Merge pull request #901 from GMLC-TDC/master_merge

Master merge for HELICS 2.3 release

.ci/.drone.yml

@@ -21,13 +21,13 @@ steps:
   image: alpine
   commands:
   - apk update
-  - apk add --no-cache build-base git bash cmake ninja boost-dev zeromq-dev swig
+  - apk add --no-cache build-base git bash cmake ninja boost-dev zeromq-dev
   - gcc --version || echo "gcc not installed"
   - clang --version || echo "clang not installed"
   - cmake --version
   - git --version
   - mkdir build && cd build
-  - cmake -GNinja ..
+  - cmake -GNinja -DHELICS_BUILD_TESTS=ON -DHELICS_BUILD_EXAMPLES=ON ..
   - cmake --build .
   - ctest -L Continuous --output-on-failure
 
@@ -55,12 +55,12 @@ steps:
   image: alpine
   commands:
   - apk update
-  - apk add --no-cache build-base git bash cmake ninja boost-dev zeromq-dev swig
+  - apk add --no-cache build-base git bash cmake ninja boost-dev zeromq-dev
   - gcc --version || echo "gcc not installed"
   - clang --version || echo "clang not installed"
   - cmake --version
   - git --version
   - mkdir build && cd build
-  - cmake -GNinja ..
+  - cmake -GNinja -DHELICS_BUILD_TESTS=ON -DHELICS_BUILD_EXAMPLES=ON ..
   - cmake --build .
   - ctest -L Continuous --output-on-failure

.ci/Brewfile-minimal.travis

@@ -0,0 +1,3 @@
+brew "ccache"
+brew "cmake"
+brew "zeromq"

.ci/Brewfile.travis

@@ -1,6 +1,4 @@
-brew "pcre"
 brew "ccache"
 brew "cmake"
 brew "swig"
 brew "zeromq"
-brew "[email protected]"

