Kamping integration

.clang-format

@@ -0,0 +1 @@
+BasedOnStyle: Google

.clangd

@@ -0,0 +1,3 @@
+CompileFlags:
+  Add: [-std=c++17]
+  Remove: [-Wgnu-zero-variadic-macro-arguments, -Wterminate]

.devcontainer/Dockerfile

@@ -0,0 +1,39 @@
+# See here for image contents: https://github.com/microsoft/vscode-dev-containers/tree/v0.187.0/containers/cpp/.devcontainer/base.Dockerfile
+
+# [Choice] Debian / Ubuntu version: debian-10, debian-9, ubuntu-20.04, ubuntu-18.04
+ARG VARIANT="buster"
+FROM mcr.microsoft.com/vscode/devcontainers/cpp:0-${VARIANT}
+
+RUN apt-get update \
+ && export DEBIAN_FRONTEND=noninteractive \
+ && apt-get -y install --no-install-recommends \
+      bison \
+      cmake \
+      flex \
+      libgmp3-dev \
+      libgtest-dev \
+      libopenmpi-dev \
+      ninja-build \
+      openmpi-bin \
+      openmpi-common \
+      python3-dev \
+      python3-pip \
+      python3-pip \
+      python3-setuptools \
+      vim \
+ && apt-get clean \
+ && rm -rf /var/lib/apt/lists/*
+
+RUN pip install \
+    beautifulsoup4 \
+    cmake \
+    lxml
+
+RUN git clone https://github.com/jeetsukumaran/DendroPy.git \
+ && cd DendroPy \
+ && python3 setup.py install \
+ && cd .. \
+ && rm -rf DendroPy
+
+RUN useradd --uid 1026 -m user
+USER user

.devcontainer/devcontainer.json

@@ -0,0 +1,30 @@
+// For format details, see https://aka.ms/devcontainer.json. For config options, see the README at:
+// https://github.com/microsoft/vscode-dev-containers/tree/v0.187.0/containers/cpp
+{
+	"name": "C++",
+	"build": {
+		"dockerfile": "Dockerfile",
+		// Update 'VARIANT' to pick an Debian / Ubuntu OS version: debian-10, debian-9, ubuntu-20.04, ubuntu-18.04
+		"args": { "VARIANT": "ubuntu-20.04" }
+	},
+	"runArgs": [ "--cap-add=SYS_PTRACE", "--security-opt", "seccomp=unconfined"],
+
+	// Set *default* container specific settings.json values on container create.
+	"settings": {},
+
+	// Add the IDs of extensions you want installed when the container is created.
+	"extensions": [
+		"ms-vscode.cpptools",
+		"twxs.cmake",
+		"ms-vscode.cmake-tools"
+	],
+
+	// 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": []
+
+	// Comment out connect as root instead. More info: https://aka.ms/vscode-remote/containers/non-root.
+	"remoteUser": "user"
+}

.gitignore

@@ -39,3 +39,11 @@ release/
 .cproject
 .project
 .settings/
+
+# CMake output files
+compile_commands.json
+
+# Other files
+run/
+.cache/
+.vscode/

.gitmodules

@@ -4,3 +4,6 @@
 [submodule "libs/terraphast"]
 	path = libs/terraphast
 	url = https://github.com/amkozlov/terraphast-one
+[submodule "libs/kamping"]
+	path = libs/kamping
+	url = [email protected]:kamping-site/kamping.git

CMakeLists.txt

@@ -35,13 +35,13 @@ else()
   set(ENABLE_GMP OFF)
 endif()
 
-#set(CMAKE_CXX_STANDARD 14)
-#set(CMAKE_CXX_EXTENSIONS OFF)
+set(CMAKE_CXX_STANDARD 17)
+set(CMAKE_CXX_EXTENSIONS OFF)
 
