2023 maintenance update

.github/workflows/build_test.yml

@@ -1,50 +1,48 @@
-name: Standard Build and Test
+name: Build & Test PR
 
 on:
   # allows us to run workflows manually
   workflow_dispatch:
-  pull_request:
-    branches:
-      - master
-    paths-ignore:
-      - '.github/workflows/docker_publish.yml'
-
   push:
-    branches:
-      - master
+  pull_request:
     paths-ignore:
+      - 'docker/Dockerfile'
       - '.github/workflows/docker_publish.yml'
 
-
 jobs:
-  BuildTest:
-    runs-on: ubuntu-latest 
+  build-dependency-and-test-img:
+    runs-on: ubuntu-latest
+
+    strategy:
+      matrix:
+        ubuntu_versions : [
+          22.04,
+          ]
+        pkg_mgr : [
+          apt,
+          conda,
+        ]
 
-    container:
-      image: cyclus/cyclus-deps
-
+    name: Installing Dependencies, Building cyclus and running tests
     steps:
-      - name: Checkout repository
-        uses: actions/checkout@v2
+      - name: Log in to the Container registry
+        uses: docker/login-action@v2
+        with:
+          registry: ghcr.io
+          username: ${{ github.repository_owner }}
+          password: ${{ secrets.GITHUB_TOKEN }}
 
-      - name: setup
-        run: |
-          echo "HOME=/github/home/" >> $GITHUB_ENV
-          echo "PATH=$PATH:${HOME}/.local/bin" >> $GITHUB_ENV
-          echo "LD_LIBRARY_PATH=$LD_LIBRARY_PATH:${HOME}/.local/lib" >> $GITHUB_ENV
-      - name: Building Cyclus
-        run: |
-          mkdir -p ${HOME}/.local/lib/python3.7/site-packages/
-          cd ${GITHUB_WORKSPACE}
-          python install.py -j 2 \
-                            --build-type=Release --core-version 999999.999999 \
-                            -DBLAS_LIBRARIES="/opt/conda/lib/libblas.so" \
-                            -DLAPACK_LIBRARIES="/opt/conda/lib/liblapack.so"
+      - name: Checkout repository
+        uses: actions/checkout@v3
 
-      - name: Unit Test
-        run: |
-          cyclus_unit_tests; exit $?
-
-      - name: Nosetest
-        run: |
-          nosetests -w ${GITHUB_WORKSPACE}/tests; exit $?
+      - name: Installing Dependencies in Docker image
+        uses: firehed/multistage-docker-build-action@v1
+        with:
+          repository: ghcr.io/${{ github.repository_owner }}/cyclus_${{ matrix.ubuntu_versions }}_${{ matrix.pkg_mgr }}
+          stages: ${{ matrix.pkg_mgr }}-deps, cyclus
+          server-stage: cyclus-test
+          quiet: false
+          parallel: true
+          tag-latest-on-default: false
+          dockerfile: docker/Dockerfile
+          build-args: pkg_mgr=${{ matrix.pkg_mgr }}

.github/workflows/changelog_test.yml

@@ -10,7 +10,6 @@ env:
 
 jobs:
   changelog_update:
-    if: ${{ github.event_name == 'pull_request' }}
     runs-on: ubuntu-latest
     container:
       image: alpine:3.14
@@ -23,10 +22,17 @@ jobs:
           git --version
 
       - name: Checkout repository
-        uses: actions/checkout@v2
-    
-      - name: Housekeeping
-        run: |
+        uses: actions/checkout@v3
+
+      - run: |
+          git config --global --add safe.directory ${GITHUB_WORKSPACE}
           cd $GITHUB_WORKSPACE
-          housekeeping_script/changelog_test.sh
+          git remote add cyclus https://github.com/cyclus/cyclus.git
+          git fetch cyclus
+          change=`git diff cyclus/master -- CHANGELOG.rst | wc -l`
+          git remote remove cyclus
+          if [ $change -eq 0 ]; then 
+            echo "CHANGELOG.rst has not been updated"
+            exit 1 
+          fi
 

