Some modernizations

.pre-commit-config.yaml

@@ -0,0 +1,7 @@
+repos:
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v4.5.0  # Use the latest stable tag
+    hooks:
+      - id: trailing-whitespace
+      - id: end-of-file-fixer
+      - id: check-added-large-files

CMakeLists.txt

@@ -1,14 +1,38 @@
 cmake_minimum_required(VERSION 3.14)
 
-# Project name
+# try to prevent modification of source directory
+# note: some files may still be written before CMake can abort and need to be removed manually
+if(${CMAKE_CURRENT_SOURCE_DIR} STREQUAL ${CMAKE_CURRENT_BINARY_DIR})
+  message(
+    FATAL_ERROR
+      "In-source build not allowed. "
+      "Please create a new directory, preferably next to the source directory, and run CMake from there. "
+      "You may want to remove CMakeCache.txt and CMakeFiles/ which were created in the source directory."
+    )
+endif()
+
 project(mirco VERSION 0.1.0)
 
-# Check for out-of-source build
-if(${CMAKE_SOURCE_DIR} STREQUAL ${CMAKE_BINARY_DIR})
-  message(FATAL_ERROR "\nIn-source builds not allowed. Please make a new directory (called a build directory) and run CMake from there.\n\nTo clean-up, you may need to remove CMakeCache.txt and CMakeFiles from your source directory.")
-endif()
+# Print CMake version to screen
+message(STATUS "Using CMake ${CMAKE_VERSION}")
 
+# Enforce the C++ standard we are using and turn off compiler-specific extensions
 set(CMAKE_CXX_STANDARD 17)
+set(CMAKE_CXX_STANDARD_REQUIRED ON)
+set(CMAKE_CXX_EXTENSIONS OFF)
+
+# We do not use C++ modules (yet). Turn off scanning to avoid issues with clang-tidy.
+# If you want to add module support, this problem needs to be revisited. Our hope
+# is that CMake and/or clang-tidy will be updated to handle modules better.
+set(CMAKE_CXX_SCAN_FOR_MODULES OFF)
+
+# Ensure cmake setup the correct runtime path when installing
+# see here for more information: https://gitlab.kitware.com/cmake/community/-/wikis/doc/cmake/RPATH-handling
+include(GNUInstallDirs)
+set(CMAKE_SKIP_BUILD_RPATH FALSE)
+set(CMAKE_BUILD_WITH_INSTALL_RPATH FALSE)
+set(CMAKE_INSTALL_RPATH "${CMAKE_INSTALL_PREFIX}/${CMAKE_INSTALL_LIBDIR}")
+set(CMAKE_INSTALL_RPATH_USE_LINK_PATH TRUE)
 
 # Add libraries
 if(GTEST_IN_MIRCO)
@@ -145,7 +169,7 @@ configure_package_config_file(cmake/mirco_libConfig.cmake.in
 
 install(FILES
   ${CMAKE_CURRENT_BINARY_DIR}/mirco_libConfig.cmake
-  DESTINATION lib/cmake/mirco 
+  DESTINATION lib/cmake/mirco
   )
 
 install(DIRECTORY ${PROJECT_SOURCE_DIR}/src/ DESTINATION include/mirco FILES_MATCHING PATTERN "*.h")

README.md

@@ -22,62 +22,83 @@ cd <someBaseDir>
 mkdir <sourceDir>
 git clone --recursive https://github.com/imcs-compsim/MIRCO.git <sourceDir>
 ```
+
 where `<someBaseDir>` is some directory in your machine and `<sourceDir>` will contain the `MIRCO` source code.
 
 If you have already cloned the repository using:
+
 ```bash
 git clone https://github.com/imcs-compsim/MIRCO.git <sourceDir>
 ```
+
 you can pull the submodules using:
+
 ```bash
 cd <sourceDir>
 git submodule update --init --recursive
 ```
+
 To update the submodules, you can use the following command from your source directory:
+
 ```bash
 git submodule update --recursive --remote
 ```
 
 ### Configure and build the code
 
 To create an out-of-source build, first create a build directory using:
+
 ```bash
 cd <someBaseDir>
 mkdir <buildDir>
 ```
+
 where `<buildDir>` is the build directory.
 
 > Note: The exact location of `<buildDir>` is arbitrary, as long as it is _not_ a subdirectory of `<sourceDir>`.
 
 Now, you have to navigate to the build directory and call the `do-configure` script in order to invoke `cmake`:
+
 ```bash
 cd <buildDir>
 <sourceDir>/do-configure
 ```
 
+Alternatively, you can use CMake presets:
+
+```bash
+cd <buildDir>
+cmake --preset=<name_of_your_preset> <sourceDir>
+```
+
 > **IMPORTANT** Make sure to set `Trilinos_DIR` to point to you Trilinos installation.
 
 Build the `mirco` executable in the build directory using:
+
 ```bash
 cd <buildDir>
 make -j <numProc>
 ```
+
 with `<numProc>` specifying the number of processes used for compilation.
 The `mirco` executable will be created in the build directory.
 
 ### Run all tests
 
 You can run the tests from the build directory using:
+
 ```bash
 ctest
 ```
 
 ### Run the code
 
 To run the code with an input file, use the following command in your build directory:
+
 ```bash
 ./mirco <sourceDir>/Input/<someInputFile.xml>
 ```
+
 where `<someInputFile.xml>` is any input file in the prescribed format.
 
 ## How to cite MIRCO?

create-mirco-python-venv

@@ -1,16 +1,30 @@
 #!/bin/bash
 
+# Exit the script at the first failure
+set -e
+
+if [ ! -f "./create-mirco-python-venv" ]; then
+    echo "Please run this script from the root directory of the repository."
+    exit 1
+fi
+
 # Path to the python virtual environment.
 PYTHON_VENV="`dirname "$0"`/utilities/mirco-python-venv"
 
 # If the virtual environment already exists, delete it.
 if [ -d "$PYTHON_VENV" ]; then rm -Rf $PYTHON_VENV; fi
 
+# Path to python
+PYTHON_PATH=${1:-python3}
+
 # Setup the virtual environment and source it.
-python3 -m venv "${PYTHON_VENV}"
+$PYTHON_PATH -m venv "${PYTHON_VENV}"
 source "${PYTHON_VENV}"/bin/activate
 
 # Install all the modules defined in requirements.txt.
 pip install --upgrade pip
 pip install wheel
 pip install -r requirements.txt
+
+# Install the pre-commit hooks.
+pre-commit install

requirements.txt

@@ -1,2 +1,3 @@
 # Python modules that will be installed into the MIRCO python virtual environment
-clang-format==14.0.0
+clang-format==14.0.0
+pre-commit==3.5.0