Update for namechange

.github/workflows/time.yml

@@ -7,7 +7,7 @@ jobs:
   cargo-run:
     runs-on: self-hosted
     env:
-      NPCORE_CONFIG_TUI: false  # Disable TUI
+      PMCORE_CONFIG_TUI: false  # Disable TUI
     steps:
     - name: Checkout Repository
       uses: actions/checkout@v2

LICENSE

@@ -636,7 +636,7 @@ copy of the Program in return for a fee.
     You should have received a copy of the GNU General Public License
     along with this program.  If not, see <https://www.gnu.org/licenses/>.
 
-    NPcore  Copyright (C) 2023  J. Otálvaro, M. Neely, LAPKB
+    PMcore  Copyright (C) 2023  J. Otálvaro, M. Neely, LAPKB
     This program comes with ABSOLUTELY NO WARRANTY; for details type `show w'.
     This is free software, and you are welcome to redistribute it
     under certain conditions; type `show c' for details.

src/entrypoints.rs

@@ -79,9 +79,9 @@ where
     Ok(())
 }
 
-/// Primary entrypoint for NPcore
+/// Primary entrypoint for PMcore
 ///
-/// This function is the primary entrypoint for NPcore, and is used to run the algorithm.
+/// This function is the primary entrypoint for PMcore, and is used to run the algorithm.
 /// The settings for this function is specified in a TOML configuration file, see `routines::settings::run` for details.
 pub fn start<S>(engine: Engine<S>, settings_path: String) -> Result<NPResult>
 where
@@ -98,7 +98,7 @@ where
     let (tx, rx) = mpsc::unbounded_channel::<Comm>();
     let maintx = tx.clone();
     logger::setup_log(&settings, tx.clone());
-    tracing::info!("Starting NPcore");
+    tracing::info!("Starting PMcore");
 
     // Read input data and remove excluded scenarios (if any)
     let mut scenarios = datafile::parse(&settings.paths.data).unwrap();

src/lib.rs

@@ -1,4 +1,4 @@
-//! NPcore is a framework for developing and running non-parametric algorithms for population pharmacokinetic modelling
+//! PMcore is a framework for developing and running non-parametric algorithms for population pharmacokinetic modelling
 
 pub mod algorithms;
 pub mod routines {

src/logger.rs

@@ -24,7 +24,7 @@ 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.config.log_level.as_str();
 
-    // Use the log file defined in configuration file, or default to npcore.log
+    // Use the log file defined in configuration file, or default to pmcore.log
     let log_path = settings.paths.log.as_ref().unwrap();
 
     let env_filter = EnvFilter::new(&log_level);

src/routines/settings.rs

@@ -6,7 +6,7 @@ use serde_derive::Serialize;
 use serde_json;
 use std::collections::HashMap;
 
-/// Contains all settings NPcore
+/// Contains all settings PMcore
 #[derive(Debug, Deserialize, Clone, Serialize)]
 #[serde(deny_unknown_fields)]
 pub struct Settings {
@@ -26,7 +26,7 @@ pub struct Paths {
     pub data: String,
     /// If provided, the log file will be written to this path.
     pub log: Option<String>,
-    /// If provided, NPcore will use this prior instead of a "uniform" prior, see `sobol::generate` for details.
+    /// If provided, PMcore will use this prior instead of a "uniform" prior, see `sobol::generate` for details.
     pub prior: Option<String>,
 }
 
@@ -160,13 +160,13 @@ impl Error {
 ///
 /// This function parses the settings from a TOML configuration file. The settings are validated, and a copy of the settings is written to file.
 ///
-/// Entries in the TOML file may be overridden by environment variables. The environment variables must be prefixed with `NPCORE_`, and the TOML entry must be in uppercase. For example, the TUI may be disabled by setting the environment variable `NPCORE_TUI=false`.
+/// Entries in the TOML file may be overridden by environment variables. The environment variables must be prefixed with `PMCORE_`, and the TOML entry must be in uppercase. For example, the TUI may be disabled by setting the environment variable `PMCORE_TUI=false`.
 pub fn read_settings(path: String) -> Result<Settings, config::ConfigError> {
     let settings_path = path;
 
     let parsed = eConfig::builder()
         .add_source(config::File::with_name(&settings_path).format(config::FileFormat::Toml))
-        .add_source(config::Environment::with_prefix("NPCORE").separator("_"))
+        .add_source(config::Environment::with_prefix("PMCORE").separator("_"))
         .build()?;
 
     // Deserialize settings to the Settings struct

src/tui/ui.rs

@@ -1,4 +1,4 @@
-//! Defines the Terminal User Interface (TUI) for NPcore
+//! Defines the Terminal User Interface (TUI) for PMcore
 
 use crossterm::execute;
 use eyre::Result;
@@ -104,7 +104,7 @@ pub fn start_ui(mut rx: UnboundedReceiver<Comm>, settings: Settings) -> Result<(
             terminal.show_cursor()?;
             crossterm::terminal::disable_raw_mode()?;
             tracing::info!("Exit signal received");
-            print!("NPcore was stopped by user");
+            print!("PMcore was stopped by user");
             exit(0);
         }
     }