- pypi wheels against the libczirw-sys submodule (self-contained Eigen build, msvc runtime alignment, bindgen flags) - and slim down publish_pypi.yml: no pinned zig/clang versions, no cmake shim, no bindgen env vars; only the ring /imsvc clang shim remains
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@@ -33,22 +33,18 @@ jobs:
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~/.osxcross
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key: cache-ubuntu-maturin-cross-compile
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- name: Install llvm, cmake and clang
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- name: Install build dependencies
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run: |
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if ! command -v llvm-dlltool >/dev/null 2>&1; then
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# the stock clang on noble (18) is too old for the 2025+ MSVC STL that
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# cargo-xwin downloads (yvals_core.h: "error STL1000: expected Clang
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# 19.0.0 or newer"), so take the newest clang / lld / libclang / llvm
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# tools from apt.llvm.org (generic package names, nothing pinned)
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sudo apt update
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sudo apt install -y llvm cmake build-essential libclang-dev clang
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fi
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# the stock clang on noble is 18, but the 2025+ MSVC STL bundled with
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# cargo-xwin requires clang >= 19 (yvals_core.h "error STL1000: expected
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# Clang 19.0.0 or newer"). Install a newer toolchain from apt.llvm.org so
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# its clang-cl driver, lld-link and libclang (bindgen) are all new enough.
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if ! command -v clang-24 >/dev/null 2>&1; then
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echo "deb [trusted=yes] https://apt.llvm.org/noble/ llvm-toolchain-noble main" | sudo tee /etc/apt/sources.list.d/llvm-toolchain-noble.list
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echo "deb [trusted=yes] https://apt.llvm.org/noble/ llvm-toolchain-noble main" | sudo tee /etc/apt/sources.list.d/llvm-toolchain-noble.list >/dev/null
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sudo apt update
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# libeigen3-dev: Eigen 3.4.0 for libczirw (see the cmake-shim step below)
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sudo apt install -y clang-24 lld-24 libclang-24-dev libeigen3-dev
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fi
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sudo apt install -y build-essential cmake clang lld libclang-dev llvm
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clang --version | head -1
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command -v clang clang-cl lld-link llvm-lib
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shell: bash
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- name: Install Rust
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@@ -65,12 +61,7 @@ jobs:
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- name: Install sccache and maturin
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run: |
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python -m pip install --upgrade pip
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# ziglang >= 0.17 ships a bundled libc++ that requires -D_LIBCPP_* config
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# macros only cargo-zigbuild >= 0.24.0 passes to bindgen; otherwise
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# libczirw-sys fails with "hardening.h ... _LIBCPP_ASSERTION_SEMANTIC_DEFAULT
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# is not defined". Pin the combo that is known to work.
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python -m pip install --upgrade maturin "ziglang==0.17.0" "cargo-zigbuild==0.24.0"
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python -m pip install --upgrade pip maturin ziglang cargo-zigbuild
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# in case an older copy was cargo-installed into the CARGO_HOME cache,
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# prevent it from shadowing the pip-installed one
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rm -f "${CARGO_HOME:?}/bin/cargo-zigbuild" || true
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@@ -95,72 +86,59 @@ jobs:
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tar -xzf osxcross.tar.gz -C ~/
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mv ~/osxcross ~/.osxcross
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fi
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shell: bash
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- name: Tune the libczirw-sys cmake build (system Eigen, dynamic CRT)
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- name: Shim clang for ring's aarch64-windows build
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run: |
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# libczirw-sys cmake build clones Eigen3 from gitlab.com (ExternalProject);
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# that clone is flaky on this runner (it is the only git-based network step
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# left in the build). noble libeigen3-dev is the same Eigen 3.4.0 that libczi
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# pins, and libczi has an upstream option to use it - flip that option for
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# the libCZI project via CMAKE_PROJECT_INCLUDE. cmake does not read that
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# variable from the environment, so a cmake shim injects it (-D); the shim is
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# scoped to invocations that look like the libczi configure (no-op for
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# --build / --version / other uses).
