ukaea · qingfengxia · Oct 15, 2020 · Oct 13, 2020 · Oct 14, 2020 · Oct 14, 2020
diff --git a/.github/workflows/conda-ci.yml b/.github/workflows/conda-ci.yml
@@ -0,0 +1,88 @@
+name: parallel-preprocessor-conda
+# https://github.com/marketplace/actions/setup-miniconda
+on: [push]
+
+jobs:
+  ppp-conda-ci:
+    name: Ex1 (${{ matrix.python-version }}, ${{ matrix.os }})
+    runs-on: ${{ matrix.os }}
+    strategy:
+      fail-fast: false
+      matrix:
+        os: ["ubuntu-latest", "windows-latest"]
+        python-version: ["3.6", "3.7"]
+    steps:
+      - uses: actions/checkout@v2
+      - uses: goanpeca/setup-miniconda@v1
+        with:
+          auto-update-conda: true
+          python-version: ${{ matrix.python-version }}
+          channels: conda-forge
+          channel-priority: flexible
+          activate-environment: foo  # the default env
+          #activate-environment: anaconda-client-env
+          #environment-file: etc/example-environment.yml
+
+      # - name: Conda install dependencies
+      #   shell: bash -l {0}
+      #   run: |
+      #         conda info
+      #         conda install cmake
+      #         #only cmake installed from conda can find the conda install package?
+      #         conda install -c conda-forge occt=7.4
+
+      # - name: compile on windows
+      #   shell: bash -l {0}
+      #   run: |
+      #         mkdir condabuild
+      #         cd condabuild
+      #         cmake -G "NMake Makefiles" ..
+      #         cmake --build .
+      #   if: matrix.os == 'windows-latest'
+
+      # - name: compile on unix-like OS
+      #   shell: bash -l {0}
+      #   run: |
+      #         mkdir condabuild
+      #         cd condabuild
+      #         cmake  ..
+      #         cmake --build .
+      #   if: matrix.os != 'windows-latest'
+
+      - name: build conda package on windows and Linux
+        #shell: bash -l {0}
+        run: |
+            conda info
+            conda install conda-build
+            conda build ../recipe/meta.yaml
+
+      - name: test built package
+        shell: bash -l {0}
+        run: |
+      	    conda install -c local ppp
+            echo "start unit test in the folder:$(pwd)"
+	          if [ ! -f "run_all_tests.sh" ]; then cp ../scripts/run_all_tests.sh ./ ; fi
+	          bash run_all_tests.sh
+        if: matrix.os != 'windows-latest'
+
+     - name: Create Release
+        id: create_release
+        uses: actions/create-release@v1  #https://github.com/actions/upload-release-asset
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+        with:
+          tag_name: ${{ github.ref }}
+          release_name: Release ${{ github.ref }}
+          draft: false
+          prerelease: false
+
+      - name: Upload Release Asset
+        id: upload-release-asset 
+        uses: actions/upload-release-asset@v1
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+        with:
+          upload_url: ${{ steps.create_release.outputs.upload_url }} # This pulls from the CREATE RELEASE step above, referencing it's ID to get its outputs object, which include a `upload_url`. See this blog post for more info: https://jasonet.co/posts/new-features-of-github-actions/#passing-data-to-future-steps 
+          asset_path: ./my-artifact.zip  # todo: tar.gz file on Linux
+          asset_name: my-artifact.zip
+          asset_content_type: application/zip
diff --git a/.github/workflows/docker-ci.yml b/.github/workflows/docker-ci.yml
@@ -1,4 +1,4 @@
-name: parallel-preprocessor-docker
+name: fedora-debian
 
 on: [push, pull_request]
 
