Update petsird to v0.2.0

.devcontainer/Dockerfile

@@ -29,29 +29,25 @@ ARG USERNAME="vscode"
 ARG USER_UID=1000
 ARG USER_GID=$USER_UID
 ARG CONDA_GID=900
-ARG CONDA_ENVIRONMENT_NAME=prd
-ARG VSCODE_DEV_CONTAINERS_SCRIPT_LIBRARY_VERSION=v0.229.0
+ARG CONDA_ENVIRONMENT_NAME=petsird
 
 RUN apt-get update && apt-get install -y \
     libc6-dbg \
     && rm -rf /var/lib/apt/lists/*
 
 # Enable non-root Docker access in container
-ARG ENABLE_NONROOT_DOCKER="true"
-# Use the OSS Moby CLI instead of the licensed Docker CLI
-ARG USE_MOBY="false"
-RUN script=$(curl -fsSL "https://raw.githubusercontent.com/microsoft/vscode-dev-containers/${VSCODE_DEV_CONTAINERS_SCRIPT_LIBRARY_VERSION}/script-library/docker-debian.sh") && bash -c "$script" -- "${ENABLE_NONROOT_DOCKER}" "/var/run/docker-host.sock" "/var/run/docker.sock" "${USERNAME}" "${USE_MOBY}"
+ARG DOCKER_VERSION="27.0.3"
+RUN script=$(curl -fsSL "https://raw.githubusercontent.com/devcontainers/features/2951f0481a488ea43a6f2ea6f18a47f0a0bf744d/src/docker-outside-of-docker/install.sh") \
+    && VERSION=${DOCKER_VERSION} DOCKERDASHCOMPOSEVERSION="none" bash -c "$script"
 
 # Setting the ENTRYPOINT to docker-init.sh will configure non-root access to
 # the Docker socket if "overrideCommand": false is set in devcontainer.json.
 # The script will also execute CMD if you need to alter startup behaviors.
 ENTRYPOINT [ "/usr/local/share/docker-init.sh" ]
 CMD [ "sleep", "infinity" ]
 
-ARG MAMBAFORGE_VERSION=22.9.0-2
-
 # Based on https://github.com/conda-forge/miniforge-images/blob/master/ubuntu/Dockerfile
-RUN wget --no-hsts --quiet https://github.com/conda-forge/miniforge/releases/download/${MAMBAFORGE_VERSION}/Mambaforge-${MAMBAFORGE_VERSION}-Linux-$(uname -m).sh -O /tmp/miniforge.sh \
+RUN wget --no-hsts --quiet https://github.com/conda-forge/miniforge/releases/latest/download/Miniforge3-$(uname)-$(uname -m).sh -O /tmp/miniforge.sh \
     && /bin/bash /tmp/miniforge.sh -b -p /opt/conda \
     && rm /tmp/miniforge.sh \
     && /opt/conda/bin/conda clean --tarballs --index-cache --packages --yes \
@@ -67,8 +63,8 @@ RUN wget --no-hsts --quiet https://github.com/conda-forge/miniforge/releases/dow
 # Create a conda environment from the environment file in the repo root.
 COPY --from=file-normalizer --chown=$USER_UID:conda /data/environment.yml /tmp/build/
 RUN umask 0002 \
-    && /opt/conda/bin/mamba env create -f /tmp/build/environment.yml \
-    && /opt/conda/bin/mamba clean -fy \
+    && /opt/conda/bin/conda env create -f /tmp/build/environment.yml \
+    && /opt/conda/bin/conda clean -fy \
     && sudo chown -R :conda /opt/conda/envs
 
 # Add a file that is to be sourced from .bashrc and from the devops pipeline stages
@@ -87,11 +83,11 @@ ENV CMAKE_GENERATOR=Ninja
 
 # Create a kits file for the VSCode CMake Tools extension, so you are not prompted for which kit to select whenever you open VSCode
 RUN mkdir -p /home/vscode/.local/share/CMakeTools \
-    && echo '[{"name":"GCC-10","compilers":{"C":"/opt/conda/envs/prd/bin/x86_64-conda_cos6-linux-gnu-gcc","CXX":"/opt/conda/envs/prd/bin/x86_64-conda_cos6-linux-gnu-g++"}}]' > /home/vscode/.local/share/CMakeTools/cmake-tools-kits.json \
+    && echo '[{"name":"GCC-10","compilers":{"C":"/opt/conda/envs/petsird/bin/x86_64-conda_cos6-linux-gnu-gcc","CXX":"/opt/conda/envs/petsird/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
 
 # Install the yardl tool
-ARG YARDL_VERSION=0.3.2
+ARG YARDL_VERSION=0.6.2
 RUN wget --quiet "https://github.com/microsoft/yardl/releases/download/v${YARDL_VERSION}/yardl_${YARDL_VERSION}_linux_x86_64.tar.gz" \
     && tar -xzf "yardl_${YARDL_VERSION}_linux_x86_64.tar.gz" \
     && mv yardl "/opt/conda/envs/${CONDA_ENVIRONMENT_NAME}/bin/" \

.devcontainer/devcontainer.bashrc

@@ -2,9 +2,8 @@
 # shellcheck source=/dev/null
 
 source /opt/conda/etc/profile.d/conda.sh
-conda activate prd
+conda activate petsird
 source <(yardl completion bash)
-source <(just --completions bash)
 
 if [[ "${BASH_ENV:-}" == "$(readlink -f "${BASH_SOURCE[0]:-}")" ]]; then
     # We don't want subshells to unnecessarily source this again.

