From 9a2f999ba78d047376f5c7937e4d10cc850707de Mon Sep 17 00:00:00 2001
From: Michael Hall <michael@mbh.sh>
Date: Tue, 21 Nov 2023 10:39:45 +1000
Subject: [PATCH] build: add anyhow

---
 Cargo.lock  |  7 +++++++
 Cargo.toml  |  2 ++
 src/lib.rs  |  9 +++------
 src/main.rs | 30 +++++++++++++++++-------------
 4 files changed, 29 insertions(+), 19 deletions(-)

diff --git a/Cargo.lock b/Cargo.lock
index 33a23b0..9302efb 100644
--- a/Cargo.lock
+++ b/Cargo.lock
@@ -59,6 +59,12 @@ dependencies = [
  "windows-sys",
 ]
 
+[[package]]
+name = "anyhow"
+version = "1.0.75"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "a4668cab20f66d8d020e1fbc0ebe47217433c1b6c8f2040faf858554e394ace6"
+
 [[package]]
 name = "bitflags"
 version = "2.4.1"
@@ -191,6 +197,7 @@ checksum = "f665ee40bc4a3c5590afb1e9677db74a508659dfd71e126420da8274909a0167"
 name = "nohuman"
 version = "0.1.0"
 dependencies = [
+ "anyhow",
  "clap",
  "env_logger",
  "log",
diff --git a/Cargo.toml b/Cargo.toml
index 8ac88fe..9a9cd86 100644
--- a/Cargo.toml
+++ b/Cargo.toml
@@ -1,5 +1,6 @@
 [package]
 name = "nohuman"
+description = "Remove human reads from a sequencing run"
 version = "0.1.0"
 edition = "2021"
 
@@ -9,4 +10,5 @@ edition = "2021"
 clap = { version = "4.4.7", features = ["derive"] }
 log = "0.4.20"
 env_logger = "0.10.0"
+anyhow = "1.0.75"
 
diff --git a/src/lib.rs b/src/lib.rs
index c076dd7..2424cf3 100644
--- a/src/lib.rs
+++ b/src/lib.rs
@@ -1,5 +1,5 @@
-use std::process::Command;
 use std::io::{self, Write};
+use std::process::Command;
 
 pub struct CommandRunner {
     pub command: String,
@@ -13,9 +13,7 @@ impl CommandRunner {
     }
 
     pub fn run(&self, args: &[&str]) -> io::Result<()> {
-        let output = Command::new(&self.command)
-            .args(args)
-            .output()?;
+        let output = Command::new(&self.command).args(args).output()?;
 
         if !output.status.success() {
             let error_message = String::from_utf8_lossy(&output.stderr);
@@ -34,7 +32,6 @@ impl CommandRunner {
     }
 }
 
-
 // add tests for each of the CommandRunner methods
 #[cfg(test)]
 mod tests {
@@ -71,4 +68,4 @@ mod tests {
         let command = CommandRunner::new("not-a-real-command");
         assert!(!command.is_executable());
     }
-}
\ No newline at end of file
+}
diff --git a/src/main.rs b/src/main.rs
index 1aebd1e..06609cc 100644
--- a/src/main.rs
+++ b/src/main.rs
@@ -1,7 +1,8 @@
-use clap::{Parser};
-use log::{info, warn, LevelFilter, error, debug};
-use nohuman::CommandRunner;
+use anyhow::{anyhow, bail, Context, Result};
+use clap::Parser;
 use env_logger::Builder;
+use log::{debug, error, info, warn, LevelFilter};
+use nohuman::CommandRunner;
 
 #[derive(Parser, Debug)]
 #[command(author, version, about, long_about = None)]
@@ -15,7 +16,7 @@ struct Args {
     verbose: bool,
 }
 
-fn main() {
+fn main() -> Result<()> {
     let args = Args::parse();
 
     // Initialize logger
@@ -46,15 +47,18 @@ fn main() {
         }
     }
 
-    if args.check {
-        if !missing_commands.is_empty() {
-            error!("The following dependencies are missing:");
-            for cmd in missing_commands {
-                error!("{}", cmd);
-            }
-            std::process::exit(1);
+    if !missing_commands.is_empty() {
+        error!("The following dependencies are missing:");
+        for cmd in missing_commands {
+            error!("{}", cmd);
         }
-        info!("Dependencies are available");
-        std::process::exit(0);
+        bail!("Missing dependencies");
     }
+
+    if args.check {
+        info!("All dependencies are available");
+        return Ok(());
+    }
+
+    Ok(())
 }