Merge pull request #32 from LAPKB/config

Reworked settings and run configuration

.gitignore

@@ -22,3 +22,4 @@ meta*.csv
 stop
 .vscode
 *.f90
+settings.json

Cargo.toml

@@ -21,6 +21,7 @@ csv = "1.2.1"
 ndarray = { version = "0.15.6", features = ["rayon"] }
 serde = "1.0.188"
 serde_derive = "1.0.188"
+serde_json = "1.0.66"
 sobol_burley = "0.5.0"
 toml = { version = "0.8.1", features = ["preserve_order"] }
 ode_solvers = "0.3.7"
@@ -46,6 +47,7 @@ faer = { version = "0.15.0", features = ["nalgebra", "ndarray"] }
 tracing = "0.1.40"
 tracing-subscriber = { version = "0.3.17", features = ["env-filter", "fmt", "time"] }
 chrono = "0.4"
+config = "0.13"
 
 [dev-dependencies]
 criterion = "0.5"

examples/bimodal_ke/config.toml

@@ -1,18 +1,19 @@
 [paths]
 data = "examples/data/bimodal_ke.csv"
-log_out = "log/bimodal_ke.log"
-#prior_dist = "theta_bimodal_ke.csv"
+log = "log/bimodal_ke.log"
+#prior = "theta_bimodal_ke.csv"
 
 [config]
 cycles = 1024
 engine = "NPAG"
-init_points = 10000
+init_points = 2129
 seed = 347
 tui = true
-pmetrics_outputs = true
+output = true
 cache = true
 idelta = 0.1
-log_level = "debug"
+log_level = "info"
+
 
 [random]
 Ke = [0.001, 3.0]

src/algorithms.rs

@@ -1,4 +1,4 @@
-use crate::prelude::{self, settings::run::Settings};
+use crate::prelude::{self, settings::Settings};
 
 use output::NPResult;
 use prelude::{datafile::Scenario, *};
@@ -9,12 +9,6 @@ mod npag;
 mod npod;
 mod postprob;
 
-// pub enum Type {
-//     NPAG,
-//     NPOD,
-//     POSTPROB,
-// }
-
 pub trait Algorithm {
     fn fit(&mut self) -> NPResult;
     fn to_npresult(&self) -> NPResult;
@@ -35,17 +29,17 @@ where
             Err(err) => panic!("Unable to remove previous stop file: {}", err),
         }
     }
-    let ranges = settings.computed.random.ranges.clone();
+    let ranges = settings.random.ranges();
     let theta = initialization::sample_space(&settings, &ranges);
 
     //This should be a macro, so it can automatically expands as soon as we add a new option in the Type Enum
-    match settings.parsed.config.engine.as_str() {
+    match settings.config.engine.as_str() {
         "NPAG" => Box::new(npag::NPAG::new(
             engine,
             ranges,
             theta,
             scenarios,
-            settings.parsed.error.poly,
+            settings.error.poly,
             tx,
             settings,
         )),
@@ -54,15 +48,15 @@ where
             ranges,
             theta,
             scenarios,
-            settings.parsed.error.poly,
+            settings.error.poly,
             tx,
             settings,
         )),
         "POSTPROB" => Box::new(postprob::POSTPROB::new(
             engine,
             theta,
             scenarios,
-            settings.parsed.error.poly,
+            settings.error.poly,
             tx,
             settings,
         )),

src/algorithms/npag.rs

@@ -7,7 +7,7 @@ use crate::{
         output::NPResult,
         output::{CycleLog, NPCycle},
         prob, qr,
-        settings::run::Settings,
+        settings::Settings,
         simulation::predict::Engine,
         simulation::predict::{sim_obs, Predict},
     },
@@ -118,15 +118,15 @@ where
             f1: f64::default(),
             cycle: 1,
             gamma_delta: 0.1,
-            gamma: settings.parsed.error.value,
-            error_type: match settings.parsed.error.class.to_lowercase().as_str() {
+            gamma: settings.error.value,
+            error_type: match settings.error.class.to_lowercase().as_str() {
                 "additive" => ErrorType::Add,
                 "proportional" => ErrorType::Prop,
                 _ => panic!("Error type not supported"),
             },
             converged: false,
-            cycle_log: CycleLog::new(&settings.computed.random.names),
-            cache: settings.parsed.config.cache.unwrap_or(false),
+            cycle_log: CycleLog::new(&settings.random.names()),
+            cache: settings.config.cache,
             tx,
             settings,
             scenarios,
@@ -277,8 +277,6 @@ where
                 gamlam: self.gamma,
             };
             self.tx.send(Comm::NPCycle(state.clone())).unwrap();
-            self.cycle_log
-                .push_and_write(state, self.settings.parsed.config.pmetrics_outputs.unwrap());
 
