Format with rustfmt

src/c_abi/mod.rs

@@ -1,5 +1,5 @@
+pub mod xdr_seek;
 #[allow(non_upper_case_globals)]
 pub mod xdrfile;
 pub mod xdrfile_trr;
 pub mod xdrfile_xtc;
-pub mod xdr_seek;

src/c_abi/xdr_seek.rs

@@ -103,12 +103,11 @@ extern "C" {
     pub fn xdr_flush(xd: *mut XDRFILE) -> ::std::os::raw::c_int;
 }
 
-
 #[cfg(test)]
 mod tests {
 
-    use super::*;
     use super::super::xdrfile_xtc::*;
+    use super::*;
     use std::ffi::CString;
 
     #[test]
@@ -129,10 +128,15 @@ mod tests {
             let tell = xdr_tell(xdr);
             assert!(tell == 0, "{}", tell);
 
-            read_xtc(xdr, num_atoms, &mut step, &mut time,
+            read_xtc(
+                xdr,
+                num_atoms,
+                &mut step,
+                &mut time,
                 box_vec.as_ptr() as *mut Matrix,
                 x_p,
-                &mut prec);
+                &mut prec,
+            );
 
             let tell = xdr_tell(xdr);
             assert!(tell > 0, "{}", tell);

src/c_abi/xdrfile.rs

@@ -1,4 +1,3 @@
-
 pub const DIM: u32 = 3;
 
 #[repr(C)]
@@ -7,7 +6,6 @@ pub struct XDRFILE {
     _unused: [u8; 0],
 }
 
-
 pub type BindgenTy1 = u32;
 pub const exdrOK: BindgenTy1 = 0;
 pub const exdrHEADER: BindgenTy1 = 1;

src/c_abi/xdrfile_trr.rs

@@ -1,6 +1,5 @@
 use super::xdrfile::*;
 
-
 extern "C" {
     pub fn read_trr_natoms(
         fn_: *const ::std::os::raw::c_char,
@@ -89,11 +88,17 @@ mod tests {
         unsafe {
             let mode = CString::new("w").unwrap();
             let xdr = xdrfile_open(tmp_path.as_ptr(), mode.as_ptr());
-            let write_code = write_trr(xdr, natoms, step, time, lambda,
+            let write_code = write_trr(
+                xdr,
+                natoms,
+                step,
+                time,
+                lambda,
                 box_vec.as_ptr() as *mut Matrix,
                 x.as_ptr() as *mut Rvec,
                 v.as_ptr() as *mut Rvec,
-                f.as_ptr() as *mut Rvec);
+                f.as_ptr() as *mut Rvec,
+            );
             assert!(write_code as u32 == exdrOK);
             xdrfile_close(xdr);
         }
@@ -111,11 +116,17 @@ mod tests {
         unsafe {
             let mode = CString::new("r").unwrap();
             let xdr = xdrfile_open(tmp_path.as_ptr(), mode.as_ptr());
-            let read_code = read_trr(xdr, natoms, &mut step2, &mut time2,
+            let read_code = read_trr(
-                &mut lambda2, box_vec2.as_ptr() as *mut Matrix,
+                xdr,
+                natoms,
+                &mut step2,
+                &mut time2,
+                &mut lambda2,
+                box_vec2.as_ptr() as *mut Matrix,
                 x2.as_ptr() as *mut Rvec,
                 v2.as_ptr() as *mut Rvec,
-                f2.as_ptr() as *mut Rvec);
+                f2.as_ptr() as *mut Rvec,
+            );
             assert!(read_code as u32 == exdrOK);
             xdrfile_close(xdr);
         }
@@ -129,5 +140,4 @@ mod tests {
         assert!(v2 == v);
         assert!(f2 == f);
     }
-
 }

src/c_abi/xdrfile_xtc.rs

@@ -1,6 +1,5 @@
 use super::xdrfile::*;
 
