- Python: tree of python objects instead of tree of dicts

- Rust: more derives

.github/workflows/publish_crates.yml

@@ -1,6 +1,6 @@
 name: Publish
 
-on: [push, pull_request, workflow_call]
+on: [workflow_dispatch]
 
 permissions:
   contents: read
@@ -11,21 +11,24 @@ jobs:
     runs-on: ubuntu-latest
     timeout-minutes: 25
     steps:
-      - uses: actions/checkout@v4
-      - uses: dtolnay/rust-toolchain@stable
-
-      - name: cargo-release Cache
-        id: cargo_release_cache
-        uses: actions/cache@v3
+      - uses: actions/checkout@v6
+      - name: Restore cache
+        uses: actions/cache/restore@v4
         with:
-          path: ~/.cargo/bin/cargo-release
-          key: ${{ runner.os }}-cargo-release
+          path: |
+            ~/.cargo
+          key: cache-ubuntu-cargo-publish
 
-      - run: cargo install cargo-release
-        if: steps.cargo_release_cache.outputs.cache-hit != 'true'
-
-      - name: cargo login
-        run: cargo login ${{ secrets.CRATES_IO_API_TOKEN }}
+      - name: Install Rust
+        run: |-
+          export PATH="$HOME/.cargo/bin:$PATH"
+          if ! command -v rustc >/dev/null 2>&1; then
+            curl --proto '=https' --tlsv1.2 -sSf https://sh.rustup.rs | sh -s -- -y
+          else
+            rustup update
+          fi
+          cargo install cargo-release
+        shell: bash
 
       # allow-branch HEAD is because GitHub actions switches
       # to the tag while building, which is a detached head
@@ -44,6 +47,8 @@ jobs:
       # have passed.
       - name: "cargo release publish"
         run: |-
+          export PATH="$HOME/.osxcross/bin:$PATH"
+          cargo login ${{ secrets.CRATES_IO_API_TOKEN }}
           cargo release \
             publish \
             --workspace \
@@ -52,3 +57,10 @@ jobs:
             --no-confirm \
             --no-verify \
             --execute
+
+      - name: Store cache
+        uses: actions/cache/save@v4
+        with:
+          path: |
+            ~/.cargo
+          key: cache-ubuntu-cargo-publish

.github/workflows/publish_pypi.yml

@@ -0,0 +1,115 @@
+name: CI
+
+on: [workflow_dispatch]
+
+permissions:
+  contents: read
+
+jobs:
+  pypi_publish:
+    name: Publish (pypi.org)
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v6
+      - uses: actions/setup-python@v5
+        with:
+          python-version: 3.x
+
+      - name: Restore cache
+        uses: actions/cache/restore@v4
+        with:
+          path: |
+            ~/.cache/pip
+            ~/.cache/pip-wheel
+            ~/.cache/sccache
+            ~/.cache/cargo-xwin
+            ~/.cargo
+            ~/.osxcross
+          key: cache-ubuntu-maturin-cross-compile
+
+      - name: Install llvm
+        run: |
+          if ! command -v llvm-dlltool >/dev/null 2>&1; then
+            sudo apt update
+            sudo apt install -y llvm
+          fi
+        shell: bash
+
+      - name: Install Rust
+        run: |
+          export PATH="$HOME/.cargo/bin:$PATH"
+          if ! command -v rustc >/dev/null 2>&1; then
+            curl --proto '=https' --tlsv1.2 -sSf https://sh.rustup.rs | sh -s -- -y
+          else
+            rustup update
+          fi
+        shell: bash
+
+      - name: Install sccache and maturin
+        run: |
+          export PATH="$HOME/.cargo/bin:$PATH"
+          python -m pip install --upgrade pip
+          pip install maturin ziglang
+          if ! command -v sccache >/dev/null 2>&1; then
+            cargo install sccache || pip install sccache
+          fi
+        shell: bash
+
+      - name: Install xwin
+        run: |
+          export PATH="$HOME/.cargo/bin:$PATH"
+          if ! command -v cargo-xwin >/dev/null 2>&1; then
+            cargo install cargo-xwin || pip install cargo-xwin
+            cargo xwin cache xwin
+          fi
+        shell: bash
+
+      - name: Install osxcross
+        run: |
+          export PATH="$HOME/.osxcross/bin:$PATH"
+          if ! command -v osxcross >/dev/null 2>&1; then
+            wget ${{ secrets.OSXCROSS_LINK }} -O osxcross.tar.gz
+            tar -xzf osxcross.tar.gz -C ~/
+            mv ~/osxcross ~/.osxcross
+          fi
+
+      - name: Build wheels
+        run: |
+          export PATH="$HOME/.cargo/bin:$HOME/.osxcross/bin:$PATH"
+          rm -rf dist
+          maturin sdist --out dist -m ome-metadata/Cargo.toml
+          rustup default nightly
+          
+          rustup target add x86_64-unknown-linux-gnu --toolchain nightly
+          maturin build --release --out ../dist --target x86_64-unknown-linux-gnu -m ome-metadata/Cargo.toml
+          rustup target add aarch64-unknown-linux-gnu --toolchain nightly
+          maturin build --release --out ../dist --target aarch64-unknown-linux-gnu --zig -m ome-metadata/Cargo.toml
+          
+          rustup target add x86_64-pc-windows-msvc --toolchain nightly
+          maturin build --release --out dist --target x86_64-pc-windows-msvc -m ome-metadata/Cargo.toml
+          rustup target add aarch64-pc-windows-msvc --toolchain nightly
+          maturin build --release --out dist --target aarch64-pc-windows-msvc -m ome-metadata/Cargo.toml
+          
+          rustup target add x86_64-apple-darwin --toolchain nightly
+          maturin build --release --out dist --target x86_64-apple-darwin --zig -m ome-metadata/Cargo.toml
+          rustup target add aarch64-apple-darwin --toolchain nightly
+          maturin build --release --out dist --target aarch64-apple-darwin --zig -m ome-metadata/Cargo.toml
+
+      - name: Store cache
+        uses: actions/cache/save@v4
+        with:
+          path: |
+            ~/.cache/pip
+            ~/.cache/pip-wheel
+            ~/.cache/sccache
+            ~/.cache/cargo-xwin
+            ~/.cargo
+            ~/.osxcross
+          key: cache-ubuntu-maturin-cross-compile
+
+      - name: Publish to PyPI
+        uses: pypa/gh-action-pypi-publish@release/v1
+        with:
+          password: ${{ secrets.PYPI_API_TOKEN }}
+        env:
+          GITHUB_WORKFLOW_REF: 1.10.1

