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| # For most projects, this workflow file will not need changing; you simply need | ||
| # to commit it to your repository. | ||
| # | ||
| # You may wish to alter this file to override the set of languages analyzed, | ||
| # or to provide custom queries or build logic. | ||
| # | ||
| # ******** NOTE ******** | ||
| # We have attempted to detect the languages in your repository. Please check | ||
| # the `language` matrix defined below to confirm you have the correct set of | ||
| # supported CodeQL languages. | ||
| # | ||
| name: "CodeQL" | ||
|
|
||
| on: | ||
| push: | ||
| branches: | ||
| - master | ||
| - aaron-dev-test | ||
| pull_request: | ||
| # The branches below must be a subset of the branches above | ||
| branches: | ||
| - master | ||
| - aaron-dev-test | ||
| schedule: | ||
| - cron: '20 18 * * 1' | ||
|
|
||
| jobs: | ||
| analyze-mpi: | ||
| name: Analyze mpi | ||
| runs-on: ubuntu-latest | ||
| permissions: | ||
| security-events: write | ||
| actions: read | ||
|
|
||
| strategy: | ||
| fail-fast: false | ||
| matrix: | ||
| language: [cpp] | ||
|
|
||
| # Specify the container in which actions will run | ||
| container: | ||
| image: ehb1/us3comp:latest | ||
| options: --cpus 2 | ||
|
|
||
| steps: | ||
| - name: Checkout repository | ||
| uses: actions/checkout@v4 | ||
| - name: Initialize CodeQL | ||
| uses: github/codeql-action/init@v3 | ||
| with: | ||
| languages: ${{ matrix.language }} | ||
| - name: Build | ||
| run: | | ||
| cp admin/codeql/docker/local.pri.mpi local.pri | ||
| cd utils | ||
| qmake | ||
| make -j4 | ||
| cd .. | ||
| cd programs/us_mpi_analysis | ||
| qmake | ||
| make -j4 | ||
| cd ../.. | ||
| - name: Perform CodeQL Analysis | ||
| uses: github/codeql-action/analyze@v3 | ||
|
|
||
| analyze-gui: | ||
| name: Analyze gui | ||
| runs-on: ubuntu-latest | ||
| permissions: | ||
| security-events: write | ||
| actions: read | ||
|
|
||
| strategy: | ||
| fail-fast: false | ||
| matrix: | ||
| language: [cpp] | ||
|
|
||
| # Specify the container in which actions will run | ||
| container: | ||
| image: ehb1/us3comp:latest | ||
| options: --cpus 2 | ||
|
|
||
| steps: | ||
| - name: Checkout repository | ||
| uses: actions/checkout@v4 | ||
| - name: Initialize CodeQL | ||
| uses: github/codeql-action/init@v3 | ||
| with: | ||
| languages: ${{ matrix.language }} | ||
| - name: Build | ||
| run: | | ||
| cp admin/codeql/docker/local.pri.gui local.pri | ||
| git config --global --add safe.directory /__w/ultrascan3/ultrascan3 | ||
| (cd programs/us && sh revision.sh) | ||
| cd qwtplot3d | ||
| qmake | ||
| make -j4 | ||
| cd .. | ||
| cd utils | ||
| qmake | ||
| make -j4 | ||
| cd .. | ||
| cd gui | ||
| qmake | ||
| make -j4 | ||
| cd .. | ||
| for d in `find programs -type d -name "us*" | grep -v 'us_mpi_analysis'` | ||
| do | ||
| echo "*** compiling in $d ***" | ||
| ( cd $d && qmake && make -j4 ) | ||
| done | ||
| - name: Perform CodeQL Analysis | ||
| uses: github/codeql-action/analyze@v3 | ||
|
|
||
| analyze-somo: | ||
| name: Analyze somo | ||
| runs-on: ubuntu-latest | ||
| permissions: | ||
| security-events: write | ||
| actions: read | ||
|
|
||
| strategy: | ||
| fail-fast: false | ||
| matrix: | ||
| language: [cpp] | ||
|
|
||
| # Specify the container in which actions will run | ||
| container: | ||
| image: ehb1/us3comp:latest | ||
| options: --cpus 2 | ||
|
|
||
| steps: | ||
| - name: Checkout repository | ||
| uses: actions/checkout@v4 | ||
| - name: Initialize CodeQL | ||
| uses: github/codeql-action/init@v3 | ||
| with: | ||
| languages: ${{ matrix.language }} | ||
| - name: Build | ||
| run: | | ||
| bdir=`pwd` | ||
| echo $bdir | ||
| pwd | ||
| export ULTRASCAN=$bdir | ||
| export us3=$bdir | ||
| cd us_somo/develop | ||
| git config --global --add safe.directory /__w/ultrascan3/ultrascan3 | ||
| ./revision.sh | ||
| ./version.sh | ||
| cp $bdir/admin/codeql/docker/local.pri.somo local.pri | ||
| qmake libus_somo.pro | ||
| make -j4 | ||
| qmake us_somo.pro | ||
| make -j4 | ||
| - name: Perform CodeQL Analysis | ||
| uses: github/codeql-action/analyze@v3 | ||
| unit-testing: | ||
| name: Unit Testing | ||
