -0,0 +1 @@
+pub mod adaptative_grid;

src/algorithms/routines/initialization/mod.rs → 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;

src/algorithms/routines/initialization/sobol.rs → 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,

src/logger.rs → 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};

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;

src/algorithms/routines/output.rs → 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