.clang-format

+BasedOnStyle: LLVM
+AlignAfterOpenBracket: true
+AlignConsecutiveAssignments: true
+IndentWidth: 4
+AlwaysBreakAfterDefinitionReturnType: None
+PenaltyReturnTypeOnItsOwnLine: 9999999
+BreakBeforeBraces: Custom
+BraceWrapping:
+  AfterCaseLabel: true
+  AfterClass: true
+  AfterControlStatement: Always
+  AfterEnum: true
+  AfterFunction: true
+  AfterNamespace: true
+  AfterStruct: true
+  AfterUnion: true
+  AfterExternBlock: true
+  BeforeCatch: true
+  BeforeElse: true
+  BeforeLambdaBody: false
+  BeforeWhile: false
+  IndentBraces: false
+  SplitEmptyFunction: true
+  SplitEmptyRecord: true
+  SplitEmptyNamespace: true
+AllowShortBlocksOnASingleLine: false
+AllowShortFunctionsOnASingleLine: None
+AllowShortCaseLabelsOnASingleLine: false
+AllowShortIfStatementsOnASingleLine: false
+AllowShortLoopsOnASingleLine: false
+IndentCaseLabels: true
+Standard: c++17
+AccessModifierOffset: -4
+BinPackParameters: true
+NamespaceIndentation: None

.clang-tidy

+Checks: "-*,\
+readability-braces-around-statements,\
+modernize-concat-nested-namespaces,\
+modernize-raw-string-literal,\
+modernize-use-nullptr,\
+modernize-use-override"

.dockerignore

+# Exclude the usual build environment stuff.
+.clang-format
+.git
+.gitignore
+.gitlab-ci.yml
+ThirdParty
+build
+builds
+.DS_Store
+
+# Make sure Dockerfiles aren't included in build context to
+# improve caching.
+docker/nektar/Dockerfile
+docker/nektar-dev/Dockerfile
+docker/nektar-workbook/Dockerfile
+docker/nektar-env/Dockerfile

.gitattributes

+# Files to ignore for export
+.gitlab-ci.yml export-ignore
+.gitlab-ci/ export-ignore
+.gitignore export-ignore
+.gitattributes export-ignore
+.gitmodules export-ignore
+/docs/tutorial export-ignore
+/library/Demos/MultiRegions/ExtraDemos/ export-ignore
+/solvers/ImageWarpingSolver/ export-ignore
+/solvers/VortexWaveInteraction/ export-ignore
+/solvers/CardiacEPSolver/Utilities/CellMLToNektar/ export-ignore
+/solvers/IncNavierStokesSolver/Utilities/HybridPerformanceModel/ export-ignore
+/utilities/Extras/ export-ignore
+
+# Attempt union merges with CHANGELOG to avoid conflicts.
+CHANGELOG.md merge=union

.gitignore

+.*
+!.gitignore
+!.gitlab-ci.yml
+!.gitattributes
+!.clang-format
+!.clang-tidy
+!.dockerignore
+!.gitlab-ci
+# Ignore builds and ThirdParty directories
+build
+buildDebug
+builds
+ThirdParty
+# Ignore .DS_Store sometimes created by OS X.
+.DS_Store
+# for the userguide
+*.pdf
+# Kdevelop project files
+*.kdev4
+# Sublime project files
+*.sublime-project
+*.sublime-workspace
+# CLion build directories
+cmake-build-*
+# Any python cache directories
+__pycache__

