Upgrade from ISMRMRD to MRD v2

.devcontainer/.vscode/launch.json

@@ -8,7 +8,7 @@
             "name": "(gdb) Launch",
             "type": "cppdbg",
             "request": "launch",
-            "program": "/opt/conda/envs/gadgetron/bin/gadgetron",
+            "program": "/opt/conda/envs/pingvin/bin/pingvin",
             "args": [],
             "stopAtEntry": false,
             "cwd": "${workspaceFolder}",

.devcontainer/.vscode/settings.json

@@ -82,10 +82,10 @@
     },
     "cmake.configureOnOpen": true,
     "cmake.preferredGenerators": ["Ninja", "Unix Makefiles"],
-    "cmake.cmakePath": "/opt/conda/envs/gadgetron/bin/cmake",
+    "cmake.cmakePath": "/opt/conda/envs/pingvin/bin/cmake",
     "cmake.configureSettings": {
         "USE_CUDA": "ON",
         "USE_MKL": "ON",
-        "CMAKE_INSTALL_PREFIX": "/opt/conda/envs/gadgetron"
+        "CMAKE_INSTALL_PREFIX": "/opt/conda/envs/pingvin"
     }
 }

.devcontainer/bootstrap-vscode.sh

@@ -9,5 +9,5 @@ else
 fi
 
 mkdir -p /home/vscode/.local/share/CMakeTools && \
-    echo '[{"name":"GCC-CONDA","compilers":{"C":"/opt/conda/envs/gadgetron/bin/x86_64-conda_cos6-linux-gnu-gcc","CXX":"/opt/conda/envs/gadgetron/bin/x86_64-conda_cos6-linux-gnu-g++"}}]' > /home/vscode/.local/share/CMakeTools/cmake-tools-kits.json && \
+    echo '[{"name":"GCC-CONDA","compilers":{"C":"/opt/conda/envs/pingvin/bin/x86_64-conda_cos6-linux-gnu-gcc","CXX":"/opt/conda/envs/pingvin/bin/x86_64-conda_cos6-linux-gnu-g++"}}]' > /home/vscode/.local/share/CMakeTools/cmake-tools-kits.json && \
     chown vscode:conda /home/vscode/.local/share/CMakeTools/cmake-tools-kits.json

.devcontainer/devcontainer.bashrc

@@ -0,0 +1,14 @@
+#! /bin/bash
+# shellcheck source=/dev/null
+
+source /opt/conda/etc/profile.d/conda.sh
+conda activate pingvin
+
+if command -v just >/dev/null ; then
+    source <(just --completions bash)
+fi
+
+if [[ "${BASH_ENV:-}" == "$(readlink -f "${BASH_SOURCE[0]:-}")" ]]; then
+    # We don't want subshells to unnecessarily source this again.
+    unset BASH_ENV
+fi

.devcontainer/devcontainer.json

@@ -1,10 +1,10 @@
 {
-	"name": "Gadgetron",
+	"name": "Pingvin",
 	"build": {
 		"dockerfile": "../Dockerfile",
-		"target": "gadgetron_dev_cuda",
+		"target": "pingvin_dev_cuda",
 		"context": "../",
-		"cacheFrom": "ghcr.io/gadgetron/gadgetron/gadgetron_ubuntu_dev_cuda:latest",
+		"cacheFrom": "ghcr.io/gadgetron/pingvin/ubuntu22.04_dev_cuda:latest",
 	},
 	"containerEnv": {
 		"DOCKER_BUILDKIT": "1",
@@ -21,11 +21,11 @@
 					"Ninja",
 					"Unix Makefiles"
 				],
-				"cmake.cmakePath": "/opt/conda/envs/gadgetron/bin/cmake",
+				"cmake.cmakePath": "/opt/conda/envs/pingvin/bin/cmake",
 				"cmake.configureSettings": {
 					"USE_CUDA": "ON",
 					"USE_MKL": "ON",
-					"CMAKE_INSTALL_PREFIX": "/opt/conda/envs/gadgetron",
+					"CMAKE_INSTALL_PREFIX": "/opt/conda/envs/pingvin",
 					"BUILD_DOCUMENTATION": "OFF"
 				},
 				"indentRainbow.includedLanguages": [ "yaml", "python" ]
@@ -34,6 +34,7 @@
 			// Add the IDs of extensions you want installed when the container is created.
 			"extensions": [
 				"ms-vscode.cpptools",
+				"ms-vscode.cpptools-extension-pack",
 				"ms-vscode.cmake-tools",
 				"ms-vscode.live-server",
 				"eamodio.gitlens",
@@ -48,10 +49,8 @@
 		}
 	},
 
