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- workflow fix

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- bump dependencies
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w.pomp committed 2026-10-01 19:27:09 +02:00
1 parent f94c77c3f8
commit 7af9cdb5a3
7 files changed
+42 -37
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.github/workflows/publish_crates.yml
+9 -8
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@@ -1,6 +1,6 @@
name: Publish_rs name: Publish_rs
on: [workflow_dispatch] on: [ workflow_dispatch ]
permissions: permissions:
contents: read contents: read
@@ -10,24 +10,25 @@ jobs:
name: Publish (crates.io) name: Publish (crates.io)
runs-on: ubuntu-latest runs-on: ubuntu-latest
timeout-minutes: 25 timeout-minutes: 25
env:
CARGO_HOME: ${{ github.workspace }}/.cargo
steps: steps:
- uses: actions/checkout@v6 - uses: actions/checkout@v6
- name: Restore cache - name: Restore cache
uses: actions/cache/restore@v4 uses: actions/cache/restore@v4
with: with:
path: | path: ${{ env.CARGO_HOME }}
~/.cargo
key: cache-ubuntu-cargo-publish key: cache-ubuntu-cargo-publish
- name: Install Rust - name: Install Rust
run: |- run: |-
export PATH="${CARGO_HOME:-$HOME/.cargo}/bin:$PATH" export PATH="$CARGO_HOME/bin:$PATH"
if ! command -v rustc >/dev/null 2>&1; then if ! command -v rustc >/dev/null 2>&1; then
curl --proto '=https' --tlsv1.2 -sSf https://sh.rustup.rs | sh -s -- -y curl --proto '=https' --tlsv1.2 -sSf https://sh.rustup.rs | sh -s -- -y
else else
rustup update rustup update
fi fi
echo "${CARGO_HOME:-$HOME/.cargo}/bin" >> "$GITHUB_PATH" echo "$CARGO_HOME/bin" >> "$GITHUB_PATH"
cargo install cargo-release cargo install cargo-release
shell: bash shell: bash
@@ -47,8 +48,9 @@ jobs:
# which is reasonable, since this job only runs after the Linux, Windows, and WASM builds # which is reasonable, since this job only runs after the Linux, Windows, and WASM builds
# have passed. # have passed.
- name: "cargo release publish" - name: "cargo release publish"
env:
CARGO_REGISTRY_TOKEN: ${{ secrets.CRATES_IO_API_TOKEN }}
run: |- run: |-
cargo login ${{ secrets.CRATES_IO_API_TOKEN }}
cargo release \ cargo release \
publish \ publish \
--workspace \ --workspace \
@@ -61,6 +63,5 @@ jobs:
- name: Store cache - name: Store cache
uses: actions/cache/save@v4 uses: actions/cache/save@v4
with: with:
path: | path: ${{ env.CARGO_HOME }}
~/.cargo
key: cache-ubuntu-cargo-publish key: cache-ubuntu-cargo-publish
.github/workflows/publish_pypi.yml
+9 -7
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@@ -1,6 +1,6 @@
name: Publish_py name: Publish_py
on: [workflow_dispatch] on: [ workflow_dispatch ]
permissions: permissions:
contents: read contents: read
@@ -9,6 +9,8 @@ jobs:
pypi_publish: pypi_publish:
name: Publish (pypi.org) name: Publish (pypi.org)
runs-on: ubuntu-latest runs-on: ubuntu-latest
env:
CARGO_HOME: ${{ github.workspace }}/.cargo
steps: steps:
- uses: actions/checkout@v6 - uses: actions/checkout@v6
- uses: actions/setup-python@v5 - uses: actions/setup-python@v5
@@ -23,7 +25,7 @@ jobs:
~/.cache/pip-wheel ~/.cache/pip-wheel
~/.cache/sccache ~/.cache/sccache
~/.cache/cargo-xwin ~/.cache/cargo-xwin
~/.cargo ${{ env.CARGO_HOME }}
~/.osxcross ~/.osxcross
key: cache-ubuntu-maturin-cross-compile key: cache-ubuntu-maturin-cross-compile
@@ -37,17 +39,18 @@ jobs:
- name: Install Rust - name: Install Rust
run: | run: |
export PATH="$HOME/.cargo/bin:$PATH" export PATH="$CARGO_HOME/bin:$PATH"
if ! command -v rustc >/dev/null 2>&1; then if ! command -v rustc >/dev/null 2>&1; then
curl --proto '=https' --tlsv1.2 -sSf https://sh.rustup.rs | sh -s -- -y curl --proto '=https' --tlsv1.2 -sSf https://sh.rustup.rs | sh -s -- -y
else else
rustup update rustup update
fi fi
echo "$CARGO_HOME/bin" >> "$GITHUB_PATH"
cargo --version
shell: bash shell: bash
- name: Install sccache and maturin - name: Install sccache and maturin
run: | run: |
export PATH="$HOME/.cargo/bin:$PATH"
python -m pip install --upgrade pip python -m pip install --upgrade pip
pip install maturin ziglang pip install maturin ziglang
if ! command -v sccache >/dev/null 2>&1; then if ! command -v sccache >/dev/null 2>&1; then
@@ -57,7 +60,6 @@ jobs:
- name: Install xwin - name: Install xwin
run: | run: |
export PATH="$HOME/.cargo/bin:$PATH"
if ! command -v cargo-xwin >/dev/null 2>&1; then if ! command -v cargo-xwin >/dev/null 2>&1; then
cargo install cargo-xwin || pip install cargo-xwin cargo install cargo-xwin || pip install cargo-xwin