-
 extern "C" {
     pub fn read_xtc_natoms(
         fn_: *const ::std::os::raw::c_char,
@@ -81,9 +80,15 @@ mod tests {
         unsafe {
             let mode = CString::new("w").unwrap();
             let xdr = xdrfile_open(tmp_path.as_ptr(), mode.as_ptr());
-            let write_code = write_xtc(xdr, natoms, step, time,
+            let write_code = write_xtc(
-                box_vec.as_ptr() as *mut Matrix, x.as_ptr() as *mut Rvec,
+                xdr,
-                1000.0);
+                natoms,
+                step,
+                time,
+                box_vec.as_ptr() as *mut Matrix,
+                x.as_ptr() as *mut Rvec,
+                1000.0,
+            );
             assert!(write_code as u32 == exdrOK);
             xdrfile_close(xdr);
         }
@@ -98,9 +103,15 @@ mod tests {
         unsafe {
             let mode = CString::new("r").unwrap();
             let xdr = xdrfile_open(tmp_path.as_ptr(), mode.as_ptr());
-            let read_code = read_xtc(xdr, natoms, &mut step2, &mut time2,
+            let read_code = read_xtc(
-                box_vec2.as_ptr() as *mut Matrix, x2.as_ptr() as *mut Rvec,
+                xdr,
-                &mut prec);
+                natoms,
+                &mut step2,
+                &mut time2,
+                box_vec2.as_ptr() as *mut Matrix,
+                x2.as_ptr() as *mut Rvec,
+                &mut prec,
+            );
             assert!(read_code as u32 == exdrOK);
             xdrfile_close(xdr);
         }

src/frame.rs

@@ -26,23 +26,28 @@ impl Default for Frame {
             step: 0,
             time: 0.0,
             box_vector: [[0.0; 3]; 3],
-            coords: Vec::with_capacity(0)
+            coords: Vec::with_capacity(0),
         }
     }
 }
 
 impl fmt::Debug for Frame {
     fn fmt(&self, f: &mut fmt::Formatter<'_>) -> fmt::Result {
-        write!(f, "Frame {{ atoms: {}, step: {}, time: {}, \
+        write!(
-            box: {:?}, coords: {:?} }}", self.num_atoms, self.step, self.time,
+            f,
-            self.box_vector, self.coords)
+            "Frame {{ atoms: {}, step: {}, time: {}, \
+            box: {:?}, coords: {:?} }}",
+            self.num_atoms, self.step, self.time, self.box_vector, self.coords
+        )
     }
 }
 
 impl Frame {
     /// Creates an empty frame with a capacity of 0
     pub fn new() -> Frame {
-        Frame{ ..Default::default() }
+        Frame {
+            ..Default::default()
+        }
     }
 
     /// Creates a frame with the given capacity
@@ -52,12 +57,13 @@ impl Frame {
             coords: vec![[0.0, 0.0, 0.0]; num_atoms as usize],
             ..Default::default()
         }
-
     }
 
     /// Filters the frame by removing all atoms not matching the given indeces.
     pub fn filter_coords(self: &mut Frame, indeces: &[usize]) {
-        self.coords = self.coords.iter() 
+        self.coords = self
+            .coords
+            .iter()
             .map(|elem| elem.clone())
             .enumerate()
             .filter(|&(i, _)| indeces.contains(&i))
@@ -72,8 +78,6 @@ impl Frame {
     }
 }
 
-
-
 #[cfg(test)]
 mod tests {
     use super::*;
@@ -91,7 +95,7 @@ mod tests {
         frame.coords[0] = [1.0, 2.0, 3.0];
         frame.coords[1] = [4.0, 5.0, 6.0];
         frame.coords[2] = [7.0, 8.0, 9.0];
-        let filter: Vec<usize> = vec![1,2];
+        let filter: Vec<usize> = vec![1, 2];
         let mut frame_new = frame.clone();
         frame_new.filter_coords(&filter);
         assert!(frame_new.num_atoms as usize == filter.len());

src/iterator.rs

@@ -1,5 +1,5 @@
-use crate::*;
 use crate::c_abi::xdrfile::exdrENDOFFILE;
+use crate::*;
 use failure::Error;
 use std::rc::Rc;
 
@@ -13,7 +13,7 @@ impl IntoIterator for XTCTrajectory {
         XTCTrajectoryIterator {
             trajectory: self,
             item: Rc::new(Frame::with_capacity(num_atoms)),
-            has_error: false
+            has_error: false,
         }
     }
 }
@@ -32,18 +32,19 @@ pub struct XTCTrajectoryIterator {
 impl Iterator for XTCTrajectoryIterator {
     type Item = Result<Rc<Frame>, Error>;
 
-    fn next(&mut self) -> Option<Self::Item> { // Reuse old frame
+    fn next(&mut self) -> Option<Self::Item> {
+        // Reuse old frame
         if self.has_error {
             return None;
         }
 
         let item: &mut Frame = match Rc::get_mut(&mut self.item) {
             Some(item) => item,
-            None => {  // caller kept frame. Create new one
+            None => {
+                // caller kept frame. Create new one
                 self.item = Rc::new(Frame::with_capacity(self.item.num_atoms));
                 Rc::get_mut(&mut self.item).unwrap()
             }
-
         };
         match self.trajectory.read(item) {
             Ok(()) => Some(Ok(Rc::clone(&self.item))),
@@ -69,7 +70,7 @@ impl IntoIterator for TRRTrajectory {
         TRRTrajectoryIterator {
             trajectory: self,
             item: Rc::new(Frame::with_capacity(num_atoms)),
-            has_error: false
+            has_error: false,
         }
     }
 }
@@ -88,18 +89,19 @@ pub struct TRRTrajectoryIterator {
 impl Iterator for TRRTrajectoryIterator {
     type Item = Result<Rc<Frame>, Error>;
 