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# the override also aligns the msvc CRT: libCZI forces the static runtime
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# (/MT) while the rest of the build (Rust std, cc-compiled vendored libs,
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# /defaultlib:msvcrt) is dynamic (/MD), and lld-link rejects the mix with
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# /failifmismatch:RuntimeLibrary. no effect on the non-windows builds.
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# ring 0.17.14 forces a plain `clang` for its C build on
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# aarch64-pc-windows-msvc (its "must use Clang on Win AArch64"
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# workaround), while the CFLAGS injected by cargo-xwin carry
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# clang-cl-style `/imsvc <dir>` pairs that plain clang rejects.
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# This shim rewrites them to `-I <dir>` and execs the real clang
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# found further down PATH; all other invocations pass through
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# untouched, and tools with other names (clang-cl, lld-link) are not
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# affected.
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mkdir -p /root/ci-shims
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cat > /root/cm-override-libczi.cmake <<'CMAKEEOF'
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if (CMAKE_PROJECT_NAME STREQUAL "libCZI")
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set(LIBCZI_BUILD_PREFER_EXTERNALPACKAGE_EIGEN3 ON CACHE BOOL "" FORCE)
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set(LIBCZI_DO_NOT_SET_MSVC_RUNTIME_LIBRARY ON CACHE BOOL "" FORCE)
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set(CMAKE_MSVC_RUNTIME_LIBRARY "MultiThreadedDLL$<$<CONFIG:Debug>:Debug>" CACHE STRING "" FORCE)
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endif()
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CMAKEEOF
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cat > /root/ci-shims/cmake <<'SHIMEOF'
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cat > /root/ci-shims/clang <<'EOF'
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#!/usr/bin/env bash
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case "$*" in
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--build*)
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exec /usr/bin/cmake "$@" ;;
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*libczi*)
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exec /usr/bin/cmake -DCMAKE_PROJECT_INCLUDE=/root/cm-override-libczi.cmake "$@" ;;
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*)
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exec /usr/bin/cmake "$@" ;;
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args=()
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prev_imsvc=0
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for a in "$@"; do
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if [ "$prev_imsvc" = "1" ]; then
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args+=("-I$a")
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prev_imsvc=0
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continue
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fi
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case "$a" in
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/imsvc) prev_imsvc=1 ;;
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/imsvc:*) args+=("-I${a#/imsvc:}") ;;
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*) args+=("$a") ;;
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esac
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SHIMEOF
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chmod +x /root/ci-shims/cmake
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echo "--- /root/cm-override-libczi.cmake ---"
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cat /root/cm-override-libczi.cmake
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echo "--- /root/ci-shims/cmake ---"
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cat /root/ci-shims/cmake
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done
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self_dir=$(CDPATH= cd -- "$(dirname -- "$0")" && pwd)
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real=""
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IFS=":" read -r -a _dirs <<< "$PATH"
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IFS=""
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for d in "${_dirs[@]}"; do
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[ "$d" = "$self_dir" ] && continue
