chore: update rust edition and clippy/fmt

jayhesselberth · jayhesselberth · commit 7de1613bf31b · 2026-01-01T09:11:50.000-07:00
diff --git a/Cargo.toml b/Cargo.toml
@@ -4,7 +4,7 @@ members = ["crates/*"]
 
 [workspace.package]
 version = "0.1.0-alpha.1"
-edition = "2021"
+edition = "2024"
 rust-version = "1.85"
 license = "MIT"
 authors = ["Jay Hesselberth"]
diff --git a/crates/charmer-core/src/lib.rs b/crates/charmer-core/src/lib.rs
@@ -6,8 +6,8 @@
 pub mod main_log;
 pub mod metadata;
 
-pub use main_log::{find_latest_log, parse_log_file, parse_main_log, SnakemakeLogInfo};
+pub use main_log::{SnakemakeLogInfo, find_latest_log, parse_log_file, parse_main_log};
 pub use metadata::{
-    decode_metadata_filename, parse_metadata_file, scan_metadata_dir, MetadataError, SnakemakeJob,
-    SnakemakeMetadata,
+    MetadataError, SnakemakeJob, SnakemakeMetadata, decode_metadata_filename, parse_metadata_file,
+    scan_metadata_dir,
 };
diff --git a/crates/charmer-lsf/src/bhist.rs b/crates/charmer-lsf/src/bhist.rs
@@ -1,7 +1,7 @@
 //! Query LSF job history via bhist.
 
 use crate::types::{LsfJob, LsfJobState};
-use charmer_parsers::{parse_memory_mb, run_command_allow_failure, MemoryFormat};
+use charmer_parsers::{MemoryFormat, parse_memory_mb, run_command_allow_failure};
 use chrono::{DateTime, Utc};
 use std::time::Duration;
 use thiserror::Error;
diff --git a/crates/charmer-lsf/src/bjobs.rs b/crates/charmer-lsf/src/bjobs.rs
@@ -2,8 +2,8 @@
 
 use crate::types::{LsfJob, LsfJobState};
 use charmer_parsers::{
-    non_empty_string, parse_lsf_timestamp, parse_memory_mb, run_command_allow_failure,
-    split_delimited, MemoryFormat,
+    MemoryFormat, non_empty_string, parse_lsf_timestamp, parse_memory_mb,
+    run_command_allow_failure, split_delimited,
 };
 use std::time::Duration;
 use thiserror::Error;
diff --git a/crates/charmer-lsf/src/failure.rs b/crates/charmer-lsf/src/failure.rs
@@ -3,8 +3,8 @@
 //! Query detailed failure information and provide actionable suggestions.
 
 use charmer_parsers::{
-    format_duration, format_duration_lsf, parse_duration_secs, parse_memory_mb,
-    run_command_allow_failure, MemoryFormat,
+    MemoryFormat, format_duration, format_duration_lsf, parse_duration_secs, parse_memory_mb,
+    run_command_allow_failure,
 };
 use thiserror::Error;
 use tokio::process::Command;
diff --git a/crates/charmer-lsf/src/lib.rs b/crates/charmer-lsf/src/lib.rs
@@ -7,7 +7,7 @@ pub mod bjobs;
 pub mod failure;
 pub mod types;
 
-pub use bhist::{query_bhist, BhistError};
-pub use bjobs::{query_bjobs, BjobsError};
-pub use failure::{analyze_failure, FailureAnalysis, FailureError, FailureMode};
+pub use bhist::{BhistError, query_bhist};
+pub use bjobs::{BjobsError, query_bjobs};
+pub use failure::{FailureAnalysis, FailureError, FailureMode, analyze_failure};
 pub use types::{LsfJob, LsfJobState};
diff --git a/crates/charmer-monitor/src/app.rs b/crates/charmer-monitor/src/app.rs
@@ -5,12 +5,12 @@ use crate::components::{
 };
 use crate::ui::Theme;
 use charmer_runs::RunInfo;
-use charmer_state::{JobStatus, PipelineState, MAIN_PIPELINE_JOB_ID};
+use charmer_state::{JobStatus, MAIN_PIPELINE_JOB_ID, PipelineState};
 use crossterm::event::{self, Event, KeyCode, KeyEvent, KeyModifiers};
 use ratatui::{
+    Frame,
     layout::{Constraint, Direction, Layout, Rect},
     widgets::Clear,
-    Frame,
 };
 use std::time::{Duration, Instant};
 