.gitignore

@@ -70,4 +70,7 @@ docs/_build/
 
 # Pyenv
 .python-version
-/Cargo.lock
+Cargo.lock
+target/
+
+.agentbridge

Cargo.toml

@@ -1,32 +1,16 @@
-[package]
-name = "ome-metadata"
-version = "0.1.0"
+[workspace]
+resolver = "3"
+members = ["ome-metadata", "ome-metadata-derive"]
+
+[workspace.package]
+version = "0.5.0"
 edition = "2024"
-rust-version = "1.85.1"
+rust-version = "1.88.0"
 authors = ["Wim Pomp <w.pomp@nki.nl>"]
-license = "MIT"
+license = "MIT OR Apache-2.0"
 description = "Ome metadata as a rust/python structure."
-homepage = "https://github.com/wimpomp/ome-metadata"
-repository = "https://github.com/wimpomp/ome-metadata"
+homepage = "https://git.pomppervova.nl/wim/ome-metadata"
+repository = "https://git.pomppervova.nl/wim/ome-metadata"
 readme = "README.md"
 keywords = ["bioformats", "imread", "ome", "metadata"]
 categories = ["multimedia::images", "science"]
-exclude = ["/tests"]
-
-# See more keys and their definitions at https://doc.rust-lang.org/cargo/reference/manifest.html
-[lib]
-name = "ome_metadata"
-crate-type = ["cdylib", "rlib"]
-
-[dependencies]
-anyhow = "1.0.98"
-serde = { version = "1.0.219", features = ["derive"] }
-quick-xml = {  version = "0.37.5", features = ["serialize"] }
-
-[dependencies.pyo3]
-version = "0.24.2"
-features = ["extension-module", "abi3-py310", "generate-import-lib", "anyhow"]
-optional = true
-
-[features]
-python = ["dep:pyo3"]

LICENSE

@@ -1,19 +0,0 @@
-Copyright (c) 2025 Wim Pomp
-
-Permission is hereby granted, free of charge, to any person obtaining a copy
-of this software and associated documentation files (the "Software"), to deal
-in the Software without restriction, including without limitation the rights
-to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
-copies of the Software, and to permit persons to whom the Software is
-furnished to do so, subject to the following conditions:
-
-The above copyright notice and this permission notice shall be included in all
-copies or substantial portions of the Software.
-
-THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
-IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
-FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
-AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
-LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
-OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
-SOFTWARE.

README.md

@@ -9,7 +9,7 @@ use ome_metadata::Ome;
 