-	"runArgs": ["--init", "--network=host"],
-
 	// To enable your local GPUs in container if they are on enabled by default devcontainer will fail to start on hosts without GPU
-	// "runArgs": ["--init", "--network=host", "--gpus=all"],
+	"runArgs": ["--init", "--network=host", "--gpus=all"],
 
 	"mounts": [
 	],

.dockerignore

@@ -6,15 +6,18 @@
 !apps/
 !cmake/
 !core/
+!doc/
 !docker/
 !gadgets/
+!justfile
+!libmrd/
 !test/
 !toolboxes/
 !environment.yml
-!chroot/
-!doc/
+!.devcontainer/devcontainer.bashrc
 
 # but also ignore:
 test/integration/data/
+test/e2e/data/
 *.Dockerfile
 docker/integration-test-image.sh

.github/workflows/pingvin-ci.yml

@@ -0,0 +1,149 @@
+name: Pingvin CI
+
+on:
+  push:
+    branches: [main]
+    tags: ["v*.*.*"]
+  pull_request:
+    branches: [main]
+  workflow_dispatch:
+
+permissions:
+  id-token: write
+  contents: read
+
+env:
+  imageBaseName: ghcr.io/gadgetron/pingvin/ubuntu22.04
+
+defaults:
+  run:
+    # See https://github.com/marketplace/actions/setup-miniconda#important
+    shell: bash -el {0}
+
+jobs:
+  build-and-test:
+    runs-on: ["self-hosted", "1ES.Pool=biomedsigproc-pingvin-NC6s_v3"]
+    strategy:
+      matrix:
+        flavor: [cuda, nocuda]
+    steps:
+      - name: checkout
+        uses: actions/checkout@v4.1.0
+
+      - name: Check GPU availability
+        run: docker run --rm --gpus=all ghcr.io/gadgetron/gadgetron/cuda:12.3.0-base-ubuntu22.04 nvidia-smi
+
+      - name: Build Docker images
+        run: ./docker/build-images.sh --type dev --type build --type rt --flavor ${{matrix.flavor}} --base-name "${{env.imageBaseName}}"
+
+      - name: Unit Test
+        run: |-
+          image_name="${{env.imageBaseName}}_build_${{matrix.flavor}}"
+          test_command=". /opt/conda/etc/profile.d/conda.sh \
+              && conda activate pingvin \
+              && /opt/code/pingvin/build/test/test_all"
+          docker run --rm --gpus=all "${image_name}" /bin/bash -c "$test_command"
+
+      - name: End-to-End Test
+        run: |-
+          image_name="${{env.imageBaseName}}_rt_${{matrix.flavor}}"
+          # Check Pingvin entrypoint
+          docker run --rm -i --gpus=all "${image_name}" --info
+          # Test Pingvin end-to-end
+          test_command=". /opt/conda/etc/profile.d/conda.sh \
+              && conda activate pingvin \
+              && cd /opt/e2e-test/ \
+              && pytest --echo-log-on-failure"
+          docker run --rm --gpus=all --entrypoint /bin/bash "${image_name}" -c "$test_command"
+
+  publish-docker-images:
+    if: github.event_name == 'push' && startsWith(github.ref, 'refs/tags')
+    needs: [build-and-test]
+    runs-on: ["self-hosted", "1ES.Pool=biomedsigproc-pingvin-NC6s_v3"]
+    strategy:
+      matrix:
+        flavor: [cuda, nocuda]
+    permissions:
+      packages: write
+    steps:
+      - name: checkout
+        uses: actions/checkout@v4.1.0
+
+      - name: Log into ghcr.io
+        uses: docker/login-action@v3
+        with:
