- 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

.github/workflows/publish_pypi.yml

@@ -33,22 +33,18 @@ jobs:
             ~/.osxcross
           key: cache-ubuntu-maturin-cross-compile
 
-      - name: Install llvm, cmake and clang
+      - name: Install build dependencies
         run: |
-          if ! command -v llvm-dlltool >/dev/null 2>&1; then
+          # the stock clang on noble (18) is too old for the 2025+ MSVC STL that
-            sudo apt update
+          # cargo-xwin downloads (yvals_core.h: "error STL1000: expected Clang
-            sudo apt install -y llvm cmake build-essential libclang-dev clang
+          # 19.0.0 or newer"), so take the newest clang / lld / libclang / llvm
-          fi
+          # tools from apt.llvm.org (generic package names, nothing pinned)
-          # the stock clang on noble is 18, but the 2025+ MSVC STL bundled with
+          sudo apt update
-          # cargo-xwin requires clang >= 19 (yvals_core.h "error STL1000: expected
+          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
-          # Clang 19.0.0 or newer"). Install a newer toolchain from apt.llvm.org so
+          sudo apt update
-          # its clang-cl driver, lld-link and libclang (bindgen) are all new enough.
+          sudo apt install -y build-essential cmake clang lld libclang-dev llvm
-          if ! command -v clang-24 >/dev/null 2>&1; then
+          clang --version | head -1
-            echo "deb [trusted=yes] https://apt.llvm.org/noble/ llvm-toolchain-noble main" | sudo tee /etc/apt/sources.list.d/llvm-toolchain-noble.list
+          command -v clang clang-cl lld-link llvm-lib
-            sudo apt update
-            # libeigen3-dev: Eigen 3.4.0 for libczirw (see the cmake-shim step below)
-            sudo apt install -y clang-24 lld-24 libclang-24-dev libeigen3-dev
-          fi
         shell: bash
 
       - name: Install Rust
@@ -65,12 +61,7 @@ jobs:
 
       - name: Install sccache and maturin
         run: |
-          python -m pip install --upgrade pip
+          python -m pip install --upgrade pip maturin ziglang cargo-zigbuild
-          # ziglang >= 0.17 ships a bundled libc++ that requires -D_LIBCPP_* config
-          # macros only cargo-zigbuild >= 0.24.0 passes to bindgen; otherwise
-          # libczirw-sys fails with "hardening.h ... _LIBCPP_ASSERTION_SEMANTIC_DEFAULT
-          # is not defined". Pin the combo that is known to work.
-          python -m pip install --upgrade maturin "ziglang==0.17.0" "cargo-zigbuild==0.24.0"
           # in case an older copy was cargo-installed into the CARGO_HOME cache,
           # prevent it from shadowing the pip-installed one
           rm -f "${CARGO_HOME:?}/bin/cargo-zigbuild" || true
@@ -95,83 +86,71 @@ jobs:
             tar -xzf osxcross.tar.gz -C ~/
             mv ~/osxcross ~/.osxcross
           fi
+        shell: bash
 