 # set these flags globally for all subprojects (libpll etc.)
-set (CMAKE_CXX_FLAGS_DEBUG    "-O3 -g" CACHE INTERNAL "")
+set (CMAKE_CXX_FLAGS_DEBUG    "-Og -g" CACHE INTERNAL "")
 set (CMAKE_CXX_FLAGS_RELEASE  "-O3"    CACHE INTERNAL "")
-set (CMAKE_C_FLAGS_DEBUG    "-O3 -g" CACHE INTERNAL "")
+set (CMAKE_C_FLAGS_DEBUG    "-Og -g" CACHE INTERNAL "")
 set (CMAKE_C_FLAGS_RELEASE  "-O3"    CACHE INTERNAL "")
 
 project (raxml-ng C CXX)
@@ -70,8 +70,8 @@ if (CMAKE_CXX_COMPILER_VERSION VERSION_LESS RAXML_COMPILER_TARGET_VERSION)
 endif()
 
 
-set (raxml-ng_VERSION_MAJOR 0)
-set (raxml-ng_VERSION_MINOR 8)
+set (raxml-ng_VERSION_MAJOR 1)
+set (raxml-ng_VERSION_MINOR 1)
 
 #set (CMAKE_BUILD_TYPE DEBUG)
 #set (CMAKE_BUILD_TYPE RELEASE)
@@ -84,7 +84,7 @@ endif()
 message (STATUS "Building ${CMAKE_BUILD_TYPE}")
 
 set (WARN_FLAGS               "-Wall -Wextra")
-set (CMAKE_CXX_FLAGS          "-std=c++11 ${WARN_FLAGS}")
+set (CMAKE_CXX_FLAGS          "${WARN_FLAGS}")
 
 if (ENABLE_GMP)
 #find_package(GMP REQUIRED)

