Merge branch 'develop' into feature/oswSpeedUp

.github/workflows/containerdeploy.yml

@@ -4,7 +4,8 @@ on:
   push:
     branches:
       - nightly
-      - 'release/**'
+    tags:
+      - "Release*"
 
 jobs:
   DeployDocker:
@@ -29,7 +30,27 @@ jobs:
       - name: Downcase REPO
         run: echo "repo=${GITHUB_REPOSITORY,,}" >> $GITHUB_OUTPUT
         id: downcase_repo
-      - name: Checkout Dockerfiles
+      - name: Checkout repository because we need to build contrib
+        uses: actions/checkout@v3
+        with:
+          submodules: true
+        if: startsWith(steps.extract_branch.outputs.branch, 'release/')
+      - name: Login to GitHub Container Registry
+        uses: docker/login-action@v2
+        with:
+          registry: ghcr.io
+          username: ${{ github.actor }}
+          password: ${{ secrets.GITHUB_TOKEN }}        
+      - name: Build contrib container using the correct submodule hash
+        uses: docker/build-push-action@v3
+        with:
+          push: true
+          context: contrib
+          file: contrib/dockerfiles/Dockerfile
+          tags: |
+            ghcr.io/openms/contrib:${{ steps.tag_name.outputs.tag }}
+        if: startsWith(steps.extract_branch.outputs.branch, 'release/')        
+      - name: Checkout Library and Executable Dockerfiles
         shell: bash # uses git bash on windows
         run: |
             git clone https://github.com/OpenMS/dockerfiles
@@ -39,12 +60,6 @@ jobs:
             then
               git checkout ${{ steps.extract_branch.outputs.branch }} || git checkout master
             fi
-      - name: Login to GitHub Container Registry
-        uses: docker/login-action@v2
-        with:
-          registry: ghcr.io
-          username: ${{ github.actor }}
-          password: ${{ secrets.GITHUB_TOKEN }}
       - name: Build and Push Docker Library Image
         uses: docker/build-push-action@v3
         with:
@@ -89,6 +104,26 @@ jobs:
         shell: bash
         run: echo "repo=${GITHUB_REPOSITORY,,}" >> $GITHUB_OUTPUT
         id: downcase_repo
+      - name: Checkout repository because we need to build contrib
+        uses: actions/checkout@v3
+        with:
+          submodules: true
+        if: startsWith(steps.extract_branch.outputs.branch, 'release/')
+      - name: Login to GitHub Container Registry
+        uses: docker/login-action@v2
+        with:
+          registry: ghcr.io
+          username: ${{ github.actor }}
+          password: ${{ secrets.GITHUB_TOKEN }}        
+      - name: Build contrib container using the correct submodule hash
+        uses: docker/build-push-action@v3
+        with:
+          push: true
+          context: contrib
+          file: contrib/dockerfiles/Dockerfile
+          tags: |
+            ghcr.io/openms/contrib:${{ steps.tag_name.outputs.tag }}
+        if: startsWith(steps.extract_branch.outputs.branch, 'release/')                
       - name: Checkout Dockerfiles
         shell: bash
         run: |

.github/workflows/knime_tests.yml

@@ -5,6 +5,7 @@ on:
 jobs:
   test-knime:
     env:
+      GH_TOKEN: ${{ github.token }}
       KNIME_MAJOR_VERSION: 4
       KNIME_MINOR_VERSION: 7
       INSTALLATION_DIR: ${{ github.workspace }}
@@ -52,3 +53,18 @@ jobs:
             -i "org.knime.features.r.feature.group,org.knime.features.chem.types.feature.group,org.rdkit.knime.feature.feature.group,org.knime.features.ext.svg.feature.group" \
             -p KNIMEProfile \
             -nosplash
+            
+      - name: Create Workspace and fill with input data
+        run: |
+          wget -c https://abibuilder.cs.uni-tuebingen.de/archive/openms/Tutorials/Example_Data.tar.gz -O - | tar -xz
+            
+      - name:  Clone Tutorials
+        run: |
+          gh repo clone OpenMS/Tutorials
+          pushd Tutorials/Workflows
+            ./executeBatch.sh "$KNIME_DIR/knime" ${INSTALLATION_DIR}
+            cat log*.txt
+          popd
+            
+
+