.gitlab-ci/Dockerfile_add_repo

+FROM %%BASE_IMAGE%%
+
+ADD --chown=nektar:nektar . /home/nektar/nektar

.gitlab-ci/build-and-test.sh

+#!/bin/bash -x
+
+declare -a CMAKEARGS
+
+[[ $OS_VERSION != "macos" ]] && ccache -s && ccache -M 5G
+
+echo "Running build with:"
+echo "  - BUILD_CC                : $BUILD_CC"
+echo "  - BUILD_CXX               : $BUILD_CXX"
+echo "  - BUILD_FC                : $BUILD_FC"
+echo "  - BUILD_TYPE              : $BUILD_TYPE"
+echo "  - BUILD_SIMD              : $BUILD_SIMD"
+echo "  - DISABLE_MCA             : $DISABLE_MCA"
+echo "  - EXPORT_COMPILE_COMMANDS : $EXPORT_COMPILE_COMMANDS"
+echo "  - NUM_CPUS                : $NUM_CPUS"
+echo "  - OS_VERSION              : $OS_VERSION"
+echo "  - PYTHON_EXECUTABLE       : $PYTHON_EXECUTABLE"
+
+if [[ $BUILD_TYPE == "default" ]]; then
+    CMAKEARGS=(..
+               "-DCMAKE_BUILD_TYPE=Release"
+               "-DNEKTAR_TEST_ALL=ON"
+               "-DNEKTAR_ERROR_ON_WARNINGS=OFF"
+              )
+elif [[ $BUILD_TYPE == "full" ]]; then
+    CMAKEARGS=(..
+               "-DCMAKE_BUILD_TYPE:STRING=Debug"
+               "-DNEKTAR_FULL_DEBUG:BOOL=ON"
+               "-DNEKTAR_TEST_ALL:BOOL=ON"
+               "-DNEKTAR_USE_ARPACK:BOOL=ON"
+               "-DNEKTAR_USE_FFTW:BOOL=ON"
+               "-DNEKTAR_USE_MPI:BOOL=ON"
+               "-DNEKTAR_USE_SCOTCH:BOOL=ON"
+               "-DNEKTAR_USE_PETSC:BOOL=ON"
+               "-DNEKTAR_USE_HDF5:BOOL=ON"
+               "-DNEKTAR_USE_METIS:BOOL=ON"
+               "-DNEKTAR_USE_MESHGEN:BOOL=ON"
+               "-DNEKTAR_USE_CCM:BOOL=ON"
+               "-DNEKTAR_USE_CGNS:BOOL=ON"
+               "-DNEKTAR_CCMIO_URL=https://www.nektar.info/ccmio/libccmio-2.6.1.tar.gz"
+               "-DNEKTAR_USE_CWIPI:BOOL=ON"
+               "-DNEKTAR_USE_VTK:BOOL=ON"
+	       "-DNEKTAR_USE_LST:BOOL=ON"
+               "-DNEKTAR_BUILD_PYTHON:BOOL=ON"
+               "-DNEKTAR_TEST_USE_HOSTFILE=ON"
+               "-DNEKTAR_UTILITY_EXTRAS=ON"
+               "-DNEKTAR_ERROR_ON_WARNINGS=OFF"
+              )
+
+    if [[ $BUILD_SIMD == "avx2" ]]; then
+        CMAKEARGS+=("-DNEKTAR_ENABLE_SIMD_AVX2:BOOL=ON")
+    elif [[ $BUILD_SIMD == "avx512" ]]; then
+        CMAKEARGS+=("-DNEKTAR_ENABLE_SIMD_AVX512:BOOL=ON")
+    fi
+elif [[ $BUILD_TYPE == "performance" ]]; then
+    CMAKEARGS=(..
+               "-DCMAKE_BUILD_TYPE=Release"
+               "-DNEKTAR_BUILD_TESTS=OFF"
+               "-DNEKTAR_BUILD_UNIT_TESTS=OFF"
+               "-DNEKTAR_BUILD_PERFORMANCE_TESTS=ON"
+               "-DNEKTAR_ERROR_ON_WARNINGS=OFF"
+              )
+fi
+
+if [[ $DO_COVERAGE != "" ]]; then
+    CMAKEARGS+=("-DCMAKE_CXX_FLAGS=-fprofile-arcs -ftest-coverage")
+    pip3 install --user fastcov lxml
+fi
+
+if [[ $BUILD_TYPE != "performance" ]]; then
+    TEST_JOBS="$NUM_CPUS"
+else 
+    TEST_JOBS="1"
+fi
+
+if [[ $EXPORT_COMPILE_COMMANDS != "" ]]; then
+    CMAKEARGS+=("-DCMAKE_EXPORT_COMPILE_COMMANDS=ON")
+fi
+
+# Custom compiler
+if [[ $BUILD_CC != "" ]]; then
+    CMAKEARGS+=("-DCMAKE_C_COMPILER=${BUILD_CC}")
+fi
+if [[ $BUILD_CXX != "" ]]; then
+    CMAKEARGS+=("-DCMAKE_CXX_COMPILER=${BUILD_CXX}")
+fi
+if [[ $BUILD_FC != "" ]]; then
+    CMAKEARGS+=("-DCMAKE_Fortran_COMPILER=${BUILD_FC}")
+fi
+
+# Custom Python executable
+if [[ $PYTHON_EXECUTABLE != "" ]]; then
+    CMAKEARGS+=("-DPython_EXECUTABLE=${PYTHON_EXECUTABLE}")
+fi
+
+rm -rf build && mkdir -p build && (cd build && cmake -G 'Unix Makefiles' "${CMAKEARGS[@]}" ..)
+
+if [[ $DISABLE_MCA != "" ]]; then
+    export OMPI_MCA_btl_base_warn_component_unused=0
+fi
+
+if [[ $EXPORT_COMPILE_COMMANDS != "" ]]; then
+    # If we are just exporting compile commands for clang-tidy, just build any
+    # third-party dependencies that we need.
+    make -C build -j $NUM_CPUS thirdparty 2>&1
+    exit_code=$?
+else
+    # Otherwise build and test the code.
+    make -C build -j $NUM_CPUS all 2>&1 && make -C build -j $NUM_CPUS install && \
+        (cd build && ctest -j $TEST_JOBS --output-on-failure)
+    exit_code=$?
+
+    # Build coverage
+    if [[ $DO_COVERAGE != "" && $exit_code -eq 0 ]]; then
+        set -e
+        $HOME/.local/bin/fastcov --exclude '/usr' --lcov -o coverage.info
+        lcov --summary coverage.info
+        python3 cmake/python/lcov_cobertura.py coverage.info
+        mkdir coverage
+        python3 cmake/python/split_cobertura.py coverage.xml coverage
+        exit 0;
+    fi
+fi
+
+if [[ $exit_code -ne 0 ]]; then
+    [[ $OS_VERSION != "macos" ]] && rm -rf build/dist
+    exit $exit_code
+fi