.github/workflows/docker_publish.yml

@@ -0,0 +1,100 @@
+name: Build & Publish docker image for CI
+
+on:
+  # allows us to run workflows manually
+  workflow_dispatch:
+  push:
+    paths:
+      - 'docker/Dockerfile'
+      - '.github/workflows/docker_publish.yml'
+
+jobs:
+  build-dependency-and-test-img:
+    runs-on: ubuntu-latest
+
+    strategy:
+      matrix:
+        ubuntu_versions : [
+          22.04,
+          ]
+        pkg_mgr : [
+          apt,
+          conda,
+        ]
+
+    name: Installing Dependencies, Building cyclus and running tests
+    steps:
+      - name: default environment
+        run: |
+          echo "tag-latest-on-default=false" >> "$GITHUB_ENV"
+
+      - name: condition on trigger parameters
+        if: ${{ github.repository_owner == 'svalinn' && github.ref == 'refs/heads/develop' }}
+        run: |
+          echo "tag-latest-on-default=true" >> "$GITHUB_ENV"
+
+      - name: Log in to the Container registry
+        uses: docker/login-action@v2
+        with:
+          registry: ghcr.io
+          username: ${{ github.repository_owner }}
+          password: ${{ secrets.GITHUB_TOKEN }}
+
+      - name: Checkout repository
+        uses: actions/checkout@v3
+
+      - name: Installing Dependencies in Docker image
+        uses: firehed/multistage-docker-build-action@v1
+        with:
+          repository: ghcr.io/${{ github.repository_owner }}/cyclus_${{ matrix.ubuntu_versions }}_${{ matrix.pkg_mgr }}
+          stages: ${{ matrix.pkg_mgr }}-deps, cyclus
+          server-stage: cyclus-test
+          quiet: false
+          parallel: true
+          tag-latest-on-default: ${{ env.tag-latest-on-default }}
+          dockerfile: docker/Dockerfile
+          build-args: pkg_mgr=${{ matrix.pkg_mgr }}
+
+
+  push_stable_ci_img:
+    needs: [build-dependency-and-test-img]
+    runs-on: ubuntu-latest
+
+    strategy:
+      matrix:
+        ubuntu_versions : [
+          22.04,
+          ]
+        pkg_mgr : [
+          apt,
+          conda,
+          ]
+
+    name: Pushing final images
+    steps:       
+      - name: Log in to the Container registry
+        if: ${{ github.repository_owner == 'cyclus' }}
+        uses: docker/login-action@v2
+        with:
+          registry: ghcr.io
+          username: ${{ github.repository_owner }}
+          password: ${{ secrets.GITHUB_TOKEN }}
+
+      - name: Store image name
+        if: ${{ github.repository_owner == 'cyclus' }}
+        run: |
+          echo "image_base_tag=ghcr.io/${{ github.repository_owner }}/cyclus_${{ matrix.ubuntu_versions }}_${{ matrix.pkg_mgr }}" >> "$GITHUB_ENV"
+
+      - name: Push Image as latest img
+        if: ${{ github.repository_owner == 'cyclus' && github.ref == 'refs/heads/develop' }}
+        uses: akhilerm/tag-push-action@v2.1.0
+        with:
+          src: ${{ env.image_base_tag }}/cyclus:latest
+          dst: ${{ env.image_base_tag }}:latest
+
+      - name: Push Image as latest img
+        if: ${{ github.repository_owner == 'cyclus' && github.ref == 'refs/heads/develop' }}
+        uses: akhilerm/tag-push-action@v2.1.0
+        with:
+          src: ${{ env.image_base_tag }}:latest
+          dst: ${{ env.image_base_tag }}:stable

CHANGELOG.rst

@@ -22,7 +22,8 @@ Since last release
 **Changed:**
 
 * Moved to unified CHANGELOG Entry and check them with GithubAction (#1571)
-
+* Major update and modernization of build (#1587)
+* Changed Json formatting for compatibility with current python standards (#1587)
 
 **Removed:**
 

CMakeLists.txt

@@ -1,4 +1,4 @@
-CMAKE_MINIMUM_REQUIRED(VERSION 2.8)
+CMAKE_MINIMUM_REQUIRED(VERSION 3.16)
 #taken from http://geant4.cern.ch/support/source/geant4/CMakeLists.txt
 IF(${CMAKE_SOURCE_DIR} STREQUAL ${CMAKE_BINARY_DIR})
     message(STATUS "Cyclus requires an out-of-source build.")
@@ -10,20 +10,16 @@ IF(${CMAKE_SOURCE_DIR} STREQUAL ${CMAKE_BINARY_DIR})
     message(FATAL_ERROR "in-source build detected")
 ENDIF()
 
-# Set some policies
-cmake_policy(SET CMP0040 OLD)
-cmake_policy(SET CMP0042 OLD)
-
 # This project name is cyclus.
 PROJECT(CYCLUS)
 