@@ -28,28 +28,39 @@ jobs:
           #   compiler: gcc
           #   compilerpp: g++
           #   package_suffix: 'rpm'
+          #   docker-image: "centos:8"
+          - os: 'debian-10'
+            compiler: gcc
+            compilerpp: g++
+            package_suffix: 'deb'
+            docker-image: "debian:10"  # version 10 buster
     container:
-      image: fedora:32
+      image: ${{ matrix.docker-image }}
     steps:
-    - name: 'install git'
-      id: 'install-git'
+    - name: 'install dependencies on fedora'
+      id: 'install-dep-fedora'
       run: |
         yum install g++ gcc cmake make rpm-build git wget copr-cli -y && yum update -y
-
-    - uses: actions/checkout@v2
-    # GitHub's actions/checkout requires git version 2.18 or later, if run inside docker
-    #- name: Checkout submodules
-    #  uses: textbook/git-checkout-submodule-action@master
-
-    - name: 'install dependencies'
-      id: 'install-dep'
-      run: |
         yum install tbb tbb-devel freetype freetype-devel freeimage freeimage-devel  \
                     glew-devel SDL2-devel SDL2_image-devel glm-devel libXmu-devel libXi-devel \
                     python3 python3-devel boost-devel -y
         yum install opencascade-foundation  opencascade-modeling opencascade-ocaf \
             opencascade-visualization opencascade-devel -y
+      if: matrix.os == 'fedora-31' || matrix.os == 'fedora-32'
+
+    - name: 'install dependencies on debian'
+      id: 'install-dep-debian'
+      run: |
+          apt-get update
+          apt-get install -y  g++ cmake git gcc build-essential
+          apt-get install -y libtbb*-dev libocct-*-dev occt-misc python3-dev python3-pybind11 libboost-dev
+          apt-get install -y libx11-dev libxmu-dev libxi-dev
+      if: matrix.os == 'debian-10'
 
+    - uses: actions/checkout@v2
+    # GitHub's actions/checkout requires git version 2.18 or later, if run inside docker
+    #- name: Checkout submodules
+    #  uses: textbook/git-checkout-submodule-action@master
 
     - name: 'build package'
       id: 'build-package'

diff --git a/.github/workflows/github-ci.yml b/.github/workflows/github-ci.yml
@@ -1,4 +1,4 @@
-name: parallel-preprocessor
+name: ubuntu-macos
 # adapted from: https://github.com/ScottishCovidResponse/Covid19_EERAModel/blob/dev/.github/workflows/eera.yml
 # Supported runners and hardware resources
 # https://docs.github.com/en/free-pro-team@latest/actions/reference/specifications-for-github-hosted-runners#supported-runners-and-hardware-resources
@@ -19,17 +19,17 @@ jobs:
         matrix:
           include:
             - os: 'ubuntu-20.04'
-              comiler: gcc
-              comilerpp: g++
+              compiler: gcc
+              compilerpp: g++
               package_suffix: 'deb'
             - os: 'ubuntu-18.04'
-              comiler: gcc
-              comilerpp: g++
+              compiler: gcc
+              compilerpp: g++
               package_suffix: 'deb'
-            # - os: 'macos-latest'
-            #   comiler: gcc
-            #   comilerpp: g++
-            #   package_suffix: 'dmg'
+            - os: 'macos-latest'
+              compiler: gcc
+              compilerpp: g++
+              package_suffix: 'dmg'
     steps:
     - uses: actions/checkout@v2
 
@@ -39,7 +39,7 @@ jobs:
            #sudo apt-get upgrade
            sudo apt-get install -y  g++ cmake clang cppcheck similarity-tester flawfinder
            sudo apt-get install -y lcov htmldoc poppler-utils graphviz doxygen
-           sudo apt-get install -y libtbb*-dev libocct-*-dev occt-misc python3-dev python3-pybind11 freecad
+           sudo apt-get install -y libtbb*-dev libocct-*-dev occt-misc python3-dev python3-pybind11 libboost-dev freecad
            sudo apt-get install -y libx11-dev libxmu-dev libxi-dev
       if: matrix.os == 'ubuntu-20.04'
       # ubuntu-20.04 has opencascade in official repo, PPA not needed, python3-pybind11 is also latest enough
@@ -49,15 +49,15 @@ jobs:
            sudo add-apt-repository ppa:freecad-maintainers/freecad-stable
            sudo apt-get update
            #sudo apt-get upgrade
-           sudo apt-get install -y libtbb*-dev libocct-*-dev occt-misc python3-dev freecad
+           sudo apt-get install -y libtbb*-dev libocct-*-dev occt-misc python3-dev freecad libboost-dev
            sudo apt-get install -y  g++ cmake clang lcov cppcheck similarity-tester flawfinder clang-format clang-tidy
            sudo apt-get install -y  libx11-dev libxmu-dev libxi-dev
       if: matrix.os == 'ubuntu-18.04'
 
