feat(micromzpaf): pack IonAnnot into a u32 and add neutral losses

Taskfile.yml

@@ -30,6 +30,11 @@ tasks:
       # dashboard.rs only exists under the opt-in feature; CI only `cargo check`s it.
       - cargo clippy -p timsseek_cli --features dashboard --all-targets -- -D warnings
 
+  # Keep workspace documentation warning-free.
+  doc:
+    cmds:
+      - RUSTDOCFLAGS="-D warnings" cargo doc --workspace --no-deps
+
   todos:
     cmds:
       - grep -nH -R TODO rust/tims*/src
@@ -81,4 +86,3 @@ tasks:
     desc: Stop local Koina server
     cmds:
       - docker stop koina-local
-

rust/apex_sim/src/plots.rs

@@ -278,7 +278,7 @@ impl Default for TraceToggles {
 }
 
 /// Bottom panel: the apex-finder intermediate traces, min-max normalized to
-/// [0,1] so heterogeneous scales overlay legibly. Apex markers overlaid.
+/// `[0,1]` so heterogeneous scales overlay legibly. Apex markers overlaid.
 pub fn traces(ui: &mut egui::Ui, score: &ScoreResult, tog: &TraceToggles, true_apex: f32) {
     let t = &score.traces;
     let mut series: Vec<(&str, &[f32])> = Vec::new();

rust/micromzpaf/Cargo.toml

@@ -7,6 +7,9 @@ license.workspace = true
 [dependencies]
 serde = { workspace = true, features = ["derive"] }
 thiserror = { workspace = true }
+# Used for the one-time warning when parsing drops a mass-error suffix.
+tracing = { workspace = true }
 
-# Workspace-inherited deps
-rustyms = { workspace = true }
+[dev-dependencies]
+# Pins the string serialization format.
+serde_json = { workspace = true }

rust/micromzpaf/src/error.rs

@@ -0,0 +1,52 @@
+//! Why an annotation could not be parsed or represented.
+
+use thiserror::Error;
+
+use crate::{
+    CHARGE_MAX,
+    CHARGE_MIN,
+    ISOTOPE_MAX,
+    ISOTOPE_MIN,
+};
+
+/// Why an annotation could not be parsed or represented.
+#[derive(Debug, Error)]
+pub enum IonParsingError {
+    #[error("Ordinal {ordinal} out of range for series '{series}'")]
+    OrdinalOutOfRange { ordinal: u8, series: char },
+    #[error("Series '{series}' requires an ordinal")]
+    MissingOrdinal { series: char },
+    #[error("Series '{series}' takes no ordinal, got {ordinal}")]
+    UnexpectedOrdinal { series: char, ordinal: u8 },
+    #[error("Unsupported fragment type: '{fragment_type}'")]
+    UnsupportedFragmentType { fragment_type: char },
+    #[error("Charge cannot be 0")]
+    ChargeCannotBeZero,
+    #[error("Charge {charge} outside the representable range {CHARGE_MIN}..={CHARGE_MAX}")]
+    ChargeOutOfRange { charge: i8 },
+    #[error(
+        "Isotope offset {isotope} outside the representable range {ISOTOPE_MIN}..={ISOTOPE_MAX}"
+    )]
+    IsotopeOutOfRange { isotope: i8 },
+    #[error("Neutral loss '{loss}' is not representable")]
+    UnsupportedNeutralLoss { loss: String },
+    #[error("Immonium ions must be a bare uppercase residue, got '{annotation}'")]
+    UnsupportedModifiedImmonium { annotation: String },
+    #[error("Ran out of distinct unknown-ion labels: the 8-bit ordinal is exhausted")]
+    UnknownIonsExhausted,
+    #[error("Could not parse '{annotation}': {context}")]
+    ParsingError {
+        annotation: String,
+        context: &'static str,
+    },
+}
+
+impl IonParsingError {
+    /// Create a parsing error with context.
+    pub(crate) fn parse(annotation: &str, context: &'static str) -> Self {
+        Self::ParsingError {
+            annotation: annotation.to_string(),
+            context,
+        }
+    }
+}