Merge branch 'qt6' of https://github.com/cbielow/OpenMS into qt6

.github/workflows/openms_ci_matrix_full.yml

@@ -216,11 +216,10 @@ jobs:
 
     - name: Install Qt (Windows)
       if: startsWith(matrix.os, 'windows')
-      uses: jurplel/install-qt-action@v3
+      uses: jurplel/install-qt-action@v4
       with:
-        version: '5.15.2' # 5.12.7 is broken https://bugreports.qt.io/browse/QTBUG-81715, > 5.15.2 is not available on official archives (https://github.com/miurahr/aqtinstall/issues/636)
+        version: '6.7.2'
         cache: 'false'
-        aqtversion: '==3.1.*'
         archives: 'qtsvg qtimageformats qtbase'
 
     - name: Setup build tools (and system contrib on Linux and Mac)
@@ -234,7 +233,7 @@ jobs:
           sudo add-apt-repository universe
           sudo apt update   
           sudo apt-get -qq install -y build-essential cmake autoconf patch libtool git automake ninja-build xvfb ccache
-          sudo apt-get -qq install -y qtbase5-dev libqt5svg5-dev libqt5opengl5-dev
+          sudo apt-get -qq install -y qt6-base-dev libqt6svg6-dev libqt6opengl6-dev libqt6openglwidgets6 libgl-dev
           sudo apt-get -qq install -y libeigen3-dev libboost-random-dev libboost-regex-dev libboost-iostreams-dev \
            libboost-date-time-dev libboost-math-dev libxerces-c-dev zlib1g-dev libsvm-dev libbz2-dev coinor-libcoinmp-dev libhdf5-dev
 
@@ -246,18 +245,18 @@ jobs:
         fi
         
         if [[ "${{ matrix.os }}" == windows-* ]]; then
-          # Qt5_DIR set by Install Qt5 step
-          echo "cmake_prefix=$Qt5_DIR/lib/cmake;$Qt5_DIR" >> $GITHUB_OUTPUT
+          # QT_ROOT_DIR set by Install Qt step
+          echo "cmake_prefix=$QT_ROOT_DIR/lib/cmake;$QT_ROOT_DIR" >> $GITHUB_OUTPUT
           choco install ccache ninja cmake -y --no-progress
           ## GH CLI "SHOULD BE" installed. Sometimes I had to manually install nonetheless. Super weird.
           # https://github.com/actions/runner-images/blob/main/images/win/scripts/Installers/Install-GitHub-CLI.ps1
           echo "C:\Program Files (x86)\GitHub CLI" >> $GITHUB_PATH
           # Install eigen from choco
           choco install eigen -y --no-progress
           echo "eigen_choco=C:\ProgramData\chocolatey\lib\eigen\share\cmake" >> $GITHUB_OUTPUT
-
+          choco install doxygen.portable ghostscript graphviz -y --no-progress
+          
           if [[ "${{ steps.set-vars.outputs.pkg_type }}" != "none" ]]; then
-            choco install doxygen.portable ghostscript graphviz -y --no-progress
             # uses a custom NSIS, which provides 8-k string support and has UltraModernUI integrated already
             curl --no-progress-meter -L -o NSIS.tar.gz https://github.com/OpenMS/NSIS/raw/main/NSIS.tar.gz
             ## overwrite existing NSIS (which has only 1k-string support)
@@ -269,12 +268,9 @@ jobs:
           ## Needed for Qt. Install before to overwrite the default softlinks on the GH runners
           brew install python3 --force --overwrite
           brew install --quiet ccache autoconf automake libtool ninja && brew link --overwrite ccache
-          brew install libsvm xerces-c boost eigen sqlite coinutils cbc cgl clp qt@5
-          echo "cmake_prefix=$(brew --prefix qt@5)/lib/cmake;$(brew --prefix qt@5)" >> $GITHUB_OUTPUT
-          echo "Qt5_DIR=$(brew --prefix qt@5)/lib/cmake/Qt5" >> $GITHUB_ENV
-          if [[ "${{ steps.set-vars.outputs.pkg_type }}" != "none" ]]; then
-            brew install --quiet doxygen ghostscript graphviz
-          fi
+          brew install libsvm xerces-c boost eigen sqlite coinutils cbc cgl clp qt
+          echo "cmake_prefix=$(brew --prefix qt)/lib/cmake;$(brew --prefix qt)" >> $GITHUB_OUTPUT
+          brew install --quiet doxygen ghostscript graphviz
         fi
 