-      - name: Tune the libczirw-sys cmake build (system Eigen, dynamic CRT)
+      - name: Shim clang for ring's aarch64-windows build
         run: |
-          # libczirw-sys cmake build clones Eigen3 from gitlab.com (ExternalProject);
+          # ring 0.17.14 forces a plain `clang` for its C build on
-          # that clone is flaky on this runner (it is the only git-based network step
+          # aarch64-pc-windows-msvc (its "must use Clang on Win AArch64"
-          # left in the build). noble libeigen3-dev is the same Eigen 3.4.0 that libczi
+          # workaround), while the CFLAGS injected by cargo-xwin carry
-          # pins, and libczi has an upstream option to use it - flip that option for
+          # clang-cl-style `/imsvc <dir>` pairs that plain clang rejects.
-          # the libCZI project via CMAKE_PROJECT_INCLUDE. cmake does not read that
+          # This shim rewrites them to `-I <dir>` and execs the real clang
-          # variable from the environment, so a cmake shim injects it (-D); the shim is
+          # found further down PATH; all other invocations pass through
-          # scoped to invocations that look like the libczi configure (no-op for
+          # untouched, and tools with other names (clang-cl, lld-link) are not
-          # --build / --version / other uses).
+          # affected.
-          # the override also aligns the msvc CRT: libCZI forces the static runtime
-          # (/MT) while the rest of the build (Rust std, cc-compiled vendored libs,
-          # /defaultlib:msvcrt) is dynamic (/MD), and lld-link rejects the mix with
-          # /failifmismatch:RuntimeLibrary. no effect on the non-windows builds.
           mkdir -p /root/ci-shims
-          cat > /root/cm-override-libczi.cmake <<'CMAKEEOF'
+          cat > /root/ci-shims/clang <<'EOF'
-          if (CMAKE_PROJECT_NAME STREQUAL "libCZI")
-            set(LIBCZI_BUILD_PREFER_EXTERNALPACKAGE_EIGEN3 ON CACHE BOOL "" FORCE)
-            set(LIBCZI_DO_NOT_SET_MSVC_RUNTIME_LIBRARY ON CACHE BOOL "" FORCE)
-            set(CMAKE_MSVC_RUNTIME_LIBRARY "MultiThreadedDLL$<$<CONFIG:Debug>:Debug>" CACHE STRING "" FORCE)
-          endif()
-          CMAKEEOF
-          cat > /root/ci-shims/cmake <<'SHIMEOF'
           #!/usr/bin/env bash
-          case "$*" in
+          args=()
-            --build*)
+          prev_imsvc=0
-              exec /usr/bin/cmake "$@" ;;
+          for a in "$@"; do
-            *libczi*)
+            if [ "$prev_imsvc" = "1" ]; then
-              exec /usr/bin/cmake -DCMAKE_PROJECT_INCLUDE=/root/cm-override-libczi.cmake "$@" ;;
+              args+=("-I$a")
-            *)
+              prev_imsvc=0
-              exec /usr/bin/cmake "$@" ;;
+              continue
-          esac
+            fi
-          SHIMEOF
+            case "$a" in
-          chmod +x /root/ci-shims/cmake
+              /imsvc)   prev_imsvc=1 ;;
-          echo "--- /root/cm-override-libczi.cmake ---"
+              /imsvc:*) args+=("-I${a#/imsvc:}") ;;
-          cat /root/cm-override-libczi.cmake
+              *)        args+=("$a") ;;
-          echo "--- /root/ci-shims/cmake ---"
+            esac
-          cat /root/ci-shims/cmake
+          done
+          self_dir=$(CDPATH= cd -- "$(dirname -- "$0")" && pwd)
+          real=""
+          IFS=":" read -r -a _dirs <<< "$PATH"
+          IFS=""
+          for d in "${_dirs[@]}"; do
+            [ "$d" = "$self_dir" ] && continue
+            if [ -x "$d/clang" ]; then real="$d/clang"; break; fi
+          done
+          [ -n "$real" ] || real=/usr/bin/clang
+          exec "$real" "${args[@]}"
+          EOF
+          chmod +x /root/ci-shims/clang
         shell: bash
 