| runs-on: ubuntu-latest | ||
| permissions: | ||
| security-events: write | ||
| actions: read | ||
|
|
||
| strategy: | ||
| fail-fast: false | ||
| matrix: | ||
| language: [ cpp ] | ||
|
|
||
| # Specify the container in which actions will run | ||
| container: | ||
| image: ehb1/us3comp:latest | ||
| options: --cpus 2 | ||
|
|
||
| steps: | ||
| - name: Checkout repository | ||
| uses: actions/checkout@v4 | ||
|
|
||
| - name: Configure and build | ||
| run: | | ||
| apt-get install -y cmake | ||
| bdir=`pwd` | ||
| echo $bdir | ||
| pwd | ||
| export ULTRASCAN=$bdir | ||
| export us3=$bdir | ||
| git config --global --add safe.directory /__w/ultrascan3/ultrascan3 | ||
| mkdir -p $bdir/build | ||
| cd build | ||
| cmake .. | ||
| make -j4 | ||
| - name: Run tests | ||
| run: | | ||
| cd build | ||
| ctest --output-on-failure -V | ||
|
|
||
|
|
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| cmake_minimum_required(VERSION 3.21) | ||
| project(UltrascanTest) | ||
|
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| set(CMAKE_CXX_STANDARD 20) | ||
| set(CMAKE_CXX_STANDARD_REQUIRED True) | ||
|
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| # Enable AUTOMOC | ||
| set(CMAKE_AUTOMOC ON) | ||
| set(CMAKE_AUTORCC ON) | ||
| set(CMAKE_AUTOUIC ON) | ||
|
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| # Enable debugging | ||
| set(CMAKE_BUILD_TYPE Debug) | ||
| set(CMAKE_CXX_FLAGS_DEBUG "-g") | ||
|
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| # Enable testing | ||
| enable_testing() | ||
|
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| # Find Qt packages | ||
| find_package(Qt5 REQUIRED COMPONENTS Core Gui Network Sql Test Xml) | ||
|
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||
| # Include the src subdirectory | ||
| add_subdirectory(utils) | ||
| add_subdirectory(test) |
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| [](https://github.com/ehb54/ultrascan3/actions/workflows/codeql-analysis.yml) | ||
|
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| This is the home of the UltraScan GUI software source code. | ||
| More information is available [here](https://ultrascan.aucsolutions.com) | ||
|
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| The UltraScan project is supported by NIH Funding GM120600 | ||
|
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| ### Licensing | ||
|
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| This project is licensed under the Lesser General Public License (LGPL). You can find the LGPL license in the LICENSE file in the root directory of this project. | ||
|
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| This project uses the Eigen library, which is licensed under the Mozilla Public License 2.0 (MPL2). | ||
| You can find the Eigen source code and license at [Eigen GitHub repository](https://gitlab.com/libeigen/eigen). | ||
|
|
||
| ### Installation | ||
|
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| The simplest way is to download and install a precompiled [binary](https://www.ultrascan3.aucsolutions.com/download.php) | ||
|
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| ### Building | ||
|
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| If you wish to compile from source, here are some notes to get you started. | ||
|
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| You will need [qt5](https://doc.qt.io/qt-5/gettingstarted.html) development and [qwt](https://qwt.sourceforge.io/) installed. | ||
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| We typically compile from source as in [ansible roles build-qt, build-qwt & build-us3](https://github.com/KJSain/us3lims-roles/tree/master/roles) | ||
|
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| One could also take hints from this [Dockerfile](https://github.com/ehb54/ultrascan3/blob/master/admin/codeql/docker/docker/Dockerfile) which uses an Ubuntu 20.04 container and qt packages. | ||
|
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| Please create an issue or [contact us](https://www.ultrascan3.aucsolutions.com/contacts.php) if you have further questions. | ||
|
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| ### Container environment | ||