     - name: Cache contrib (Windows)
@@ -458,8 +454,8 @@ jobs:
         type: 'tar'
         directory: ${{ github.workspace }}
         path: OpenMS
-        exclusions: 'bld/* ./source.tar.gz THIRDPARTY/* .git/*'
-        filename: 'source.tar.gz'
+        exclusions: 'bld/* ./OpenMS-${{ steps.create_changelog.outputs.version_number }}.tar.gz THIRDPARTY/* .git/*'
+        filename: 'OpenMS-${{ steps.create_changelog.outputs.version_number }}.tar.gz'
 
 
 
@@ -468,9 +464,9 @@ jobs:
       if: steps.set-vars.outputs.pkg_type != 'none' && startsWith(matrix.os, 'ubuntu')
       uses: actions/upload-artifact@v4
       with:
-        name: source.tar.gz
+        name: OpenMS-${{ steps.create_changelog.outputs.version_number }}.tar.gz
         path: |
-          ${{ github.workspace }}/source.tar.gz
+          ${{ github.workspace }}/OpenMS-${{ steps.create_changelog.outputs.version_number }}.tar.gz
 
 
     # Only upload docs when we are building the package, use the ubuntu build simply 'cause its fast
@@ -539,7 +535,7 @@ jobs:
       - name: Download source archive as artifact
         uses: actions/download-artifact@v4
         with:
-          name: source.tar.gz
+          name: OpenMS-${{ steps.create_changelog.outputs.version_number }}.tar.gz
 
       - name: Download changelog as artifact
         if: inputs.do_release

.github/workflows/pyopenms-wheels.yml

@@ -7,6 +7,11 @@ name: pyopenms-wheels-and-packages
 # events but only for the master branch
 on:
   workflow_dispatch:
+    inputs:
+      upload-to-pypi:
+        type: boolean
+        description: actually upload the release package to pypi.org
+        default: false
   push:
     tags:
       - 'Release*'
@@ -26,8 +31,12 @@ jobs:
       with:
         cmake-version: '3.25.x'
 
-    - name: Reduce PATH
-      run: echo "PATH=C:\hostedtoolcache\windows\Python\3.7.9\x64\Scripts;C:\hostedtoolcache\windows\Python\3.7.9\x64;C:\hostedtoolcache\windows\Ruby\2.5.8\x64\bin;C:\Program Files\Java\jdk8u265-b01\bin;C:\ProgramData\kind;C:\vcpkg;C:\cf-cli;C:\Program Files (x86)\NSIS;C:\windows\system32;C:\windows;C:\windows\System32\Wbem;C:\windows\System32\WindowsPowerShell\v1.0;C:\windows\System32\OpenSSH;C:\ProgramData\Chocolatey\bin;C:\Program Files\Docker;C:\Program Files\PowerShell\7;C:\Program Files\OpenSSL\bin;C:\Strawberry\c\bin;C:\Strawberry\perl\site\bin;C:\Strawberry\perl\bin;C:\Program Files\Git\cmd;C:\Program Files\Git\mingw64\bin;C:\Program Files\Git\usr\bin;C:\Program Files (x86)\Microsoft Visual Studio\2019\\Enterprise\Common7\IDE\CommonExtensions\Microsoft\CMake\CMake\bin" | Out-File -FilePath $env:GITHUB_ENV -Encoding utf8 -Append
+    - name: Reduce PATH # This fixes a bug described in https://github.com/facebook/watchman/commit/59bcfbf91d2a24ab580b8a78e384f133cc202383
+      run: echo "DISTUTILS_USE_SDK=1"
+
+    - name: Get number of CPU cores
+      uses: SimenB/github-actions-cpu-cores@v2
+      id: cpu-cores
 
     - name: Install Qt
       uses: jurplel/install-qt-action@v3
@@ -46,20 +55,26 @@ jobs:
             curl -o $MINICONDA_FILENAME "https://repo.anaconda.com/miniconda/$MINICONDA_FILENAME"
             ./Miniconda3-latest-Windows-x86_64.exe //InstallationType=JustMe //RegisterPython=0 //S //D=$HOME/miniconda3
 
+
+    - name: Download contrib build from archive (Windows)
+      shell: bash
+      env:
+        GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+      run: |
+          cd OpenMS/contrib
+          # Download the file using the URL fetched from GitHub
+          gh release download -R OpenMS/contrib --pattern 'contrib_build-Windows.tar.gz'
+          # Extract the archive
+          7z x -so contrib_build-Windows.tar.gz | 7z x -si -ttar
+          rm contrib_build-Windows.tar.gz
+          ls -la
+
     # https://github.com/marketplace/actions/visual-studio-shell
     - name: Set up Visual Studio shell
       uses: egor-tensin/vs-shell@v2
       with:
         arch: x64
 