 let xml = read_to_string($file)?;
 let ome: Ome = xml.parse()?;
-let image = &ome.image.unwrap()[0];
+let image = &ome.image[0];
 println!("acquisition date: {:#?}", image.acquisition_date);
 ```
 

ome-metadata-derive/Cargo.toml

@@ -0,0 +1,11 @@
+[package]
+name = "ome-metadata-derive"
+version = "0.5.0"
+edition = "2024"
+
+[dependencies]
+quote = "1"
+syn = "2"
+
+[lib]
+proc-macro = true

ome-metadata-derive/LICENSE-APACHE

@@ -0,0 +1,201 @@
+                              Apache License
+                        Version 2.0, January 2004
+                     http://www.apache.org/licenses/
+
+TERMS AND CONDITIONS FOR USE, REPRODUCTION, AND DISTRIBUTION
+
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+
+APPENDIX: How to apply the Apache License to your work.
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+   To apply the Apache License to your work, attach the following
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ome-metadata-derive/LICENSE-MIT

@@ -0,0 +1,27 @@
+Copyright (c) 2015 - 2021 Ulrik Sverdrup "bluss",
+			  Jim Turner,
+			  and ndarray developers
+
+Permission is hereby granted, free of charge, to any
+person obtaining a copy of this software and associated
+documentation files (the "Software"), to deal in the
+Software without restriction, including without
+limitation the rights to use, copy, modify, merge,
+publish, distribute, sublicense, and/or sell copies of
+the Software, and to permit persons to whom the Software
+is furnished to do so, subject to the following
+conditions:
+
+The above copyright notice and this permission notice
+shall be included in all copies or substantial portions
+of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF
+ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED
+TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A
+PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT
+SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY
+CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION
+OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR
+IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
+DEALINGS IN THE SOFTWARE.

ome-metadata-derive/README.md

@@ -0,0 +1 @@
+# Derive macros for ome-metadata

ome-metadata-derive/src/lib.rs

@@ -0,0 +1,297 @@
+use proc_macro::TokenStream;
+use quote::quote;
+use syn::{Data, DeriveInput, Fields, Visibility, parse_macro_input};
+
+#[proc_macro_derive(OmeXML)]
+pub fn ome_metadata_derive_xml(input: TokenStream) -> TokenStream {
+    let input = parse_macro_input!(input as DeriveInput);
+    let ident = input.ident;
+
+    let expanded = quote! {
+        impl #ident {
+            pub fn from_xml<T: AsRef<str>>(s: T) -> Result<Self, Error> {
+                Ok(from_str(s.as_ref())?)
+            }
+
+            pub fn to_xml(&self) -> Result<String, Error> {
+                Ok(to_string(self)?)
+            }
+        }
+    };
+
+    TokenStream::from(expanded)
+}
+
+#[proc_macro_derive(PyOmeComplexEnum)]
+pub fn ome_metadata_derive_complex_enum(input: TokenStream) -> TokenStream {
+    let input = parse_macro_input!(input as DeriveInput);
+    let ident = input.ident;
+
+    let mut variants = Vec::new();
+
+    match input.data {
+        Data::Enum(s) => {
+            for variant in &s.variants {
+                let variant_ident = &variant.ident;
+                variants.push(quote! {
+                    Self::#variant_ident(v) => v.clone().into_bound_py_any(py)?,
+                });
+            }
+        }
+        _ => {
+            return syn::Error::new_spanned(ident, "PyOmeComplexEnum only supports structs")
+                .to_compile_error()
+                .into();
+        }
+    };
+
+    let expanded = quote! {
+        impl PyDisplay for #ident {
+            fn py_str(&self) -> String {
+                format!("{:?}", self)
+            }
+        }
+
+        #[pyo3::prelude::pymethods]
+        impl #ident {
+            /// all possible variants of this enum that can be constructed or converted into
+            #[staticmethod]
+            fn variants() -> Vec<String> {
+                Self::VARIANTS.iter().map(|v| v.trim_matches('"').to_string()).collect()
+            }
+
+            fn __repr__(&self) -> String {
+                self.py_str()
+            }
+
+            fn __str__(&self) -> String {
+                self.py_str()
+            }
+
+            fn __getnewargs__<'py>(&self, py: Python<'py>) -> PyResult<(Bound<'py, PyAny>,)> {
+                Ok((match self { #(#variants)* },))
+            }
+
+            #[staticmethod]
+            #[pyo3(name = "from_xml")]
+            fn py_from_xml(xml: &str) -> PyResult<Self> {
+                Ok(Self::from_xml(xml)?)
+            }
+
+            #[pyo3(name = "to_xml")]
+            fn py_to_xml(&self) -> PyResult<String> {
+                Ok(self.to_xml()?)
+            }
+        }
+    };
+
+    TokenStream::from(expanded)
+}
+
+#[proc_macro_derive(PyOmeEnum)]
+pub fn ome_metadata_derive_enum(input: TokenStream) -> TokenStream {
+    let input = parse_macro_input!(input as DeriveInput);
+    let name = input.ident;
+
+    let expanded = quote! {
+        impl PyDisplay for #name {
+            fn py_str(&self) -> String {
+                format!("{}", self)
+            }
+        }
+
+        #[pyo3::prelude::pymethods]
+        impl #name {
+            #[new]
+            fn new(unit: &str) -> PyResult<Self> {
+                unit.parse().map_err(|_| PyErr::new::<pyo3::exceptions::PyValueError, _>(format!("could not parse {}", unit)))