.devcontainer/devcontainer.json

@@ -1,7 +1,6 @@
-// For format details, see https://aka.ms/devcontainer.json. For config options, see the README at:
-// https://github.com/microsoft/vscode-dev-containerdevcotns/tree/v0.238.0/containers/go
+// For format details, see https://aka.ms/devcontainer.json.
 {
-  "name": "prd",
+  "name": "petsird",
   "build": {
     "dockerfile": "Dockerfile",
     "context": ".."
@@ -48,7 +47,7 @@
         "cmake.buildDirectory": "${workspaceFolder}/cpp/build",
         "cmake.configureOnOpen": false,
 
-        "python.defaultInterpreterPath": "/opt/conda/envs/prd/bin/python",
+        "python.defaultInterpreterPath": "/opt/conda/envs/petsird/bin/python",
         "python.analysis.typeCheckingMode": "strict",
         "python.analysis.diagnosticMode": "workspace",
         "python.analysis.diagnosticSeverityOverrides": {
@@ -88,7 +87,7 @@
           "gitlens.showWhatsNewAfterUpgrades": false
         },
 
-        "gcovViewer.gcovBinary": "/opt/conda/envs/prd/bin/x86_64-conda-linux-gnu-gcov",
+        "gcovViewer.gcovBinary": "/opt/conda/envs/petsird/bin/x86_64-conda-linux-gnu-gcov",
         "gcovViewer.buildDirectories": ["${workspaceFolder}/cpp/build"],
 
         "search.useIgnoreFiles": false,
@@ -109,19 +108,17 @@
         "ms-python.python",
         "ms-vscode.cmake-tools",
         "ms-vscode.cpptools",
-        "sclu1034.justfile",
         "timonwong.shellcheck",
         "twxs.cmake"
       ]
     }
   },
 
-  // Use 'forwardPorts' to make a list of ports inside the container available locally.
-  // "forwardPorts": [],
-
-  // Use 'postCreateCommand' to run commands after the container is created.
-  // "postCreateCommand": "go version",
+  "overrideCommand": false,
+  "mounts": [
+    // Bind mount docker socket under an alias to support docker-from-docker
+    "source=/var/run/docker.sock,target=/var/run/docker-host.sock,type=bind"
+  ],
 
-  // Comment out to connect as root instead. More info: https://aka.ms/vscode-remote/containers/non-root.
   "remoteUser": "vscode"
 }

.github/workflows/ci.yml

@@ -23,7 +23,7 @@ jobs:
     runs-on: ubuntu-latest
 
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
         with:
           submodules: recursive
 
@@ -46,11 +46,6 @@ jobs:
           cd PETSIRD/model
           yardl generate
 
-      - name: Python
-        run: |
-          cd python
-          python start.py
-
       - name: Cpp
         run: |
           cd cpp && mkdir -p build && cd build

.gitmodules

@@ -1,3 +1,4 @@
 [submodule "PETSIRD"]
 	path = PETSIRD
-	url = https://github.com/ETSInitiative/PRDdefinition
+	url = https://github.com/ETSInitiative/PETSIRD
+        branch=main

cpp/CMakeLists.txt

@@ -1,5 +1,5 @@
 cmake_minimum_required(VERSION 3.12.0) # older would work, but could give warnings on policy CMP0074
-project(PETSIRDUseCaseTemplate VERSION 0.1.0)
+project(root_to_petsird VERSION 0.2.0)
 
 set(CMAKE_CXX_STANDARD 17)
 
@@ -16,11 +16,14 @@ else()
   add_compile_options(-Wall -Wextra -pedantic)
 endif()
 
-add_subdirectory(../PETSIRD/cpp/generated PETSIRD_generated)
+set(PETSIRD_dir ../PETSIRD/cpp/generated)
+add_subdirectory(${PETSIRD_dir} PETSIRD_generated)
 
 find_package(ROOT REQUIRED COMPONENTS Core Imt RIO Net Hist Graf Graf3d Gpad Tree TreePlayer Rint Postscript Matrix Physics MathCore Thread MultiProc ROOTDataFrame)
 add_executable(root_to_petsird main.cpp)
-include_directories(root_to_petsird PUBLIC ../PETSIRD/cpp/generated)
-target_link_libraries(root_to_petsird PUBLIC prd_generated)
+target_include_directories(root_to_petsird PUBLIC ${PETSIRD_dir})
+# needed for helpers
+target_include_directories(root_to_petsird PUBLIC ${PETSIRD_dir}/..)
+target_link_libraries(root_to_petsird PUBLIC petsird_generated)
 target_link_libraries(root_to_petsird PUBLIC ROOT::Core ROOT::Imt ROOT::RIO ROOT::Net ROOT::Hist ROOT::Graf ROOT::Graf3d ROOT::Gpad ROOT::Tree ROOT::TreePlayer ROOT::Rint ROOT::Postscript ROOT::Matrix ROOT::Physics ROOT::MathCore ROOT::Thread ROOT::MultiProc ROOT::ROOTDataFrame)
 install(TARGETS root_to_petsird DESTINATION bin)