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Merge pull request #2 from Yoshanuikabundi/open-ergonomics

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Improved ergonomics for opening files
This commit is contained in:
Daniel Bauer
2020-11-08 09:57:43 +01:00
committed by GitHub
parent e77f43d8ae c998ded6bb
commit ca7624fe1a
4 changed files with 52 additions and 35 deletions
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8
README.md
View File

@@ -11,11 +11,9 @@ files with a safe api.
### Basic usage
```rust
use xdrfile::*;
use std::path::Path;
let mut path = Path::new("tests/1l2y.xtc");
// get a handle to the file
let mut trj = XTCTrajectory::open(path, FileMode::Read).unwrap();
let mut trj = XTCTrajectory::open_read("tests/1l2y.xtc").unwrap();
// find number of atoms in the file
let num_atoms = trj.get_num_atoms().unwrap();
@@ -48,11 +46,9 @@ Rc is required)
```rust
use xdrfile::*;
use std::path::Path;
let mut path = Path::new("tests/1l2y.xtc");
// get a handle to the file
let trj = XTCTrajectory::open(path, FileMode::Read).unwrap();
let trj = XTCTrajectory::open_read("tests/1l2y.xtc").unwrap();
// iterate over all frames
for (idx, frame) in trj.into_iter().filter_map(Result::ok).enumerate() {

4
src/iterator.rs
View File

@@ -122,7 +122,7 @@ mod tests {
#[test]
pub fn test_xtc_trajectory_iterator() {
let traj = XTCTrajectory::open(Path::new("tests/1l2y.xtc"), FileMode::Read).unwrap();
let traj = XTCTrajectory::open_read("tests/1l2y.xtc").unwrap();
let frames: Vec<Rc<Frame>> = traj.into_iter().filter_map(Result::ok).collect();
assert!(frames.len() == 38);
assert!(frames[0].step == 1, frames[0].step);
@@ -131,7 +131,7 @@ mod tests {
#[test]
pub fn test_trr_trajectory_iterator() {
let traj = TRRTrajectory::open(Path::new("tests/1l2y.trr"), FileMode::Read).unwrap();
let traj = TRRTrajectory::open_read("tests/1l2y.trr").unwrap();
let frames: Vec<Rc<Frame>> = traj.into_iter().filter_map(Result::ok).collect();
assert!(frames.len() == 38);
assert!(frames[0].step == 1, frames[0].step);