+            }
+
+            /// all possible variants of this enum that can be constructed or converted into
+            #[staticmethod]
+            fn variants() -> Vec<String> {
+                Self::VARIANTS.iter().map(|v| v.trim_matches('"').to_string()).collect()
+            }
+
+            fn __repr__(&self) -> String {
+                self.py_str()
+            }
+
+            fn __str__(&self) -> String {
+                self.py_str()
+            }
+
+            fn __getnewargs__(&self) -> (String,) {
+                (format!("{}", self),)
+            }
+
+            #[staticmethod]
+            #[pyo3(name = "from_xml")]
+            fn py_from_xml(xml: &str) -> PyResult<Self> {
+                Ok(Self::from_xml(xml)?)
+            }
+
+            #[pyo3(name = "to_xml")]
+            fn py_to_xml(&self) -> PyResult<String> {
+                Ok(self.to_xml()?)
+            }
+        }
+    };
+
+    TokenStream::from(expanded)
+}
+
+#[proc_macro_derive(PyOmeUnit)]
+pub fn ome_metadata_derive_unit(input: TokenStream) -> TokenStream {
+    let input = parse_macro_input!(input as DeriveInput);
+    let name = input.ident;
+
+    let expanded = quote! {
+        impl PyDisplay for #name {
+            fn py_str(&self) -> String {
+                format!("{}", self)
+            }
+        }
+
+        #[pyo3::prelude::pymethods]
+        impl #name {
+            #[new]
+            fn new(unit: &str) -> PyResult<Self> {
+                unit.parse().map_err(|_| PyErr::new::<pyo3::exceptions::PyValueError, _>(format!("could not parse {}", unit)))
+            }
+
+            /// convert a value between units
+            #[pyo3(name = "convert")]
+            fn py_convert(&self, unit: &Self, value: f64) -> PyResult<f64> {
+                Ok(self.convert(unit, value)?)
+            }
+
+            /// all possible variants of this enum that can be constructed or converted into
+            #[staticmethod]
+            fn variants() -> Vec<String> {
+                Self::VARIANTS.iter().map(|v| v.trim_matches('"').to_string()).collect()
+            }
+
+            fn __repr__(&self) -> String {
+                self.py_str()
+            }
+
+            fn __str__(&self) -> String {
+                self.py_str()
+            }
+
+            fn __getnewargs__(&self) -> (String,) {
+                (format!("{}", self),)
+            }
+
+            #[staticmethod]
+            #[pyo3(name = "from_xml")]
+            fn py_from_xml(xml: &str) -> PyResult<Self> {
+                Ok(Self::from_xml(xml)?)
+            }
+
+            #[pyo3(name = "to_xml")]
+            fn py_to_xml(&self) -> PyResult<String> {
+                Ok(self.to_xml()?)
+            }
+        }
+    };
+
+    TokenStream::from(expanded)
+}
+
+#[proc_macro_derive(PyOme)]
+pub fn ome_metadata_derive(input: TokenStream) -> TokenStream {
+    let input = parse_macro_input!(input as DeriveInput);
+    let name = input.ident;
+
+    // Only support named structs
+    let fields = match input.data {
+        Data::Struct(s) => match s.fields {
+            Fields::Named(named) => named.named,
+            _ => {
+                return syn::Error::new_spanned(name, "PyOme only supports named structs")
+                    .to_compile_error()
+                    .into();
+            }
+        },
+        _ => {
+            return syn::Error::new_spanned(name, "PyOme only supports structs")
+                .to_compile_error()
+                .into();
+        }
+    };
+
+    let mut idents = Vec::new();
+    let mut types = Vec::new();
+    let mut f = Vec::new();
+    let mut ps = Vec::new();
+    let mut new_kwargs = Vec::new();
+    let mut s = Vec::new();
+
+    for field in fields.iter() {
+        let ty = &field.ty;
+        if let Some(ident) = &field.ident
+            && let Visibility::Public(_) = field.vis
+        {
+            let tmp = ident.to_string();
+            let field_name = tmp.trim_start_matches("r#");
+            idents.push(quote! {
+                self.#ident
+            });
+            types.push(quote! { #ty });
+            f.push(quote! {
+                pub #ident: #ty
+            });
+            ps.push(quote! {
+                self.#ident.py_str()
+            });
+            new_kwargs.push(quote! {
+                (#field_name, self.#ident.clone().into_bound_py_any(py)?)
+            });
+            s.push(format!("{}: {{}}", field_name));
+        } else {
+            return syn::Error::new_spanned(field, "PyOme type only supports public named fields")
+                .to_compile_error()
+                .into();
+        }
+    }
+    let fmt = format!("{}({})", name, s.join(", "));
+
+    // Generate the token stream
+    let expanded = quote! {
+        impl PyDisplay for #name {
+            fn py_str(&self) -> String {
+                format!(#fmt, #(#ps,)*)
+            }
+        }
+
+        #[pyo3::prelude::pymethods]
+        impl #name {
+            fn __getnewargs_ex__<'py>(&self, py: Python<'py>) -> PyResult<((), std::collections::HashMap<&str, Bound<'py, PyAny>>)> {
+                Ok(((), std::collections::HashMap::from_iter([#(#new_kwargs,)*])))
+            }
+
+            fn __repr__(&self) -> String {
+                self.py_str()
+            }
+
+            fn __str__(&self) -> String {
+                self.py_str()
+            }
+
+            #[staticmethod]
+            #[pyo3(name = "from_xml")]