-    - name: Load contrib build
-      run: |
-          mkdir contribbld
-          cd contribbld
-          curl -o contribbld.tar.gz https://abibuilder.cs.uni-tuebingen.de/archive/openms/contrib/windows/x64/msvc-14.2/contrib_build.tar.gz
-          tar -xzf contribbld.tar.gz
-          rm contribbld.tar.gz
-
     - name: Setup conda paths
       shell: bash
       run: |
@@ -74,7 +89,7 @@ jobs:
         pushd bld
         # TODO: set generator via variable, then we can share this step
         cmake --version
-        cmake -G "Visual Studio 17 2022" -A x64 -DOPENMS_CONTRIB_LIBS="$GITHUB_WORKSPACE/contribbld" -DCMAKE_PREFIX_PATH="$(echo $Qt5_Dir)/lib/cmake;${Qt5_Dir}" ../OpenMS
+        cmake -G "Visual Studio 17 2022" -A x64 -DOPENMS_CONTRIB_LIBS="$GITHUB_WORKSPACE/OpenMS/contrib" -DCMAKE_PREFIX_PATH="$(echo $Qt5_Dir)/lib/cmake;${Qt5_Dir}" ../OpenMS
         # Note: multiple --targets only supported by CMake 3.15+
         cmake --build . --config Release --target OpenMS
       
@@ -103,14 +118,14 @@ jobs:
           pip install -U pip
           pip install -U autowrap
           pip install -U pytest
-          pip install -U numpy
+          pip install 'numpy<=1.26.4'
           pip install -U wheel
 
           echo $CURRENT_PYTHON_EXECUTABLE
 
           # build pyopenms distribution
           cmake --version
-          cmake -DPYTHON_EXECUTABLE:FILEPATH=$CURRENT_PYTHON_EXECUTABLE -DPYOPENMS=ON -DPY_NUM_THREADS=4 .
+          cmake -DPYTHON_EXECUTABLE:FILEPATH=$CURRENT_PYTHON_EXECUTABLE -DPYOPENMS=ON -DPY_NUM_THREADS=${{ steps.cpu-cores.outputs.count }} .
           cmake --build . --config Release --target pyopenms
 
           # copy to directory
@@ -139,6 +154,10 @@ jobs:
       with:
         path: OpenMS
 
+    - name: Get number of CPU cores
+      uses: SimenB/github-actions-cpu-cores@v2
+      id: cpu-cores
+
     - name: Setup cmake
       uses: jwlawson/actions-setup-cmake@v2
       with:
@@ -187,7 +206,7 @@ jobs:
         pushd bld
         # Use -DCMAKE_FIND_DEBUG_MODE=ON for debug
         cmake -DCMAKE_BUILD_TYPE="Release" -DCMAKE_PREFIX_PATH="$(brew --prefix libomp);$(echo $Qt5_Dir)/lib/cmake;${Qt5_Dir}" -DCMAKE_OSX_DEPLOYMENT_TARGET=12 -DBOOST_USE_STATIC=OFF ../OpenMS
-        make -j4 OpenMS
+        make -j${{ steps.cpu-cores.outputs.count }} OpenMS
 
         mkdir pyopenms_whls
 
@@ -205,13 +224,13 @@ jobs:
           pip install -U pip
           pip install -U autowrap
           pip install -U pytest
-          pip install -U numpy
+          pip install 'numpy<=1.26.4'
           pip install -U wheel
           pip install -U pandas
 
           # build pyopenms distribution (macOS)
-          cmake -DPYTHON_EXECUTABLE:FILEPATH=$CURRENT_PYTHON_EXECUTABLE -DPYOPENMS=ON -DPY_NUM_THREADS=4 .
-          make -j4 pyopenms
+          cmake -DPYTHON_EXECUTABLE:FILEPATH=$CURRENT_PYTHON_EXECUTABLE -DPYOPENMS=ON -DPY_NUM_THREADS=${{ steps.cpu-cores.outputs.count }} .
+          make -j${{ steps.cpu-cores.outputs.count }} pyopenms
 
           # copy to directory
           cp pyOpenMS/dist/*.whl pyopenms_whls/
@@ -249,6 +268,10 @@ jobs:
       with:
         path: OpenMS
 
