From 705ca163791c702f44189e8f0db7cb8a48c956c9 Mon Sep 17 00:00:00 2001
From: "w.pomp" <w.pomp@nki.nl>
Date: Mon, 23 Feb 2026 19:54:58 +0100
Subject: [PATCH] start using semver, fix doc.rs issue

---
 Cargo.toml      | 19 ++++++++++---------
 README.md       |  2 ++
 src/lib.rs      |  2 +-
 src/metadata.rs |  2 +-
 src/py.rs       |  5 +++--
 5 files changed, 17 insertions(+), 13 deletions(-)

diff --git a/Cargo.toml b/Cargo.toml
index dc51480..90b75dc 100644
--- a/Cargo.toml
+++ b/Cargo.toml
@@ -1,13 +1,13 @@
 [package]
 name = "ndbioimage"
-version = "2026.1.2"
+version = "0.1.0"
 edition = "2024"
-rust-version = "1.85.1"
+rust-version = "1.87.0"
 authors = ["Wim Pomp <w.pomp@nki.nl>"]
 license = "MIT"
 description = "Read bio image formats using the bio-formats java package."
-homepage = "https://github.com/wimpomp/ndbioimage/tree/rs"
-repository = "https://github.com/wimpomp/ndbioimage/tree/rs"
+homepage = "https://git.wimpomp.nl/wim/ndbioimage/src/branch/rs"
+repository = "https://git.wimpomp.nl/wim/ndbioimage/src/branch/rs"
 documentation = "https://docs.rs/ndbioimage"
 readme = "README.md"
 keywords = ["bioformats", "imread", "ndarray", "metadata"]
@@ -21,6 +21,7 @@ crate-type = ["cdylib", "rlib"]
 
 [dependencies]
 clap = { version = "4", features = ["derive"] }
+color-eyre = { version = "0.6", optional = true }
 ffmpeg-sidecar = { version = "2", optional = true }
 itertools = "0.14"
 indexmap = { version = "2", features = ["serde"] }
@@ -28,21 +29,21 @@ indicatif = { version = "0.18", features = ["rayon"], optional = true }
 j4rs = "0.24"
 ndarray = { version = "0.17", features = ["serde"] }
 num = "0.4"
-numpy = { version = "0.27", optional = true }
+numpy = { version = "0.28", optional = true }
 ordered-float = "5"
 rayon = { version = "1", optional = true }
 serde = { version = "1", features = ["rc"] }
 serde_json = { version = "1", optional = true }
 serde_with = "3"
-tiffwrite = { version = "2025.12.0", optional = true}
+tiffwrite = { version = ">=2026.1.1, <2026.2.0", optional = true}
 thread_local = "1"
 ome-metadata = "0.4"
 lazy_static = "1"
 thiserror = "2"
 
 [dependencies.pyo3]
-version = "0.27"
-features = ["extension-module", "abi3-py310", "generate-import-lib", "anyhow"]
+version = "0.28"
+features = ["extension-module", "abi3-py310", "eyre", "generate-import-lib"]
 optional = true
 
 [dev-dependencies]
@@ -60,7 +61,7 @@ retry = "2"
 # Enables formats for which code in bioformats with a GPL license is needed
 gpl-formats = []
 # Enables python ffi using pyO3
-python = ["dep:pyo3", "dep:numpy", "dep:serde_json"]
+python = ["dep:pyo3", "dep:numpy", "dep:serde_json", "dep:color-eyre"]
 # Enables writing as tiff
 tiff = ["dep:tiffwrite", "dep:indicatif", "dep:rayon"]
 # Enables writing as mp4 using ffmpeg
diff --git a/README.md b/README.md
index 0d6d5e4..88a38f1 100644
--- a/README.md
+++ b/README.md
@@ -14,6 +14,8 @@ it on the fly to the image.
 Currently, it supports imagej tif files, czi files, micromanager tif sequences and anything
 [bioformats](https://www.openmicroscopy.org/bio-formats/) can handle.
 
+To transition to semver, versions before 0.1.0 were yanked from crates.io.
+
 ## Installation
 
 ```
diff --git a/src/lib.rs b/src/lib.rs
index da7c4f9..9c56367 100644
--- a/src/lib.rs
+++ b/src/lib.rs
@@ -1,4 +1,4 @@
-#![cfg_attr(docsrs, feature(doc_auto_cfg))]
+#![cfg_attr(docsrs, feature(doc_cfg))]
 
 mod bioformats;
 
diff --git a/src/metadata.rs b/src/metadata.rs
index 0e34489..969c126 100644
--- a/src/metadata.rs
+++ b/src/metadata.rs
@@ -15,7 +15,7 @@ impl Metadata for Ome {
 
     fn get_image(&self) -> Option<&Image> {
         if let Some(image) = &self.image.first() {
-            Some(&image)
+            Some(image)
         } else {
             None
         }
diff --git a/src/py.rs b/src/py.rs
index d469e75..34c3753 100644
--- a/src/py.rs
+++ b/src/py.rs
@@ -19,7 +19,7 @@ use std::sync::Arc;
 
 impl From<crate::error::Error> for PyErr {
     fn from(err: crate::error::Error) -> PyErr {
-        PyErr::new::<PyValueError, _>(err.to_string())
+        color_eyre::eyre::Report::from(err).into()
     }
 }
 
@@ -49,7 +49,7 @@ impl ViewConstructor {
     }
 }
 
-#[pyclass(subclass, module = "ndbioimage.ndbioimage_rs")]
+#[pyclass(subclass, from_py_object, module = "ndbioimage.ndbioimage_rs")]
 #[pyo3(name = "View")]
 #[derive(Clone, Debug, Serialize, Deserialize)]
 struct PyView {
@@ -982,6 +982,7 @@ fn py_download_bioformats(gpl_formats: bool) -> PyResult<()> {
 #[pymodule]
 #[pyo3(name = "ndbioimage_rs")]
 fn ndbioimage_rs(m: &Bound<PyModule>) -> PyResult<()> {
+    color_eyre::install()?;
     m.add_class::<PyView>()?;
     m.add_class::<ViewConstructor>()?;
     m.add_function(wrap_pyfunction!(py_download_bioformats, m)?)?;