feat: cli verbosity flag

Cargo.toml

@@ -12,7 +12,7 @@ members = [
 ]
 
 [workspace.package]
-version = "0.24.0"
+version = "0.25.0"
 edition = "2024"
 authors = ["Sebastian Paez"]
 license = "Apache-2.0"

pyproject.toml

@@ -1,6 +1,6 @@
 [project]
 name = "timsseek-workspace"
-version = "0.24.0"
+version = "0.25.0"
 requires-python = ">=3.11,<3.13"
 dependencies = [
     "jupyter[python]>=1.1.1",
@@ -55,7 +55,7 @@ packages = [
 ]
 
 [tool.bumpver]
-current_version = "0.24.0"
+current_version = "0.25.0"
 version_pattern = "MAJOR.MINOR.PATCH[-PYTAGNUM]"
 tag_message = "v{new_version}"
 commit_message = "chore: bump version to {new_version}"

python/speclib_builder/pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "hatchling.build"
 
 [project]
 name = "speclib_builder"
-version = "0.24.0"
+version = "0.25.0"
 requires-python = ">=3.11,<3.13"
 dependencies = [
   "rich",

python/timsseek_rescore/pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "hatchling.build"
 
 [project]
 name = "timsseek_rescore"
-version = "0.24.0"
+version = "0.25.0"
 requires-python = ">=3.11,<3.13"
 dependencies = [
   "polars",

python/timsseek_rts_receiver/pyproject.toml

@@ -1,6 +1,6 @@
 [project]
 name = "timsseek_rts_receiver"
-version = "0.24.0"
+version = "0.25.0"
 requires-python = ">=3.11,<3.13"
 description = "Add your description here"
 dependencies = [

rust/timsquery_cli/src/cli.rs

@@ -7,6 +7,14 @@ use std::path::PathBuf;
 #[derive(Parser, Debug)]
 #[command(author, version, about, long_about = None)]
 pub struct Args {
+    /// Increase logging verbosity (can be repeated: -v for debug, -vv for trace)
+    #[arg(short, long, action = clap::ArgAction::Count, global = true)]
+    pub verbose: u8,
+
+    /// Decrease logging verbosity (can be repeated: -q for warn, -qq for error)
+    #[arg(short, long, action = clap::ArgAction::Count, global = true)]
+    pub quiet: u8,
+
     #[command(subcommand)]
     pub command: Option<Commands>,
 }

rust/timsquery_cli/src/main.rs

@@ -30,14 +30,39 @@ use mimalloc::MiMalloc;
 #[global_allocator]
 static GLOBAL: MiMalloc = MiMalloc;
 
+/// Converts verbosity flags to a log level string.
+/// Returns the log level based on verbose/quiet counts.
+/// If RUST_LOG is set, it takes precedence.
+fn get_log_level(verbose: u8, quiet: u8) -> String {
+    // RUST_LOG environment variable takes precedence
+    if std::env::var("RUST_LOG").is_ok() {
+        return std::env::var("RUST_LOG").unwrap();
+    }
+
+    // Calculate effective verbosity: positive = more verbose, negative = more quiet
+    let effective = verbose as i8 - quiet as i8;
+
+    match effective {
+        2.. => "trace".to_string(),
+        1 => "debug".to_string(),
+        0 => "info".to_string(),
+        -1 => "warn".to_string(),
+        _ => "error".to_string(),
+    }
+}
+
 fn main() -> Result<(), CliError> {
-    let env_filter = EnvFilter::try_from_default_env().unwrap_or_else(|_| EnvFilter::new("info"));
+    let args = Args::parse();
+
+    let log_level = get_log_level(args.verbose, args.quiet);
+    let env_filter = EnvFilter::builder()
+        .with_default_directive(log_level.parse().unwrap())
+        .from_env_lossy();
     let subscriber = Registry::default()
         .with(env_filter)
         .with(tracing_subscriber::fmt::layer().with_span_events(FmtSpan::CLOSE));
 
     set_global_default(subscriber).expect("Setting default subscriber failed");
-    let args = Args::parse();
 
     match args.command {
         Some(Commands::QueryIndex(args)) => main_query_index(args)?,

