Add VSC dev container config files (#425)

* Add devcontainer and update dockerfiles

* Update documentation

* Update VSC settings

.devcontainer/Dockerfile

@@ -0,0 +1,18 @@
+FROM mcr.microsoft.com/devcontainers/cpp:0-ubuntu-22.04
+
+ARG REINSTALL_CMAKE_VERSION_FROM_SOURCE="3.25.2"
+
+# Optionally install the cmake for vcpkg
+COPY ./reinstall-cmake.sh /tmp/
+
+RUN if [ "${REINSTALL_CMAKE_VERSION_FROM_SOURCE}" != "none" ]; then \
+        chmod +x /tmp/reinstall-cmake.sh && /tmp/reinstall-cmake.sh ${REINSTALL_CMAKE_VERSION_FROM_SOURCE}; \
+    fi \
+    && rm -f /tmp/reinstall-cmake.sh
+
+# [Optional] Uncomment this section to install additional vcpkg ports.
+# RUN su vscode -c "${VCPKG_ROOT}/vcpkg install <your-port-name-here>"
+
+# [Optional] Uncomment this section to install additional packages.
+# RUN apt-get update && export DEBIAN_FRONTEND=noninteractive \
+#     && apt-get -y install --no-install-recommends <your-package-list-here>

.devcontainer/devcontainer.json

@@ -0,0 +1,26 @@
+// For format details, see https://aka.ms/devcontainer.json. For config options, see the
+// README at: https://github.com/devcontainers/templates/tree/main/src/cpp
+{
+	"name": "C++",
+	"build": {
+		"dockerfile": "Dockerfile"
+	},
+	"features": {
+		"ghcr.io/rocker-org/devcontainer-features/miniforge:1": {}
+	}
+
+	// Features to add to the dev container. More info: https://containers.dev/features.
+	// "features": {},
+
+	// 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": "gcc -v",
+
+	// Configure tool-specific properties.
+	// "customizations": {},
+
+	// Uncomment to connect as root instead. More info: https://aka.ms/dev-containers-non-root.
+	// "remoteUser": "root"
+}

.devcontainer/reinstall-cmake.sh

@@ -0,0 +1,58 @@
+#!/usr/bin/env bash
+#-------------------------------------------------------------------------------------------------------------
+# Copyright (c) Microsoft Corporation. All rights reserved.
+# Licensed under the MIT License. See https://go.microsoft.com/fwlink/?linkid=2090316 for license information.
+#-------------------------------------------------------------------------------------------------------------
+#
+set -e
+
+CMAKE_VERSION=${1:-"none"}
+
+if [ "${CMAKE_VERSION}" = "none" ]; then
+    echo "No CMake version specified, skipping CMake reinstallation"
+    exit 0
+fi
+
+# Cleanup temporary directory and associated files when exiting the script.
+cleanup() {
+    EXIT_CODE=$?
+    set +e
+    if [[ -n "${TMP_DIR}" ]]; then
+        echo "Executing cleanup of tmp files"
+        rm -Rf "${TMP_DIR}"
+    fi
+    exit $EXIT_CODE
+}
+trap cleanup EXIT
+
+
+echo "Installing CMake..."
+apt-get -y purge --auto-remove cmake
+mkdir -p /opt/cmake
+
+architecture=$(dpkg --print-architecture)
+case "${architecture}" in
+    arm64)
+        ARCH=aarch64 ;;
+    amd64)
+        ARCH=x86_64 ;;
+    *)
+        echo "Unsupported architecture ${architecture}."
+        exit 1
+        ;;
+esac
+
+CMAKE_BINARY_NAME="cmake-${CMAKE_VERSION}-linux-${ARCH}.sh"
+CMAKE_CHECKSUM_NAME="cmake-${CMAKE_VERSION}-SHA-256.txt"
+TMP_DIR=$(mktemp -d -t cmake-XXXXXXXXXX)
+
+echo "${TMP_DIR}"
+cd "${TMP_DIR}"
+
+curl -sSL "https://github.com/Kitware/CMake/releases/download/v${CMAKE_VERSION}/${CMAKE_BINARY_NAME}" -O
+curl -sSL "https://github.com/Kitware/CMake/releases/download/v${CMAKE_VERSION}/${CMAKE_CHECKSUM_NAME}" -O
+
+sha256sum -c --ignore-missing "${CMAKE_CHECKSUM_NAME}"
+sh "${TMP_DIR}/${CMAKE_BINARY_NAME}" --prefix=/opt/cmake --skip-license
+
+ln -s /opt/cmake/bin/cmake /usr/local/bin/cmake