65
src/lib.rs
View File

@@ -8,11 +8,9 @@
//! # Basic usage example
//! ```rust
//! use xdrfile::*;
//! use std::path::Path;
//!
//! let mut path = Path::new("tests/1l2y.xtc");
//! // get a handle to the file
//! let mut trj = XTCTrajectory::open(path, FileMode::Read).unwrap();
//! let mut trj = XTCTrajectory::open_read("tests/1l2y.xtc").unwrap();
//!
//! // find number of atoms in the file
//! let num_atoms = trj.get_num_atoms().unwrap();
@@ -45,11 +43,9 @@
//!
//! ```rust
//! use xdrfile::*;
//! use std::path::Path;
//!
//! let mut path = Path::new("tests/1l2y.xtc");
//! // get a handle to the file
//! let trj = XTCTrajectory::open(path, FileMode::Read).unwrap();
//! let trj = XTCTrajectory::open_read("tests/1l2y.xtc").unwrap();
//!
//! // iterate over all frames
//! for (idx, frame) in trj.into_iter().filter_map(Result::ok).enumerate() {
@@ -157,7 +153,8 @@ struct XDRFile {
}
impl XDRFile {
pub fn open(path: &Path, filemode: FileMode) -> Result<XDRFile> {
pub fn open(path: impl AsRef<Path>, filemode: FileMode) -> Result<XDRFile> {
let path = path.as_ref();
let path_p = path_to_cstring(path).into_raw();
let mode_p = CString::new(filemode.value()).unwrap().into_raw();
@@ -211,7 +208,7 @@ pub struct XTCTrajectory {
}
impl XTCTrajectory {
pub fn open(path: &Path, filemode: FileMode) -> Result<XTCTrajectory> {
pub fn open(path: impl AsRef<Path>, filemode: FileMode) -> Result<XTCTrajectory> {
let xdr = XDRFile::open(path, filemode)?;
Ok(XTCTrajectory {
handle: xdr,
@@ -219,6 +216,21 @@ impl XTCTrajectory {
num_atoms: Lazy::new(),
})
}
/// Open a file in read mode
pub fn open_read(path: impl AsRef<Path>) -> Result<Self> {
Self::open(path, FileMode::Read)
}
/// Open a file in append mode
pub fn open_append(path: impl AsRef<Path>) -> Result<Self> {
Self::open(path, FileMode::Append)
}
/// Open a file in write mode
pub fn open_write(path: impl AsRef<Path>) -> Result<Self> {
Self::open(path, FileMode::Write)
}
}
impl Trajectory for XTCTrajectory {
@@ -299,13 +311,28 @@ pub struct TRRTrajectory {
}
impl TRRTrajectory {
pub fn open(path: &Path, filemode: FileMode) -> Result<TRRTrajectory> {
pub fn open(path: impl AsRef<Path>, filemode: FileMode) -> Result<TRRTrajectory> {
let xdr = XDRFile::open(path, filemode)?;
Ok(TRRTrajectory {
handle: xdr,
num_atoms: Lazy::new(),
})
}
/// Open a file in read mode
pub fn open_read(path: impl AsRef<Path>) -> Result<Self> {
Self::open(path, FileMode::Read)
}
/// Open a file in append mode
pub fn open_append(path: impl AsRef<Path>) -> Result<Self> {
Self::open(path, FileMode::Append)
}
/// Open a file in write mode
pub fn open_write(path: impl AsRef<Path>) -> Result<Self> {
Self::open(path, FileMode::Write)
}
}
impl Trajectory for TRRTrajectory {
@@ -404,7 +431,7 @@ mod tests {
box_vector: [[1.0, 2.0, 3.0], [2.0, 1.0, 3.0], [3.0, 2.0, 1.0]],
coords: vec![[1.0, 1.0, 1.0], [1.0, 1.0, 1.0]],
};
let mut f = XTCTrajectory::open(tmp_path, FileMode::Write).unwrap();
let mut f = XTCTrajectory::open_write(&tmp_path).unwrap();
let write_status = f.write(&frame);
match write_status {
Err(_) => panic!("Failed"),
@@ -413,7 +440,7 @@ mod tests {
f.flush().unwrap();
let mut new_frame = Frame::with_capacity(natoms);
let mut f = XTCTrajectory::open(tmp_path, FileMode::Read).unwrap();
let mut f = XTCTrajectory::open_read(tmp_path).unwrap();
let num_atoms = f.get_num_atoms().unwrap();
assert_eq!(num_atoms, natoms);
@@ -443,7 +470,7 @@ mod tests {
box_vector: [[1.0, 2.0, 3.0], [2.0, 1.0, 3.0], [3.0, 2.0, 1.0]],
coords: vec![[1.0, 1.0, 1.0], [1.0, 1.0, 1.0]],
};
let mut f = TRRTrajectory::open(tmp_path, FileMode::Write).unwrap();
let mut f = TRRTrajectory::open_write(tmp_path).unwrap();
let write_status = f.write(&frame);
match write_status {
Err(_) => panic!("Failed"),
@@ -452,7 +479,7 @@ mod tests {
f.flush().unwrap();
let mut new_frame = Frame::with_capacity(natoms);
let mut f = TRRTrajectory::open(tmp_path, FileMode::Read).unwrap();
let mut f = TRRTrajectory::open_read(tmp_path).unwrap();
// let num_atoms = f.get_num_atoms().unwrap();
// assert_eq!(num_atoms, natoms);
@@ -472,11 +499,11 @@ mod tests {
#[test]
fn test_err_could_not_open() {
let file_name = "non-existent.xtc";
let path = Path::new(&file_name);
if let Err(e) = XDRFile::open(path, FileMode::Read) {
let expexted_path = Path::new(&file_name);
if let Err(e) = XDRFile::open(file_name, FileMode::Read) {
match e {
Error::CouldNotOpenFile(err_path, err_mode) => {
assert_eq!(path, err_path);
assert_eq!(expexted_path, err_path);
assert!(FileMode::Read == err_mode)
}
_ => panic!("Wrong Error type"),
@@ -487,8 +514,7 @@ mod tests {
#[test]
fn test_err_could_not_read_atom_nr() {
let file_name = "README.md"; // not a trajectory
let path = Path::new(&file_name);
let mut trr = TRRTrajectory::open(path, FileMode::Read).unwrap();
let mut trr = TRRTrajectory::open_read(file_name).unwrap();
if let Err(e) = trr.get_num_atoms() {
match e {
Error::CouldNotReadAtomNumber(code) => {
@@ -502,9 +528,8 @@ mod tests {
#[test]
fn test_err_could_not_read() {
let file_name = "README.md"; // not a trajectory
let path = Path::new(&file_name);
let mut frame = Frame::with_capacity(1);
let mut trr = TRRTrajectory::open(path, FileMode::Read).unwrap();
let mut trr = TRRTrajectory::open_read(file_name).unwrap();
if let Err(e) = trr.read(&mut frame) {
match e {
Error::CouldNotRead(code) => {

10
tests/integration.rs
View File

@@ -1,15 +1,13 @@
#[cfg(test)]
mod integration {
use std::path::Path;
use std::rc::Rc;
use xdrfile::*;
#[test]
fn test_use_library() {
let path = Path::new("tests/1l2y.xtc");
let mut trj = XTCTrajectory::open(path, FileMode::Read).unwrap();
let mut trj = XTCTrajectory::open_read("tests/1l2y.xtc").unwrap();
let num_atoms = trj.get_num_atoms().unwrap();
let mut frame = Frame::with_capacity(num_atoms);
@@ -20,9 +18,7 @@ mod integration {
#[test]
fn test_use_library_iterator() {
let path = Path::new("tests/1l2y.xtc");
let trj = XTCTrajectory::open(path, FileMode::Read).unwrap();
let trj = XTCTrajectory::open_read("tests/1l2y.xtc").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);