First attempt at github actions

.github/workflows/ci-github-actions.yaml

@@ -0,0 +1,83 @@
+name: GitHub Actions CI
+
+on: 
+  push:
+    branches: 
+    - develop
+    - feature-gh-actions
+  pull_request:
+    branches: 
+    - develop
+
+jobs:
+
+  linux:
+    runs-on: ubuntu-latest
+    container: ${{ matrix.container }}
+    env:
+      GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+      GH_JOBNAME: ${{ matrix.jobname }}
+      GH_OS: Linux
+    strategy:
+      fail-fast: false
+      matrix:
+        jobname: [
+          ubuntu22-gcc,
+          ubuntu22-clang,
+        ]
+        include:
+        - jobname: ubuntu22-gcc
+          container: 
+            image: ghcr.io/philipfackler/xolotl-ci:ubuntu22-dev
+            options: -u root 
+        - jobname: ubuntu22-clang
+          container: 
+            image: ghcr.io/philipfackler/xolotl-ci:ubuntu22-dev
+            options: -u root
+
+    steps:
+    - name: Checkout Action
+      uses: actions/checkout@v1
+
+    - name: Configure
+      run: CI/scripts/run_step.sh configure
+
+    - name: Build
+      run: CI/scripts/run_step.sh build
+
+    - name: Test
+      run: CI/scripts/run_step.sh test
+
+
+  macos:
+    runs-on: macos-latest
+    env:
+      GH_YML_JOBNAME: ${{ matrix.jobname }}
+      GH_YML_OS: macOS
+
+    strategy:
+      fail-fast: false
+      matrix:
+        jobname: [
+          macos1015-xcode11 
+        ]
+
+    steps:
+    - name: Checkout Action
+      uses: actions/checkout@v1
+
+    - name: Setup Dependencies
+      run: |
+        brew install boost open-mpi hdf5-mpi make [email protected]
+        echo "PATH=/opt/homebrew/opt/[email protected]/libexec/bin:$PATH" >> $GITHUB_ENV
+
+    - name: Configure
+      run: CI/scripts/run_step.sh configure
+      env:
+        PATH: ${{ env.PATH }}
+
+    - name: Build
+      run: CI/scripts/run_step.sh build
+
+    - name: Test
+      run: CI/scripts/run_step.sh test

CI/docker/ubuntu22/Dockerfile

@@ -0,0 +1,34 @@
+FROM ubuntu:22.04
+
+ENV DEBIAN_FRONTEND noninteractive
+
+# Install dependencies
+RUN apt-get update -y
+RUN apt-get upgrade -y
+RUN apt-get install -y \
+        python3 \
+        clang \
+        clang-tidy \
+        g++ \
+        git \
+        gdb \
+        make \
+        cmake \
+        cmake-curses-gui \
+        mpi-default-dev \
+        libblas-dev \
+        liblapack-dev \
+        libhdf5-mpi-dev \
+        libboost-filesystem-dev \
+        libboost-program-options-dev \
+        libboost-test-dev \
+        libboost-log-dev \
+        bzip2 \
+        sudo
+
+RUN useradd -mr -u 10000 builduser
+RUN adduser builduser sudo
+RUN echo "builduser:builduser" | chpasswd
+
+USER builduser
+WORKDIR /home/builduser

CI/scripts/run_step.sh

@@ -0,0 +1,55 @@
+#!/bin/bash
+
+echo -e "\nCheck gcc and clang compilers\n"
+gcc --version
+clang --version
+
+case "$1" in 
+
+  configure)
+
+    git config --global --add safe.directory ${GITHUB_WORKSPACE}
+
+    case "${GH_JOBNAME}" in
+      *"clang"*)
+        export CC=clang
+        export CXX=clang++
+        export OMPI_CC=clang
+        export OMPI_CXX=clang++
+      ;;
+      *)
+      ;;
+    esac
+
+    cd ${GITHUB_WORKSPACE}/..
+
+    git clone https://gitlab.com/petsc/petsc.git -b v3.21.6 petsc
+    cd petsc
+    bash ${GITHUB_WORKSPACE}/../xolotl/scripts/build_petsc.sh \
+        --prefix=${GITHUB_WORKSPACE}/../install \
+        --skip-pull
+
+    cd ${GITHUB_WORKSPACE}/..
+    mkdir build
+    cd build
+
+    cmake -DCMAKE_PREFIX_PATH=${GITHUB_WORKSPACE}/../install ${GITHUB_WORKSPACE}
+
+    ;;
+
+  build)
+    cd ${GITHUB_WORKSPACE}/../build
+    make -j4
+    ;;
+
+  test)
+    cd ${GITHUB_WORKSPACE}/../build
+    ctest -VV --label-exclude xolotl.tests.system
+    ./test/system/SystemTester -- -t
+    ;;
+
+  *)
+    echo " Invalid step" "$1"
+    exit -1
+    ;;
+esac

xolotl/util/include/xolotl/util/StepSequence.h

@@ -1,5 +1,7 @@
 #pragma once
 
+#include <cstdint>
+
 #include <xolotl/util/IStepSequence.h>
 
 namespace xolotl