rust/timsquery_viewer/src/cli.rs

@@ -4,6 +4,14 @@ use std::path::PathBuf;
 #[derive(Parser, Debug)]
 #[command(author, version, about, long_about = None)]
 pub struct Cli {
+    /// Increase logging verbosity (can be repeated: -v for debug, -vv for trace)
+    #[arg(short, long, action = clap::ArgAction::Count, global = true)]
+    pub verbose: u8,
+
+    /// Decrease logging verbosity (can be repeated: -q for warn, -qq for error)
+    #[arg(short, long, action = clap::ArgAction::Count, global = true)]
+    pub quiet: u8,
+
     #[arg(
         long,
         value_name = "FILE",

rust/timsquery_viewer/src/main.rs

@@ -25,34 +25,55 @@ use mimalloc::MiMalloc;
 #[global_allocator]
 static GLOBAL: MiMalloc = MiMalloc;
 
-fn setup_logger() {
-    let app_level = std::env::var("RUST_LOG").unwrap_or_else(|_| "info".to_string());
-    let env_filter = match EnvFilter::builder().parse(&app_level) {
+/// Converts verbosity flags to a log level string.
+/// Returns the log level based on verbose/quiet counts.
+/// If RUST_LOG is set, it takes precedence.
+fn get_log_level(verbose: u8, quiet: u8) -> String {
+    // RUST_LOG environment variable takes precedence
+    if std::env::var("RUST_LOG").is_ok() {
+        return std::env::var("RUST_LOG").unwrap();
+    }
+
+    // Calculate effective verbosity: positive = more verbose, negative = more quiet
+    let effective = verbose as i8 - quiet as i8;
+
+    match effective {
+        2.. => "trace".to_string(),
+        1 => "debug".to_string(),
+        0 => "info".to_string(),
+        -1 => "warn".to_string(),
+        _ => "error".to_string(),
+    }
+}
+
+fn setup_logger(verbose: u8, quiet: u8) {
+    let log_level = get_log_level(verbose, quiet);
+    let env_filter = match EnvFilter::builder().parse(&log_level) {
         Ok(filter) => filter,
         Err(_) => {
             let mut warning_msg = String::new();
             let _ = writeln!(
                 &mut warning_msg,
-                "Warning: Invalid RUST_LOG value: {}. Falling back to 'info'.",
-                app_level
+                "Warning: Invalid log level: {}. Falling back to 'info'.",
+                log_level
             );
             eprintln!("{}", warning_msg);
             EnvFilter::new("info")
         }
     };
 
-    // 5. Initialize Subscriber
+    // Initialize Subscriber
     let subscriber = Registry::default()
         .with(env_filter)
         .with(tracing_subscriber::fmt::layer().with_span_events(FmtSpan::CLOSE));
 
-    subscriber.init(); // simpler than set_global_default + expect
+    subscriber.init();
 }
 
 fn main() -> eframe::Result {
     let args = cli::Cli::parse();
 
-    setup_logger();
+    setup_logger(args.verbose, args.quiet);
     let options = eframe::NativeOptions {
         viewport: egui::ViewportBuilder::default()
             .with_inner_size([1400.0, 800.0])

rust/timsseek_cli/src/cli.rs

@@ -5,6 +5,14 @@ use timsseek::DecoyStrategy;
 #[derive(Parser, Debug)]
 #[command(author, version, about, long_about = None)]
 pub struct Cli {
+    /// Increase logging verbosity (can be repeated: -v for debug, -vv for trace)
+    #[arg(short, long, action = clap::ArgAction::Count, global = true)]
+    pub verbose: u8,
+
+    /// Decrease logging verbosity (can be repeated: -q for warn, -qq for error)
+    #[arg(short, long, action = clap::ArgAction::Count, global = true)]
+    pub quiet: u8,
+
     /// Path to the JSON configuration file (optional, uses defaults if not provided)
     #[arg(short, long)]
     pub config: Option<PathBuf>,