.github/workflows/openms-ci.yml

@@ -24,11 +24,12 @@ jobs:
     - name: Install Qt
       uses: jurplel/install-qt-action@v3
       with:
-        version: '5.12.6' # 5.12.7 is broken https://bugreports.qt.io/browse/QTBUG-81715
+        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)
         host: 'windows' # default: win64_msvc2017_64
         target: 'desktop'
         install-deps: 'true'
         cache: 'false'
+        aqtversion: '==3.1.*'
 
     # https://github.com/marketplace/actions/visual-studio-shell
     - name: Set up Visual Studio shell
@@ -105,7 +106,7 @@ jobs:
           mkdir $GITHUB_WORKSPACE/OpenMS/bld/
           ctest --output-on-failure -V -S ../OpenMS/OpenMS/tools/ci/cibuild.cmake
       env:
-          #OS_PREFIX_PATH: "${{ env.Qt5_Dir }}/lib/cmake;${{ env.Qt5_Dir }}"
+          #OS_PREFIX_PATH: "${{ env.Qt5_DIR }}/lib/cmake;${{ env.Qt5_DIR }}"
           CONTRIB_BUILD_DIRECTORY: "${{ github.workspace }}/OpenMS/contrib"
           CI_PROVIDER: "GitHub-Actions"
           CMAKE_GENERATOR: "Ninja"
@@ -178,12 +179,13 @@ jobs:
     - name: Install Qt
       uses: jurplel/install-qt-action@v3
       with:
-        version: '5.12.7'
+        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)
         host: 'mac'
         target: 'desktop'
         install-deps: 'true'
         cache: 'false'
         setup-python: 'false' # see https://github.com/jurplel/install-qt-action/issues/130
+        aqtversion: '==3.1.*'
 
     - name: Install build tools
       run: brew install autoconf automake libtool ninja
@@ -213,17 +215,18 @@ jobs:
           done
 
           # create symlinks like brew https://github.com/Homebrew/homebrew-core/blob/master/Formula/qt.rb#L61
-          pushd $Qt5_Dir/include
-            for f in $Qt5_Dir/lib/*.framework/Headers
+          # Warning: Qt5_DIR will change meaning in the new jurplel/install-qt-action. Use QT_ROOT_DIR instead
+          # https://github.com/jurplel/install-qt-action/blob/master/README_upgrade_guide.md
+          pushd $Qt5_DIR/include
+            for f in $Qt5_DIR/lib/*.framework/Headers
             do
               lnknm=$(basename "${f%/*}" ".framework")
               ln -s $f $lnknm
             done
-            for f in $Qt5_Dir/lib/*.framework/Versions/5/Qt*
+            for f in $Qt5_DIR/lib/*.framework/Versions/5/Qt*
             do
               install_name_tool -id $f $f
             done
-            otool -L /Users/runner/work/OpenMS/Qt/5.12.7/clang_64/lib/QtCore.framework/Versions/5/QtCore
           popd
 
     - name: Add THIRDPARTY
@@ -459,7 +462,7 @@ jobs:
             mkdir $GITHUB_WORKSPACE/OpenMS/bld/
             ctest --output-on-failure -V -S $GITHUB_WORKSPACE/OpenMS/tools/ci/cibuild.cmake
       env:
-          OS_PREFIX_PATH: "${{ env.Qt5_Dir }}/lib/cmake;${{ env.Qt5_Dir }}"
+          OS_PREFIX_PATH: "${{ env.Qt5_DIR }}/lib/cmake;${{ env.Qt5_DIR }}"
           CONTRIB_BUILD_DIRECTORY: "/contrib-build"
           CI_PROVIDER: "GitHub-Actions"
           CMAKE_GENERATOR: "Ninja"