@@ -113,11 +113,11 @@ pub struct App {
     command_expanded: bool,                    // Whether command section is expanded in details
 
     // Run management
-    pub runs: Vec<RunInfo>,              // Available runs
-    pub selected_run: Option<String>,    // Currently selected run UUID
-    pub show_run_picker: bool,           // Whether run picker modal is open
-    pub run_picker_index: usize,         // Selected index in run picker
-    pub show_all_jobs: bool,             // Whether to show all jobs or just snakemake jobs
+    pub runs: Vec<RunInfo>,           // Available runs
+    pub selected_run: Option<String>, // Currently selected run UUID
+    pub show_run_picker: bool,        // Whether run picker modal is open
+    pub run_picker_index: usize,      // Selected index in run picker
+    pub show_all_jobs: bool,          // Whether to show all jobs or just snakemake jobs
 }
 
 impl App {
@@ -627,7 +627,10 @@ impl App {
                     if let Some(run) = self.runs.get(self.run_picker_index) {
                         self.selected_run = Some(run.run_uuid.clone());
                         self.status_message = Some((
-                            format!("Selected run: {}", &run.run_uuid[..8.min(run.run_uuid.len())]),
+                            format!(
+                                "Selected run: {}",
+                                &run.run_uuid[..8.min(run.run_uuid.len())]
+                            ),
                             Instant::now(),
                         ));
                     }
@@ -836,11 +839,7 @@ impl App {
                     &run.run_uuid
                 };
 
-                let jobs_str = format!(
-                    "{}/{}",
-                    run.completed_jobs,
-                    run.total_jobs.unwrap_or(0)
-                );
+                let jobs_str = format!("{}/{}", run.completed_jobs, run.total_jobs.unwrap_or(0));
 
                 let time_ago = format_time_ago(run.last_updated);
 
diff --git a/crates/charmer-monitor/src/components/footer.rs b/crates/charmer-monitor/src/components/footer.rs
@@ -1,11 +1,11 @@
 //! Footer component with keyboard shortcuts and status messages.
 
 use ratatui::{
+    Frame,
     layout::{Constraint, Direction, Layout, Rect},
     style::{Color, Modifier, Style},
     text::{Line, Span},
     widgets::Paragraph,
-    Frame,
 };
 
 /// Version from Cargo.toml
diff --git a/crates/charmer-monitor/src/components/header.rs b/crates/charmer-monitor/src/components/header.rs
@@ -3,11 +3,11 @@
 use charmer_state::PipelineState;
 use chrono::Local;
 use ratatui::{
+    Frame,
     layout::Rect,
     style::{Color, Modifier, Style},
     text::{Line, Span},
     widgets::{Block, Borders, Paragraph},
-    Frame,
 };
 
 pub struct Header;
diff --git a/crates/charmer-monitor/src/components/job_detail.rs b/crates/charmer-monitor/src/components/job_detail.rs
@@ -3,11 +3,11 @@
 use charmer_state::{EnvType, ExecutionEnvironment, FailureMode, Job, JobStatus, PipelineState};
 use chrono::Utc;
 use ratatui::{
+    Frame,
     layout::Rect,
     style::{Color, Modifier, Style},
     text::{Line, Span},
     widgets::{Block, Borders, Paragraph},
-    Frame,
 };
 