             // Increasing objf signals instability or model misspecification.
             if self.last_objf > self.objf {
@@ -292,6 +290,9 @@ where
             self.w = self.lambda.clone();
             let pyl = self.psi.dot(&self.w);
 
+            self.cycle_log
+                .push_and_write(state, self.settings.config.output);
+
             // Stop if we have reached convergence criteria
             if (self.last_objf - self.objf).abs() <= THETA_G && self.eps > THETA_E {
                 self.eps /= 2.;
@@ -309,7 +310,7 @@ where
             }
 
             // Stop if we have reached maximum number of cycles
-            if self.cycle >= self.settings.parsed.config.cycles {
+            if self.cycle >= self.settings.config.cycles {
                 tracing::warn!("Maximum number of cycles reached");
                 break;
             }

src/algorithms/npod.rs

@@ -9,7 +9,7 @@ use crate::{
         output::NPResult,
         output::{CycleLog, NPCycle},
         prob, qr,
-        settings::run::Settings,
+        settings::Settings,
         simulation::predict::Engine,
         simulation::predict::{sim_obs, Predict},
     },
@@ -111,15 +111,15 @@ where
             objf: f64::INFINITY,
             cycle: 1,
             gamma_delta: 0.1,
-            gamma: settings.parsed.error.value,
-            error_type: match settings.parsed.error.class.as_str() {
+            gamma: settings.error.value,
+            error_type: match settings.error.class.as_str() {
                 "additive" => ErrorType::Add,
                 "proportional" => ErrorType::Prop,
                 _ => panic!("Error type not supported"),
             },
             converged: false,
-            cycle_log: CycleLog::new(&settings.computed.random.names),
-            cache: settings.parsed.config.cache.unwrap_or(false),
+            cycle_log: CycleLog::new(&settings.random.names()),
+            cache: settings.config.cache,
             tx,
             settings,
             scenarios,
@@ -296,7 +296,7 @@ where
             }
 
             // Stop if we have reached maximum number of cycles
-            if self.cycle >= self.settings.parsed.config.cycles {
+            if self.cycle >= self.settings.config.cycles {
                 tracing::warn!("Maximum number of cycles reached");
                 break;
             }
@@ -308,7 +308,7 @@ where
             }
             //TODO: the cycle migh break before reaching this point
             self.cycle_log
-                .push_and_write(state, self.settings.parsed.config.pmetrics_outputs.unwrap());
+                .push_and_write(state, self.settings.config.output);
 
             self.cycle += 1;
 

src/algorithms/postprob.rs

@@ -6,7 +6,7 @@ use crate::{
         ipm,
         output::NPResult,
         prob,
-        settings::run::Settings,
+        settings::Settings,
         simulation::predict::Engine,
         simulation::predict::{sim_obs, Predict},
     },
@@ -82,8 +82,8 @@ where
             objf: f64::INFINITY,
             cycle: 0,
             converged: false,
-            gamma: settings.parsed.error.value,
-            error_type: match settings.parsed.error.class.as_str() {
+            gamma: settings.error.value,
+            error_type: match settings.error.class.as_str() {
                 "additive" => ErrorType::Add,
                 "proportional" => ErrorType::Prop,
                 _ => panic!("Error type not supported"),

src/entrypoints.rs

@@ -5,7 +5,7 @@ use crate::prelude::{
     *,
 };
 use crate::routines::datafile::Scenario;
-use crate::routines::settings::run::Settings;
+use crate::routines::settings::*;
 
 use csv::{ReaderBuilder, WriterBuilder};
 use eyre::Result;
@@ -35,16 +35,16 @@ pub fn simulate<S>(engine: Engine<S>, settings_path: String) -> Result<()>
 where
     S: Predict<'static> + std::marker::Sync + std::marker::Send + 'static + Clone,
 {
-    let settings = settings::simulator::read(settings_path);
-    let theta_file = File::open(settings.paths.theta).unwrap();
+    let settings: Settings = read_settings(settings_path).unwrap();
+    let theta_file = File::open(settings.paths.prior.unwrap()).unwrap();
     let mut reader = ReaderBuilder::new()
         .has_headers(true)
         .from_reader(theta_file);
     let theta: Array2<f64> = reader.deserialize_array2_dynamic().unwrap();
 
