Merge branch 'ml/misc' into 'main'

Various changes to build files (CMake & devcontainer)

See merge request naaice/poet!38

.devcontainer/Dockerfile

@@ -1,12 +1,53 @@
-FROM mcr.microsoft.com/vscode/devcontainers/base:debian
+FROM gcc:11.2.0
 
-RUN sudo apt-get update && export DEBIAN_FRONTEND=noninteractive \
+ENV DEBIAN_FRONTEND=noninteractive
-    && sudo apt-get install -y \
+
-        cmake \
+RUN apt-get update \
-        git \
+    && apt-get install -y \
-        libeigen3-dev \
+    git \
-        libopenmpi-dev \
+    sudo \
-        r-base-dev 
+    ninja-build \
+    fzf \
+    libblas-dev && \
+    apt-get clean && \
+    rm -rf /var/lib/apt/lists/*
+
+WORKDIR /tmp
+
+RUN curl -Ls https://download.open-mpi.org/release/open-mpi/v5.0/openmpi-5.0.5.tar.gz | tar xz && \
+    cd openmpi-5.0.5 && \
+    ./configure --prefix=/usr/local && \
+    make -j $(nproc) && \
+    make install && \
+    rm -rf /tmp/openmpi-5.0.5
+
+RUN curl -Lo cmake.sh https://github.com/Kitware/CMake/releases/download/v3.30.5/cmake-3.30.5-linux-x86_64.sh \
+    && bash ./cmake.sh --skip-license --prefix=/usr/local \
+    && rm cmake.sh
+
+RUN curl -Ls https://github.com/Reference-LAPACK/lapack/archive/refs/tags/v3.12.0.tar.gz | tar xz && \
+    cd lapack-3.12.0 && \
+    mkdir build && \
+    cd build && \
+    cmake .. -G Ninja -DBUILD_SHARED_LIBS=ON && \
+    ninja install && \
+    rm -rf /tmp/lapack-3.12.0
+
+RUN curl -Ls https://cran.r-project.org/src/base/R-4/R-4.4.2.tar.gz | tar xz && \
+    cd R-4.4.2 && \
+    ./configure --prefix=/usr/local --enable-R-shlib --with-blas --with-lapack && \
+    make -j $(nproc) && \
+    make install && \
+    rm -rf /tmp/R-4.4.2
+
+RUN  /usr/local/bin/R -q -e "install.packages(c('Rcpp', 'RInside', 'qs'), repos='https://cran.rstudio.com/')"
+
+RUN curl -Ls https://gitlab.com/libeigen/eigen/-/archive/3.4.0/eigen-3.4.0.tar.bz2 | tar xj \
+    && mkdir /tmp/eigen-3.4.0/build \
+    && cd /tmp/eigen-3.4.0/build \
+    && cmake .. -G Ninja \
+    && ninja install \
+    && rm -rf /tmp/eigen-3.4.0
 
 RUN git clone https://github.com/doctest/doctest.git /doctest \
     && cd /doctest \
@@ -14,7 +55,16 @@ RUN git clone https://github.com/doctest/doctest.git /doctest \
     && cd build \
     && cmake .. \
     && make install \
-    && cd / \
     && rm -rf /doctest
 
-RUN  /usr/bin/R -q -e "install.packages(c('Rcpp', 'RInside'))"
+RUN useradd -m -s /bin/bash -G sudo vscode \
+    && echo "vscode ALL=(ALL) NOPASSWD:ALL" >> /etc/sudoers
+
+USER vscode
+
+ENV LD_LIBRARY_PATH=/usr/local/lib:$LD_LIBRARY_PATH
+
+RUN sh -c "$(wget -O- https://github.com/deluan/zsh-in-docker/releases/download/v1.2.1/zsh-in-docker.sh)" -- \ 
+    -t agnoster 
+
+WORKDIR /home/vscode

.devcontainer/devcontainer.json

@@ -21,7 +21,8 @@
 	},
 	// in case you want to push/pull from remote repositories using ssh
 	"mounts": [
-		"source=${localEnv:HOME}/.ssh,target=/home/vscode/.ssh,type=bind,consistency=cached"
+		"source=${localEnv:HOME}/.ssh,target=/home/vscode/.ssh,type=bind,consistency=cached",
+		"source=${localEnv:HOME}/.gitconfig,target=/home/vscode/.gitconfig,type=bind,consistency=cached"
 	]
 	// Uncomment to connect as an existing user other than the container default. More info: https://aka.ms/dev-containers-non-root.
 	// "remoteUser": "devcontainer"

CMake/FindRRuntime.cmake

@@ -1,28 +1,27 @@
 # prepare R environment (Rcpp + RInside)
-find_program(R_EXE "R")
+find_program(R_EXE "R"
+  REQUIRED
+)
 
 # search for R executable, R header file and library path
-if(R_EXE)
+execute_process(
-  execute_process(
+  COMMAND ${R_EXE} RHOME
-    COMMAND ${R_EXE} RHOME
+  OUTPUT_VARIABLE R_ROOT_DIR
-    OUTPUT_VARIABLE R_ROOT_DIR
+  OUTPUT_STRIP_TRAILING_WHITESPACE
-    OUTPUT_STRIP_TRAILING_WHITESPACE
+)
-  )
 
-  find_path(
+find_path(
-    R_INCLUDE_DIR R.h
+  R_INCLUDE_DIR R.h
-    HINTS ${R_ROOT_DIR}
+  HINTS /usr/include /usr/local/include /usr/share ${R_ROOT_DIR}/include
-    PATHS /usr/include /usr/local/include /usr/share
+  PATH_SUFFIXES R/include R
-    PATH_SUFFIXES include/R R/include
+  REQUIRED
-  )
+)
 
-  find_library(
+find_library(
-    R_LIBRARY libR.so
+  R_LIBRARY libR.so
-    HINTS ${R_ROOT_DIR}/lib
+  HINTS ${R_ROOT_DIR}/lib
-  )
+  REQUIRED
-else()
+)
-  message(FATAL_ERROR "No R runtime found!")
-endif()
 
 set(R_LIBRARIES ${R_LIBRARY})
 set(R_INCLUDE_DIRS ${R_INCLUDE_DIR})
@@ -71,11 +70,8 @@ list(APPEND R_INCLUDE_DIRS ${R_RInside_INCLUDE_DIR})
 # putting all together into interface library
 
 add_library(RRuntime INTERFACE IMPORTED)
-set_target_properties(
+target_link_libraries(RRuntime INTERFACE ${R_LIBRARIES})
-  RRuntime PROPERTIES
+target_include_directories(RRuntime INTERFACE ${R_INCLUDE_DIRS})
-  INTERFACE_LINK_LIBRARIES "${R_LIBRARIES}"
-  INTERFACE_INCLUDE_DIRECTORIES "${R_INCLUDE_DIRS}"
-)
 
 unset(R_LIBRARIES)
 unset(R_INCLUDE_DIRS)