.ci/azure-pipelines.yml

@@ -0,0 +1,112 @@
+jobs:
+- job: Windows
+  strategy:
+    matrix:
+      VS2015-64bit:
+        imageName: "vs2015-win2012r2"
+        langArch: "x64"
+        vsArch: "x64"
+      VS2017-32bit:
+        imageName: "vs2017-win2016"
+        langArch: "x86"
+        vsArch: "Win32"
+      VS2017-64bit:
+        imageName: "vs2017-win2016"
+        langArch: "x64"
+        vsArch: "x64"
+      VS2019-64bit:
+        imageName: "windows-2019"
+        langArch: "x64"
+        vsArch: "x64"
+  pool:
+    vmImage: $(imageName)
+
+  steps:
+  # -----------------------
+  # Install dependencies
+  # -----------------------
+  - powershell: |
+      Set-ExecutionPolicy Bypass -Scope Process -Force; iex ((New-Object System.Net.WebClient).DownloadString('https://chocolatey.org/install.ps1'))
+      echo "##vso[task.prependpath]C:\\ProgramData\\chocolatey\\bin"
+      choco install boost-msvc-14.1 cmake --yes --limit-output
+      echo "##vso[task.prependpath]C:\\Program Files\\CMake\\bin"
+    condition: eq( variables['imageName'], 'vs2015-win2012r2' )
+    displayName: Install chocolatey, boost, and newer cmake
+    
+  - bash: choco install swig --yes --limit-output
+    condition: eq( variables['Agent.OS'], 'Windows_NT' )
+    displayName: Install swig
+
+  - task: UsePythonVersion@0
+    inputs:
+      versionSpec: '3.4'
+      architecture: $(langArch)
+    condition: ne( variables['imageName'], 'vs2015-win2012r2' )
+
+  - bash: pip3 install pytest
+    condition: ne( variables['imageName'], 'vs2015-win2012r2' )
+    displayName: Install pytest
+
+  # -----------------------
+  # Configure HELICS
+  # -----------------------
+  - task: CMake@1
+    inputs:
+      cmakeArgs: -A $(vsArch) -DHELICS_ENABLE_SWIG=ON -DHELICS_BUILD_CXX_SHARED_LIB=ON -DHELICS_ENABLE_PACKAGE_BUILD=ON -DHELICS_BUILD_TESTS=ON -DHELICS_BUILD_EXAMPLES=ON ..
+    displayName: 'Configure HELICS'
+    condition: eq( variables['Agent.OS'], 'Windows_NT' )
+
+#  - task: CMake@1
+#    inputs:
+#      cmakeArgs: -DBUILD_PYTHON_INTERFACE=ON .
+#    displayName: 'Configure Python interface'
+#    condition: and(ne( variables['imageName'], 'vs2015-win2012r2' ), eq( variables['langArch'], 'x64' ))
+
+  - task: CMake@1
+    inputs:
+      cmakeArgs: -DBUILD_JAVA_INTERFACE=ON .
+    displayName: 'Configure Java interface'
+    condition: and(ne( variables['imageName'], 'vs2015-win2012r2' ), eq( variables['langArch'], 'x64' ))
+
+  # -----------------------
+  # Build HELICS
+  # -----------------------
+  - bash: cmake --build . --config Release
+    displayName: 'Build HELICS'
+    workingDirectory: build
+
+  # -----------------------
+  # Package HELICS
+  # -----------------------
+  - bash: |
+      cpack_dir="$(which cmake)"
+      cpack_dir="${cpack_dir%/cmake}"
+      "${cpack_dir}/cpack" -G "NSIS" -C Release -B "$PWD/installer-output"
+    displayName: 'Package HELICS'
+    workingDirectory: build
+    condition: ne( variables['imageName'], 'vs2015-win2012r2' )
+    
+  - task: CopyFiles@2
+    inputs:
+      sourceFolder: '$(Build.SourcesDirectory)/build/installer-output'
+      contents: '*.exe'
+      TargetFolder: '$(Build.ArtifactStagingDirectory)'
+    condition: ne( variables['imageName'], 'vs2015-win2012r2' )
+
+  - task: PublishBuildArtifacts@1
+    inputs:
+      pathtoPublish: '$(Build.ArtifactStagingDirectory)'
+      artifactName: installer
+    condition: ne( variables['imageName'], 'vs2015-win2012r2' )
+
+  # -----------------------
+  # Test HELICS
+  # -----------------------
+  - bash: ctest --output-on-failure --timeout 480 -C Release -L "Continuous"
+    displayName: 'Test HELICS'
+    workingDirectory: build
+
+  # Packaging tests
+  - bash: ctest --output-on-failure --timeout 480 -C Release -L "PackagingFast"
+    displayName: 'Test HELICS packaging'
+    workingDirectory: build

.circleci/asan_blacklist.txt

@@ -1 +1,2 @@
 src:*/libzmq/*
+src:*/badInputTests.cpp

.circleci/config.yml

@@ -35,51 +35,45 @@ jobs:
       - image: helics/octave:latest
     environment:
       OCTAVETEST: "/root/project/tests/octave"
-      CMAKE_FLAGS: "-DBUILD_OCTAVE_INTERFACE=ON"
+      CMAKE_FLAGS: "-DBUILD_OCTAVE_INTERFACE=ON -DHELICS_BUILD_TESTS=ON"
     steps:
       - checkout
-      - setup_remote_docker: 
-         docker_layer_caching: true   # Save time when caching
       - run: *setup_helics
       - run: *run_octave_tests
 