 /// Color palette for wildcard values (matches job_list.rs).
diff --git a/crates/charmer-monitor/src/components/job_list.rs b/crates/charmer-monitor/src/components/job_list.rs
@@ -2,16 +2,16 @@
 
 use crate::app::ViewMode;
 use crate::components::ViewTabs;
-use charmer_state::{Job, JobCounts, JobStatus, PipelineState, MAIN_PIPELINE_JOB_ID};
+use charmer_state::{Job, JobCounts, JobStatus, MAIN_PIPELINE_JOB_ID, PipelineState};
 use ratatui::{
+    Frame,
     layout::{Constraint, Direction, Layout, Rect},
     style::{Color, Modifier, Style},
     text::{Line, Span},
     widgets::{
         Block, Borders, Gauge, List, ListItem, ListState, Paragraph, Scrollbar,
         ScrollbarOrientation, ScrollbarState,
     },
-    Frame,
 };
 use std::collections::{HashMap, HashSet};
 
diff --git a/crates/charmer-monitor/src/components/log_viewer.rs b/crates/charmer-monitor/src/components/log_viewer.rs
@@ -1,11 +1,11 @@
 //! Log viewer component for displaying job log files.
 
 use ratatui::{
+    Frame,
     layout::Rect,
     style::{Color, Style},
     text::{Line, Span},
     widgets::{Block, Borders, Paragraph, Scrollbar, ScrollbarOrientation, ScrollbarState, Wrap},
-    Frame,
 };
 use std::fs;
 use std::io;
diff --git a/crates/charmer-monitor/src/components/rule_summary.rs b/crates/charmer-monitor/src/components/rule_summary.rs
@@ -4,13 +4,13 @@ use crate::app::ViewMode;
 use crate::components::ViewTabs;
 use charmer_state::{JobStatus, PipelineState};
 use ratatui::{
+    Frame,
     layout::{Constraint, Rect},
     style::{Color, Modifier, Style},
     text::Span,
     widgets::{
         Block, Borders, Row, Scrollbar, ScrollbarOrientation, ScrollbarState, Table, TableState,
     },
-    Frame,
 };
 
 /// Statistics for a single rule.
diff --git a/crates/charmer-parsers/src/lib.rs b/crates/charmer-parsers/src/lib.rs
@@ -7,8 +7,8 @@ pub mod command;
 pub mod memory;
 pub mod time;
 
-pub use command::{run_command, run_command_allow_failure, CommandError};
-pub use memory::{parse_memory_mb, MemoryFormat};
+pub use command::{CommandError, run_command, run_command_allow_failure};
+pub use memory::{MemoryFormat, parse_memory_mb};
 pub use time::{
     format_duration, format_duration_lsf, format_duration_slurm, parse_duration,
     parse_duration_secs, parse_exit_code, parse_lsf_timestamp, parse_slurm_timestamp,
diff --git a/crates/charmer-runs/src/store.rs b/crates/charmer-runs/src/store.rs
@@ -78,7 +78,10 @@ mod tests {
         let store = RunStore::new(working_dir);
 
         let mut state = RunsState::default();
-        state.upsert_run(RunInfo::new("test-run".to_string(), working_dir.to_path_buf()));
+        state.upsert_run(RunInfo::new(
+            "test-run".to_string(),
+            working_dir.to_path_buf(),
+        ));
 
         store.save(&state).unwrap();
         assert!(store.path().exists());
diff --git a/crates/charmer-runs/src/types.rs b/crates/charmer-runs/src/types.rs
@@ -138,7 +138,8 @@ impl RunsState {
             self.runs.push(run);
         }
         // Sort by last_updated descending
-        self.runs.sort_by(|a, b| b.last_updated.cmp(&a.last_updated));
+        self.runs
+            .sort_by(|a, b| b.last_updated.cmp(&a.last_updated));
         // Keep only last N runs
         self.runs.truncate(Self::MAX_RUNS);
     }
diff --git a/crates/charmer-slurm/src/failure.rs b/crates/charmer-slurm/src/failure.rs
@@ -3,8 +3,8 @@
 //! Query detailed failure information and provide actionable suggestions.
 