-    fn next(&mut self) -> Option<Self::Item> { // Reuse old frame
+    fn next(&mut self) -> Option<Self::Item> {
+        // Reuse old frame
         if self.has_error {
             return None;
         }
 
         let item: &mut Frame = match Rc::get_mut(&mut self.item) {
             Some(item) => item,
-            None => {  // caller kept frame. Create new one
+            None => {
+                // caller kept frame. Create new one
                 self.item = Rc::new(Frame::with_capacity(self.item.num_atoms));
                 Rc::get_mut(&mut self.item).unwrap()
             }
-
         };
         match self.trajectory.read(item) {
             Ok(()) => Some(Ok(Rc::clone(&self.item))),

src/lib.rs

@@ -58,33 +58,33 @@
 //! }
 //! ```
 
-
 #[cfg(test)]
-#[macro_use] extern crate assert_approx_eq;
+#[macro_use]
+extern crate assert_approx_eq;
 extern crate lazy_init;
 
+pub mod c_abi;
 mod frame;
 mod iterator;
-pub mod c_abi; 
 pub use frame::Frame;
 pub use iterator::*;
 
+use c_abi::xdr_seek;
 use c_abi::xdrfile;
 use c_abi::xdrfile::XDRFILE;
-use c_abi::xdr_seek;
-use c_abi::xdrfile_xtc;
 use c_abi::xdrfile_trr;
+use c_abi::xdrfile_xtc;
 
+use failure::{err_msg, Error};
+use lazy_init::Lazy;
+use std::cell::Cell;
 use std::ffi::CString;
 use std::path::Path;
-use failure::{Error,err_msg};
-use std::cell::Cell;
-use lazy_init::Lazy;
 
 pub enum FileMode {
     Write,
     Append,
-    Read    
+    Read,
 }
 
 impl FileMode {
@@ -99,7 +99,7 @@ impl FileMode {
 
 fn path_to_cstring(path: &Path) -> CString {
     CString::new(path.to_str().unwrap()).unwrap()
-    }
+}
 
 /// A safe wrapper around the c implementation of an XDRFile
 struct XDRFile {
@@ -109,7 +109,6 @@ struct XDRFile {
 }
 
 impl XDRFile {
-
     pub fn open(path: &Path, filemode: FileMode) -> Result<XDRFile, Error> {
         let path_p = path_to_cstring(path).into_raw();
         let mode_p = CString::new(filemode.value()).unwrap().into_raw();
@@ -117,10 +116,15 @@ impl XDRFile {
         unsafe {
             let xdrfile = xdrfile::xdrfile_open(path_p, mode_p);
 
-            if ! xdrfile.is_null() {
+            if !xdrfile.is_null() {
                 let path = String::from(path.to_str().unwrap());
-                Ok(XDRFile { xdrfile, filemode, path })
+                Ok(XDRFile {
-            } else {  // Something went wrong. But the C api does not tell us what
+                    xdrfile,
+                    filemode,
+                    path,
+                })
+            } else {
+                // Something went wrong. But the C api does not tell us what
                 Err(err_msg("Failed to open trajectory file"))
             }
         }
@@ -138,7 +142,6 @@ impl Drop for XDRFile {
 
 /// The trajectory trait defines shared methods for xtc and trr trajectories
 pub trait Trajectory {
-
     /// Read the next step of the trajectory into the frame object
     fn read(&mut self, frame: &mut Frame) -> Result<(), Error>;
 
