- better python errors

pyproject.toml

@@ -27,7 +27,7 @@ dependencies = [
 ]
 
 [project.optional-dependencies]
-test = ["pytest"]
+test = ["pytest", "tiffwrite"]
 
 [project.scripts]
 ndbioimage = "ndbioimage:ndbioimage_rs.main"
@@ -38,7 +38,6 @@ python-source = "py"
 features = ["python", "bioformats_java", "tiffwrite"]
 module-name = "ndbioimage.ndbioimage_rs"
 include = ["py/ndbioimage/jassets/j4rs*", "py/ndbioimage/deps/libj4rs*"]
-strip = true
 
 [tool.isort]
 line_length = 119

src/error.rs

@@ -1,6 +1,7 @@
+use strum::IntoStaticStr;
 use thiserror::Error;
 
-#[derive(Debug, Error)]
+#[derive(Debug, Error, IntoStaticStr)]
 pub enum Error {
     #[error(transparent)]
     IO(#[from] std::io::Error),
@@ -113,3 +114,9 @@ pub enum Error {
     #[error("cannot remove axes {0}, size {1} != 1")]
     SizeMismatch(String, usize),
 }
+
+impl Error {
+    pub fn variant_name(&self) -> &'static str {
+        self.into()
+    }
+}

src/py.rs

@@ -14,7 +14,9 @@ use numpy::{
 use ome_metadata::Ome;
 use postcard::{from_bytes, to_stdvec};
 use pyo3::IntoPyObjectExt;
-use pyo3::exceptions::{PyIndexError, PyNotImplementedError, PyTypeError, PyValueError};
+use pyo3::exceptions::{
+    PyIndexError, PyNotImplementedError, PyRuntimeError, PyTypeError, PyValueError,
+};
 use pyo3::prelude::*;
 use pyo3::types::{
     PyBytes, PyEllipsis, PyInt, PyList, PyNone, PySlice, PySliceMethods, PyString, PyTuple,
@@ -24,11 +26,25 @@ use pyo3_stub_gen::inventory::submit;
 use pyo3_stub_gen::{StubGenConfig, StubInfo};
 use serde::{Deserialize, Serialize};
 use std::collections::HashSet;
+use std::error::Error as StdError;
 use std::path::PathBuf;
 
+fn format_error_chain(err: &crate::error::Error) -> String {
+    let mut msg = format!("[{}] {err}", err.variant_name());
+    let mut source = err.source();
+    while let Some(s) = source {
+        msg.push_str(&format!("\n  |-> {s}"));
+        source = s.source();
+    }
+    msg
+}
+
 impl From<crate::error::Error> for PyErr {
+    #[track_caller]
     fn from(err: crate::error::Error) -> PyErr {
-        color_eyre::eyre::Report::from(err).into()
+        let location = std::panic::Location::caller();
+        let msg = format!("{}: {}", location, format_error_chain(&err));
+        PyRuntimeError::new_err(msg)
     }
 }
 
@@ -200,7 +216,7 @@ impl PyView {
                 let dtype_str = name.extract::<String>()?;
                 dtype_str.parse()?
             } else {
-                PixelType::U16
+                *view.pixel_type()
             };
             let ome = view.metadata()?;
             Ok(Self {

tests/test_open.py

@@ -13,7 +13,7 @@ from ndbioimage import Imread
         for path in (Path(__file__).parent / "files").iterdir()
         if path.is_dir() and path.name != "czi_xml"
         for file in path.iterdir()
-        if not file.suffix == ".pzl"
+        if file.suffix.lower() not in [".pzl", ".xml", "", ".txt"]
     ],
 )
 def test_open(file):

tests/test_slicing.py

@@ -18,7 +18,7 @@ def array():
 @pytest.fixture()
 def image(array):
     with tempfile.TemporaryDirectory() as folder:
-        file = Path(folder) / "tiff" / "test.tif"
+        file = Path(folder) / "test.tif"
         tiffwrite(file, array, "yxczt")
         with Imread(file, axes="yxczt") as im:
             yield im