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| Assuming you are experienced with containers... | ||
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| A containerized development image is also available | ||
| ```docker pull ehb1/us3comp``` | ||
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| The source is in `/ultrascan3` | ||
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| Run and export the containers display in Linux | ||
| ```docker run -it --rm -e DISPLAY=${DISPLAY} -v /tmp/.X11-unix:/tmp/.X11-unix -v $HOME/.Xauthority:/home/xterm/.Xauthority --hostname $(hostname) ehb1/us3comp bash``` | ||
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| N.B. the `--rm` above will delete the container after you exit, so any changes will be lost after exiting. | ||
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| Update the ultrascan3 code ```cd /ultrascan3 && git pull``` | ||
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| Compile both `us` and `us3_somo` ```cd /ultrascan3 && ./makeall.sh && ./makesomo.sh``` | ||
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| Run the compiled application ```LD_LIBRARY_PATH=/ultrascan3/lib:/qwt-6.1.5/lib /ultrascan3/bin/us``` | ||
|
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| Note - subprocesses do not currently run in the container, so you must run any compiled application individually, e.g. `us_fematch` | ||
|
|
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| FROM ubuntu:22.04 | ||
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| # dockerfile for us3 compiles | ||
|
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| ARG DEBIAN_FRONTEND=noninteractive | ||
|
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| # basic install stuff | ||
|
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| RUN apt-get update | ||
| RUN apt-get install -y --no-install-recommends apt-utils | ||
| RUN apt-get install -y build-essential | ||
| RUN apt-get install -y tzdata | ||
| RUN apt-get install -y software-properties-common | ||
| RUN apt-get install -y bind9-host | ||
| RUN apt-get install -y subversion git libssl-dev bc curl wget | ||
| RUN apt-get install -y zlib1g-dev | ||
| RUN apt-get install -y pkg-config | ||
| RUN apt-get install -y re2c | ||
| RUN apt-get install -y openssh-server | ||
| RUN apt-get install -y vim | ||
| RUN apt-get install -y emacs-nox | ||
| RUN apt-get install -y xorg | ||
| RUN apt-get install -y x11-apps | ||
| RUN apt-get install -y telnet | ||
| RUN apt-get install -y cmake | ||
|
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| # qt | ||
| RUN apt-get install -y qtbase5-dev | ||
| RUN apt-get install -y libqt5svg5-dev | ||
| RUN apt-get install -y libqt5sql5-mysql | ||
| RUN apt-get install -y libqt5sql5-psql | ||
| RUN apt-get install -y qtmultimedia5-dev | ||
| RUN apt-get install -y libqt5datavisualization5 | ||
| RUN apt-get install -y libqt5datavisualization5-dev | ||
|
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| # qt support | ||
|
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| # RUN apt-get install -y libmariadbclient-dev | ||
| RUN apt-get install -y libmysqlclient-dev | ||
| RUN apt-get install -y mpich | ||
|
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| # install qwt | ||
| RUN wget https://versaweb.dl.sourceforge.net/project/qwt/qwt/6.1.6/qwt-6.1.6.tar.bz2 | ||
| RUN tar jxf qwt-6.1.6.tar.bz2 | ||
| RUN cd qwt-6.1.6 && qmake && make -j12 && make install | ||
|
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| # get source | ||
| RUN git clone https://github.com/ehb54/ultrascan3.git | ||
|
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| # setup initial local.pri's | ||
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| RUN cp /ultrascan3/admin/codeql/docker/local.pri.somo /ultrascan3/us_somo/develop/local.pri | ||
| RUN cp /ultrascan3/admin/codeql/docker/local.pri.gui /ultrascan3/local.pri | ||
|
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| # somo version setup | ||
| RUN cd /ultrascan3/us_somo/develop && env ULTRASCAN=/ultrascan3 ./revision.sh && env us3=/ultrascan3 ./version.sh |
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