 use charmer_parsers::{
-    format_duration, format_duration_slurm, parse_duration_secs, parse_memory_mb,
-    run_command_allow_failure, MemoryFormat,
+    MemoryFormat, format_duration, format_duration_slurm, parse_duration_secs, parse_memory_mb,
+    run_command_allow_failure,
 };
 use thiserror::Error;
 use tokio::process::Command;
@@ -108,9 +108,18 @@ impl FailureAnalysis {
             FailureMode::ExitCode { code, signal } => {
                 let explanation = if let Some(sig) = signal {
                     match sig {
-                        9 => format!("Job killed with signal {} (SIGKILL). Exit code: {}", sig, code),
-                        11 => format!("Job crashed with signal {} (SIGSEGV - segmentation fault). Exit code: {}", sig, code),
-                        15 => format!("Job terminated with signal {} (SIGTERM). Exit code: {}", sig, code),
+                        9 => format!(
+                            "Job killed with signal {} (SIGKILL). Exit code: {}",
+                            sig, code
+                        ),
+                        11 => format!(
+                            "Job crashed with signal {} (SIGSEGV - segmentation fault). Exit code: {}",
+                            sig, code
+                        ),
+                        15 => format!(
+                            "Job terminated with signal {} (SIGTERM). Exit code: {}",
+                            sig, code
+                        ),
                         _ => format!("Job exited with code {} and signal {}", code, sig),
                     }
                 } else {
diff --git a/crates/charmer-slurm/src/lib.rs b/crates/charmer-slurm/src/lib.rs
@@ -7,7 +7,7 @@ pub mod sacct;
 pub mod squeue;
 pub mod types;
 
-pub use failure::{analyze_failure, FailureAnalysis, FailureError, FailureMode};
-pub use sacct::{query_resource_usage, query_sacct, SacctError, SlurmResourceUsage};
-pub use squeue::{query_squeue, SqueueError};
+pub use failure::{FailureAnalysis, FailureError, FailureMode, analyze_failure};
+pub use sacct::{SacctError, SlurmResourceUsage, query_resource_usage, query_sacct};
+pub use squeue::{SqueueError, query_squeue};
 pub use types::{SlurmJob, SlurmJobState};
diff --git a/crates/charmer-slurm/src/sacct.rs b/crates/charmer-slurm/src/sacct.rs
@@ -2,8 +2,8 @@
 
 use crate::types::{SlurmJob, SlurmJobState};
 use charmer_parsers::{
-    non_empty_string, parse_duration, parse_duration_secs, parse_exit_code, parse_memory_mb,
-    parse_slurm_timestamp, run_command, split_delimited, MemoryFormat,
+    MemoryFormat, non_empty_string, parse_duration, parse_duration_secs, parse_exit_code,
+    parse_memory_mb, parse_slurm_timestamp, run_command, split_delimited,
 };
 use chrono::{DateTime, Utc};
 use std::time::Duration;
@@ -20,8 +20,7 @@ pub enum SacctError {
 
 /// sacct output format (--parsable2 uses | delimiter)
 /// JobIDRaw, JobName, State, Partition, Submit, Start, End, NodeList, AllocCPUS, ReqMem, Timelimit, Comment, ExitCode
-const SACCT_FORMAT: &str =
-    "JobIDRaw,JobName,State,Partition,Submit,Start,End,NodeList,AllocCPUS,ReqMem,Timelimit,Comment,ExitCode";
+const SACCT_FORMAT: &str = "JobIDRaw,JobName,State,Partition,Submit,Start,End,NodeList,AllocCPUS,ReqMem,Timelimit,Comment,ExitCode";
 