 # check for and enable c++11 support (required for cyclus)
 INCLUDE(CheckCXXCompilerFlag)
-CHECK_CXX_COMPILER_FLAG("-std=c++11" COMPILER_SUPPORTS_CXX11)
+CHECK_CXX_COMPILER_FLAG("-std=c++14" COMPILER_SUPPORTS_CXX14)
 IF(COMPILER_SUPPORTS_CXX11)
-    SET(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -std=c++11")
+    SET(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -std=c++14")
 ELSE()
-    MESSAGE(STATUS "The compiler ${CMAKE_CXX_COMPILER} has no C++11 support. Please use a different C++ compiler.")
+    MESSAGE(STATUS "The compiler ${CMAKE_CXX_COMPILER} has no C++14 support. Please use a different C++ compiler.")
 ENDIF()
 
 # enable assembly
@@ -108,8 +104,10 @@ IF(NOT CYCLUS_DOC_ONLY)
     endif()
 
     # Tell CMake where the modules are
-    LIST(APPEND CMAKE_MODULE_PATH
-        "${CMAKE_DIR}/share/cmake-2.8/Modules" "${PROJECT_SOURCE_DIR}/cmake")
+    MESSAGE("-- CMAKE_MODULE_PATH: ${CMAKE_MODULE_PATH}")
+    LIST(APPEND CMAKE_MODULE_PATH ${CMAKE_MODULE_PATH}
+ #       "/opt/conda/share/cmake-3.25/Modules" 
+        "${PROJECT_SOURCE_DIR}/cmake")
 
     # Include macros
     INCLUDE(CopyWhenDiffMacro)
@@ -162,24 +160,29 @@ IF(NOT CYCLUS_DOC_ONLY)
     MESSAGE("-- Dependency Binary Hints (DEPS_BIN_HINTS): ${DEPS_BIN_HINTS}")
     MESSAGE("-- Dependency Library Hints (DEPS_LIB_HINTS): ${DEPS_LIB_HINTS}")
     MESSAGE("-- Dependency Include Hints (DEPS_INCLUDE_HINTS): ${DEPS_INCLUDE_HINTS}")
+    MESSAGE("CMAKE_MODULE_PATH: ${CMAKE_MODULE_PATH}")
+
+    # Search pkg-config utility first
+    find_package(PkgConfig REQUIRED)
+
 
     # Debian installs useful LibXML2 files to /usr/include/libxml2/libxml
     # libxml2 is required for relaxng schema validation
-    FIND_PACKAGE(LibXml2 ${DEPS_HINTS})
-    IF(NOT LIBXML2_LIBRARIES)
-        FIND_LIBRARY(LibXml2 REQUIRED ${DEPS_HINTS})
-    ENDIF()
+
+    FIND_PACKAGE(LibXml2 REQUIRED)
     ADD_DEFINITIONS(${LIBXML2_DEFINITIONS})
     SET(LIBS ${LIBS} ${LIBXML2_LIBRARIES})
-
-    # Find LibXML++ and dependencies
-    FIND_PACKAGE(LibXML++)
-    IF(NOT LibXML++_LIBRARIES)
-        FIND_LIBRARY(LibXML++ REQUIRED ${DEPS_HINTS})
-    ENDIF()
-    SET(LIBS ${LIBS} ${LibXML++_LIBRARIES})
-    message("-- LibXML++ Include Dir: ${LibXML++_INCLUDE_DIR}")
-
+    message("-- LibXML2 Include Dir: ${LIBXML2_INCLUDE_DIR}")
+
+    # Then use pkg-config for locate specific package
+    pkg_check_modules(LIBXMLXX IMPORTED_TARGET libxml++-4.0)
+    IF ( NOT LIBXMLXX_LIBRARIES )
+       pkg_check_modules(LIBXMLXX REQUIRED IMPORTED_TARGET libxml++-2.6)
+    ENDIF ( NOT LIBXMLXX_LIBRARIES )
+    SET(LIBS ${LIBS} ${LIBXMLXX_LIBRARIES})
+    message("-- LibXML++ Include Dir: ${LIBXMLXX_INCLUDE_DIRS}")
+    message("-- LibXML++ Librarires: ${LIBXMLXX_LIBRARIES}")
+
     # find lapack and link to it
     FIND_PACKAGE(LAPACK REQUIRED)
     set(LIBS ${LIBS} ${LAPACK_LIBRARIES})
@@ -188,8 +191,9 @@ IF(NOT CYCLUS_DOC_ONLY)
     MESSAGE("-- Found BLAS Libraries: ${BLAS_LIBRARIES}")
 