.gitlab-ci/check-compiled-files.py

+###############################################################################
+##
+## File: check-compiled-files.py
+##
+## For more information, please see: http://www.nektar.info
+##
+## The MIT License
+##
+## Copyright (c) 2006 Division of Applied Mathematics, Brown University (USA),
+## Department of Aeronautics, Imperial College London (UK), and Scientific
+## Computing and Imaging Institute, University of Utah (USA).
+##
+## Permission is hereby granted, free of charge, to any person obtaining a
+## copy of this software and associated documentation files (the "Software"),
+## to deal in the Software without restriction, including without limitation
+## the rights to use, copy, modify, merge, publish, distribute, sublicense,
+## and/or sell copies of the Software, and to permit persons to whom the
+## Software is furnished to do so, subject to the following conditions:
+##
+## The above copyright notice and this permission notice shall be included
+## in all copies or substantial portions of the Software.
+##
+## THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS
+## OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+## FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL
+## THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+## LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+## FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
+## DEALINGS IN THE SOFTWARE.
+##
+## Description: Check for compiled files using compile_commands.json
+##
+###############################################################################
+
+import json, sys, glob, os
+
+# Should be run from root source directory.
+cwd = os.getcwd()
+
+# Folders and extensions to check
+folders = ['library', 'solvers', 'tests', 'utilities']
+exts = ['cpp', 'c']
+
+# Presently some stuff is not in the CI.
+ignore_sources = [
+    # CADfix API
+    "library/NekMesh/CADSystem/CFI/CADSystemCFI.cpp",
+    "library/NekMesh/CADSystem/CFI/CADSurfCFI.cpp",
+    "library/NekMesh/CADSystem/CFI/CADCurveCFI.cpp",
+    "library/NekMesh/CADSystem/CFI/CADVertCFI.cpp",
+    "library/NekMesh/Module/InputModules/InputCADfix.cpp",
+    "library/NekMesh/Module/OutputModules/OutputCADfix.cpp",
+    # Likwid
+    "solvers/CompressibleFlowSolver/Utilities/TimeRiemann.cpp",
+    "solvers/CompressibleFlowSolver/Utilities/TimeRoeKernel.cpp",
+    # Template for PWS
+    "solvers/PulseWaveSolver/EquationSystems/TemplatePressureArea.cpp",
+]
+
+ignore_sources = [ os.path.join(cwd, os.path.normpath(p)) for p in ignore_sources ]
+
+with open(sys.argv[1], 'r') as f:
+    compilation_data = json.load(f)
+    compiled_files = [ entry['file'] for entry in compilation_data ]
+
+    # Search for all c/cpp files in library, solvers and utilities folder.
+    found_files = []
+    for folder in folders:
+        for ext in exts:
+            found_files += glob.glob(os.path.join(cwd, folder, '**', '*.{:s}'.format(ext)), recursive=True)
+
+    # Compare the lists of files.
+    all_good = True
+    for f in found_files:
+        if f in ignore_sources:
+            continue
+
+        if f not in compiled_files:
+            print('Uncompiled file: ' + f)
+            all_good = False
+
+    if not all_good:
+        exit(1)

.gitlab-ci/checkformatXMLfile.sh

+#!/bin/bash
+XML_INDEX="    " find -type f -name "*.xml" -print0 | xargs -0 -I % $(dirname "$0")/formatXMLfile.sh % --no-output
+exit $?