     - name: Compile on Linux (debug)
       # env:
-      #         CC: ${{ matrix.config.compiler }}
-      #         CXX: ${{ matrix.config.compilerpp }}
+      #         CC: ${{ matrix.compiler }}
+      #         CXX: ${{ matrix.compilerpp }}
       run: |
         git submodule update --init --recursive
         mkdir build

diff --git a/CMakeLists.txt b/CMakeLists.txt
@@ -247,24 +247,25 @@ if (UNIX)
     if (${CMAKE_OS_NAME} STREQUAL "Debian" OR ${CMAKE_OS_NAME} STREQUAL "Ubuntu")
         # Tell CPack to generate a .deb package
         set(CPACK_GENERATOR "DEB")
-        set(CPACK_PACKAGE_NAME "parallel-preprocessor_${CMAKE_OS_ID}-${CMAKE_OS_VERSION}")
-        # -${CPACK_DEBIAN_PACKAGE_ARCHITECTURE}  not defined variable
-        string( TOLOWER "${PACKAGE_NAME}-${PACKAGE_VERSION_NAME}_${CMAKE_OS_ID}-${CMAKE_OS_VERSION}" 
-                CPACK_PACKAGE_FILE_NAME )
+        set(CPACK_PACKAGE_NAME ${PACKAGE_NAME})
     endif()
     if (${CMAKE_OS_NAME} STREQUAL "RedHat" OR ${CMAKE_OS_NAME} STREQUAL "Fedora")
         set(CPACK_GENERATOR "RPM")
-        set(CPACK_PACKAGE_NAME "parallel-preprocessor_${CMAKE_OS_ID}-${CMAKE_OS_VERSION}")
+        set(CPACK_PACKAGE_NAME ${PACKAGE_NAME})
     endif()
     if (APPLE)
         set(CPACK_GENERATOR "DragNDrop")
-        set(CPACK_PACKAGE_NAME "parallel-preprocessor_${CMAKE_OS_ID}-${CMAKE_OS_VERSION}")
+        set(CPACK_PACKAGE_NAME ${PACKAGE_NAME})
     endif()
+
+    # -${CPACK_DEBIAN_PACKAGE_ARCHITECTURE}  not defined variable
+    string( TOLOWER "${PACKAGE_NAME}-${PACKAGE_VERSION_NAME}_${CMAKE_OS_ID}-${CMAKE_OS_VERSION}" 
+    CPACK_PACKAGE_FILE_NAME )
 endif()
 if(WIN32)
     # NSIS can be generated by opencascade and Qt dll are not bundled, so not quite working
     set(CPACK_GENERATOR "NSIS64")  # zip 7z are other choices
-    set(CPACK_PACKAGE_NAME "parallel-preprocessor-${CMAKE_OS_VERSION}_${CMAKE_OS_ID}")
+    set(CPACK_PACKAGE_NAME ${PACKAGE_NAME})
     set(CPACK_PACKAGE_INSTALL_REGISTRY_KEY ${PACKAGE_NAME})
 endif()
 
@@ -275,16 +276,18 @@ set(CPACK_DEBIAN_PACKAGE_MAINTAINER "Qingfeng Xia @ UKAEA")
 set(CPACK_PACKAGE_DESCRIPTION, "${CMAKE_CURRENT_SOURCE_DIR}/Readme.md")
 # Set a Package Version
 set(CPACK_PACKAGE_VERSION ${PACKAGE_VERSION_NAME})
-#set(CPACK_PACKAGE_FILE_NAME "${CPACK_PACKAGE_NAME}")
+if (NOT APPLE)
+# this LICENSE file's end of line caused problem during dmg package generation on MacOS
 set(CPACK_RESOURCE_FILE_LICENSE "${CMAKE_CURRENT_SOURCE_DIR}/LICENSE")
+endif()
 
 message(STATUS "CPACK_PACKAGE_FILE_NAME: ${CPACK_PACKAGE_FILE_NAME}")
 
 ################################################################
 
 #set(CPACK_IGNORE_FILES "\.psd$;/\.git/;/backup/;\.#;/#;\.tar.gz$;/stage/;/build/;/condabuild/;\.diff$;\.DS_Store")
-set(CPACK_SOURCE_GENERATOR "TGZ")
-set(CPACK_SOURCE_PACKAGE_FILE_NAME "${CPACK_PACKAGE_NAME}")
+set(CPACK_SOURCE_GENERATOR "ZIP")
+set(CPACK_SOURCE_PACKAGE_FILE_NAME "${CPACK_PACKAGE_NAME}-${PACKAGE_VERSION_NAME}")
 set(CPACK_SOURCE_IGNORE_FILES ${CPACK_IGNORE_FILES})
 
