[pull] main from metno:main

.github/workflows/ci.yml

@@ -10,8 +10,9 @@ on:
   schedule:
     - cron: '0 18 * * *'
 
+# Ensure this workflow gets cancelled if a newer commit has been pushed on the same branch (unless it's the default branch)
 concurrency:
-  group: ${{ github.workflow }}-@{{ github.ref }}
+  group: ${{ github.workflow }}-${{ github.head_ref || github.run_id }}
   cancel-in-progress: true
 
 env:
@@ -23,9 +24,9 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Checkout code
-        uses: actions/checkout@v4
+        uses: actions/checkout@v7
       - name: Check spelling
-        uses: crate-ci/typos@7bc041cbb7ca9167c9e0e4ccbb26f48eb0f9d4e0 # v1.30.2
+        uses: crate-ci/typos@8a48f81b6c64dcfea44b3633223084c4be58ac5f # v1.49.0
 
   lint:
     name: lint
@@ -38,7 +39,7 @@ jobs:
           - {command: clippy, rust: stable}
     steps:
       - name: Checkout repository
-        uses: actions/checkout@v4
+        uses: actions/checkout@v7
       - name: Install Rust (${{matrix.rust}})
         uses: dtolnay/rust-toolchain@stable
         with: {toolchain: '${{matrix.rust}}', components: 'rustfmt, clippy'}
@@ -51,15 +52,15 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Checkout repository
-        uses: actions/checkout@v4
+        uses: actions/checkout@v7
         with: {submodules: true}
-      - name: Install Rust (${{matrix.rust}})
+      - name: Install Rust
         uses: dtolnay/rust-toolchain@stable
-        with: {toolchain: nightly}
+        with: {toolchain: "nightly-2025-09-01"}
       - name: Document workspace
         env:
           RUSTDOCFLAGS: "--cfg docsrs"
-        run: cargo doc --features static,zlib,blosc-all,lzf,f16,complex
+        run: cargo doc --features static,zlib,blosc-all,lzf,f16,complex --no-deps
 
   brew:
     name: brew
@@ -68,12 +69,12 @@ jobs:
       fail-fast: false
       matrix:
         include:
-          - {version: hdf5@1.10}
-          - {version: hdf5@1.14}
+          - {version: hdf5@2.1}
+          - {version: hdf5}
           - {version: hdf5-mpi, mpi: true}
     steps:
       - name: Checkout repository
-        uses: actions/checkout@v4
+        uses: actions/checkout@v7
         with: {submodules: true}
       - name: Install Rust (${{matrix.rust}})
         uses: dtolnay/rust-toolchain@stable
@@ -94,22 +95,19 @@ jobs:
         include:
           - {os: ubuntu-latest, version: 1.8.16, channel: conda-forge, rust: stable}
           - {os: windows-latest, version: 1.8.17, channel: conda-forge, rust: stable}
-          - {os: macos-13, version: 1.8.18, channel: anaconda, rust: stable}
           - {os: ubuntu-latest, version: 1.8.20, channel: anaconda, rust: beta}
           - {os: ubuntu-latest, version: 1.10.1, channel: anaconda, rust: nightly}
           - {os: windows-latest, version: 1.10.2, channel: anaconda, rust: beta}
           - {os: ubuntu-latest, version: 1.10.3, channel: conda-forge, rust: nightly}
           - {os: windows-latest, version: 1.10.4, channel: anaconda, rust: nightly}
           - {os: ubuntu-latest, version: 1.10.4, mpi: openmpi, channel: conda-forge, rust: stable}
           - {os: ubuntu-latest, version: 1.10.5, channel: conda-forge, rust: beta}
-          - {os: macos-13, version: 1.10.5, mpi: openmpi, channel: conda-forge, rust: beta}
           - {os: ubuntu-latest, version: 1.10.6, channel: anaconda, rust: stable}
           - {os: ubuntu-latest, version: 1.10.6, mpi: mpich, channel: conda-forge, rust: nightly}
-          # - {os: ubuntu, version: 1.10.8, channel: conda-forge, rust: stable}
           - {os: ubuntu-latest, version: 1.12.0, mpi: openmpi, channel: conda-forge, rust: stable}
-          - {os: macos-latest, version: 1.12.0, channel: conda-forge, rust: stable}
           - {os: windows-latest, version: 1.12.0, channel: conda-forge, rust: stable}
           - {os: ubuntu-latest, version: 1.12.1, channel: conda-forge, rust: stable}
+          - {os: macos-14, version: 1.12.1, mpi: openmpi, channel: conda-forge, rust: beta}
           - {os: macos-latest, version: 1.14.0, channel: conda-forge, rust: stable}
           - {os: windows-latest, version: 1.14.0, channel: conda-forge, rust: stable}
           - {os: ubuntu-latest, version: 1.14.0, channel: conda-forge, rust: stable}
@@ -118,13 +116,13 @@ jobs:
         shell: bash -l {0}
     steps:
       - name: Checkout repository
-        uses: actions/checkout@v4
+        uses: actions/checkout@v7
         with: {submodules: true}
       - name: Install Rust (${{matrix.rust}})
         uses: dtolnay/rust-toolchain@stable
         with: {toolchain: '${{matrix.rust}}'}
       - name: Install conda
-        uses: conda-incubator/setup-miniconda@v3
+        uses: conda-incubator/setup-miniconda@v4
         with: {auto-update-conda: false, activate-environment: testenv, miniconda-version: latest}
       - name: Set conda for Arm64
         if: runner.arch == 'arm64' && runner.os == 'macOS'
@@ -138,6 +136,12 @@ jobs:
           export HDF5_DIR="$CONDA_PREFIX"
           [ "${{matrix.mpi}}" != "" ] && FEATURES=mpio
           [ "${{runner.os}}" != "Windows" ] && export RUSTFLAGS="-C link-args=-Wl,-rpath,$CONDA_PREFIX/lib"
+          # doctests are linked separately by rustdoc and need the rpath too
+          [ "${{runner.os}}" != "Windows" ] && export RUSTDOCFLAGS="-C link-args=-Wl,-rpath,$CONDA_PREFIX/lib"
+          # conda's MPICH uses UCX, which tries to open an RDMA transport on the runner's NIC
+          # and aborts MPI_Init when it is unsupported. Restrict UCX to TCP and shared memory,
+          # which is all a single-process test needs.
+          [ "${{matrix.mpi}}" == "mpich" ] && export UCX_TLS=tcp,self,sm
           [ "${{matrix.mpi}}" == "mpich" ] && [ "${{runner.os}}" == "Linux" ] && export MPICH_CC=$(which gcc)
           [ "${{matrix.mpi}}" == "openmpi" ] && [ "${{runner.os}}" == "Linux" ] && export OMPI_CC=$(which gcc)
           cargo test -vv --features="$FEATURES"
@@ -155,7 +159,7 @@ jobs:
           - {os: macos, rust: stable}
     steps:
       - name: Checkout repository
-        uses: actions/checkout@v4
+        uses: actions/checkout@v7
         with: {submodules: true}
       - name: Install Rust (${{matrix.rust}})
         uses: dtolnay/rust-toolchain@stable
@@ -167,13 +171,16 @@ jobs:
         if: matrix.rust != 'stable-gnu'
       - name: Run examples
         run: |
-          cargo r --example simple --features hdf5-sys/static,hdf5-sys/zlib,lzf,blosc-all
-          cargo r --example chunking --features hdf5-sys/static,hdf5-sys/zlib,lzf,blosc-all
+          cargo r --example simple --features ${{ env.FEATURES }}
+          cargo r --example chunking --features ${{ env.FEATURES }}
+          cargo r --example continuously_rw_1d --features ${{ env.FEATURES }}
         if: matrix.rust != 'stable-gnu'
+        env:
+          FEATURES: hdf5-sys/static,hdf5-sys/zlib,lzf,blosc-all
 