@@ -156,25 +159,29 @@ pub trait Trajectory {
 pub struct XTCTrajectory {
     handle: XDRFile,
     precision: Cell<f32>, // internal mutability required for read method
-    num_atoms: Lazy<Result<u32, Error>>
+    num_atoms: Lazy<Result<u32, Error>>,
 }
 
 impl XTCTrajectory {
     pub fn open(path: &Path, filemode: FileMode) -> Result<XTCTrajectory, Error> {
         let xdr = XDRFile::open(path, filemode)?;
-        Ok(XTCTrajectory { handle: xdr, precision: Cell::new(1000.0), num_atoms: Lazy::new() })
+        Ok(XTCTrajectory {
+            handle: xdr,
+            precision: Cell::new(1000.0),
+            num_atoms: Lazy::new(),
+        })
     }
 }
 
 impl Trajectory for XTCTrajectory {
-
     fn read(&mut self, frame: &mut Frame) -> Result<(), Error> {
         unsafe {
             // C lib requires an i32 to be passed, but step is exposed it as u32
             // (A step cannot be negative, can it?). So we need to create a step
             // variable to pass to read_xtc and cast it afterwards to u32
             let mut step: i32 = 0;
-            let code = xdrfile_xtc::read_xtc(self.handle.xdrfile,
+            let code = xdrfile_xtc::read_xtc(
+                self.handle.xdrfile,
                 frame.num_atoms as i32,
                 &mut step,
                 &mut frame.time,
@@ -185,23 +192,31 @@ impl Trajectory for XTCTrajectory {
             frame.step = step as u32;
             match code {
                 xdrfile::exdrOK => Ok(()),
-                _ => Err(err_msg(format!("Failed to read trajectory. Error code: {}", code))), 
+                _ => Err(err_msg(format!(
+                    "Failed to read trajectory. Error code: {}",
+                    code
+                ))),
             }
         }
     }
 
     fn write(&mut self, frame: &Frame) -> Result<(), Error> {
         unsafe {
-            let code = xdrfile_xtc::write_xtc(self.handle.xdrfile,
+            let code = xdrfile_xtc::write_xtc(
+                self.handle.xdrfile,
                 frame.num_atoms as i32,
                 frame.step as i32,
                 frame.time,
                 frame.box_vector.as_ptr() as *mut [[f32; 3]; 3],
                 frame.coords[..].as_ptr() as *mut [f32; 3],
-                1000.0) as u32;
+                1000.0,
+            ) as u32;
             match code {
                 xdrfile::exdrOK => Ok(()),
-                _ => Err(err_msg(format!("Failed to write trajectory. Error code: {}", code)))
+                _ => Err(err_msg(format!(
+                    "Failed to write trajectory. Error code: {}",
+                    code
+                ))),
             }
         }
     }
@@ -211,7 +226,10 @@ impl Trajectory for XTCTrajectory {
             let code = xdr_seek::xdr_flush(self.handle.xdrfile) as u32;
             match code {
                 xdrfile::exdrOK => Ok(()),
-                _ => Err(err_msg(format!("Failed to flush trajectory. Error code: {}", code)))
+                _ => Err(err_msg(format!(
+                    "Failed to flush trajectory. Error code: {}",
+                    code
+                ))),
             }
         }
     }
@@ -222,37 +240,42 @@ impl Trajectory for XTCTrajectory {
             unsafe {
                 let path = CString::new(self.handle.path.as_str()).unwrap();
                 let path_p = path.into_raw();
-                let code = xdrfile_xtc::read_xtc_natoms(path_p, &mut num_atoms as *const i32) as u32;
+                let code =
+                    xdrfile_xtc::read_xtc_natoms(path_p, &mut num_atoms as *const i32) as u32;
                 match code {
                     xdrfile::exdrOK => Ok(num_atoms as u32),
-                    _ => Err(err_msg(format!("Failed to read atom number from trajectory. Error code: {}", code)))
+                    _ => Err(err_msg(format!(
+                        "Failed to read atom number from trajectory. Error code: {}",
+                        code
+                    ))),
                 }
             }
         });
         match result {
             Ok(val) => Ok(*val),
             // ugly hack because failure::Error is not "Clone"
-            Err(err) => Err(err_msg(format!("{}", err)))
+            Err(err) => Err(err_msg(format!("{}", err))),
         }
     }
 }
 
-
 /// Read/Write TRR Trajectories
 pub struct TRRTrajectory {
     handle: XDRFile,
-    num_atoms: Lazy<Result<u32, Error>>
+    num_atoms: Lazy<Result<u32, Error>>,
 }
 
 impl TRRTrajectory {
     pub fn open(path: &Path, filemode: FileMode) -> Result<TRRTrajectory, Error> {
         let xdr = XDRFile::open(path, filemode)?;
-        Ok(TRRTrajectory { handle: xdr, num_atoms: Lazy::new() })
+        Ok(TRRTrajectory {
+            handle: xdr,
+            num_atoms: Lazy::new(),
+        })
     }
 }
 