+    - name: Get number of CPU cores
+      uses: SimenB/github-actions-cpu-cores@v2
+      id: cpu-cores
+
     - name: Setup cmake
       uses: jwlawson/actions-setup-cmake@v2
       with:
@@ -297,7 +320,7 @@ jobs:
         pushd bld
         # Use -DCMAKE_FIND_DEBUG_MODE=ON for debug
         cmake -DCMAKE_BUILD_TYPE="Release" -DCMAKE_PREFIX_PATH="$(brew --prefix libomp);$(echo $Qt5_Dir)/lib/cmake;${Qt5_Dir}" -DCMAKE_OSX_DEPLOYMENT_TARGET=12 -DBOOST_USE_STATIC=OFF ../OpenMS
-        make -j4 OpenMS
+        make -j${{ steps.cpu-cores.outputs.count }} OpenMS
 
         mkdir pyopenms_whls
 
@@ -315,13 +338,13 @@ jobs:
           pip install -U pip
           pip install -U autowrap
           pip install -U pytest
-          pip install -U numpy
+          pip install 'numpy<=1.26.4'
           pip install -U wheel
           pip install -U pandas
 
           # build pyopenms distribution (macOS)
-          cmake -DPYTHON_EXECUTABLE:FILEPATH=$CURRENT_PYTHON_EXECUTABLE -DPYOPENMS=ON -DPY_NUM_THREADS=4 .
-          make -j4 pyopenms
+          cmake -DPYTHON_EXECUTABLE:FILEPATH=$CURRENT_PYTHON_EXECUTABLE -DPYOPENMS=ON -DPY_NUM_THREADS=${{ steps.cpu-cores.outputs.count }} .
+          make -j${{ steps.cpu-cores.outputs.count }} pyopenms
 
           # copy to directory
           cp pyOpenMS/dist/*.whl pyopenms_whls/
@@ -357,6 +380,10 @@ jobs:
       with:
         path: OpenMS
 
+    - name: Get number of CPU cores
+      uses: SimenB/github-actions-cpu-cores@v2
+      id: cpu-cores
+
     - name: Setup cmake
       uses: jwlawson/actions-setup-cmake@v2
       with:
@@ -377,7 +404,7 @@ jobs:
         mkdir openms-build
         cd openms-build
         cmake -DCMAKE_BUILD_TYPE="Release" -DOPENMS_CONTRIB_LIBS="/contrib-build/" -DCMAKE_PREFIX_PATH="/contrib-build/" $GITHUB_WORKSPACE/OpenMS
-        make -j4 OpenMS
+        make -j${{ steps.cpu-cores.outputs.count }} OpenMS
 
         # compile and configure OpenMS
         for py in $(echo "${PYTHON_VERSIONS}" | jq -r '.[]'); do
@@ -393,13 +420,13 @@ jobs:
           "$PYBIN/bin/pip" install -U Cython
           "$PYBIN/bin/pip" install -U setuptools
           "$PYBIN/bin/pip" install -U wheel
-          "$PYBIN/bin/pip" install -U numpy
+          "$PYBIN/bin/pip" install 'numpy<=1.26.4'
           "$PYBIN/bin/pip" install -U pytest
           "$PYBIN/bin/pip" install -U autowrap
 
           # configure (don't copy deps since we use auditwheel)
-          cmake -DNO_DEPENDENCIES=ON -DOPENMS_CONTRIB_LIBS="/contrib-build/" -DCMAKE_PREFIX_PATH="/contrib-build/" -DPYOPENMS=On -DPython_ROOT_DIR=$PYBIN -DPython_FIND_STRATEGY="LOCATION" -DPY_NUM_THREADS=4 $GITHUB_WORKSPACE/OpenMS
-          make -j4 pyopenms
+          cmake -DNO_DEPENDENCIES=ON -DOPENMS_CONTRIB_LIBS="/contrib-build/" -DCMAKE_PREFIX_PATH="/contrib-build/" -DPYOPENMS=On -DPython_ROOT_DIR=$PYBIN -DPython_FIND_STRATEGY="LOCATION" -DPY_NUM_THREADS=${{ steps.cpu-cores.outputs.count }} $GITHUB_WORKSPACE/OpenMS
+          make -j${{ steps.cpu-cores.outputs.count }} pyopenms
           
           # ensure auditwheel can find the libraries
           export LD_LIBRARY_PATH=$LD_OLD_LIBRARY_PATH:`pwd`/lib
@@ -551,18 +578,20 @@ jobs:
             ls -la wheels/
 
     - name: Publish package to nightly PyPI
-      if: "contains(github.ref, 'develop') || contains(github.ref, 'nightly')"
+        # Upload the wheels to our pypi server for develop, nightly and release branches (unless it's explictly stated to upload it to pypi.org)
+      if: contains(github.ref, 'develop') || contains(github.ref, 'nightly') || (contains(github.ref, 'Release') && inputs.upload-to-pypi == 'false')
       uses: pypa/gh-action-pypi-publish@release/v1
       with:
-        repository_url: https://pypi.cs.uni-tuebingen.de/
+        repository-url: https://pypi.cs.uni-tuebingen.de/
         user: openms
         password: ${{ secrets.abiservices_pypi_pw }}
         packages-dir: ${{ github.workspace }}/wheels
 