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if [ -x "$d/clang" ]; then real="$d/clang"; break; fi
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done
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[ -n "$real" ] || real=/usr/bin/clang
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exec "$real" "${args[@]}"
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EOF
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chmod +x /root/ci-shims/clang
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shell: bash
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- name: Build wheels
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env:
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# ziglang >= 0.17's bundled libc++ needs these -D_LIBCPP_* macros when
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# parsed by bindgen/libclang; cargo-zigbuild >= 0.24.0 supplies them, but
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# the runner may still resolve an older 0.23.1 — pre-set them so any
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# cargo-zigbuild version works (it appends its own flags to these)
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BINDGEN_EXTRA_CLANG_ARGS_x86_64-apple-darwin: "-D_LIBCPP_ASSERTION_SEMANTIC_DEFAULT=_LIBCPP_ASSERTION_SEMANTIC_ENFORCE -D_LIBCPP_PSTL_BACKEND_SERIAL -D_LIBCPP_HAS_VENDOR_AVAILABILITY_ANNOTATIONS=0 -D_LIBCPP_HAS_TERMINAL -D_LIBCPP_HAS_RANDOM_DEVICE -D_LIBCPP_HAS_NO_STD_MODULES -D_LIBCPP_HAS_FILESYSTEM=1"
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BINDGEN_EXTRA_CLANG_ARGS_aarch64-apple-darwin: "-D_LIBCPP_ASSERTION_SEMANTIC_DEFAULT=_LIBCPP_ASSERTION_SEMANTIC_ENFORCE -D_LIBCPP_PSTL_BACKEND_SERIAL -D_LIBCPP_HAS_VENDOR_AVAILABILITY_ANNOTATIONS=0 -D_LIBCPP_HAS_TERMINAL -D_LIBCPP_HAS_RANDOM_DEVICE -D_LIBCPP_HAS_NO_STD_MODULES -D_LIBCPP_HAS_FILESYSTEM=1"
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BINDGEN_EXTRA_CLANG_ARGS_x86_64-unknown-linux-gnu: "-D_LIBCPP_ASSERTION_SEMANTIC_DEFAULT=_LIBCPP_ASSERTION_SEMANTIC_ENFORCE -D_LIBCPP_PSTL_BACKEND_SERIAL -D_LIBCPP_HAS_VENDOR_AVAILABILITY_ANNOTATIONS=0 -D_LIBCPP_HAS_TERMINAL -D_LIBCPP_HAS_RANDOM_DEVICE -D_LIBCPP_HAS_NO_STD_MODULES -D_LIBCPP_HAS_FILESYSTEM=1"
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BINDGEN_EXTRA_CLANG_ARGS_aarch64-unknown-linux-gnu: "-D_LIBCPP_ASSERTION_SEMANTIC_DEFAULT=_LIBCPP_ASSERTION_SEMANTIC_ENFORCE -D_LIBCPP_PSTL_BACKEND_SERIAL -D_LIBCPP_HAS_VENDOR_AVAILABILITY_ANNOTATIONS=0 -D_LIBCPP_HAS_TERMINAL -D_LIBCPP_HAS_RANDOM_DEVICE -D_LIBCPP_HAS_NO_STD_MODULES -D_LIBCPP_HAS_FILESYSTEM=1"
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BINDGEN_EXTRA_CLANG_ARGS_x86_64-unknown-linux-musl: "-D_LIBCPP_ASSERTION_SEMANTIC_DEFAULT=_LIBCPP_ASSERTION_SEMANTIC_ENFORCE -D_LIBCPP_PSTL_BACKEND_SERIAL -D_LIBCPP_HAS_VENDOR_AVAILABILITY_ANNOTATIONS=0 -D_LIBCPP_HAS_TERMINAL -D_LIBCPP_HAS_RANDOM_DEVICE -D_LIBCPP_HAS_NO_STD_MODULES -D_LIBCPP_HAS_FILESYSTEM=1"
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BINDGEN_EXTRA_CLANG_ARGS_aarch64-unknown-linux-musl: "-D_LIBCPP_ASSERTION_SEMANTIC_DEFAULT=_LIBCPP_ASSERTION_SEMANTIC_ENFORCE -D_LIBCPP_PSTL_BACKEND_SERIAL -D_LIBCPP_HAS_VENDOR_AVAILABILITY_ANNOTATIONS=0 -D_LIBCPP_HAS_TERMINAL -D_LIBCPP_HAS_RANDOM_DEVICE -D_LIBCPP_HAS_NO_STD_MODULES -D_LIBCPP_HAS_FILESYSTEM=1"
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shell: bash
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run: |
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export PATH="$HOME/.osxcross/bin:$PATH"
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# put the cmake shim (system-Eigen override for libczirw) in front
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export PATH="/root/ci-shims:$PATH"
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command -v cmake
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echo "HOME=$HOME CARGO_HOME=$CARGO_HOME RUSTUP_HOME=$RUSTUP_HOME"
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command -v cargo-zigbuild || echo "cargo-zigbuild: not on PATH"
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cargo-zigbuild --version 2>&1 || true
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command -v rustup
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command -v cargo
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rustup show
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cargo --version
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# the shim (for ring's forced plain `clang`) goes in front of the
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# llvm tools so clang-cl / lld-link (distinct names) still resolve to
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# the real toolchain; bindgen finds libclang via LIBCLANG_PATH
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LLVM_BIN=$(dirname "$(readlink -f "$(command -v clang)")")