   helicsTSan:
     docker:
       - image: helics/clang-tsan:latest
     environment:
-      CMAKE_FLAGS: '-DCMAKE_CXX_COMPILER=clang++ -DCMAKE_C_COMPILER=clang -DCMAKE_CXX_FLAGS="-fsanitize=thread -stdlib=libc++ -L/root/develop/libcxx_tsan/lib -lc++abi -I/root/develop/libcxx_tsan/include -I/root/develop/libcxx_tsan/include/c++/v1 -Wno-unused-command-line-argument -g -O1 -Wl,-rpath=/root/develop/libcxx_tsan/lib"  -DBUILD_HELICS_BOOST_TESTS=OFF -DZMQ_SUBPROJECT=ON  -DZMQ_FORCE_SUBPROJECT=ON -DDISABLE_SYSTEM_CALL_TESTS=ON'
+      CMAKE_FLAGS: '-DCMAKE_CXX_COMPILER=clang++ -DCMAKE_C_COMPILER=clang -DCMAKE_CXX_FLAGS="-fsanitize=thread -stdlib=libc++ -L/root/develop/libcxx_tsan/lib -lc++abi -I/root/develop/libcxx_tsan/include -I/root/develop/libcxx_tsan/include/c++/v1 -Wno-unused-command-line-argument -g -O1 -Wl,-rpath=/root/develop/libcxx_tsan/lib"  -DHELICS_BUILD_TESTS=ON -DHELICS_ZMQ_SUBPROJECT=ON  -DHELICS_ZMQ_FORCE_SUBPROJECT=ON -DHELICS_DISABLE_SYSTEM_CALL_TESTS=ON'
+      TSAN_OPTIONS: 'second_deadlock_stack=1 suppressions=/root/project/.circleci/tsan_suppression.txt'
 
     steps:
       - checkout
-      - setup_remote_docker: 
-         docker_layer_caching: true   # Save time when caching
       - run: *setup_helics
       - run: *run_helics_tests
 
   helicsASan:
     docker:
-      - image: helics/clang-asan:latest
+      - image: helics/buildenv:sanitizers
     environment:
-      CMAKE_FLAGS: '-DCMAKE_CXX_COMPILER=clang++ -DCMAKE_C_COMPILER=clang -DCMAKE_CXX_FLAGS="-fsanitize=undefined,address -stdlib=libc++ -L/root/develop/libcxx_asan/lib -lc++abi -I/root/develop/libcxx_asan/include -I/root/develop/libcxx_asan/include/c++/v1 -Wno-unused-command-line-argument -fno-omit-frame-pointer -g -O1 -Wl,-rpath=/root/develop/libcxx_asan/lib -fsanitize-blacklist=/root/project/.circleci/asan_blacklist.txt"  -DBUILD_HELICS_BOOST_TESTS=OFF -DZMQ_SUBPROJECT=ON  -DZMQ_FORCE_SUBPROJECT=ON'
+      CMAKE_FLAGS: '-DCMAKE_CXX_COMPILER=clang++ -DCMAKE_C_COMPILER=clang -DCMAKE_CXX_FLAGS="-fsanitize=undefined,address -fsanitize-address-use-after-scope -stdlib=libc++ -L/root/develop/libcxx_asan/lib -lc++abi -I/root/develop/libcxx_asan/include -I/root/develop/libcxx_asan/include/c++/v1 -Wno-unused-command-line-argument -fno-omit-frame-pointer -g -O1 -Wl,-rpath=/root/develop/libcxx_asan/lib -fsanitize-blacklist=/root/project/.circleci/asan_blacklist.txt"  -DHELICS_BUILD_TESTS=ON -DHELICS_ZMQ_SUBPROJECT=ON  -DHELICS_ZMQ_FORCE_SUBPROJECT=ON'
       LSAN_OPTIONS: 'suppressions=/root/project/.circleci/leak_suppression.txt'
+      UBSAN_OPTIONS: 'print_stacktrace=1'
 
     steps:
       - checkout
-      - setup_remote_docker: 
-         docker_layer_caching: true   # Save time when caching
       - run: *setup_helics
       - run: *run_helics_tests
 
