refactor(cli): initial branch commit

crates/sage-cli/Cargo.toml

@@ -10,6 +10,10 @@ license = "MIT"
 
 # See more keys and their definitions at https://doc.rust-lang.org/cargo/reference/manifest.html
 
+[lib]
+name = "sage_cli"
+path = "src/lib.rs"
+
 [[bin]]
 name = "sage"
 path = "src/main.rs"
@@ -20,7 +24,7 @@ sage-cloudpath = { path = "../sage-cloudpath", features = ["parquet"] }
 
 anyhow = "1.0"
 csv = "1"
-clap = { version="4.0", features = ["cargo", "unicode"] }
+clap = { version = "4.0", features = ["cargo", "unicode"] }
 env_logger = "0.8.4"
 fnv = "1.0"
 log = "0.4.0"
@@ -29,6 +33,6 @@ num_cpus = "1.13"
 rayon = "1.5"
 regex = "1.0"
 ryu = "1.0"
-serde = { version="1.0", features = ["derive"] }
+serde = { version = "1.0", features = ["derive"] }
 serde_json = "1.0"
 sysinfo = "0.29"

crates/sage-cli/src/input.rs

@@ -49,38 +49,38 @@ pub struct Search {
 #[derive(Deserialize)]
 /// Input search parameters deserialized from JSON file
 pub struct Input {
-    database: Builder,
-    precursor_tol: Tolerance,
-    fragment_tol: Tolerance,
-    report_psms: Option<usize>,
-    chimera: Option<bool>,
-    wide_window: Option<bool>,
-    min_peaks: Option<usize>,
-    max_peaks: Option<usize>,
-    max_fragment_charge: Option<u8>,
-    min_matched_peaks: Option<u16>,
-    precursor_charge: Option<(u8, u8)>,
-    override_precursor_charge: Option<bool>,
-    isotope_errors: Option<(i8, i8)>,
-    deisotope: Option<bool>,
-    quant: Option<QuantOptions>,
-    predict_rt: Option<bool>,
-    output_directory: Option<String>,
-    mzml_paths: Option<Vec<String>>,
-    bruker_spectrum_processor: Option<BrukerSpectrumProcessor>,
-
-    annotate_matches: Option<bool>,
-    write_pin: Option<bool>,
-    score_type: Option<ScoreType>,
+    pub database: Builder,
+    pub precursor_tol: Tolerance,
+    pub fragment_tol: Tolerance,
+    pub report_psms: Option<usize>,
+    pub chimera: Option<bool>,
+    pub wide_window: Option<bool>,
+    pub min_peaks: Option<usize>,
+    pub max_peaks: Option<usize>,
+    pub max_fragment_charge: Option<u8>,
+    pub min_matched_peaks: Option<u16>,
+    pub precursor_charge: Option<(u8, u8)>,
+    pub override_precursor_charge: Option<bool>,
+    pub isotope_errors: Option<(i8, i8)>,
+    pub deisotope: Option<bool>,
+    pub quant: Option<QuantOptions>,
+    pub predict_rt: Option<bool>,
+    pub output_directory: Option<String>,
+    pub mzml_paths: Option<Vec<String>>,
+    pub bruker_spectrum_processor: Option<BrukerSpectrumProcessor>,
+
+    pub annotate_matches: Option<bool>,
+    pub write_pin: Option<bool>,
+    pub score_type: Option<ScoreType>,
 }
 
 #[derive(Serialize, Deserialize, Debug)]
 pub struct LfqOptions {
-    peak_scoring: Option<sage_core::lfq::PeakScoringStrategy>,
-    integration: Option<sage_core::lfq::IntegrationStrategy>,
-    spectral_angle: Option<f64>,
-    ppm_tolerance: Option<f32>,
-    combine_charge_states: Option<bool>,
+    pub peak_scoring: Option<sage_core::lfq::PeakScoringStrategy>,
+    pub integration: Option<sage_core::lfq::IntegrationStrategy>,
+    pub spectral_angle: Option<f64>,
+    pub ppm_tolerance: Option<f32>,
+    pub combine_charge_states: Option<bool>,
 }
 
 impl From<LfqOptions> for LfqSettings {
@@ -108,11 +108,11 @@ impl From<LfqOptions> for LfqSettings {
 
 #[derive(Serialize, Deserialize, Debug)]
 pub struct TmtOptions {
-    level: Option<u8>,
-    sn: Option<bool>,
+    pub level: Option<u8>,
+    pub sn: Option<bool>,
 }
 
-#[derive(Copy, Clone, Serialize)]
+#[derive(Copy, Clone, Serialize, Debug)]
 pub struct TmtSettings {
     pub level: u8,
     pub sn: bool,

crates/sage-cli/src/lib.rs

@@ -0,0 +1,4 @@
+pub mod input;
+pub mod output;
+pub mod runner;
+pub mod telemetry;