 #################################################################

diff --git a/Readme.md b/Readme.md
@@ -16,11 +16,20 @@ Dr Andrew Davis of UKAEA, has contributed his technical insight,  test geometrie
 
 [**doxygen generated API documentation with wiki pages**](https://ukaea.github.io/parallel-preprocessor/site/doxygen-docs.html)
 
-## Overview
+## Feature overview
 
-Although this software aims to be a framework for more CAE/CAE preprocessing operatons, currently, this software provides only multi-threading geometry imprint and collision check, via command line user interface. This software has demonstrated faster and more controllable geometry imprinting on large geometry assemblies (10k+ parts) that is not possible on most existing CAD tools.
+This software aims to be a framework for more CAE/CAE **preprocessing operatons** for large geometry assemblies upto 1 millions parts, such as such as fusion reactor, areoplane, areo-engine as a whole, using high performance computation  infrastructure like Exa-scale super-computer. see more [Technical Overview](./wiki/TechOverview.md) on why a parallel preprocessor is needed in the era of E-scale (10^18 FLops) computation.
 
-Technical backgroud will be added later
+Currently, this software provides only multi-threading geometry imprint and collision check, via command line user interface. This software has demonstrated faster and more controllable geometry **collision-detection, imprinting** on **large geometry assemblies (10k+ parts)** that is not possible on most existing CAD tools.
+
+![CPU usage of parallel-preprocessor using 64 threads on a 32-core CPU](./wiki/assets/ppp_multithreading_cpu_usage.png)
+
+Screenshot for the CPU usage of parallel-preprocessor using 64 threads on a 32-core CPU (Source: Dr Andy Davis)
+
+
+## Future plan
+
+[wiki/Roadmap.md](wiki/Roadmap.md): lists short-term and long-term plan, depends on funding status. Partially sponsoring this project is welcomed to enhance existing modules or develop new modules.
 
 ## Disclaimer
 
@@ -32,39 +41,50 @@ According to the open source [license](./LICENSE),  **there is no warranty for t
 
 This project has been designed to be cross-platform, but only Linux is supported as the baseline platform.
 
-+ Ubuntu as the primary/baseline development platform, with deb binary package generated 
++ Ubuntu latest LTS as the primary/baseline development platform, with deb binary package generated 
+    - Debian package should be achievable, since OpenCASCADE are available in official repository
 
-+ Fedora, Centos can compile ppp from source, with OpenCascade 7.x source code or copr package.
++ Fedora 30+  with OpenCascade 7.x package available from official repository, with rpm binary package generated.
 
-+ Centos8 should work without much effort; Centos7 software stack is outdated, using docker/singularity instead.
++ Compiling from source code for other Linux platforms is straight-forward,  driven by cmake and cpack, guidance provided. 
+    - Centos8 should work without much effort, but OpenCASCADE must be compiled from source at first.
+    - Centos7 software stack is outdated for compiler and cmake , using docker/singularity instead.
 
 + Windows 10 users are encouraged to use WSL with one of the supported Linux distributions, while guide to compile on Windows has been added.
 
-+ MacOS should be possible through homebrew, and compiling instruction has been provided.
++ MacOS compiling and packaging is done via homebrew, DragNDrop binary package is available.
 
 Conda package and Linux native package for Ubuntu LTS may be available in the future, see [packaging.md](wiki/Packaging.md)
 
 ## Installation guide
 
-### Download binary package
+**Note: user must install runtime dependencies (TBB, OpenCASCADE, etc, see Compile guide wiki pages for each platform) then install the downloaded binary package. Hint: if user have freecad installed, then all dependencies should have installed**
+
+### Download (x86_64 architecture) binary packages
 Ubuntu deb package and fedora 30+ rpm package, conda packages for windows, it should be available to download on **github Release** for this public github. The unstable package build from the latest code on the main branch can be downloaded here <https://github.com/ukaea/parallel-preprocessor/releases/tag/dev>
 
 **Note: choose the correct operation system, and the package is targeting at system-wide python3**
 
-The package file has the name pattern: `parallel-preprocessor-<this_software_version>-dev_<OS name>-<OS version>.<package_suffix>`
-If your OS is not supported, you need to compile it by yourself,  there is documentation for installation dependency and build for all major platforms.
+The package file has the name pattern: `parallel-preprocessor-<this_software_version>-dev_<OS name>-<OS version>.<package_suffix>` If your OS is not supported, you need to compile it by yourself,  there is documentation for installation dependency and build for all major platforms.
 