+            fn py_from_xml(xml: &str) -> PyResult<Self> {
+                Ok(Self::from_xml(xml)?)
+            }
+
+            #[pyo3(name = "to_xml")]
+            fn py_to_xml(&self) -> PyResult<String> {
+                Ok(self.to_xml()?)
+            }
+        }
+    };
+
+    TokenStream::from(expanded)
+}

ome-metadata/Cargo.toml

@@ -0,0 +1,32 @@
+[package]
+name = "ome-metadata"
+version = "0.5.0"
+edition = "2024"
+rust-version = "1.88.0"
+authors = ["Wim Pomp <w.pomp@nki.nl>"]
+license = "MIT OR Apache-2.0"
+description = "Ome metadata as a rust/python structure."
+homepage = "https://git.pomppervova.nl/wim/ome-metadata"
+repository = "https://git.pomppervova.nl/wim/ome-metadata"
+documentation = "https://docs.rs/ome-metadata"
+readme = "README.md"
+keywords = ["bioformats", "imread", "ome", "metadata"]
+categories = ["multimedia::images", "science"]
+exclude = ["/tests"]
+
+# See more keys and their definitions at https://doc.rust-lang.org/cargo/reference/manifest.html
+[lib]
+name = "ome_metadata"
+crate-type = ["cdylib", "rlib"]
+
+[dependencies]
+color-eyre = { version = "0.6", optional = true }
+ome-metadata-derive = { path = "../ome-metadata-derive" }
+pyo3 = { version = "0.29", features = ["abi3-py310", "anyhow", "eyre", "generate-import-lib"], optional = true}
+quick-xml = { version = "0.40", features = ["serialize"] }
+serde = { version = "1", features = ["derive"] }
+strum = { version = "0.28", features = ["derive"] }
+thiserror = "2"
+
+[features]
+python = ["dep:pyo3", "dep:color-eyre"]

ome-metadata/LICENSE-APACHE

@@ -0,0 +1,201 @@
+                              Apache License
+                        Version 2.0, January 2004
+                     http://www.apache.org/licenses/
+
+TERMS AND CONDITIONS FOR USE, REPRODUCTION, AND DISTRIBUTION
+
+1. Definitions.
+
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+   and distribution as defined by Sections 1 through 9 of this document.
+
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+
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+
+   "You" (or "Your") shall mean an individual or Legal Entity
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+
+7. Disclaimer of Warranty. Unless required by applicable law or
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+   Contributor provides its Contributions) on an "AS IS" BASIS,
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+8. Limitation of Liability. In no event and under no legal theory,
+   whether in tort (including negligence), contract, or otherwise,
+   unless required by applicable law (such as deliberate and grossly
+   negligent acts) or agreed to in writing, shall any Contributor be
+   liable to You for damages, including any direct, indirect, special,
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+   on Your own behalf and on Your sole responsibility, not on behalf
+   of any other Contributor, and only if You agree to indemnify,
+   defend, and hold each Contributor harmless for any liability
+   incurred by, or claims asserted against, such Contributor by reason
+   of your accepting any such warranty or additional liability.
+
+END OF TERMS AND CONDITIONS
+
+APPENDIX: How to apply the Apache License to your work.
+
+   To apply the Apache License to your work, attach the following
+   boilerplate notice, with the fields enclosed by brackets "[]"
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+   file or class name and description of purpose be included on the
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+Copyright [yyyy] [name of copyright owner]
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+	http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.

ome-metadata/LICENSE-MIT

@@ -0,0 +1,27 @@
+Copyright (c) 2015 - 2021 Ulrik Sverdrup "bluss",
+			  Jim Turner,
+			  and ndarray developers
+
+Permission is hereby granted, free of charge, to any
+person obtaining a copy of this software and associated
+documentation files (the "Software"), to deal in the
+Software without restriction, including without
+limitation the rights to use, copy, modify, merge,
+publish, distribute, sublicense, and/or sell copies of
+the Software, and to permit persons to whom the Software
+is furnished to do so, subject to the following
+conditions:
+
+The above copyright notice and this permission notice
+shall be included in all copies or substantial portions
+of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF
+ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED
+TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A
+PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT
+SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY
+CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION
+OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR
+IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
+DEALINGS IN THE SOFTWARE.

ome-metadata/README.md

@@ -0,0 +1,25 @@
+# ome-metadata
+
+Open Microscopy XML metadata (https://www.openmicroscopy.org/Schemas/) as a collection of Rust structs and enums, with translation to Python.
+
+## Rust
+``` 
+use std::fs::read_to_string;
+use ome_metadata::Ome;
+
+let xml = read_to_string($file)?;
+let ome: Ome = xml.parse()?;
+let image = &ome.image[0];
+println!("acquisition date: {:#?}", image.acquisition_date);
+```
+
+## Python
+```
+from ome_metadata import Ome
+
+with open($file) as f:
+    xml = f.read()
+ome = Ome.from_xml(xml)
+image = ome.image[0]
+print(f"acquisition date: {image.acquisition_date}")