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export PATH="/root/ci-shims:$LLVM_BIN:$PATH"
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export LIBCLANG_PATH="$(dirname "$LLVM_BIN")/lib"
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rm -rf dist
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maturin sdist --out dist -m ndbioimage/Cargo.toml
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@@ -170,8 +148,9 @@ jobs:
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maturin build --release --out dist --target aarch64-apple-darwin --zig --auditwheel repair -m ndbioimage/Cargo.toml
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rustup target add x86_64-unknown-linux-gnu
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# the x86_64-gnu build links the runner's host liblzma (lzma-sys), which needs
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# glibc symbols up to 2.34 - higher than the default manylinux_2_17 baseline
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# the x86_64-gnu build links the runner's host liblzma (lzma-sys),
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# which needs glibc symbols up to 2.34 - higher than the
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# manylinux_2_17 baseline
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maturin build --release --out dist --target x86_64-unknown-linux-gnu --zig --auditwheel repair --compatibility manylinux_2_34 -m ndbioimage/Cargo.toml
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rustup target add aarch64-unknown-linux-gnu
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maturin build --release --out dist --target aarch64-unknown-linux-gnu --zig --auditwheel repair --compatibility manylinux_2_34 -m ndbioimage/Cargo.toml
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@@ -180,14 +159,6 @@ jobs:
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rustup target add aarch64-unknown-linux-musl
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maturin build --release --out dist --target aarch64-unknown-linux-musl --zig --auditwheel repair -m ndbioimage/Cargo.toml
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# cargo-xwin resolves clang-cl / lld-link through PATH and bindgen finds
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# libclang via LIBCLANG_PATH, so prefer the >=19 toolchain over the stock
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# clang-18 (rejected by the 2025+ MSVC STL with STL1000) for the msvc builds
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export PATH="/usr/lib/llvm-24/bin:$PATH"
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export LIBCLANG_PATH="/usr/lib/llvm-24/lib"
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command -v clang-cl
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clang-cl --version
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command -v lld-link
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rustup target add x86_64-pc-windows-msvc
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maturin build --release --out dist --target x86_64-pc-windows-msvc --auditwheel repair -m ndbioimage/Cargo.toml
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rustup target add aarch64-pc-windows-msvc
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@@ -4,3 +4,6 @@
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[submodule "image-registration"]
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path = image-registration
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url = https://git.pomppervova.nl/wim/image-registration.git
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[submodule "libczirw-sys"]
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path = libczirw-sys
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url = https://git.pomppervova.nl/wim/libczirw-sys.git
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@@ -23,3 +23,10 @@ debug = true
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[profile.dev.package.backtrace]
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opt-level = 3
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# Build against the libczirw-sys checkout in the submodule of that name:
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# its fixes (self-contained cmake build via vendored Eigen, msvc C runtime
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# alignment for xwin, bindgen flags for zig's libc++) are not yet published
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# to crates.io; drop this patch once a release containing them is available
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[patch.crates-io]
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libczirw-sys = { path = "libczirw-sys" }
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Submodule
+1
Submodule libczirw-sys added at d6fe6ec733.
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