+`apt remove parallel-preprocessor`
+`dpkg -i parallel-preprocessor*.deb`
  [Download parallel-preprocessor for ubuntu version 18.04](https://github.com/ukaea/parallel-preprocessor/releases/download/dev/parallel-preprocessor-0.3-dev_ubuntu-18.04.deb)
 
  [Download parallel-preprocessor for ubuntu version 20.04](https://github.com/ukaea/parallel-preprocessor/releases/download/dev/parallel-preprocessor-0.3-dev_ubuntu-20.04.deb)
 
+[Download parallel-preprocessor for debian version 10](https://github.com/ukaea/parallel-preprocessor/releases/download/dev/parallel-preprocessor-0.3-dev_debian-10.deb)
+
+
  [Download parallel-preprocessor for fedora version 31](https://github.com/ukaea/parallel-preprocessor/releases/download/dev/parallel-preprocessor-0.3-dev_fedora-31.rpm)
 
  [Download parallel-preprocessor for fedora version 32](https://github.com/ukaea/parallel-preprocessor/releases/download/dev/parallel-preprocessor-0.3-dev_fedora-32.rpm)
 
  Coming soon: 
  [Download parallel-preprocessor for MacOS 10.15](https://github.com/ukaea/parallel-preprocessor/releases/download/dev/parallel-preprocessor-0.3-dev_macos-latest.dmg)
 
+ Coming later:   Conda package for Windows 10.
+
 ### Compile from source
 [wiki/BuildOnLinux.md](wiki/BuildOnLinux.md): Guide to install dependencies and compile on Linux (Centos, Fedora, Ubuntu), build instructions.
 
@@ -105,13 +125,6 @@ If your OS is not supported, you need to compile it by yourself,  there is docum
 ### Guide to packaging
 [wiki/Packaging.md](wiki/Packaging.md) deb/rpm package generation by CPack, distribution strategy.
 
----
-
-## Future plan
-
-[wiki/Roadmap.md](wiki/Roadmap.md): lists short-term and long-term plan, depends on funding status. Partially sponsoring this project is welcomed to enhance existing modules or develop new modules.
-
-
 ---
 
 ## License consideration
@@ -125,4 +138,5 @@ Note:  the main branch of this repo is `main` not `master`.
 
 ## Acknowledgement
 
-Funding source: STEP project in UKAEA <http://www.ccfe.ac.uk/step.aspx>
+Funding from August 2019 ~ April 2020: STEP project in UKAEA <http://www.ccfe.ac.uk/step.aspx>
+
diff --git a/src/CMakeLists.txt b/src/CMakeLists.txt
@@ -123,9 +123,8 @@ endif(PPP_USE_PYTHON)
 
 
 ############################################################
-# unit test module
+# unit test module, PropertyContainer is header only
 ############################################################
 if(PPP_USE_TEST)
-    add_subdirectory(test)
     add_subdirectory (PropertyContainer)  # Catch2 must be add() before this subdirectionary
 endif()
diff --git a/src/Geom/GeomTests/CMakeLists.txt b/src/Geom/GeomTests/CMakeLists.txt
@@ -20,11 +20,19 @@ if(OCC_FOUND)
 target_link_libraries(geom_tests ${OCC_LIBS}) # list should be used without quote
 endif()
 
+####################### standalone app #####################
+add_executable(UniqueIdValidator "UniqueIdValidator.cpp") #
+target_link_libraries(UniqueIdValidator ${OCC_LIBS})
+
+install(TARGETS UniqueIdValidator
+        RUNTIME DESTINATION bin
+        COMPONENT applications)
+
 ##################### standalone app ###########################
 if (${PPP_USE_QT})
     # relies on QT, but user may not enable QT GUI
     add_executable(OccBVHdemo "OccBVHdemo.cpp") #
-    target_link_libraries(OccBVHdemo ${OCC_LIBS}) # compiled but does not work with OCCT 7.3
+    target_link_libraries(OccBVHdemo ${OCC_LIBS})
     target_link_libraries(OccBVHdemo ${OCC_VIZ_LIBRARIES}) # list should be used without quote
     install(TARGETS OccBVHdemo
         RUNTIME DESTINATION bin