cargo xwin cache xwin cargo xwin cache xwin
@@ -75,7 +77,7 @@ jobs:
- name: Build wheels - name: Build wheels
run: | run: |
export PATH="$HOME/.cargo/bin:$HOME/.osxcross/bin:$PATH" export PATH="$HOME/.osxcross/bin:$PATH"
rustup default stable rustup default stable
rm -rf dist rm -rf dist
maturin sdist --out dist -m ome-metadata/Cargo.toml maturin sdist --out dist -m ome-metadata/Cargo.toml
@@ -107,7 +109,7 @@ jobs:
~/.cache/pip-wheel ~/.cache/pip-wheel
~/.cache/sccache ~/.cache/sccache
~/.cache/cargo-xwin ~/.cache/cargo-xwin
~/.cargo ${{ env.CARGO_HOME }}
~/.osxcross ~/.osxcross
key: cache-ubuntu-maturin-cross-compile key: cache-ubuntu-maturin-cross-compile
.gitignore
+1
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@@ -1,4 +1,5 @@
/target /target
/.cargo/
# Byte-compiled / optimized / DLL files # Byte-compiled / optimized / DLL files
__pycache__/ __pycache__/
ome-metadata-derive/Cargo.toml
+2 -2
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@@ -1,6 +1,6 @@
[package] [package]
name = "ome-metadata-derive" name = "ome-metadata-derive"
version = "0.5.0" version = "0.6.0"
edition = "2024" edition = "2024"
rust-version = "1.88.0" rust-version = "1.88.0"
authors = ["Wim Pomp <w.pomp@nki.nl>"] authors = ["Wim Pomp <w.pomp@nki.nl>"]
@@ -13,7 +13,7 @@ readme = "README.md"
[dependencies] [dependencies]
quote = "1" quote = "1"
syn = "2" syn = "3"
[lib] [lib]
proc-macro = true proc-macro = true
ome-metadata/Cargo.toml
+3 -3
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@@ -1,6 +1,6 @@
[package] [package]
name = "ome-metadata" name = "ome-metadata"
version = "0.5.0" version = "0.6.0"
edition = "2024" edition = "2024"
rust-version = "1.88.0" rust-version = "1.88.0"
authors = ["Wim Pomp <w.pomp@nki.nl>"] authors = ["Wim Pomp <w.pomp@nki.nl>"]
@@ -21,9 +21,9 @@ crate-type = ["cdylib", "rlib"]
[dependencies] [dependencies]
color-eyre = { version = "0.6", optional = true } color-eyre = { version = "0.6", optional = true }
ome-metadata-derive = { path = "../ome-metadata-derive", version = "0.5.0" } ome-metadata-derive = { path = "../ome-metadata-derive", version = "0.6.0" }
pyo3 = { version = "0.29", features = ["abi3-py310", "anyhow", "eyre", "generate-import-lib"], optional = true} pyo3 = { version = "0.29", features = ["abi3-py310", "anyhow", "eyre", "generate-import-lib"], optional = true}
quick-xml = { version = "0.40", features = ["serialize"] } quick-xml = { version = "0.42", features = ["serialize"] }
serde = { version = "1", features = ["derive"] } serde = { version = "1", features = ["derive"] }
strum = { version = "0.28", features = ["derive"] } strum = { version = "0.28", features = ["derive"] }
thiserror = "2" thiserror = "2"
ome-metadata/src/lib.rs
+9 -5
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@@ -50,7 +50,7 @@ mod tests {
assert_eq!( assert_eq!(
namespace, namespace,
quick_xml::name::ResolveResult::Bound(quick_xml::name::Namespace( quick_xml::name::ResolveResult::Bound(quick_xml::name::Namespace(
b"http://www.openmicroscopy.org/Schemas/OME/2016-06" "http://www.openmicroscopy.org/Schemas/OME/2016-06"
)) ))
); );
let root = match event { let root = match event {
@@ -59,18 +59,22 @@ mod tests {
} }
event => panic!("expected OME root, got {event:?}"), event => panic!("expected OME root, got {event:?}"),
}; };
assert_eq!(root.name().as_ref(), b"OME"); assert_eq!(root.name().as_ref(), "OME");
assert_eq!( assert_eq!(
root.try_get_attribute("xmlns:xsi") root.try_get_attribute("xmlns:xsi")
.unwrap() .unwrap()
.unwrap() .unwrap()
.value .value
.as_ref(), .as_ref(),
b"http://www.w3.org/2001/XMLSchema-instance" "http://www.w3.org/2001/XMLSchema-instance"
); );
assert_eq!( assert_eq!(
root.try_get_attribute("xsi:schemaLocation").unwrap().unwrap().value.as_ref(), root.try_get_attribute("xsi:schemaLocation")
b"http://www.openmicroscopy.org/Schemas/OME/2016-06 http://www.openmicroscopy.org/Schemas/OME/2016-06/ome.xsd" .unwrap()
.unwrap()
.value
.as_ref(),
"http://www.openmicroscopy.org/Schemas/OME/2016-06 http://www.openmicroscopy.org/Schemas/OME/2016-06/ome.xsd"
); );
assert_eq!(Ome::from_xml(&xml)?, ome); assert_eq!(Ome::from_xml(&xml)?, ome);
ome-metadata/src/xml.rs
+9 -12
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@@ -15,33 +15,30 @@ pub(crate) fn to_string<T: Serialize>(value: &T) -> Result<String, Error> {
// Serde sees an escaped string; the public XML API sees an XML fragment. // Serde sees an escaped string; the public XML API sees an XML fragment.
fn rewrite_values(xml: &str, writing: bool) -> Result<String, Error> { fn rewrite_values(xml: &str, writing: bool) -> Result<String, Error> {
let mut reader = quick_xml::Reader::from_str(xml); let mut reader = quick_xml::Reader::from_str(xml);
let mut stack: Vec<(Vec<u8>, BTreeMap<String, String>)> = Vec::new(); let mut stack: Vec<(String, BTreeMap<String, String>)> = Vec::new();
let mut output = String::new(); let mut output = String::new();
let mut copied = 0; let mut copied = 0;
loop { loop {
match reader.read_event().map_err(quick_xml::DeError::from)? { match reader.read_event().map_err(quick_xml::DeError::from)? {
Event::Start(ref start) => { Event::Start(ref start) => {
let name = start.local_name(); let name = start.local_name();
let is_value = (name.as_ref() == b"Value" let is_value = (name.as_ref() == "Value"
&& stack && stack
.last() .last()
.is_some_and(|(name, _)| name.as_slice() == b"XMLAnnotation")) .is_some_and(|(name, _)| name == "XMLAnnotation"))
|| (stack.is_empty() && name.as_ref() == b"XmlAnnotationValue"); || (stack.is_empty() && name.as_ref() == "XmlAnnotationValue");
let mut namespaces = stack.last().map(|(_, ns)| ns.clone()).unwrap_or_default(); let mut namespaces = stack.last().map(|(_, ns)| ns.clone()).unwrap_or_default();
for attribute in start.attributes() { for attribute in start.attributes() {
let attribute = attribute let attribute = attribute
.map_err(quick_xml::Error::from) .map_err(quick_xml::Error::from)
.map_err(quick_xml::DeError::from)?; .map_err(quick_xml::DeError::from)?;
let key = attribute.key.as_ref(); let key = attribute.key.as_ref();
if key == b"xmlns" || key.starts_with(b"xmlns:") { if key == "xmlns" || key.starts_with("xmlns:") {
namespaces.insert( namespaces.insert(
String::from_utf8_lossy(key).into_owned(), key.to_owned(),
quick_xml::escape::escape( quick_xml::escape::escape(
attribute attribute
.decoded_and_normalized_value( .normalized_value(quick_xml::XmlVersion::Implicit1_0)
quick_xml::XmlVersion::Implicit1_0,
reader.decoder(),
)
.map_err(quick_xml::DeError::from)?, .map_err(quick_xml::DeError::from)?,
) )
.into_owned(), .into_owned(),
@@ -74,7 +71,7 @@ fn rewrite_values(xml: &str, writing: bool) -> Result<String, Error> {
} }
copied = inner_end; copied = inner_end;
} else { } else {
stack.push((name.as_ref().to_vec(), namespaces)); stack.push((name.as_ref().to_owned(), namespaces));
} }
} }
Event::End(_) => { Event::End(_) => {
@@ -160,7 +157,7 @@ fn retain_namespaces(
let attribute = attribute let attribute = attribute
.map_err(quick_xml::Error::from) .map_err(quick_xml::Error::from)
.map_err(quick_xml::DeError::from)?; .map_err(quick_xml::DeError::from)?;
declared.push(String::from_utf8_lossy(attribute.key.as_ref()).into_owned()); declared.push(attribute.key.as_ref().to_owned());
} }
let insertion = before + 1 + start.name().as_ref().len(); let insertion = before + 1 + start.name().as_ref().len();
output.push_str(&fragment[copied..insertion]); output.push_str(&fragment[copied..insertion]);