     - name: Publish package to PyPI
-      if: "contains(github.ref, 'Release')"
+      if: contains(github.ref, 'Release') && inputs.upload-to-pypi
       uses: pypa/gh-action-pypi-publish@release/v1
       with:
         user: __token__
+        repository-url: https://test.pypi.org/
         password: ${{ secrets.pypi_api_token_release }}
         packages-dir: ${{ github.workspace }}/wheels

.github/workflows/test_pyopenms.yml

@@ -1,9 +1,9 @@
-name: Test nightly pyOpenMS on different platforms
+name: Test pyOpenMS on different platforms
 
 on:
   workflow_dispatch: # Trigger manually
-  workflow_run:
-    workflows: [ pyopenms-wheels ]
+  workflow_run: # Trigger on pyopenms-wheels
+    workflows: ["pyopenms-wheels-and-packages"]
     types:
       - completed
 
@@ -15,11 +15,11 @@ jobs:
       matrix: ${{ steps.python_versions.outputs.content }}
     steps:
       - name: Checkout repository
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
 
       - name: Read python_versions.json
         id: python_versions
-        uses: juliangruber/read-file-action@v1
+        uses: juliangruber/read-file-action@v1.1.7
         with:
           path: .github/workflows/python_versions.json
 
@@ -35,7 +35,7 @@ jobs:
         python-version: ${{ fromJson(needs.read-python-versions.outputs.matrix) }}
     steps:
       - name: Set up Python ${{ matrix.python-version }}
-        uses: actions/setup-python@v2
+        uses: actions/setup-python@v5
         with:
           python-version: ${{ matrix.python-version }}
 

.github/workflows/update_nightly.yml

@@ -69,3 +69,10 @@ jobs:
         gh workflow run openms-ci-full --ref develop
       env:
         GH_TOKEN: ${{ github.token }}
+
+    - name: Build wheels
+      if: steps.compare_branches.outputs.behind == 'true' || inputs.force
+      run: |
+        gh workflow run pyopenms-wheels-and-packages --ref nightly
+      env:
+        GH_TOKEN: ${{ github.token }}

CHANGELOG

@@ -87,6 +87,8 @@ Cleanup/Removal:
   - PeakPickerCWT_test
   - PeakShape_test
 
+- Deprecated (and likely removed in the next release)
+  - XTandemAdapter
 ------------------------------------------------------------------------------------------
 ----                                OpenMS 3.1     (released 10/2023)                 ----
 ------------------------------------------------------------------------------------------

doc/CMakeLists.txt

@@ -122,7 +122,7 @@ if(ENABLE_DOCS)
     set(DOXYGEN_MIN_REQUIRED "1.8.13")
 
     if (DOXYGEN_VERSION VERSION_LESS DOXYGEN_MIN_REQUIRED )
-      message(STATUS "Warning: Doxygen ( vers. installed = ${DOXYGEN_VERSION} < ${DOXYGEN_MIN_REQUIRED}) does not correctly process \\includedoc commands in developer's installation instructions. This will make them incomplete. Upgrade Doxygen to fix.")
+      message(STATUS "Warning: Doxygen ( vers. installed = ${DOXYGEN_VERSION} < ${DOXYGEN_MIN_REQUIRED}) does not correctly process \\include commands in developer's installation instructions. This will make them incomplete. Upgrade Doxygen to fix.")
     endif()
 
     ## if not found, use empty string to avoid `warning: the dot tool could not be found as 'DOXYGEN_DOT_EXECUTABLE-NOTFOUND/dot.exe'` in doxygen-error.log

doc/doxygen/install/install-linux.doxygen

@@ -233,7 +233,7 @@
   <tt>HAS_XSERVER=Off</tt>, especially as you may not have compiled Qt with
   OpenGL and you may not have an X server.
 
-  \includedoc "../doxygen/install/common-cmake-parameters.doxygen"
+  \include "../doxygen/install/common-cmake-parameters.doxygen"
 
   A full list of the CMake variables is shown when you execute
 

doc/doxygen/install/install-macs.doxygen

@@ -191,7 +191,7 @@
   </ol>
 
 
-  \includedoc "../doxygen/install/common-cmake-parameters.doxygen"
+  \include "../doxygen/install/common-cmake-parameters.doxygen"
 
   After CMake was executed, you can list the make targets by calling: