fixup! Merge branch 'upstream-nanobind' into migrate-to-nanobind

vicentebolea · vicentebolea · commit 8ae60210d89e · 2026-03-12T19:53:21.000-04:00
diff --git a/.github/workflows/everything.yml b/.github/workflows/everything.yml
@@ -427,53 +427,55 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        baseos: [ubuntu-bionic]
+        baseos: [ubuntu-22.04]
 
     steps:
       - uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v4
         with:
           ref: ${{ github.event.pull_request.head.sha }}
           path: ci-source
-      - name: Re-configure docker daemon
+
+      - name: Install Podman
+        if: ${{ matrix.base-img != 'self-hosted' }}
         run: |
-            sudo systemctl stop docker
-            echo $'{\n    "experimental": true\n}' | \
-                sudo tee /etc/docker/daemon.json
-            sudo systemctl start docker
+          sudo apt-get update
+          sudo apt-get install -y podman
+
+
       - name: Build image
         run: |
-            docker build \
-                --rm --squash \
+            podman build \
+                --rm \
                 -t ornladios/adios2:ci-tmp \
-                --build-arg baseos=${{ matrix.baseos }} \
                 --build-arg ci_source_dir=ci-source \
-                -f ci-source/scripts/ci/images/spack/Dockerfile \
+                -f ci-source/scripts/ci/images/spack/adios2-container-dist.dockerfile \
                 .
+
       - name: Save image as a tar file
         run: |
-            docker save -o ci-docker.tar ornladios/adios2:ci-tmp
-            ls -lah ci-docker.tar
+            podman save -o ci-podman.tar ornladios/adios2:ci-tmp
+            ls -lah ci-podman.tar
       - name: Upload
         uses: actions/upload-artifact@bbbca2ddaa5d8feaa63e36b76fdaad77386f024f # v4
         with:
           retention-days: 1
-          name: ci-docker ${{ matrix.baseos }} ${{ github.sha }}
-          path: ci-docker.tar
-      - name: Push image to Docker Hub
+          name: ci-podman ${{ matrix.baseos }} ${{ github.sha }}
+          path: ci-podman.tar
+
+      - name: Log in to GitHub Container Registry
+        if: github.event_name == 'push'
+        run: |
+          echo "${{ secrets.GITHUB_TOKEN }}" | podman login ghcr.io -u ${{ github.repository_owner }} --password-stdin
+
+      - name: Push image to GitHub Container Registry
         if: github.event_name == 'push'
-        env:
-          DOCKERHUB_USERNAME: ${{ secrets.DOCKERHUB_USERNAME }}
-          DOCKERHUB_PASSWORD: ${{ secrets.DOCKERHUB_PASSWORD }}
         run: |
             target_tag="${GITHUB_REF##refs/heads/}-${{ matrix.baseos }}"
-            docker tag \
+            podman tag \
                 ornladios/adios2:ci-tmp \
-                ornladios/adios2:${target_tag}
-            docker login \
-                --username="${DOCKERHUB_USERNAME}" \
-                --password="${DOCKERHUB_PASSWORD}"
-            docker push \
-                ornladios/adios2:${target_tag}
+                "ghcr.io/${{ github.repository }}/ornladios/adios2:${target_tag}"
+            podman push \
+                "ghcr.io/${{ github.repository }}/ornladios/adios2:${target_tag}"
 
 #######################################
 # Contract testing jobs
@@ -504,7 +506,7 @@ jobs:
           - code: tau
     defaults:
       run:
-        shell: bash -c "docker exec adios2-ci bash --login -e $(echo {0} | sed 's|/home/runner/work|/__w|g')"
+        shell: bash -c "podman exec adios2-ci bash --login -e $(echo {0} | sed 's|/home/runner/work|/__w|g')"
 
     steps:
       - uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v4
@@ -516,18 +518,18 @@ jobs:
       - name: Download CI docker image
         uses: actions/download-artifact@70fc10c6e5e1ce46ad2ea6f2b72d43f7d47b13c3 # v4
         with:
-          name: ci-docker ubuntu-bionic ${{ github.sha }}
+          name: ci-podman ubuntu-22.04 ${{ github.sha }}
       - name: Initialize containers
         shell: bash -e {0}
         run: |
             sudo chown 1000:1000 .
-            docker load -i ci-docker.tar
-            docker create \
+            podman load -i ci-podman.tar
+            podman create \
                 --name adios2-ci --workdir /__w/ADIOS2/ADIOS2 \
                 -v "/home/runner/work":"/__w" \
                 --entrypoint "tail" ornladios/adios2:ci-tmp \
                 "-f" "/dev/null"
-            docker start adios2-ci
+            podman start adios2-ci
       - name: Dependencies
         run: /opt/adios2/source/testing/contract/${{ matrix.code }}/depends.sh
       - name: Configure
diff --git a/.github/workflows/external.yml b/.github/workflows/external.yml
@@ -12,7 +12,7 @@ permissions:
 