     # Find Sqlite3
-    FIND_PACKAGE(Sqlite3 REQUIRED)
-    SET(LIBS ${LIBS} ${SQLITE3_LIBRARIES})
+    FIND_PACKAGE(SQLite3 REQUIRED)
+    SET(LIBS ${LIBS} ${SQLite3_LIBRARIES})
+    MESSAGE("-- Found SQLite3 Libraries: ${SQLite3_LIBRARIES}")
 
     # Find HDF5
     FIND_PACKAGE(HDF5 REQUIRED COMPONENTS HL)
@@ -300,8 +304,8 @@ IF(NOT CYCLUS_DOC_ONLY)
     # Cython & Python Bindings
     #
     # Use new Python library finder
-    find_package(PythonInterp)
-    find_package(PythonLibs)
+    find_package (Python3 COMPONENTS Interpreter Development NumPy)
+
     execute_process(COMMAND "${PYTHON_EXECUTABLE}" -c
                             "import site; print(site.getsitepackages(['${CMAKE_INSTALL_PREFIX}'])[0])"
                     OUTPUT_VARIABLE PYTHON_SITE_PACKAGES
@@ -321,7 +325,6 @@ IF(NOT CYCLUS_DOC_ONLY)
         endif()
         include(UseCython)
 
-        find_package(Numpy REQUIRED)
         find_package(Jinja2 REQUIRED)
         find_package(Pandas REQUIRED)
 
@@ -362,10 +365,10 @@ IF(NOT CYCLUS_DOC_ONLY)
     # ${Glibmm_INCLUDE_DIRS} breaks Ubuntu 12.04
     set(inc_dirs
         "${LIBXML2_INCLUDE_DIR}"
-        "${LibXML++_INCLUDE_DIR}"
+        "${LIBXMLXX_INCLUDE_DIRS}"
         "${Glibmm_INCLUDE_DIRS}"
-        "${LibXML++Config_INCLUDE_DIR}"
-        "${SQLITE3_INCLUDE_DIR}"
+        "${LIBXMLXXConfig_INCLUDE_DIR}"
+        "${SQLite3_INCLUDE_DIR}"
         "${HDF5_INCLUDE_DIRS}"
         "${Boost_INCLUDE_DIR}"
         "${COIN_INCLUDE_DIRS}")
@@ -376,8 +379,7 @@ IF(NOT CYCLUS_DOC_ONLY)
 
 
     if(Cython_FOUND)
-        INCLUDE_DIRECTORIES(AFTER "${PYTHON_INCLUDE_DIRS}"
-            "${NUMPY_INCLUDE_DIRS}")
+        INCLUDE_DIRECTORIES(AFTER "${PYTHON_INCLUDE_DIRS}" "${_Python3_NumPy_INCLUDE_DIR}")
     endif(Cython_FOUND)
     # set core version, one way or the other
     IF(NOT "${CORE_VERSION}" STREQUAL "")
@@ -403,7 +405,7 @@ IF(NOT CYCLUS_DOC_ONLY)
     if(Cython_FOUND)
         ADD_SUBDIRECTORY("${CYCLUS_PYSOURCE_DIR}")
     endif(Cython_FOUND)
-
+    
     ##############################################################################################
     ####################################### end includes #########################################
     ##############################################################################################
@@ -489,7 +491,7 @@ IF(NOT CYCLUS_DOC_ONLY)
     SET(CPACK_DEBIAN_PACKAGE_DEPENDS "${CPACK_DEBIAN_PACKAGE_DEPENDS}, libboost-program-options-dev (>= 1.54.0)")
     SET(CPACK_DEBIAN_PACKAGE_DEPENDS "${CPACK_DEBIAN_PACKAGE_DEPENDS}, libboost-serialization-dev (>= 1.54.0)")
     SET(CPACK_DEBIAN_PACKAGE_DEPENDS "${CPACK_DEBIAN_PACKAGE_DEPENDS}, libhdf5-dev (>= 1.8.11)")
-    SET(CPACK_DEBIAN_PACKAGE_DEPENDS "${CPACK_DEBIAN_PACKAGE_DEPENDS}, libxml++2.6-dev (>= 2.36.0)")
+    SET(CPACK_DEBIAN_PACKAGE_DEPENDS "${CPACK_DEBIAN_PACKAGE_DEPENDS}, libxml++4.0-dev (>= 4.0.0)")
     SET(CPACK_DEBIAN_PACKAGE_DEPENDS "${CPACK_DEBIAN_PACKAGE_DEPENDS}, coinor-libcbc-dev (>= 2.8.7)")
     MESSAGE("CPACK_DEBIAN_PACKAGE_DEPENDS ${CPACK_DEBIAN_PACKAGE_DEPENDS}")