   apt:
     name: apt
-    runs-on: ubuntu-20.04
+    runs-on: ubuntu-22.04
     strategy:
       fail-fast: false
       matrix:
@@ -182,7 +189,7 @@ jobs:
           - {mpi: openmpi, rust: stable}
     steps:
       - name: Checkout repository
-        uses: actions/checkout@v4
+        uses: actions/checkout@v7
         with: {submodules: true}
       - name: Install Rust (${{matrix.rust}})
         uses: dtolnay/rust-toolchain@stable
@@ -192,6 +199,7 @@ jobs:
           [ "${{matrix.mpi}}" == "mpich" ] && PACKAGES="libhdf5-mpich-dev mpich"
           [ "${{matrix.mpi}}" == "openmpi" ] && PACKAGES="libhdf5-openmpi-dev openmpi-bin"
           [ "${{matrix.mpi}}" == "serial" ] && PACKAGES="libhdf5-dev"
+          sudo apt-get update
           sudo apt-get install $PACKAGES
       - name: Build and test all crates
         run: |
@@ -214,7 +222,7 @@ jobs:
         version: ["1.8", "1.10", "1.12", "1.14"]
     steps:
       - name: Checkout repository
-        uses: actions/checkout@v4
+        uses: actions/checkout@v7
         with: {submodules: true}
       - name: Install Rust (${{matrix.rust}})
         uses: dtolnay/rust-toolchain@stable
@@ -260,7 +268,7 @@ jobs:
   #       rust: [stable]
   #   steps:
   #     - name: Checkout repository
-  #       uses: actions/checkout@v4
+  #       uses: actions/checkout@v7
   #       with: {submodules: true}
   #     - name: Install Rust (${{matrix.rust}})
   #       uses: dtolnay/rust-toolchain@stable
@@ -279,22 +287,22 @@ jobs:
 
   msrv:
     name: Minimal Supported Rust Version
-    runs-on: ubuntu-20.04
+    runs-on: ubuntu-22.04
     strategy:
       fail-fast: false
     steps:
       - name: Checkout repository
-        uses: actions/checkout@v4
+        uses: actions/checkout@v7
         with: {submodules: true}
       - name: Install Rust
         uses: dtolnay/rust-toolchain@stable
-        with: {toolchain: "1.80"}
+        with: {toolchain: "1.85.1"}
       - name: Create lock-file
         run:
           cargo update
-      - name: Override deps
-        run:
-          cargo update half@2.5.0 --precise 2.4.1
+      # - name: Override deps
+      #   run: |
+      #     cargo update half@2.7.1 --precise 2.4.1
       - name: Build and test all crates
         run:
           cargo test --locked --workspace -vv --features=hdf5-sys/static,hdf5-sys/zlib --exclude=hdf5-metno-derive
@@ -304,7 +312,7 @@ jobs:
   #   runs-on: ubuntu-latest
   #   steps:
   #     - name: Checkout repository
-  #       uses: actions/checkout@v4
+  #       uses: actions/checkout@v7
   #       with: {submodules: true}
   #     - name: Install Rust
   #       uses: dtolnay/rust-toolchain@stable
@@ -321,12 +329,15 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Checkout repository
-        uses: actions/checkout@v4
+        uses: actions/checkout@v7
         with: {submodules: true}
       - name: Install Rust
         uses: dtolnay/rust-toolchain@stable
         with: {toolchain: nightly, profile: minimal, override: true}
       - name: Run test with sanitizer
         env:
           RUSTFLAGS: "-Z sanitizer=address"
+          # Doctests are linked by rustdoc separately, so without this they miss the sanitizer
+          # runtime and fail to link against the instrumented library
+          RUSTDOCFLAGS: "-Z sanitizer=address"
         run: cargo test --features hdf5-sys/static --target x86_64-unknown-linux-gnu --workspace --exclude hdf5-metno-derive

.github/workflows/release.yml

@@ -19,7 +19,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
     - name: Checkout repository
-      uses: actions/checkout@v4
+      uses: actions/checkout@v7
       with:
         submodules: true
     - name: Install libhdf5

.gitignore

@@ -8,3 +8,5 @@ target/
 *.ipynb*
 .idea/
 sweep.timestamp
+.cargo/
+.cargo/config.toml

.typos.toml

@@ -8,3 +8,8 @@ extend-exclude = [
 extend-ignore-identifiers-re = [
   "Dout",
 ]
+# Intentional historical HDF5 misspellings, normalized in error.rs scrub()
+extend-ignore-re = [
+  "accessability",
+  "accessibilty",
+]