       - name: Build wheels
-        env:
-          # ziglang >= 0.17's bundled libc++ needs these -D_LIBCPP_* macros when
-          # parsed by bindgen/libclang; cargo-zigbuild >= 0.24.0 supplies them, but
-          # the runner may still resolve an older 0.23.1 — pre-set them so any
-          # cargo-zigbuild version works (it appends its own flags to these)
-          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"
-          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"
-          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"
-          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"
-          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"
-          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"
         shell: bash
         run: |
           export PATH="$HOME/.osxcross/bin:$PATH"
-          # put the cmake shim (system-Eigen override for libczirw) in front
+          # the shim (for ring's forced plain `clang`) goes in front of the
-          export PATH="/root/ci-shims:$PATH"
+          # llvm tools so clang-cl / lld-link (distinct names) still resolve to
-          command -v cmake
+          # the real toolchain; bindgen finds libclang via LIBCLANG_PATH
-          echo "HOME=$HOME CARGO_HOME=$CARGO_HOME RUSTUP_HOME=$RUSTUP_HOME"
+          LLVM_BIN=$(dirname "$(readlink -f "$(command -v clang)")")
-          command -v cargo-zigbuild || echo "cargo-zigbuild: not on PATH"
+          export PATH="/root/ci-shims:$LLVM_BIN:$PATH"
-          cargo-zigbuild --version 2>&1 || true
+          export LIBCLANG_PATH="$(dirname "$LLVM_BIN")/lib"
-          command -v rustup
-          command -v cargo
-          rustup show
-          cargo --version
           rm -rf dist
           maturin sdist --out dist -m ndbioimage/Cargo.toml
-          
+
           rustup target add x86_64-apple-darwin
           maturin build --release --out dist --target x86_64-apple-darwin --zig --auditwheel repair -m ndbioimage/Cargo.toml
           rustup target add aarch64-apple-darwin
           maturin build --release --out dist --target aarch64-apple-darwin --zig --auditwheel repair -m ndbioimage/Cargo.toml
-          
+
           rustup target add x86_64-unknown-linux-gnu
-          # the x86_64-gnu build links the runner's host liblzma (lzma-sys), which needs
+          # the x86_64-gnu build links the runner's host liblzma (lzma-sys),
-          # glibc symbols up to 2.34 - higher than the default manylinux_2_17 baseline
+          # which needs glibc symbols up to 2.34 - higher than the
+          # manylinux_2_17 baseline
           maturin build --release --out dist --target x86_64-unknown-linux-gnu --zig --auditwheel repair --compatibility manylinux_2_34 -m ndbioimage/Cargo.toml
           rustup target add aarch64-unknown-linux-gnu
           maturin build --release --out dist --target aarch64-unknown-linux-gnu --zig --auditwheel repair --compatibility manylinux_2_34 -m ndbioimage/Cargo.toml
@@ -179,15 +158,7 @@ jobs:
           maturin build --release --out dist --target x86_64-unknown-linux-musl --zig --auditwheel repair -m ndbioimage/Cargo.toml
           rustup target add aarch64-unknown-linux-musl
           maturin build --release --out dist --target aarch64-unknown-linux-musl --zig --auditwheel repair -m ndbioimage/Cargo.toml
-          
+
-          # cargo-xwin resolves clang-cl / lld-link through PATH and bindgen finds
-          # libclang via LIBCLANG_PATH, so prefer the >=19 toolchain over the stock
-          # clang-18 (rejected by the 2025+ MSVC STL with STL1000) for the msvc builds
-          export PATH="/usr/lib/llvm-24/bin:$PATH"
-          export LIBCLANG_PATH="/usr/lib/llvm-24/lib"
-          command -v clang-cl
-          clang-cl --version
-          command -v lld-link
           rustup target add x86_64-pc-windows-msvc
           maturin build --release --out dist --target x86_64-pc-windows-msvc --auditwheel repair -m ndbioimage/Cargo.toml
           rustup target add aarch64-pc-windows-msvc

.gitmodules

@@ -4,3 +4,6 @@
 [submodule "image-registration"]
 	path = image-registration
 	url = https://git.pomppervova.nl/wim/image-registration.git
+[submodule "libczirw-sys"]
+	path = libczirw-sys
+	url = https://git.pomppervova.nl/wim/libczirw-sys.git

Cargo.toml

@@ -23,3 +23,10 @@ debug = true
 
 [profile.dev.package.backtrace]
 opt-level = 3
+
+# Build against the libczirw-sys checkout in the submodule of that name:
+# its fixes (self-contained cmake build via vendored Eigen, msvc C runtime
+# alignment for xwin, bindgen flags for zig's libc++) are not yet published
+# to crates.io; drop this patch once a release containing them is available
+[patch.crates-io]
+libczirw-sys = { path = "libczirw-sys" }