.gitlab-ci/formatXMLfile.sh

+#!/bin/bash
+
+# Indentation level
+if [[ $XML_INDENT ]]; then
+    indent=$XML_INDENT
+else
+    indent="    "
+fi
+
+# Filename
+if [[ $1 ]]; then
+    filename=$1
+else
+    echo "Please specify xml filename"
+    exit 1 # exit with error
+fi
+
+
+# Exit if not xml file
+[[ "$filename" =~ ^.*\.xml$ ]] || exit 1
+
+# Format file
+rm -f tmp
+tab=""
+dos2unix $filename 2> /dev/null
+while read -r line || [[ -n "$line" ]]; do
+    # Print empty line
+    if [[ $line == "" ]]; then
+        echo "" >> tmp
+        continue
+    fi
+
+    # Just print line if comment
+    if [[ $line == "<!--"*"-->" ]]; then
+        echo "${tab}${line}" >> tmp
+        continue
+    fi
+
+    # Remove tab
+    if [[ $line == "</"*">"* ]] || [[ $line == "/>"* ]] || 
+       [[ $line == "-->" ]]; then
+        tab=${tab::-4}
+    fi
+
+    # Print line
+    echo "${tab}${line}" >> tmp
+
+    # Add tab
+    if [[ $line == "<!--" ]] || [[ $line == "<!--"* ]]; then
+        # Comment tag
+        tab=${tab}"    "
+    elif [[ $line == "<"* ]] && [[ $line == !("</"*) ]]; then
+        # Opening tag
+        if [[ $line == !("<?"*"?>") ]]; then
+            tab=${tab}"    "
+        fi
+    fi
+
+    # Remove tab
+    if  [[ $line == "-->" ]]; then
+        # Comment tag
+        continue
+    elif  [[ $line == *"-->" ]] && [[ $line == !(*">"*"-->") ]] && 
+          [[ $line == !(*"</"*"-->") ]]; then
+        tab=${tab::-4}
+    elif [[ $line == "<"*"</"*">"* ]] || [[ $line == "<"*"/>"* ]] || 
+     ( [[ $line == !("<"*) ]] && [[ $line == !("/>"*) ]] && [[ $line == *"/>"* ]] ); then
+        # Closing tag
+        tab=${tab::-4}
+    fi
+
+done < $filename
+
+# Rename file
+if [[ $2 == !(--no-output) ]]; then
+    if [[ $2 ]]; then
+        mv tmp $2
+    else 
+        cat tmp
+    fi
+else
+    if cmp -s tmp $filename; then 
+       rm -f tmp
+    else
+        echo "$filename not formatted properly"
+        rm -f tmp
+        exit 2 # exit with error
+    fi
+fi
+rm -f tmp
+
+# Exit script
+exit 0

.gitlab-ci/header-format-filename.sh

+#!/bin/bash
+error=0
+for file in $(find $TARGETS -type f); do
+    filename=${file##*/}
+    if [[ ! $(grep -F "$filename" $file) ]]; then
+        if [[ "${filename##*.}" == "h" ]]; then
+            echo $file does not contains file name
+            error=1
+        fi
+        if [[ "${filename##*.}" == "cpp" ]]; then
+            echo $file does not contains file name
+            error=1
+        fi
+        if [[ "${filename##*.}" == "hpp" ]]; then
+            echo $file does not contains file name
+            error=1
+        fi
+    fi
+done
+
+if [[ $error -eq 1 ]]; then
+    exit 1 # exit with an error
+fi

.gitlab-ci/header-format-license.sh

+#!/bin/bash
+error=0
+for file in $(find $TARGETS -type f); do
+    filename=${file##*/}
+    if [[ ! $(grep -F "MIT License" $file) ]]; then
+        if [[ "${filename##*.}" == "h" ]]; then
+            echo $file does not contains MIT License
+            error=1
+        fi
+        if [[ "${filename##*.}" == "cpp" ]]; then
+            echo $file does not contains MIT License
+            error=1
+        fi
+        if [[ "${filename##*.}" == "hpp" ]]; then
+            echo $file does not contains MIT License
+            error=1
+        fi
+    fi
+done
+
+if [[ $error -eq 1 ]]; then
+    exit 1 # exit with an error
+fi

.gitlab-ci/packaging-exclude

+build*
+docs/tutorial
+docker
+pkg
+ThirdParty
+nektar++*.tar.gz

.gitlab-ci/prepare_failed.sh

+#!/bin/bash
+
+rm -rf nektar/build/dist
+tar czf nektar.tar.gz nektar
+rm -rf nektar

.gitmodules

+[submodule "docs/tutorial"]
+    branch = master
+    path = docs/tutorial
+    url = https://gitlab.nektar.info/nektar/tutorial.git
+    ignore = all