.github/workflows/pyopenms-wheels.yml

@@ -24,7 +24,7 @@ jobs:
     - name: Setup cmake
       uses: jwlawson/actions-setup-cmake@v1.13
       with:
-        cmake-version: '3.23.x'
+        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
@@ -140,7 +140,7 @@ jobs:
     - name: Setup cmake
       uses: jwlawson/actions-setup-cmake@v1.13
       with:
-        cmake-version: '3.23.x'
+        cmake-version: '3.25.x'
 
     - name: Install Qt
       uses: jurplel/install-qt-action@v3
@@ -244,10 +244,6 @@ jobs:
           pip install -U wheel
           pip install -U pandas
 
-          #conda deactivate
-
-          echo $CURRENT_PYTHON_EXECUTABLE
-
           # build pyopenms distribution (macOS)
           cmake -DPYTHON_EXECUTABLE:FILEPATH=$CURRENT_PYTHON_EXECUTABLE -DPYOPENMS=ON .
           make -j4 pyopenms
@@ -298,7 +294,7 @@ jobs:
     - name: Setup cmake
       uses: jwlawson/actions-setup-cmake@v1.13
       with:
-        cmake-version: '3.23.x'
+        cmake-version: '3.25.x'
 
     - name: Build on manylinux2014
       shell: bash
@@ -350,6 +346,10 @@ jobs:
             mv wheelhouse/* $GITHUB_WORKSPACE/data/wheelhouse/
           popd
           export LD_LIBRARY_PATH=$LD_OLD_LIBRARY_PATH
+          
+          # clean previous pyopenms libs
+          rm pyOpenMS/pyopenms/_pyopenms*.so
+        
         done
 
     - uses: actions/upload-artifact@v3
@@ -468,6 +468,7 @@ jobs:
             ls -la wheels/
 
     - name: Publish package to nightly PyPI
+      if: "contains(github.ref, 'develop') || contains(github.ref, 'nightly')"
       uses: pypa/gh-action-pypi-publish@release/v1
       with:
         repository_url: https://pypi.cs.uni-tuebingen.de/

.github/workflows/update_version_numbers.yml

@@ -15,10 +15,10 @@ jobs:
   updating_package_version_number:
     runs-on: macos-latest
     steps:
-# Getting files (OpenMS)
+      # Getting files (OpenMS)
       - uses: actions/checkout@v3
 
-# Update files with new package version numbers
+      # Update files with new package version numbers
       - name: update files
         run: |
           # setting variables
@@ -44,7 +44,26 @@ jobs:
           # update INIs in tests topp:
           find ./src/tests/topp/ -type f -name '*.ini' -exec grep -q "<ITEM name=\"version\" value=\".*\" type=\"string\"" {} \; -exec sed -i '' "s#<ITEM name=\"version\" value=\".*\" type=\"string\"#<ITEM name=\"version\" value=\"$package_version\" type=\"string\"#g" {} \;
 
-# Check for changes
+          # Update Changelog
+          # Define the new section using a here-doc
+          section_header=$(cat <<EOF
+          ------------------------------------------------------------------------------------------
+          ----                                OpenMS ${package_version}     (under development)              ----
+          ------------------------------------------------------------------------------------------
+          
+          
+          .    # ends with a period for preserve trailing newlines
+          EOF
+          )
+          section_header=${section_header%.*}   # remove the period
+
+          # Get the line number of the first line starting with more than 10 "-"
+          line_num=$(grep -n "^-\{10,\}" CHANGELOG | head -n 1 | cut -d ":" -f 1)
+
+          # Use perl to insert the text at the specified line number in the file
+          perl -i -pe "print '${section_header}' if \$. == ${line_num}" CHANGELOG
+
+      # Check for changes
       - name: check for changed files
         id: changed-files
         run: |
@@ -54,13 +73,15 @@ jobs:
             echo "changes_exist=true" >> $GITHUB_ENV
           fi
 
-# Commit and PR updated files
+      # Commit and PR updated files
       - name: Commit and PR updated files
         if: env.changes_exist
         uses: peter-evans/create-pull-request@v4
         with:
           commit-message: 'Updated OpenMS package version number'
-          committer: ${{ github.actor	}}
+          committer: GitHub <noreply@github.com>
+          author: ${{ github.actor }} <${{ github.actor }}@users.noreply.github.com>
+          signoff: false
           branch: update_package_number
           delete-branch: true
-          title: '[ByGitAction] Updated OpenMS package version number'
+          title: '[ByGHAction] Updated OpenMS package version numbers'

