v0.9.3

Cargo.lock

@@ -293,7 +293,7 @@ source = "registry+https://github.com/rust-lang/crates.io-index"
 
 [[package]]
 name = "wham"
-version = "0.9.1"
+version = "0.9.2"
 dependencies = [
  "GSL 1.0.0 (registry+https://github.com/rust-lang/crates.io-index)",
  "clap 2.32.0 (registry+https://github.com/rust-lang/crates.io-index)",

Cargo.toml

@@ -1,6 +1,6 @@
 [package]
 name = "wham"
-version = "0.9.1"
+version = "0.9.3"
 authors = ["D. Bauer <bauer@bio.tu-darmstadt.de>"]
 description = "An implementation of the weighted histogram analysis method"
 license = "GPL-3.0"
@@ -17,4 +17,4 @@ rayon = "1.0.3"
 opt-level = 2
 
 [features]
-default = ["GSL/v2"]
+default = ["GSL/v2"]

src/io.rs

@@ -7,6 +7,7 @@ use std::io::{BufReader,BufWriter};
 use k_B;
 use std::path::Path;
 use super::errors::*;
+use f64;
 
 // Returns the path to path2 relative to path1
 // path1: "path/to/file.dat"
@@ -112,7 +113,7 @@ fn is_in_hist_boundaries(values: &Vec<f64>, cfg: &Config) -> bool {
 // parse a timeseries file into a histogram
 fn read_window_file(window_file: &str, cfg: &Config) -> Result<Histogram> {
 	let f = File::open(window_file)
-        .chain_err(|| format!("Failed to open sample data file {}", window_file))?;
+        .chain_err(|| format!("Failed to open sample data file {}.", window_file))?;
     let mut buf = BufReader::new(&f);
 
     // total number of bins is the product of all dimensions length
@@ -126,7 +127,9 @@ fn read_window_file(window_file: &str, cfg: &Config) -> Result<Histogram> {
 
     // read and parse each timeseries line
     let mut line = String::new();
+    let mut linecount = 0;
     while buf.read_line(&mut line).chain_err(|| "Failed to read line")? > 0 {
+        linecount += 1;
         // skip comments and empty lines
         if line.starts_with("#") || line.starts_with("@") || line.len() == 0 {
             line.clear();
@@ -134,12 +137,17 @@ fn read_window_file(window_file: &str, cfg: &Config) -> Result<Histogram> {
         }
 
         {
-            let mut split = line.split_whitespace();
 
-            split.next(); // skip time/step column
-            let values: Vec<f64> = (0..cfg.dimens).collect::<Vec<usize>>().iter().map(|_| {
-                split.next().unwrap().parse::<f64>().unwrap()
-            }).collect();
+            let split: Vec<&str> = line.split_whitespace().collect();
+            if split.len() < cfg.dimens+1 {
+                bail!(format!("Wrong number of columns in line {} of window file {}. Empty Line?.", linecount, window_file));
+            }
+
+            let mut values: Vec<f64> = vec![f64::NAN; cfg.dimens];
+            for i in 0..values.len() {
+                values[i] = split[i+1].parse::<f64>()
+                    .chain_err(|| format!("Failed to parse line {} of window file {}.", linecount, window_file))?;
+            }
 
             if is_in_hist_boundaries(&values, cfg) {
                 let bin_indeces = (0..cfg.dimens).map(|dimen: usize| {

tests/COLVAR_unparseable_1.xvg

@@ -0,0 +1,11 @@
+84.840004  -2.878293
+84.860004  -2.827750
+84.880004  -2.962375
+84.900004  
+84.920004  -2.748589
+84.940004  -2.726197
+84.960004  -2.802982
+84.980004  -2.771980
+85.000004  -2.706482
+85.020004  -2.776983
+85.040004  -2.883180

tests/COLVAR_unparseable_2.xvg

@@ -0,0 +1,11 @@
+84.840004  -2.878293
+84.860004  -2.827750
+84.880004  -2.962375
+84.900004   qwee
+84.920004  -2.748589
+84.940004  -2.726197
+84.960004  -2.802982
+84.980004  -2.771980
+85.000004  -2.706482
+85.020004  -2.776983
+85.040004  -2.883180

tests/integration.rs

@@ -77,6 +77,36 @@ mod integration {
         ));
     }
 
+    #[test]
+    fn unparseable_timeseries() {
+        let output = Command::new("./target/debug/wham")
+            .args(&["--bins", "100", "--min", "-3.0", "--max", "3.0", "-T", "300"])
+            .args(&["-f", "tests/metadata_unparseable3.dat"])
+            .args(&["-o", "/dev/null"])
+            .output()
+            .expect("failed to execute process");
+        let output = String::from_utf8_lossy(&output.stderr);
+        println!("{}", output);
+        assert!(output.to_string().contains(
+            "Failed to parse line"
+        ));
+    }
+
+    #[test]
+    fn unparseable_timeseries_empty() {
+        let output = Command::new("./target/debug/wham")
+            .args(&["--bins", "100", "--min", "-3.0", "--max", "3.0", "-T", "300"])
+            .args(&["-f", "tests/metadata_unparseable4.dat"])
+            .args(&["-o", "/dev/null"])
+            .output()
+            .expect("failed to execute process");
+        let output = String::from_utf8_lossy(&output.stderr);
+        println!("{}", output);
+        assert!(output.to_string().contains(
+            "Wrong number of columns in line"
+        ));
+    }
+
     #[test]
     fn wham_1d() {;
         Command::new("./target/debug/wham")

tests/metadata_unparseable3.dat

@@ -0,0 +1 @@
+COLVAR_unparseable_2.xvg     -3.0       100

tests/metadata_unparseable4.dat

@@ -0,0 +1 @@
+COLVAR_unparseable_1.xvg     -3.0       100