   helicsMSan:
     docker:
-      - image: helics/clang-msan:latest
+      - image: helics/buildenv:sanitizers
     environment:
-      CMAKE_FLAGS: '-DCMAKE_CXX_COMPILER=clang++ -DCMAKE_C_COMPILER=clang -DCMAKE_CXX_FLAGS="-fsanitize=memory -stdlib=libc++ -L/root/develop/libcxx_msan/lib -lc++abi -I/root/develop/libcxx_msan/include -I/root/develop/libcxx_msan/include/c++/v1 -Wno-unused-command-line-argument -fno-omit-frame-pointer -g -O1 -Wl,-rpath=/root/develop/libcxx_msan/lib"  -DBUILD_HELICS_BOOST_TESTS=OFF -DZMQ_SUBPROJECT=ON  -DZMQ_FORCE_SUBPROJECT=ON'
+      CMAKE_FLAGS: '-DCMAKE_CXX_COMPILER=clang++ -DCMAKE_C_COMPILER=clang -DCMAKE_CXX_FLAGS="-fsanitize=memory -stdlib=libc++ -L/root/develop/libcxx_msan/lib -lc++abi -I/root/develop/libcxx_msan/include -I/root/develop/libcxx_msan/include/c++/v1 -Wno-unused-command-line-argument -fno-omit-frame-pointer -g -O1 -Wl,-rpath=/root/develop/libcxx_msan/lib"  -DHELICS_BUILD_TESTS=ON -DHELICS_ZMQ_SUBPROJECT=ON  -DHELICS_ZMQ_FORCE_SUBPROJECT=ON'
 
     steps:
       - checkout
-      - setup_remote_docker: 
-         docker_layer_caching: true   # Save time when caching
       - run: *setup_helics
       - run: *run_helics_tests
 

.circleci/tsan_suppression.txt

@@ -0,0 +1,2 @@
+# This is a known purposeful leak and possible resulting race condition detection on closing of shared libraries
+

.clang-format

@@ -12,6 +12,7 @@ BreakBeforeBinaryOperators: false
 BreakBeforeBraces: Allman
 BreakBeforeTernaryOperators: false
 BreakConstructorInitializersBeforeComma: false
+IndentPPDirectives: AfterHash
 ColumnLimit: 115
 CommentPragmas: ''
 KeepEmptyLinesAtTheStartOfBlocks: false

.cmake-format.json

@@ -1,11 +1,11 @@
 {
-  "line_width": 80,
+  "line_width": 88,
   "dangle_parens": true,
   "command_case": "lower",
   "separate_fn_name_with_space": false,
   "always_wrap": [],
   "separate_ctrl_name_with_space": false,
-  "max_subargs_per_line": 3,
+  "max_subargs_per_line": 4,
   "tab_size": 4,
   "keyword_case": "upper",
   "enum_char": ".",

.github/actions/create-file-update-pr/Dockerfile

@@ -0,0 +1,12 @@
+FROM alpine:latest
+
+RUN apk add --no-cache \
+    bash \
+    jq \
+    git \
+    ca-certificates \
+    curl
+
+COPY entrypoint.sh /entrypoint.sh
+
+ENTRYPOINT ["/entrypoint.sh"]

.github/actions/create-file-update-pr/action.yml

@@ -0,0 +1,5 @@
+name: 'Create File Update PR'
+description: 'Pushes a new branch with changed files and opens a PR for updating the changed files in the base branch'
+runs:
+  using: 'docker'
+  image: 'Dockerfile'

