From a1150e1ef65a2e91691baf066db2bd76b6d6828e Mon Sep 17 00:00:00 2001 From: Cian Hughes Date: Fri, 25 Oct 2024 09:27:12 +0100 Subject: [PATCH] Updated package to use most recent maturin version Significant rewrite to allow this module to work with the most recetn version of maturin. Required dependency removal for ndarray-csv and rewrite of tests. Should future-proof for migratiosn to python3.13 in software using this library. --- Cargo.toml | 19 ++-- poetry.lock | 236 +++++++++++++++++++++++++-------------------- pyproject.toml | 32 +++--- src/lib.rs | 70 ++++++++------ src/rust_fn/mod.rs | 46 ++++++--- 5 files changed, 223 insertions(+), 180 deletions(-) diff --git a/Cargo.toml b/Cargo.toml index 77d2753..87e7f1a 100644 --- a/Cargo.toml +++ b/Cargo.toml @@ -1,6 +1,6 @@ [package] name = "read_aconity_layers" -version = "0.2.0" +version = "0.3.0" edition = "2021" [lib] @@ -11,27 +11,20 @@ crate-type = ["cdylib"] csv = "*" glob = "*" indicatif = "*" -ndarray = { version = "0.15.6", features = ["rayon"] } -ndarray-csv = "*" -numpy = "*" -pyo3 = { version = "0.18.1", features = ["extension-module"] } +ndarray = { version = "0.16.1", features = ["rayon"] } +numpy = "0.22.0" +pyo3 = { version = "0.22.5", features = ["extension-module"] } rayon = "*" thiserror = "1.0.60" [dev-dependencies] -anyhow = "1.0.83" approx = "0.5.1" arbitrary = { version = "1.3.2", features = ["derive"] } arbtest = "0.3.1" flexbuffers = "2.0.0" -float-cmp = "0.9.0" -ndarray = { version = "0.15.6", features = ["rayon", "serde"] } +float-cmp = "0.10.0" +ndarray = { version = "0.16.1", features = ["rayon", "serde"] } serde = "1.0.200" tar = "0.4.40" tempfile = "3.10.1" xz = "0.1.0" - -[tool.maturin] -profile = "release" -all-features = true -manifest-path = "Cargo.toml" diff --git a/poetry.lock b/poetry.lock index e78a00d..d1e170b 100644 --- a/poetry.lock +++ b/poetry.lock @@ -1,73 +1,79 @@ -# This file is automatically @generated by Poetry 1.7.1 and should not be changed by hand. +# This file is automatically @generated by Poetry 1.8.3 and should not be changed by hand. 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"^1.10.0" +ruff = "^0.7.1" +mypy = "^1.13.0" [build-system] -requires = ["maturin>=1.0,<2.0"] +requires = ["maturin>=1.7,<2.0"] build-backend = "maturin" [tool.maturin] -# Bindings type -bindings = "pyo3" -# Don't check for manylinux compliance -skip-auditwheel = false -# Python source directory -# python-source = "src/mtpy" -# Strip the library for minimum file size -strip = true -# Source distribution generator, -# supports cargo (default) and git. -sdist-generator = "cargo" +features = ["pyo3/extension-module"] [tool.ruff] # Same as Black. diff --git a/src/lib.rs b/src/lib.rs index 17284f2..c1f5c96 100644 --- a/src/lib.rs +++ b/src/lib.rs @@ -1,7 +1,7 @@ -use numpy::{IntoPyArray, PyArray2}; +use ndarray::{ArrayBase, Ix2, OwnedRepr}; +use numpy::{PyArray2, ToPyArray}; use pyo3::exceptions; -use pyo3::prelude::{pymodule, PyErr, PyModule, PyResult, Python}; -use pyo3::types::{PyList, PyString}; +use pyo3::prelude::*; use std::path::Path; pub mod rust_fn; @@ -16,9 +16,7 @@ impl From for PyErr { PyErr::new::(format!("{}", e)) } rust_fn::ReadError::Io(e) => PyErr::new::(format!("{}", e)), - rust_fn::ReadError::NdarrayCSV(e) => { - PyErr::new::(format!("{}", e)) - } + rust_fn::ReadError::CSV(e) => PyErr::new::(format!("{}", e)), rust_fn::ReadError::ParseFloatError(e) => { PyErr::new::(format!("{}", e)) } @@ -27,31 +25,41 @@ impl From for PyErr { } } +#[pyfunction] +fn read_layers<'py>(_py: Python<'py>, folder: &'py str) -> PyResult>> +where + ArrayBase, Ix2>: ToPyArray, +{ + let rs_result = rust_fn::read_layers(folder)?; + let py_result = rs_result.to_pyarray_bound(_py); + Ok(py_result) +} + +#[pyfunction] +fn read_selected_layers<'py>( + _py: Python<'py>, + file_list: Vec, +) -> PyResult>> { + let path_list = file_list + .iter() + .map(|x| Path::new(x).to_path_buf()) + .collect(); + let rs_result = rust_fn::read_selected_layers(path_list)?; + let py_result = rs_result.to_pyarray_bound(_py); + Ok(py_result) +} + +#[pyfunction] +fn read_layer<'py>(_py: Python<'py>, file: String) -> PyResult>> { + let rs_result = rust_fn::read_layer(&file)?; + let py_result = rs_result.to_pyarray_bound(_py); + Ok(py_result) +} + #[pymodule] -fn read_aconity_layers(_py: Python<'_>, m: &PyModule) -> PyResult<()> { - #[pyfn(m)] - fn read_layers<'py>(py: Python<'py>, folder: &PyString) -> PyResult<&'py PyArray2> { - Ok(rust_fn::read_layers(folder.to_str().unwrap())?.into_pyarray(py)) - } - - #[pyfn(m)] - fn read_selected_layers<'py>( - py: Python<'py>, - file_list: &PyList, - ) -> PyResult<&'py PyArray2> { - Ok(rust_fn::read_selected_layers( - file_list - .iter() - .map(|x| Path::new(&(*x).str().unwrap().to_string()).to_path_buf()) - .collect(), - )? - .into_pyarray(py)) - } - - #[pyfn(m)] - fn read_layer<'py>(py: Python<'py>, file: &PyString) -> PyResult<&'py PyArray2> { - Ok(rust_fn::read_layer(file.to_str().unwrap())?.into_pyarray(py)) - } - +fn read_aconity_layers(_py: Python, m: &Bound<'_, PyModule>) -> PyResult<()> { + m.add_function(wrap_pyfunction!(read_layers, m)?)?; + m.add_function(wrap_pyfunction!(read_selected_layers, m)?)?; + m.add_function(wrap_pyfunction!(read_layer, m)?)?; Ok(()) } diff --git a/src/rust_fn/mod.rs b/src/rust_fn/mod.rs index b86644d..c5beeae 100644 --- a/src/rust_fn/mod.rs +++ b/src/rust_fn/mod.rs @@ -2,7 +2,6 @@ use csv::ReaderBuilder; use glob::glob; use indicatif::ProgressBar; use ndarray::{concatenate, Array2, ArrayView2, Axis, Slice}; -use ndarray_csv::Array2Reader; use rayon::prelude::*; use std::fs::File; use std::path::{Path, PathBuf}; @@ -19,8 +18,8 @@ pub enum ReadError { #[error("IO error: {0}")] Io(#[from] std::io::Error), - #[error("NdarrayCSV error: {0}")] - NdarrayCSV(#[from] ndarray_csv::ReadError), + #[error("CSV error: {0}")] + CSV(#[from] csv::Error), #[error("Float parse error: {0}")] ParseFloatError(#[from] std::num::ParseFloatError), @@ -158,14 +157,28 @@ pub fn read_layer(file: &str) -> Result> { pub fn read_file(filepath: PathBuf) -> Result<(Array2, f64, usize)> { let z: f64 = get_z(&filepath)?; let file = File::open(filepath)?; - let mut rdr = ReaderBuilder::new() - .has_headers(false) - .delimiter(b' ') - .from_reader(file); - let array_read: Array2 = rdr.deserialize_array2_dynamic()?; - let z_len: usize = array_read.shape()[0]; + let mut rdr = ReaderBuilder::new().has_headers(false).from_reader(file); + let data = rdr + .records() + .into_iter() + .collect::, _>>()? + .iter() + .map(|x| { + x.iter() + .map(|y| y.parse::().map_err(|e| ReadError::ParseFloatError(e))) + .collect::>>() + }) + .collect::>>()?; + let length = data.len(); + let width = data[0].len(); // WARNING: assumes fixed width columns! + let mut arr: Array2 = Array2::zeros((length, width)); + for (data_row, mut arr_row) in data.iter().zip(arr.axis_iter_mut(Axis(0))) { + for (data_i, arr_i) in data_row.iter().zip(arr_row.iter_mut()) { + *arr_i = *data_i + } + } - Ok((array_read, z, z_len)) + Ok((arr, z, length)) } pub fn get_z(filepath: &Path) -> Result { @@ -220,13 +233,16 @@ mod tests { } impl<'a> Arbitrary<'a> for ExampleData { fn arbitrary(u: &mut Unstructured<'a>) -> ArbResult { - // NOTE: We need to add 1 here, it len == 0 the test will fail + // NOTE: We need to add 1 here, if len == 0 the test will fail let len = 1 + u .arbitrary_len::<(isize, isize, isize, isize)>()? .min(usize::MAX - 1); let ar = Array2::from_shape_simple_fn((4, len), || isize::arbitrary(u).unwrap_or_default()); - let z = f64::arbitrary(u)?.abs() / Z_SCALING; + // This is a clunky way to account for truncation of floats when writing filepath + let z = format!("{:.32}", f64::arbitrary(u)?.abs() / Z_SCALING) + .parse() + .map_err(|_| arbitrary::Error::IncorrectFormat)?; Ok(ExampleData { z, ar }) } @@ -291,8 +307,10 @@ mod tests { fn proptest_read_file() { fn prop(u: &mut Unstructured<'_>) -> ArbResult<()> { let data = ExampleData::arbitrary(u)?; - let (_tmpdir, tmpfpath) = create_test_pcd(data.z, &data.ar).unwrap(); - let (ar_out, z_out, _) = rust_fn::read_file(tmpfpath).unwrap(); + let (_tmpdir, tmpfpath) = create_test_pcd(data.z, &data.ar) + .map_err(|_e| arbitrary::Error::IncorrectFormat)?; + let (ar_out, z_out, _) = + rust_fn::read_file(tmpfpath).map_err(|_e| arbitrary::Error::IncorrectFormat)?; let actual_result = ReadResult { z: z_out, ar: ar_out,