.github/workflows/update_year_number.yml

@@ -1,11 +1,13 @@
 name: Update year number
 
-# Trigger this action manually
+# Trigger this action manually and on a yearly schedule
 on:
   workflow_dispatch:
     inputs:
       year_number:
         required: true
+  schedule:
+    - cron: '0 0 1 1 *'
 
 jobs:
   updating_year_number:
@@ -21,13 +23,15 @@ jobs:
           year_number="${{ github.event.inputs.year_number }}"
           # Find and replace in all files
           find . -type f ! -path "./.git/*" -exec grep -q "Freie Universitaet Berlin 2002-20" {} \; -exec sed -i '' -E "s#and Freie Universitaet Berlin 2002-20[0-9]{2}.#and Freie Universitaet Berlin 2002-$year_number.#g" {} \;
-
+          
+          # Find and replace in LICENSE.md
+          sed -i -E "s#2002-20[0-9]{2}, The OpenMS Team -- Eberhard Karls University#2002-$year_number, The OpenMS Team -- Eberhard Karls University#g" LICENSE.md
+          
 # Commit and PR updated files
       - name: Commit and PR updated files
-        uses: peter-evans/create-pull-request@v4
+        uses: peter-evans/create-pull-request@v5
         with:
           commit-message: 'Updated year number'
-          committer: ${{github.actor}}
           branch: update_year_number
           delete-branch: true
           title: '[ByGitAction] Updated year number in the header of files'

AUTHORS

@@ -2,7 +2,7 @@
                  OpenMS -- Open Source Mass Spectrometry
 =========================================================================
 
-The following authors contributed to OpenMS at some point. For the 
+The following authors contributed to OpenMS at some point. For the
 authors contributing to a specific piece of code, please refer to
 the authors tag in the respective file header.
  - Ahmed Khalil
@@ -48,7 +48,7 @@ the authors tag in the respective file header.
  - Holger Franken
  - Holger Plattfaut
  - Immanuel Luhn
- - Jang Jang Jin 
+ - Jang Jang Jin
  - Jihyung Kim
  - Johan Teleman
  - Johannes Junker
@@ -90,6 +90,7 @@ the authors tag in the respective file header.
  - Ruben Grünberg
  - Samuel Wein
  - Sandro Andreotti
+ - Simon Gene Gottlieb
  - Steffen Sass
  - Stephan Aiche
  - Sven Nahnsen

CHANGELOG

@@ -14,6 +14,11 @@ UTIL - An executable, just like a TOPP tool, but usually experimental or of less
 #<number>, e.g. #4957 - a reference to an issue or pull request on GitHub, visit https://github.com/OpenMS/OpenMS/pull/4957 for details
 
 
+------------------------------------------------------------------------------------------
+----                                OpenMS 3.1.0     (under development)              ----
+------------------------------------------------------------------------------------------
+
+
 ------------------------------------------------------------------------------------------
 ----                                OpenMS 3.0     (releases 4/2022)                  ----
 ------------------------------------------------------------------------------------------
@@ -38,9 +43,13 @@ reference and advanced developer documentation remains inside OpenMS doxygen
 documentation.
 - Add support for user defined ribonucleotides with phosphorothioate linkages
 - Add support for JSON based ribonucleotides and updated to latest Modomics database
+- fix bug in GaussFilter when using ppm as width (#6830)
+- Add support to load parameter values from a JSON formatted .json file. (Accessible via -ini. This will be
+  helpful for Common Workflow Language users and others)
 
 New Tools:
 - FLASHDeconv -- Ultra-fast high-quality deconvolution enables online processing of top-down MS data (TOPP)
+- FLASHDeconvWizard -- An GUI assistant for FLASHDeconv execution.
 
 ------------------------------------------------------------------------------------------
 ----                                OpenMS 2.8     (released 2/2022)                  ----