.vscode/settings.json

@@ -0,0 +1,4 @@
+{
+    "cmake.configureOnOpen": false,
+    "cmake.preferredGenerators": [ "Unix Makefiles" ]
+}

docs/_docs/install.md

@@ -45,6 +45,9 @@ alias faunus='docker exec --interactive -u 1000 faunuslab faunus'
 faunus < input.json # piping input to docker
 ~~~
 
+For development using VSC, we also provide a `devcontainer` configuration for setting
+up a Linux development environment, see description below.
+
 
 ## Build from source code
 
@@ -166,10 +169,18 @@ where `{tbb-root}` is the installation directory of TBB, _e.g._
 
 # Development
 
-The development of Faunus is done mainly in Jetbrain's [CLion](https://www.jetbrains.com/clion)
-(free academic license) but any other IDE or merely a text editor can be used.
-We recommend to use tools that respect the provided `.clang-format` which will ease merging
+We recommend to use an IDE or text editor that respect the provided `.clang-format` which will ease merging
 changes into the codebase, see below.
+For Visual Studio Code (VSC) users, it is very easy to setup a development environment using Docker and
+[Dev Containers](https://marketplace.visualstudio.com/items?itemName=ms-vscode-remote.remote-containers):
+
+~~~ bash
+cd faunus
+code .
+~~~
+
+(when asked, select "open in devcontainer", assuming you have Docker running)
+
 
 ## Code Style
 

scripts/Dockerfile

@@ -12,7 +12,7 @@
 # - clone of mlund/chemistry-notebooks
 #
 ARG OWNER=jupyter
-ARG BASE_CONTAINER=jupyter/scipy-notebook:lab-3.3.2
+ARG BASE_CONTAINER=jupyter/scipy-notebook:lab-3.6.1
 FROM $BASE_CONTAINER
 
 LABEL maintainer="the faun"
@@ -26,19 +26,18 @@ RUN apt-get update --yes && \
     apt-get install --yes --no-install-recommends \
     software-properties-common
 
-RUN add-apt-repository -y ppa:ubuntu-toolchain-r/test && \
-    apt-get update --yes && \
+RUN apt-get update --yes && \
     apt-get install --yes --no-install-recommends \
-    cmake \
-    gcc-11 \
-    g++-11 \
+    gcc \
+    g++ \
     libopenmpi-dev openmpi-bin openmpi-common \
     zlib1g-dev && \
     apt autoremove --yes && \
     apt-get clean && rm -rf /var/lib/apt/lists/*
 
 USER ${NB_UID}
 RUN mamba install --quiet --yes \
+    'cmake' \
     'jsonschema' \
     'jinja2' \
     'pypandoc' \
@@ -54,8 +53,8 @@ RUN git clone https://github.com/mlund/chemistry-notebooks.git
 
 USER root
 RUN git clone https://github.com/mlund/faunus.git && \
-    export CXX=g++-11 && \
-    export CC=gcc-11 && \
+    export CXX=g++ && \
+    export CC=gcc && \
     cd faunus && \
     cmake -DENABLE_PYTHON=on -DENABLE_OPENMP=on -DENABLE_MPI=on -DCMAKE_BUILD_TYPE=RelWithDebInfo -DPYBIND11_FINDPYTHON=on . && \
     make faunus && \

scripts/environment.yml

@@ -10,7 +10,7 @@ channels:
 dependencies:
     - clangdev
     - libcxx
-    - cmake>=3.16
+    - cmake>=3.25
     - python=3
     - pandoc=2
     - pypandoc=1