     // Expand data
-    let idelta = settings.config.idelta.unwrap_or(0.0);
-    let tad = settings.config.tad.unwrap_or(0.0);
+    let idelta = settings.config.idelta;
+    let tad = settings.config.tad;
     let mut scenarios = datafile::parse(&settings.paths.data).unwrap();
     scenarios.iter_mut().for_each(|scenario| {
         *scenario = scenario.add_event_interval(idelta, tad);
@@ -88,17 +88,23 @@ where
     S: Predict<'static> + std::marker::Sync + std::marker::Send + 'static + Clone,
 {
     let now = Instant::now();
-    let settings = settings::run::read(settings_path);
+    let settings = match read_settings(settings_path) {
+        Ok(s) => s,
+        Err(e) => {
+            eprintln!("Error reading settings: {:?}", e);
+            std::process::exit(-1);
+        }
+    };
     let (tx, rx) = mpsc::unbounded_channel::<Comm>();
     let maintx = tx.clone();
     logger::setup_log(&settings, tx.clone());
     tracing::info!("Starting NPcore");
 
     // Read input data and remove excluded scenarios (if any)
-    let mut scenarios = datafile::parse(&settings.parsed.paths.data).unwrap();
-    if let Some(exclude) = &settings.parsed.config.exclude {
+    let mut scenarios = datafile::parse(&settings.paths.data).unwrap();
+    if let Some(exclude) = &settings.config.exclude {
         for val in exclude {
-            scenarios.remove(val.as_integer().unwrap() as usize);
+            scenarios.remove(val.as_ptr() as usize);
         }
     }
 
@@ -111,7 +117,7 @@ where
 
     // Spawn new thread for TUI
     let settings_tui = settings.clone();
-    let handle = if settings.parsed.config.tui {
+    let handle = if settings.config.tui {
         spawn(move || {
             start_ui(rx, settings_tui).expect("Failed to start TUI");
         })
@@ -128,10 +134,10 @@ where
     tracing::info!("Total time: {:.2?}", now.elapsed());
 
     // Write output files (if configured)
-    if let Some(write) = &settings.parsed.config.pmetrics_outputs {
-        let idelta = settings.parsed.config.idelta.unwrap_or(0.0);
-        let tad = settings.parsed.config.tad.unwrap_or(0.0);
-        result.write_outputs(*write, &engine, idelta, tad);
+    if settings.config.output {
+        let idelta = settings.config.idelta;
+        let tad = settings.config.tad;
+        result.write_outputs(true, &engine, idelta, tad);
     }
 
     tracing::info!("Program complete");

src/lib.rs

@@ -16,10 +16,7 @@ pub mod routines {
         pub mod adaptative_grid;
     }
 
-    pub mod settings {
-        pub mod run;
-        pub mod simulator;
-    }
+    pub mod settings;
     pub mod evaluation {
 
         pub mod ipm;

src/logger.rs

@@ -1,4 +1,4 @@
-use crate::routines::settings::run::Settings;
+use crate::routines::settings::Settings;
 use crate::tui::ui::Comm;
 use std::io::{self, Write};
 use tokio::sync::mpsc::UnboundedSender;
@@ -22,14 +22,10 @@ use tracing_subscriber::EnvFilter;
 /// If not, the log messages are written to stdout.
 pub fn setup_log(settings: &Settings, ui_tx: UnboundedSender<Comm>) {
     // Use the log level defined in configuration file, or default to info
-    let log_level = settings
-        .parsed
-        .config
-        .log_level
-        .as_ref()
-        .map(|level| level.as_str())
-        .unwrap_or("info")
-        .to_lowercase();
+    let log_level = settings.config.log_level.as_str();
+
+    // Use the log file defined in configuration file, or default to npcore.log
+    let log_path = settings.paths.log.as_ref().unwrap();
 
     let env_filter = EnvFilter::new(&log_level);
 
@@ -41,7 +37,7 @@ pub fn setup_log(settings: &Settings, ui_tx: UnboundedSender<Comm>) {
         .create(true)
         .write(true)
         .truncate(true)
-        .open(&settings.parsed.paths.log_out)
+        .open(log_path)
         .expect("Failed to open log file - does the directory exist?");
 
     let file_layer = fmt::layer()
@@ -50,7 +46,7 @@ pub fn setup_log(settings: &Settings, ui_tx: UnboundedSender<Comm>) {
         .with_timer(CompactTimestamp);
 
     // Define layer for stdout
-    let stdout_layer = if !settings.parsed.config.tui {
+    let stdout_layer = if !settings.config.tui {
         let layer = fmt::layer()
             .with_writer(std::io::stdout)
             .with_ansi(true)
@@ -66,7 +62,7 @@ pub fn setup_log(settings: &Settings, ui_tx: UnboundedSender<Comm>) {
         ui_tx: ui_tx.clone(),
     };
 
-    let tui_layer = if settings.parsed.config.tui {
+    let tui_layer = if settings.config.tui {
         let layer = fmt::layer()
             .with_writer(tui_writer_closure)
             .with_ansi(false)