.github/actions/create-file-update-pr/entrypoint.sh

@@ -0,0 +1,46 @@
+#!/bin/bash
+
+PR_URL=$(jq --raw-output .repository.pulls_url "$GITHUB_EVENT_PATH")
+PR_URL=${PR_URL%\{*}
+API_VERSION=v3
+API_HEADER="Accept: application/vnd.github.${API_VERSION}+json; application/vnd.github.shadow-cat-preview+json; application/vnd.github.symmetra-preview+json; application/vnd.github.sailor-v-preview+json"
+AUTH_HEADER="Authorization: token ${GITHUB_TOKEN}"
+
+# Only commit and open a PR if files have changed
+files_changed=$(git diff --staged --name-only)
+if [[ "$files_changed" != "" ]];
+then
+  hash=$(sha256sum ${files_changed} | sha256sum | cut -c 1-12 -)
+  current_branch=${GITHUB_REF#refs/heads/}
+
+  # Set the git origin url for committing using a GITHUB_TOKEN
+  git remote set-url origin "https://x-access-token:${GITHUB_TOKEN}@github.com/${GITHUB_REPOSITORY}"
+  git config user.name "${INPUT_GIT_NAME}"
+  git config user.email "${INPUT_GIT_EMAIL}"
+
+  # Make sure a branch with the same name (hash + base branch) doesn't already exist
+  pr_branch="${INPUT_BRANCH_PREFIX}update-${current_branch}-${hash}"
+  git ls-remote --exit-code . "origin/${pr_branch}"
+  rv=$?
+  if [[ "$rv" != "0" ]];
+  then
+    # Commit the changed files and push the branch to GitHub
+    git checkout -b "${pr_branch}"
+    git commit -m "${INPUT_COMMIT_MSG}"
+    git push -u origin "${pr_branch}"
+
+    # Format string values for GitHub API JSON payload
+    PR_TITLE="$(echo -n "${INPUT_PR_TITLE}" | jq --raw-input --slurp ".")"
+    PR_BODY="$(echo -n "${INPUT_PR_BODY}" | jq --raw-input --slurp ".")"
+    PR_BASE="$(echo -n "${current_branch}" | jq --raw-input --slurp ".")"
+    PR_HEAD="$(echo -n "${pr_branch}" | jq --raw-input --slurp ".")"
+    pr_api_data="{\"title\":${PR_TITLE}, \"body\":${PR_BODY}, \"base\":${PR_BASE}, \"head\":${PR_HEAD}, \"draft\":false}"
+
+    # Open up the GitHub PR
+    curl -XPOST -fsSL \
+         -H "${AUTH_HEADER}" \
+         -H "${API_HEADER}" \
+         --data "${pr_api_data}" \
+         "${PR_URL}"
+  fi
+fi

.github/workflows/interface_gen_script.sh

@@ -0,0 +1,16 @@
+#!/usr/bin/sh
+
+# Generate Matlab interface using swig matlab
+mkdir build_matlab
+pushd build_matlab
+cmake -DBUILD_MATLAB_INTERFACE=ON -DHELICS_SWIG_GENERATE_INTERFACE_FILES_ONLY=ON -DHELICS_OVERWRITE_INTERFACE_FILES=ON -DHELICS_BUILD_EXAMPLES=OFF -DENABLE_ZMQ_CORE=OFF -DHELICS_BUILD_TESTS=OFF -DHELICS_BUILD_APP_EXECUTABLES=OFF -DHELICS_DISABLE_BOOST=ON -DHELICS_ENABLE_SWIG=ON -DSWIG_EXECUTABLE=/root/swig-matlab/bin/swig ..
+make -j2 mfile_overwrite
+popd
+
+# Generate Python and Java interfaces
+mkdir build_interface
+pushd build_interface
+cmake -DBUILD_PYTHON_INTERFACE=ON -DBUILD_JAVA_INTERFACE=ON -DHELICS_SWIG_GENERATE_INTERFACE_FILES_ONLY=ON -DHELICS_OVERWRITE_INTERFACE_FILES=ON -DHELICS_BUILD_EXAMPLES=OFF -DENABLE_ZMQ_CORE=OFF -DHELICS_BUILD_TESTS=OFF -DHELICS_BUILD_APP_EXECUTABLES=OFF -DHELICS_DISABLE_BOOST=ON -DHELICS_ENABLE_SWIG=ON ..
+make -j2 pyfile_overwrite
+make -j2 javafile_overwrite
+popd