Jenkinsfile

@@ -0,0 +1,184 @@
+#!groovy
+
+pipeline {
+
+    agent {
+        label 'cme-eastwatch'
+    }
+
+    options {
+        timeout(time: 1, unit: 'HOURS')
+    }
+
+    parameters {
+        string(name: 'BUILD_DIR_CLANG', defaultValue: 'build-clang-12')
+        string(name: 'BUILD_DIR_GCC', defaultValue: 'build-gcc-11')
+        string(name: 'BUILD_DIR_GCC_OPENMPI', defaultValue: 'build-gcc-11-openmpi')
+    }
+
+    stages {
+        stage('Submodules') {
+            agent {
+                dockerfile {
+                    reuseNode true
+                    filename 'dockerfile-clang-12'
+                    dir 'ci'
+                }
+            }
+            steps {
+                sh '''
+                    git submodule update --init --recursive
+                    git submodule add https://github.com/amkozlov/ngtest.git
+                '''
+            }
+        }
+        stage('Build') {
+            parallel {
+                stage('clang-12') {
+                    agent {
+                        dockerfile {
+                            reuseNode true
+                            filename 'dockerfile-clang-12'
+                            dir 'ci'
+                        }
+                    }
+                    steps {
+                        sh """
+                            rm -fr ${params.BUILD_DIR_CLANG} && mkdir -p ${params.BUILD_DIR_CLANG} && cd ${params.BUILD_DIR_CLANG}
+                            cmake -DCMAKE_BUILD_TYPE=Release .. 2>&1 |tee cmake.out
+                            make 2>&1 |tee make.out
+                        """
+                    }
+                    post {
+                        always {
+                            recordIssues enabledForFailure: true, aggregatingResults: false,
+                                tool: clang(id: 'clang-12', pattern: "${params.BUILD_DIR_CLANG}/make.out")
+                        }
+                    }
+                }
+                stage('gcc-11') {
+                    agent {
+                        dockerfile {
+                            reuseNode true
+                            filename 'dockerfile-gcc-11'
+                            dir 'ci'
+                        }
+                    }
+                    steps {
+                        sh """
+                            rm -fr ${params.BUILD_DIR_GCC} && mkdir -p ${params.BUILD_DIR_GCC} && cd ${params.BUILD_DIR_GCC}
+                            cmake -DCMAKE_BUILD_TYPE=Release .. 2>&1 |tee cmake.out
+                            make 2>&1 |tee make.out
+                        """
+                    }
+                    post {
+                        always {
+                            recordIssues enabledForFailure: true, aggregatingResults: false,
+                                tool: clang(id: 'gcc-11', pattern: "${params.BUILD_DIR_GCC}/make.out")
+                        }
+                    }
+                }
+                stage('gcc-11-openmpi') {
+                    agent {
+                        dockerfile {
+                            reuseNode true
+                            filename 'dockerfile-gcc-11'
+                            dir 'ci'
+                        }
+                    }
+                    steps {
+                        sh """
+                            rm -fr ${params.BUILD_DIR_GCC_OPENMPI} && mkdir -p ${params.BUILD_DIR_GCC_OPENMPI} && cd ${params.BUILD_DIR_GCC_OPENMPI}
+                            cmake -DCMAKE_BUILD_TYPE=Release -DUSE_MPI=ON .. 2>&1 |tee cmake.out
+                            make 2>&1 |tee make.out
+                        """
+                    }
+                    post {
+                        always {
+                            recordIssues enabledForFailure: true, aggregatingResults: false,
+                                tool: clang(id: "${STAGE_NAME}", pattern: "${params.BUILD_DIR_GCC_OPENMPI}/make.out")
+                        }
+                    }
+                }
+            }
+        }
+        stage('Unit tests') {
+            parallel {
+                stage('clang-12') {
+                    agent {
+                        dockerfile {
+                            reuseNode true
+                            filename 'dockerfile-clang-12'
+                            dir 'ci'
+                        }
+                    }
+                    steps {
+                        sh "cd ${params.BUILD_DIR_CLANG} && make test"
+                    }
+                    post {
+                        always {
+                            step([
+                                $class: 'XUnitPublisher',
+                                thresholds: [[$class: 'FailedThreshold', unstableThreshold: '1']],
+                                tools: [[$class: 'GoogleTestType', pattern: "${params.BUILD_DIR_CLANG}/test/*.xml"]]
+                            ])
+                        }
+                    }
+                }
+                stage('gcc-11') {
+                    agent {
+                        dockerfile {
+                            reuseNode true
+                            filename 'dockerfile-gcc-11'
+                            dir 'ci'
+                        }
+                    }
+                    steps {
+                        sh "cd ${params.BUILD_DIR_GCC} && make test"
+                    }
+                    post {
+                        always {
+                            step([
+                                $class: 'XUnitPublisher',
+                                thresholds: [[$class: 'FailedThreshold', unstableThreshold: '1']],
+                                tools: [[$class: 'GoogleTestType', pattern: "${params.BUILD_DIR_GCC}/test/*.xml"]]
+                            ])
+                        }
+                    }
+                }
+            }
+        }
+        stage('Regression tests') {
+            agent {
+                dockerfile {
+                    reuseNode true
+                    filename 'dockerfile-clang-12'
+                    dir 'ci'
+                }
+            }
+            steps {
+                sh """
+                    ngtest/runtest.py ${params.BUILD_DIR_CLANG}/bin/raxml-ng
+                    cd ci && ./generate_html.py ../ngtest/out/1.1.0-master/T1W1
+                """
+            }
+            post {
+                always {
+                    publishHTML(target : [
+                    allowMissing: false,
+                    alwaysLinkToLastBuild: true,
+                    keepAll: true,
+                    reportDir: 'ci',
+                    reportFiles: 'benchmark.html',
+                    reportName: 'Benchmark',
+                    reportTitles: 'Benchmark'])
+                }
+            }
+        }
+    }
+    post {
+        failure {
+            mail to: '[email protected]', subject: "FAILURE: ${currentBuild.fullDisplayName}", body: "Failed."
+        }
+    }
+}