+```

ome-metadata/pyproject.toml

@@ -0,0 +1,33 @@
+[build-system]
+requires = ["maturin>=1.9.4,<2.0"]
+build-backend = "maturin"
+
+[project]
+name = "ome-metadata"
+requires-python = ">=3.10"
+classifiers = [
+    "License :: OSI Approved :: MIT License",
+    "License :: OSI Approved :: Apache Software License",
+    "Programming Language :: Rust",
+    "Programming Language :: Python",
+    "Programming Language :: Python :: 3",
+]
+dynamic = [
+    "version",
+    "description",
+    "readme",
+    "license",
+    "license-files",
+    "authors",
+    "maintainers",
+    "keywords",
+    "urls",
+]
+
+[tool.maturin]
+features = ["python"]
+module-name = "ome_metadata"
+strip = true
+
+[tool.isort]
+line_length = 119

ome-metadata/src/error.rs

@@ -0,0 +1,15 @@
+use thiserror::Error;
+
+#[derive(Debug, Error)]
+pub enum Error {
+    #[error(transparent)]
+    IO(#[from] std::io::Error),
+    #[error(transparent)]
+    XmlDe(#[from] quick_xml::DeError),
+    #[error(transparent)]
+    XmlSe(#[from] quick_xml::SeError),
+    #[error("size of {0} is unknown")]
+    SizeOfUnknown(String),
+    #[error("no conversion to K by multiplication only")]
+    TemparatureConversion,
+}

ome-metadata/src/lib.rs

@@ -1,34 +1,26 @@
 #![allow(non_camel_case_types)]
 pub mod ome;
 
+pub mod error;
 #[cfg(feature = "python")]
-mod py;
+pub mod py;
 
-use anyhow::{Error, Result};
 pub use ome::Ome;
-use quick_xml::de::from_str;
-use std::str::FromStr;
-
-impl FromStr for Ome {
-    type Err = Error;
-
-    fn from_str(s: &str) -> Result<Self> {
-        Ok(from_str(s)?)
-    }
-}
 
 #[cfg(test)]
 mod tests {
-    use super::*;
+    use crate::Ome;
+    use crate::error::Error;
     use std::fs::read_to_string;
 
     macro_rules! test_read {
         ($($name:ident: $file:expr $(,)?)*) => {
             $(
                 #[test]
-                fn $name() -> Result<()> {
+                fn $name() -> Result<(), Error> {
                     let file = read_to_string(format!("tests/{}.xml", $file))?;
-                    let _ome: Ome = file.parse()?;
+                    let ome = Ome::from_xml(file)?;
+                    let _xml = ome.to_xml()?;
                     Ok(())
                 }
             )*
@@ -47,5 +39,6 @@ mod tests {
         i: "beads_2023_05_04__19_00_22"
         j: "20230511-p53-4x-CMV-1min-4h-01-Airyscan Processing-01"
         k: "YTL1849A131_2023_05_04__13_36_36"
+        l: "multi-channel.ome"
     );
 }

ome-metadata/src/py.rs

@@ -0,0 +1,487 @@
+use crate::error::Error;
+use crate::ome::{ExperimentType, MetadataOnly, MicrobeamManipulationType, XmlAnnotationValue};
+use pyo3::prelude::*;
+use pyo3::types::PyTuple;
+
+impl From<crate::error::Error> for PyErr {
+    fn from(err: crate::error::Error) -> PyErr {
+        color_eyre::eyre::Report::from(err).into()
+    }
+}
+
+pub(crate) trait PyDisplay {
+    fn py_str(&self) -> String;
+}
+
+impl PyDisplay for String {
+    fn py_str(&self) -> String {
+        self.clone()
+    }
+}
+
+impl PyDisplay for bool {
+    fn py_str(&self) -> String {
+        self.to_string()
+    }
+}
+
+impl PyDisplay for i32 {
+    fn py_str(&self) -> String {
+        self.to_string()
+    }
+}
+impl PyDisplay for i64 {
+    fn py_str(&self) -> String {
+        self.to_string()
+    }
+}
+impl PyDisplay for f32 {
+    fn py_str(&self) -> String {
+        self.to_string()
+    }
+}
+impl PyDisplay for f64 {
+    fn py_str(&self) -> String {
+        self.to_string()
+    }
+}
+impl<T> PyDisplay for Option<T>
+where
+    T: PyDisplay,
+{
+    fn py_str(&self) -> String {
+        if let Some(val) = self {
+            val.py_str()
+        } else {
+            "None".to_string()
+        }
+    }
+}
+
+impl<T> PyDisplay for Vec<T>
+where
+    T: PyDisplay,
+{
+    fn py_str(&self) -> String {
+        format!(
+            "[{}]",
+            self.iter()
+                .map(|x| x.py_str())
+                .collect::<Vec<_>>()
+                .join(", ")
+        )
+    }
+}
+impl PyDisplay for MetadataOnly {
+    fn py_str(&self) -> String {
+        "MetadataOnly".into()
+    }
+}
+impl<'a, 'py> FromPyObject<'a, 'py> for MetadataOnly {
+    type Error = Error;
+
+    fn extract(_obj: Borrowed<'a, 'py, PyAny>) -> Result<Self, Self::Error> {
+        Ok(Self {})
+    }
+}
+impl PyDisplay for MicrobeamManipulationType {
+    fn py_str(&self) -> String {
+        format!(
+            "[{}]",
+            self.0
+                .iter()
+                .map(|i| i.py_str())
+                .collect::<Vec<_>>()
+                .join(", ")
+        )
+    }
+}
+impl<'a, 'py> FromPyObject<'a, 'py> for XmlAnnotationValue {
+    type Error = Error;
+
+    fn extract(_obj: Borrowed<'a, 'py, PyAny>) -> Result<Self, Self::Error> {
+        Ok(Self {})
+    }
+}
+impl PyDisplay for XmlAnnotationValue {
+    fn py_str(&self) -> String {
+        "XmlAnnotationValue".to_string()
+    }
+}
+impl PyDisplay for ExperimentType {
+    fn py_str(&self) -> String {
+        format!(
+            "[{}]",
+            self.0
+                .iter()
+                .map(|i| i.py_str())
+                .collect::<Vec<_>>()
+                .join(", ")
+        )
+    }
+}
+
+#[pymethods]
+impl MetadataOnly {
+    fn __getnewargs__<'py>(&self, py: Python<'py>) -> Bound<'py, PyTuple> {
+        PyTuple::empty(py)
+    }
+    fn __repr__(&self) -> String {
+        "MetadataOnly".into()
+    }
+    fn __str__(&self) -> String {
+        "MetadataOnly".into()
+    }
+}
+
+#[pyfunction]