 /// Parse sacct state string with exit code info.
 fn parse_state(state_str: &str, exit_code_str: &str) -> SlurmJobState {
diff --git a/crates/charmer-slurm/src/squeue.rs b/crates/charmer-slurm/src/squeue.rs
@@ -2,8 +2,8 @@
 
 use crate::types::{SlurmJob, SlurmJobState};
 use charmer_parsers::{
-    non_empty_string, parse_duration, parse_memory_mb, parse_slurm_timestamp, run_command,
-    split_delimited, MemoryFormat,
+    MemoryFormat, non_empty_string, parse_duration, parse_memory_mb, parse_slurm_timestamp,
+    run_command, split_delimited,
 };
 use std::time::Duration;
 use thiserror::Error;
diff --git a/crates/charmer-state/src/lib.rs b/crates/charmer-state/src/lib.rs
@@ -11,6 +11,6 @@ pub use merge::{
 };
 pub use types::{
     DataSources, EnvType, ExecutionEnvironment, FailureAnalysis, FailureMode, Job, JobCounts,
-    JobError, JobResources, JobStatus, JobTiming, PipelineError, PipelineErrorType, PipelineState,
-    ResourceUsage, MAIN_PIPELINE_JOB_ID,
+    JobError, JobResources, JobStatus, JobTiming, MAIN_PIPELINE_JOB_ID, PipelineError,
+    PipelineErrorType, PipelineState, ResourceUsage,
 };
diff --git a/crates/charmer/src/main.rs b/crates/charmer/src/main.rs
@@ -7,14 +7,14 @@ use charmer_cli::Args;
 use charmer_core::{parse_main_log, parse_metadata_file, scan_metadata_dir};
 use charmer_monitor::App;
 use charmer_runs::{RunStatus, RunStore};
-use charmer_state::{merge_snakemake_jobs, PipelineState};
+use charmer_state::{PipelineState, merge_snakemake_jobs};
 use clap::Parser;
 use crossterm::{
     execute,
-    terminal::{disable_raw_mode, enable_raw_mode, EnterAlternateScreen, LeaveAlternateScreen},
+    terminal::{EnterAlternateScreen, LeaveAlternateScreen, disable_raw_mode, enable_raw_mode},
 };
 use miette::{IntoDiagnostic, Result};
-use polling::{init_polling, PollingConfig};
+use polling::{PollingConfig, init_polling};
 use ratatui::prelude::*;
 use std::collections::HashMap;
 use std::io;
@@ -98,9 +98,10 @@ async fn main() -> Result<()> {
     let _polling_handle = init_polling(Arc::clone(&state), poll_config).await;
 
     // Determine selected run (from args or auto-detect from runs state)
-    let selected_run = args.run_uuid.clone().or_else(|| {
-        runs_state.current_run().map(|r| r.run_uuid.clone())
-    });
+    let selected_run = args
+        .run_uuid
+        .clone()
+        .or_else(|| runs_state.current_run().map(|r| r.run_uuid.clone()));
 
     // Initialize app with a clone of the initial state
     let initial_state = {
@@ -199,10 +200,10 @@ async fn run_app(
                         let path_str = path.to_string();
                         let now = std::time::Instant::now();
 
-                        if let Some(last_time) = debounce_map.get(&path_str) {
-                            if now.duration_since(*last_time) < debounce_duration {
-                                continue; // Skip this event - too soon
-                            }
+                        if let Some(last_time) = debounce_map.get(&path_str)
+                            && now.duration_since(*last_time) < debounce_duration
+                        {
+                            continue; // Skip this event - too soon
                         }
 
                         debounce_map.insert(path_str, now);
@@ -242,11 +243,11 @@ async fn run_app(
             let working_dir = state_guard.working_dir.clone();
             drop(state_guard);
 
-            if let Ok(jobs) = scan_metadata_dir(&working_dir) {
-                if !jobs.is_empty() {
-                    let mut state_guard = shared_state.lock().await;
-                    merge_snakemake_jobs(&mut state_guard, jobs);
-                }
+            if let Ok(jobs) = scan_metadata_dir(&working_dir)
+                && !jobs.is_empty()
+            {
+                let mut state_guard = shared_state.lock().await;
+                merge_snakemake_jobs(&mut state_guard, jobs);
             }
             last_rescan = std::time::Instant::now();
         }
diff --git a/crates/charmer/src/polling.rs b/crates/charmer/src/polling.rs
diff --git a/crates/charmer/src/watcher.rs b/crates/charmer/src/watcher.rs