 impl Trajectory for TRRTrajectory {
-
     fn read(&mut self, frame: &mut Frame) -> Result<(), Error> {
         unsafe {
             // C lib requires an i32 to be passed, but step is exposed it as u32
@@ -261,7 +284,8 @@ impl Trajectory for TRRTrajectory {
             // Similar for lambda.
             let mut step: i32 = 0;
             let mut lambda: f32 = 0.0;
-            let code = xdrfile_trr::read_trr(self.handle.xdrfile,
+            let code = xdrfile_trr::read_trr(
+                self.handle.xdrfile,
                 frame.num_atoms as i32,
                 &mut step,
                 &mut frame.time,
@@ -269,19 +293,23 @@ impl Trajectory for TRRTrajectory {
                 &mut frame.box_vector,
                 frame.coords.as_ptr() as *mut [f32; 3],
                 std::ptr::null_mut(),
-                std::ptr::null_mut()
+                std::ptr::null_mut(),
             ) as u32;
             frame.step = step as u32;
             match code {
                 xdrfile::exdrOK => Ok(()),
-                _ => Err(err_msg(format!("Failed to read trajectory. Error code: {}", code)))
+                _ => Err(err_msg(format!(
+                    "Failed to read trajectory. Error code: {}",
+                    code
+                ))),
             }
         }
     }
 
     fn write(&mut self, frame: &Frame) -> Result<(), Error> {
         unsafe {
-            let code = xdrfile_trr::write_trr(self.handle.xdrfile,
+            let code = xdrfile_trr::write_trr(
+                self.handle.xdrfile,
                 frame.num_atoms as i32,
                 frame.step as i32,
                 frame.time,
@@ -289,10 +317,14 @@ impl Trajectory for TRRTrajectory {
                 frame.box_vector.as_ptr() as *mut [[f32; 3]; 3],
                 frame.coords[..].as_ptr() as *mut [f32; 3],
                 std::ptr::null_mut(),
-                std::ptr::null_mut()) as u32;
+                std::ptr::null_mut(),
+            ) as u32;
             match code {
                 xdrfile::exdrOK => Ok(()),
-                _ => Err(err_msg(format!("Failed to write trajectory. Error code: {}", code)))
+                _ => Err(err_msg(format!(
+                    "Failed to write trajectory. Error code: {}",
+                    code
+                ))),
             }
         }
     }
@@ -302,7 +334,10 @@ impl Trajectory for TRRTrajectory {
             let code = xdr_seek::xdr_flush(self.handle.xdrfile) as u32;
             match code {
                 xdrfile::exdrOK => Ok(()),
-                _ => Err(err_msg(format!("Failed to flush trajectory. Error code: {}", code))) 
+                _ => Err(err_msg(format!(
+                    "Failed to flush trajectory. Error code: {}",
+                    code
+                ))),
             }
         }
     }
@@ -313,22 +348,25 @@ impl Trajectory for TRRTrajectory {
             unsafe {
                 let path = CString::new(self.handle.path.as_str()).unwrap();
                 let path_p = path.into_raw();
-                let code = xdrfile_trr::read_trr_natoms(path_p, &mut num_atoms as *const i32) as u32;
+                let code =
+                    xdrfile_trr::read_trr_natoms(path_p, &mut num_atoms as *const i32) as u32;
                 match code {
                     xdrfile::exdrOK => Ok(num_atoms as u32),
-                    _ => Err(err_msg(format!("Failed to read atom number from trajectory. Error code: {}", code)))
+                    _ => Err(err_msg(format!(
+                        "Failed to read atom number from trajectory. Error code: {}",
+                        code
+                    ))),
                 }
             }
         });
         match result {
             Ok(val) => Ok(*val),
             // ugly hack because failure::Error is not "Clone"
-            Err(err) => Err(err_msg(format!("{}", err)))
+            Err(err) => Err(err_msg(format!("{}", err))),
         }
     }
 }
 
-
 #[cfg(test)]
 mod tests {
 
@@ -413,4 +451,3 @@ mod tests {
         assert_eq!(new_frame.coords, frame.coords);
     }
 }
-

tests/integration.rs

@@ -1,9 +1,9 @@
 #[cfg(test)]
 mod integration {
 
+    use std::path::Path;
     use std::rc::Rc;
     use xdrfile::*;
-    use std::path::Path;
 
     #[test]
     fn test_use_library() {
@@ -25,8 +25,7 @@ mod integration {
         let trj = XTCTrajectory::open(path, FileMode::Read).unwrap();
         let frames: Vec<Rc<Frame>> = trj.into_iter().filter_map(Result::ok).collect();
         for (idx, frame) in frames.iter().enumerate() {
-            assert_eq!(frame.step as usize, idx+1);
+            assert_eq!(frame.step as usize, idx + 1);
         }
     }
-
 }