+          registry: ghcr.io
+          username: ${{ github.actor }}
+          password: ${{ secrets.GITHUB_TOKEN }}
+
+      - name: Publish Docker images
+        run: |-
+          PINGVIN_VERSION_MAJOR=$(grep -Po '(?<=set\(PINGVIN_VERSION_MAJOR )([^\)]+)' CMakeLists.txt)
+          PINGVIN_VERSION_MINOR=$(grep -Po '(?<=set\(PINGVIN_VERSION_MINOR )([^\)]+)' CMakeLists.txt)
+          PINGVIN_VERSION_PATCH=$(grep -Po '(?<=set\(PINGVIN_VERSION_PATCH )([^\)]+)' CMakeLists.txt)
+          PINGVIN_VERSION="${PINGVIN_VERSION_MAJOR}.${PINGVIN_VERSION_MINOR}.${PINGVIN_VERSION_PATCH}"
+
+          ./docker/build-images.sh --type dev --type rt --flavor ${{matrix.flavor}} --base-name "${{env.imageBaseName}}" --tag "${PINGVIN_VERSION}" --push
+          ./docker/build-images.sh --type dev --type rt --flavor ${{matrix.flavor}} --base-name "${{env.imageBaseName}}" --tag latest --push
+
+
+  build-conda-package:
+    runs-on: ["self-hosted", "1ES.Pool=biomedsigproc-pingvin-NC6s_v3"]
+    steps:
+      - name: checkout
+        uses: actions/checkout@v4.1.0
+
+      - name: Install Yardl
+        run: |-
+          YARDL_VERSION=$(grep -Po '(?<=YARDL_VERSION=)(.+)' Dockerfile)
+          mkdir -p "/tmp/yardl_${YARDL_VERSION}_linux_x86_64"
+          cd "/tmp/yardl_${YARDL_VERSION}_linux_x86_64"
+          wget --quiet "https://github.com/microsoft/yardl/releases/download/v${YARDL_VERSION}/yardl_${YARDL_VERSION}_linux_x86_64.tar.gz"
+          tar -xzf "yardl_${YARDL_VERSION}_linux_x86_64.tar.gz"
+          pwd >> $GITHUB_PATH
+
+      - name: Setup Miniforge
+        uses: conda-incubator/setup-miniconda@v3
+        with:
+          miniforge-version: latest
+          environment-file: conda/environment.yml
+          activate-environment: pingvin-build
+
+      - name: Build conda package
+        run: ./conda/package.sh
+
+      - name: Upload Conda package
+        uses: actions/upload-artifact@v4
+        with:
+          name: conda-packages
+          path: conda/build_pkg/**/pingvin*.tar.bz2
+
+  publish-conda-package:
+    if: github.event_name == 'push' && startsWith(github.ref, 'refs/tags')
+    needs: [build-conda-package]
+    runs-on: ["self-hosted", "1ES.Pool=biomedsigproc-pingvin-NC6s_v3"]
+    steps:
+      - name: checkout
+        uses: actions/checkout@v4.1.0
+
+      - name: Setup Miniforge
+        uses: conda-incubator/setup-miniconda@v3
+        with:
+          miniforge-version: latest
+          environment-file: conda/environment.yml
+          activate-environment: pingvin-build
+
+      - name: Download Conda package
+        uses: actions/download-artifact@v4
+        with:
+          name: conda-packages
+          path: conda/build_pkg/
+
+      - name: Publish conda package
+        env:
+          ANACONDA_TOKEN: ${{ secrets.ANACONDA_TOKEN }}
+        run: |
+          for p in $(find conda/build_pkg -name pingvin*.tar.bz2)
+          do
+            ./conda/publish_package.sh -u gadgetron -t "$ANACONDA_TOKEN" -p "$p"
+          done