 jobs:
   generate_statuses:
-    runs-on: ubuntu-latest
+    runs-on: ubuntu-slim
     permissions:
       contents: read
       statuses: write
diff --git a/scripts/ci/images/build-ubuntu.sh b/scripts/ci/images/build-ubuntu.sh
@@ -20,7 +20,7 @@ TAG_PREFIX="${IMAGE_TAG_PREFIX:-ghcr.io/ornladios/adios2}"
 # Build the base image
 ${BUILD_TOOL} build --progress=plain \
   --build-arg PATCH_VARIANT_XROOTD=ON \
-  --build-arg EXTRA_SPECS="sz3" \
+  --build-arg EXTRA_SPECS="sz3 zstd" \
   --rm -f ./Dockerfile.ci-spack-ubuntu22.04-base \
   -t "${TAG_PREFIX}:ci-spack-ubuntu22.04-base" \
   .
diff --git a/scripts/ci/images/spack/Dockerfile b/scripts/ci/images/spack/Dockerfile
diff --git a/scripts/ci/images/spack/adios2-container-dist.dockerfile b/scripts/ci/images/spack/adios2-container-dist.dockerfile
@@ -0,0 +1,31 @@
+FROM  ghcr.io/ornladios/adios2/adios2-deps
+
+RUN echo ${ADIOS2_SPEC}
+
+# Install from CI source
+ARG ci_source_dir=ci-source
+COPY ${ci_source_dir} /opt/adios2/source
+RUN . /spack/share/spack/setup-env.sh && \
+    spack dev-build \
+        -j$(grep -c '^processor' /proc/cpuinfo) \
+        -d /opt/adios2/source \
+        --no-checksum \
+        --skip-patch \
+        --reuse \
+        adios2@master ${ADIOS2_SPEC} ^gcc && \
+    spack uninstall --all --yes-to-all gcc && \
+    spack clean -a
+
+RUN . /spack/share/spack/setup-env.sh && \
+    spack config add "concretizer:unify:false" && \
+    spack env create --without-view adios2 && \
+    spack -e adios2 add $(spack find --format "/{hash}") && \
+    spack -e adios2 install -v && \
+    rm -rf /root/.spack && \
+    spack env activate adios2 && \
+    spack env deactivate && \
+    echo "source /spack/share/spack/setup-env.sh" >> ~/.bash_profile && \
+    echo "spack load adios2" >> ~/.bash_profile
+
+ENTRYPOINT []
+CMD ["bash", "--login"]
diff --git a/scripts/ci/images/spack/adios2-deps.dockerfile b/scripts/ci/images/spack/adios2-deps.dockerfile
@@ -0,0 +1,63 @@
+FROM ubuntu:22.04
+
+ARG SPACK_VERSION=v1.0.2
+ARG SPACK_MIRROR="https://binaries.spack.io/v2025.07.0"
+ARG ADIOS2_SPEC="~mpi~mgard~libcatalyst~bzip2~png"
+
+RUN apt update && \
+    DEBIAN_FRONTEND=noninteractive apt install -y --no-install-recommends \
+    bzip2 \
+    ca-certificates \
+    curl \
+    file \
+    g++-12 \
+    gfortran-12 \
+    git \
+    gzip \
+    lsb-release \
+    patch \
+    python3 \
+    tar \
+    unzip \
+    xz-utils \
+    zstd \
+    \
+    && \
+    apt clean -y && \
+    rm -rf /var/lib/apt/lists/*
+
+# Clone and patch spack
+WORKDIR /
+RUN if ! [ -d /spack ]; then \
+      git clone --depth 1 --single-branch --branch ${SPACK_VERSION} https://github.com/spack/spack; \
+    else \
+      git fetch --all && git checkout -t origin/${SPACK_VERSION}; \
+    fi && \
+    mkdir -p /root/.spack
+
+COPY packages.yaml /root/.spack/packages.yaml
+
+# Install base specs
+RUN . /spack/share/spack/setup-env.sh && \
+    spack repo update --branch "releases/v2025.07" builtin && \
+    spack mirror add binaries "${SPACK_MIRROR}" && \
+    spack config add "packages:all:target:[haswell]" && \
+    spack config add "config:checksum:false" && \
+    spack config add "config:build_jobs:$(nproc)" && \
+    spack config add "concretizer:reuse:true"
+
+RUN . /spack/share/spack/setup-env.sh && \
+    spack install \
+      -j$(nproc) \
+      --include-build-deps \
+      --no-check-signature \
+      --fail-fast \
+      --only dependencies \
+      adios2@master ${ADIOS2_SPEC} cmake%gcc && \
+      spack clean -a && \
+    echo "source /spack/share/spack/setup-env.sh" >> ~/.bash_profile
+
+ENV ADIOS2_SPEC="${ADIOS2_SPEC}"
+
+ENTRYPOINT []
+CMD ["bash", "--login"]
diff --git a/scripts/ci/images/spack/packages.yaml b/scripts/ci/images/spack/packages.yaml
@@ -0,0 +1,11 @@
+packages:
+  gcc:
+    externals:
+    - spec: gcc@12.3.0 languages='c,c++,fortran'
+      prefix: /usr
+      extra_attributes:
+        compilers:
+          c: /usr/bin/gcc-12
+          cxx: /usr/bin/g++-12
+          fortran: /usr/bin/gfortran-12
+    buildable: false

Original file line number	Diff line number	Diff line change
`@@ -20,7 +20,7 @@ TAG_PREFIX="${IMAGE_TAG_PREFIX:-ghcr.io/ornladios/adios2}"`
`20`	`20`	`# Build the base image`
`21`	`21`	`${BUILD_TOOL} build --progress=plain \`
`22`	`22`	`--build-arg PATCH_VARIANT_XROOTD=ON \`
`23`		`- --build-arg EXTRA_SPECS="sz3" \`
	`23`	`+ --build-arg EXTRA_SPECS="sz3 zstd" \`
`24`	`24`	`--rm -f ./Dockerfile.ci-spack-ubuntu22.04-base \`
`25`	`25`	`-t "${TAG_PREFIX}:ci-spack-ubuntu22.04-base" \`
`26`	`26`	`.`