+fn parse_ome(text: &str) -> PyResult<crate::Ome> {
+    Ok(crate::ome::Ome::from_xml(text)?)
+}
+
+#[pyfunction]
+fn to_xml(ome: crate::ome::Ome) -> PyResult<String> {
+    Ok(ome.to_xml()?)
+}
+
+#[pymodule]
+#[pyo3(name = "ome_metadata")]
+pub mod ome_metadata {
+    use pyo3::prelude::*;
+
+    #[pymodule_export]
+    use super::parse_ome;
+
+    #[pymodule_export]
+    use super::to_xml;
+
+    #[pymodule_export]
+    use crate::ome::AffineTransform;
+
+    #[pymodule_export]
+    use crate::ome::Annotation;
+
+    #[pymodule_export]
+    use crate::ome::AnnotationRef;
+
+    #[pymodule_export]
+    use crate::ome::Arc;
+
+    #[pymodule_export]
+    use crate::ome::BinData;
+
+    #[pymodule_export]
+    use crate::ome::BinaryFile;
+
+    #[pymodule_export]
+    use crate::ome::BooleanAnnotation;
+
+    #[pymodule_export]
+    use crate::ome::Channel;
+
+    #[pymodule_export]
+    use crate::ome::CommentAnnotation;
+
+    #[pymodule_export]
+    use crate::ome::Dataset;
+
+    #[pymodule_export]
+    use crate::ome::Detector;
+
+    #[pymodule_export]
+    use crate::ome::DetectorSettings;
+
+    #[pymodule_export]
+    use crate::ome::Dichroic;
+
+    #[pymodule_export]
+    use crate::ome::DoubleAnnotation;
+
+    #[pymodule_export]
+    use crate::ome::Ellipse;
+
+    #[pymodule_export]
+    use crate::ome::Experiment;
+
+    #[pymodule_export]
+    use crate::ome::ExperimentType;
+
+    #[pymodule_export]
+    use crate::ome::Experimenter;
+
+    #[pymodule_export]
+    use crate::ome::ExperimenterGroup;
+
+    #[pymodule_export]
+    use crate::ome::External;
+
+    #[pymodule_export]
+    use crate::ome::Filament;
+
+    #[pymodule_export]
+    use crate::ome::FileAnnotation;
+
+    #[pymodule_export]
+    use crate::ome::Filter;
+
+    #[pymodule_export]
+    use crate::ome::FilterSet;
+
+    #[pymodule_export]
+    use crate::ome::Folder;
+
+    #[pymodule_export]
+    use crate::ome::GenericExcitationSource;
+
+    #[pymodule_export]
+    use crate::ome::Image;
+
+    #[pymodule_export]
+    use crate::ome::ImagingEnvironment;
+
+    #[pymodule_export]
+    use crate::ome::Instrument;
+
+    #[pymodule_export]
+    use crate::ome::Label;
+
+    #[pymodule_export]
+    use crate::ome::Laser;
+
+    #[pymodule_export]
+    use crate::ome::LightEmittingDiode;
+
+    #[pymodule_export]
+    use crate::ome::LightPath;
+
+    #[pymodule_export]
+    use crate::ome::LightSourceType;
+
+    #[pymodule_export]
+    use crate::ome::LightSourceSettings;
+
+    #[pymodule_export]
+    use crate::ome::Line;
+
+    #[pymodule_export]
+    use crate::ome::LongAnnotation;
+
+    #[pymodule_export]
+    use crate::ome::MapType;
+
+    #[pymodule_export]
+    use crate::ome::MapAnnotation;
+
+    #[pymodule_export]
+    use crate::ome::MapM;
+
+    #[pymodule_export]
+    use crate::ome::Mask;
+
+    #[pymodule_export]
+    use crate::ome::MetadataOnly;
+
+    #[pymodule_export]
+    use crate::ome::MicrobeamManipulation;
+
+    #[pymodule_export]
+    use crate::ome::MicrobeamManipulationType;
+
+    #[pymodule_export]
+    use crate::ome::Microscope;
+
+    #[pymodule_export]
+    use crate::ome::Ome;
+
+    #[pymodule_export]
+    use crate::ome::Objective;
+
+    #[pymodule_export]
+    use crate::ome::ObjectiveSettings;
+
+    #[pymodule_export]
+    use crate::ome::OmeBinaryOnly;
+
+    #[pymodule_export]
+    use crate::ome::Pixels;
+
+    #[pymodule_export]
+    use crate::ome::Plane;
+
+    #[pymodule_export]
+    use crate::ome::Plate;
+
+    #[pymodule_export]
+    use crate::ome::PlateAcquisition;
+
+    #[pymodule_export]
+    use crate::ome::Polygon;
+
+    #[pymodule_export]
+    use crate::ome::Polyline;
+
+    #[pymodule_export]
+    use crate::ome::Project;
+
+    #[pymodule_export]
+    use crate::ome::Roi;
+
+    #[pymodule_export]
+    use crate::ome::Reagent;
+
+    #[pymodule_export]
+    use crate::ome::Rectangle;
+
+    #[pymodule_export]
+    use crate::ome::Rights;
+
+    #[pymodule_export]
+    use crate::ome::RoiUnion;
+
+    #[pymodule_export]
+    use crate::ome::Screen;
+
+    #[pymodule_export]
+    use crate::ome::ShapeType;
+
+    #[pymodule_export]
+    use crate::ome::StageLabel;
+
+    #[pymodule_export]
+    use crate::ome::StructuredAnnotations;
+
+    #[pymodule_export]
+    use crate::ome::TiffData;
+
+    #[pymodule_export]
+    use crate::ome::TiffDataUuid;
+
+    #[pymodule_export]
+    use crate::ome::TransmittanceRange;
+
+    #[pymodule_export]
+    use crate::ome::Well;
+
+    #[pymodule_export]
+    use crate::ome::WellSample;
+
+    #[pymodule_export]
+    use crate::ome::XmlAnnotation;
+
+    #[pymodule_export]
+    use crate::ome::XmlAnnotationValue;
+
+    #[pymodule_export]
+    use crate::ome::ArcType;
+
+    #[pymodule_export]
+    use crate::ome::BinDataCompressionType;
+
+    #[pymodule_export]
+    use crate::ome::BinaryFileContent;
+
+    #[pymodule_export]
+    use crate::ome::BinningType;
+
+    #[pymodule_export]
+    use crate::ome::ChannelAcquisitionModeType;
+
+    #[pymodule_export]
+    use crate::ome::ChannelContrastMethodType;
+
+    #[pymodule_export]
+    use crate::ome::ChannelIlluminationType;
+
+    #[pymodule_export]
+    use crate::ome::DetectorType;
+
+    #[pymodule_export]
+    use crate::ome::ExperimentItemType;
+
+    #[pymodule_export]
+    use crate::ome::FilamentType;
+
+    #[pymodule_export]
+    use crate::ome::FilterType;
+
+    #[pymodule_export]
+    use crate::ome::FontFamilyType;
+
+    #[pymodule_export]
+    use crate::ome::LaserLaserMediumType;