rust/timsseek_cli/src/main.rs

@@ -309,10 +309,34 @@ fn process_single_file(
     Ok(())
 }
 
+/// Converts verbosity flags to a log level string.
+/// Returns the log level based on verbose/quiet counts.
+/// If RUST_LOG is set, it takes precedence.
+fn get_log_level(verbose: u8, quiet: u8) -> String {
+    // RUST_LOG environment variable takes precedence
+    if std::env::var("RUST_LOG").is_ok() {
+        return std::env::var("RUST_LOG").unwrap();
+    }
+
+    // Calculate effective verbosity: positive = more verbose, negative = more quiet
+    let effective = verbose as i8 - quiet as i8;
+
+    match effective {
+        2.. => "trace".to_string(),
+        1 => "debug".to_string(),
+        0 => "info".to_string(),
+        -1 => "warn".to_string(),
+        _ => "error".to_string(),
+    }
+}
+
 fn main() -> std::result::Result<(), errors::CliError> {
+    // Parse command line arguments first to get verbosity flags
+    let args = Cli::parse();
+
+    let log_level = get_log_level(args.verbose, args.quiet);
     let fmt_filter = EnvFilter::builder()
-        .with_default_directive("info".parse().unwrap())
-        .with_env_var("RUST_LOG")
+        .with_default_directive(log_level.parse().unwrap())
         .from_env_lossy();
 
     #[cfg(feature = "instrumentation")]
@@ -356,9 +380,6 @@ fn main() -> std::result::Result<(), errors::CliError> {
 
     reg.init();
 
-    // Parse command line arguments
-    let args = Cli::parse();
-
     // Load and parse configuration, or use defaults
     let mut config = match args.config {
         Some(ref config_path) => {

rust/timsseek_cli/src/sample_speclib.rs

@@ -8,10 +8,22 @@ use clap::{
 };
 // use serde_json::to_string_pretty;
 use timsseek::Speclib;
+use tracing_subscriber::EnvFilter;
+use tracing_subscriber::fmt::format::FmtSpan;
+use tracing_subscriber::prelude::*;
+use tracing_subscriber::registry::Registry;
 
 #[derive(Parser)]
 #[command(version, about, long_about = None)]
 struct Cli {
+    /// Increase logging verbosity (can be repeated: -v for debug, -vv for trace)
+    #[arg(short, long, action = clap::ArgAction::Count, global = true)]
+    verbose: u8,
+
+    /// Decrease logging verbosity (can be repeated: -q for warn, -qq for error)
+    #[arg(short, long, action = clap::ArgAction::Count, global = true)]
+    quiet: u8,
+
     #[command(subcommand)]
     command: SubCommands,
 }
@@ -41,19 +53,44 @@ fn parse_speclib(speclib_file: &str) -> Result<(), timsseek::errors::LibraryRead
     Ok(())
 }
 
+/// Converts verbosity flags to a log level string.
+/// Returns the log level based on verbose/quiet counts.
+/// If RUST_LOG is set, it takes precedence.
+fn get_log_level(verbose: u8, quiet: u8) -> String {
+    // RUST_LOG environment variable takes precedence
+    if std::env::var("RUST_LOG").is_ok() {
+        return std::env::var("RUST_LOG").unwrap();
+    }
+
+    // Calculate effective verbosity: positive = more verbose, negative = more quiet
+    let effective = verbose as i8 - quiet as i8;
+
+    match effective {
+        2.. => "trace".to_string(),
+        1 => "debug".to_string(),
+        0 => "info".to_string(),
+        -1 => "warn".to_string(),
+        _ => "error".to_string(),
+    }
+}
+
+fn setup_logger(verbose: u8, quiet: u8) {
+    let log_level = get_log_level(verbose, quiet);
+    let env_filter = EnvFilter::builder()
+        .with_default_directive(log_level.parse().unwrap())
+        .from_env_lossy();
+    let subscriber = Registry::default()
+        .with(env_filter)
+        .with(tracing_subscriber::fmt::layer().with_span_events(FmtSpan::CLOSE));
+    subscriber.init();
+}
+
 fn main() -> Result<(), timsseek::errors::LibraryReadingError> {
-    // This is a placeholder for the main function.
-    // The actual implementation would depend on the specific requirements of the application.
     let cli = Cli::parse();
+    setup_logger(cli.verbose, cli.quiet);
 
     match &cli.command {
-        // SubCommands::Sample => {
-        //     // Generate a sample speclib
-        //     generate_sample_speclib();
-        //     Ok(())
-        // }
         SubCommands::Parse { speclib_file } => {
-            // Parse the provided speclib file
             parse_speclib(speclib_file)?;
             Ok(())
         }