+
+    #[pymodule_export]
+    use crate::ome::LaserPulseType;
+
+    #[pymodule_export]
+    use crate::ome::LaserType;
+
+    #[pymodule_export]
+    use crate::ome::LightSourceGroup;
+
+    #[pymodule_export]
+    use crate::ome::MarkerType;
+
+    #[pymodule_export]
+    use crate::ome::MicrobeamManipulationItemType;
+
+    #[pymodule_export]
+    use crate::ome::MicroscopeType;
+
+    #[pymodule_export]
+    use crate::ome::NamingConventionType;
+
+    #[pymodule_export]
+    use crate::ome::ObjectiveCorrectionType;
+
+    #[pymodule_export]
+    use crate::ome::ObjectiveImmersionType;
+
+    #[pymodule_export]
+    use crate::ome::ObjectiveSettingsMediumType;
+
+    #[pymodule_export]
+    use crate::ome::PixelType;
+
+    #[pymodule_export]
+    use crate::ome::PixelsDimensionOrderType;
+
+    #[pymodule_export]
+    use crate::ome::ShapeFillRuleType;
+
+    #[pymodule_export]
+    use crate::ome::ShapeFontStyleType;
+
+    #[pymodule_export]
+    use crate::ome::ShapeGroup;
+
+    #[pymodule_export]
+    use crate::ome::StructuredAnnotationsContent;
+
+    #[pymodule_export]
+    use crate::ome::UnitsElectricPotential;
+
+    #[pymodule_export]
+    use crate::ome::UnitsFrequency;
+
+    #[pymodule_export]
+    use crate::ome::UnitsLength;
+
+    #[pymodule_export]
+    use crate::ome::UnitsPower;
+
+    #[pymodule_export]
+    use crate::ome::UnitsPressure;
+
+    #[pymodule_export]
+    use crate::ome::UnitsTemperature;
+
+    #[pymodule_export]
+    use crate::ome::UnitsTime;
+
+    #[pymodule_init]
+    fn init(_: &Bound<'_, PyModule>) -> PyResult<()> {
+        let _ = color_eyre::install();
+        Ok(())
+    }
+}

ome-metadata/tests/multi-channel.ome.xml

@@ -0,0 +1 @@
+<?xml version="1.0" encoding="UTF-8"?><OME xmlns="http://www.openmicroscopy.org/Schemas/OME/2016-06" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" Creator="OME Bio-Formats 5.2.2" UUID="urn:uuid:bebd2be7-8253-4b90-be93-4df567ffe1be" xsi:schemaLocation="http://www.openmicroscopy.org/Schemas/OME/2016-06 http://www.openmicroscopy.org/Schemas/OME/2016-06/ome.xsd"><Image ID="Image:0" Name="multi-channel.ome.tif"><Pixels BigEndian="true" DimensionOrder="XYZCT" ID="Pixels:0" Interleaved="false" SignificantBits="8" SizeC="3" SizeT="1" SizeX="439" SizeY="167" SizeZ="1" Type="int8"><Channel ID="Channel:0:0" SamplesPerPixel="1"><LightPath/></Channel><Channel ID="Channel:0:1" SamplesPerPixel="1"><LightPath/></Channel><Channel ID="Channel:0:2" SamplesPerPixel="1"><LightPath/></Channel><TiffData FirstC="0" FirstT="0" FirstZ="0" IFD="0" PlaneCount="1"><UUID FileName="multi-channel.ome.tif">urn:uuid:bebd2be7-8253-4b90-be93-4df567ffe1be</UUID></TiffData><TiffData FirstC="1" FirstT="0" FirstZ="0" IFD="1" PlaneCount="1"><UUID FileName="multi-channel.ome.tif">urn:uuid:bebd2be7-8253-4b90-be93-4df567ffe1be</UUID></TiffData><TiffData FirstC="2" FirstT="0" FirstZ="0" IFD="2" PlaneCount="1"><UUID FileName="multi-channel.ome.tif">urn:uuid:bebd2be7-8253-4b90-be93-4df567ffe1be</UUID></TiffData></Pixels></Image></OME>

py/ome_metadata/__init__.py

@@ -1,38 +0,0 @@
-from __future__ import annotations
-
-from . import ome_metadata_rs as rs  # noqa
-
-
-class Ome(dict):
-    @staticmethod
-    def from_xml(xml: str) -> Ome:
-        """Create the OME structure from an XML string"""
-        new = Ome()
-        new.update(rs.ome(str(xml)))
-        return new
-
-    def __dir__(self) -> list[str]:
-        return list(self.keys()) + list(super().__dir__())
-
-    def __getattr__(self, key: str) -> Ome | OmeList | int | float | str:
-        try:
-            new = self.__getitem__(key)
-        except KeyError:
-            raise AttributeError(f"'Ome' object has no attribute '{key}'")
-        if isinstance(new, dict):
-            return Ome(**new)
-        elif isinstance(new, list):
-            return OmeList(new)
-        else:
-            return new
-
-
-class OmeList(list):
-    def __getitem__(self, item: int) -> Ome | OmeList | int | float | str:
-        new = super().__getitem__(item)
-        if isinstance(new, dict):
-            return Ome(**new)
-        elif isinstance(new, list):
-            return OmeList(new)
-        else:
-            return new

pyproject.toml

@@ -1,32 +0,0 @@
-[build-system]
-requires = ["maturin>=1.8,<2.0"]
-build-backend = "maturin"
-
-[project]
-name = "ome-metadata"
-keywords = ["bioformats", "imread", "ome", "metadata"]
-requires-python = ">=3.10"
-classifiers = [
-    "License :: OSI Approved :: MIT License",
-    "Programming Language :: Rust",
-    "Programming Language :: Python",
-    "Programming Language :: Python :: 3",
-    "Programming Language :: Python :: 3 :: Only",
-    "Programming Language :: Python :: 3.10",
-    "Programming Language :: Python :: 3.11",
-    "Programming Language :: Python :: 3.12",
-    "Programming Language :: Python :: 3.13",
-    "Programming Language :: Python :: 3.14",
-]
-dynamic = ["version", "description", "authors", "license", "readme"]
-
-[project.urls]
-Repository = "https://github.com/wimpomp/ome-metadata"
-
-[tool.maturin]
-python-source = "py"
-features = ["pyo3/extension-module", "python"]
-module-name = "ome_metadata.ome_metadata_rs"
-
-[tool.isort]
-line_length = 119

src/py.rs

@@ -1,13 +0,0 @@
-use crate::Ome;
-use pyo3::prelude::*;
-
-#[pymodule]
-#[pyo3(name = "ome_metadata_rs")]
-fn ome_metadata_rs(m: &Bound<'_, PyModule>) -> PyResult<()> {
-    #[pyfn(m)]
-    fn ome(text: &str) -> PyResult<Ome> {
-        Ok(text.parse()?)
-    }
-
-    Ok(())
-}