add intensity-weighted average peak picker

.clang-format

@@ -7,7 +7,7 @@ AlignOperands: true
 AllowAllArgumentsOnNextLine: false
 AllowAllConstructorInitializersOnNextLine: true
 AllowAllParametersOfDeclarationOnNextLine: false
-AllowShortBlocksOnASingleLine: Always
+AllowShortBlocksOnASingleLine: true
 AllowShortCaseLabelsOnASingleLine: false
 AllowShortFunctionsOnASingleLine: None
 AllowShortIfStatementsOnASingleLine: Never
@@ -33,34 +33,39 @@ BreakBeforeBinaryOperators: None
 BreakBeforeTernaryOperators: false
 BreakConstructorInitializers: AfterColon
 BreakInheritanceList: AfterColon
-ColumnLimit: 0
+ColumnLimit: 200
 CompactNamespaces: false
-ContinuationIndentWidth: 4
+ContinuationIndentWidth: 2
+FixNamespaceComments: true
+IncludeBlocks: Regroup
 IndentCaseLabels: true
 IndentPPDirectives: BeforeHash
 IndentWidth: 2
-KeepEmptyLinesAtTheStartOfBlocks: true
+KeepEmptyLinesAtTheStartOfBlocks: false
 MaxEmptyLinesToKeep: 2
 NamespaceIndentation: All
 ObjCSpaceAfterProperty: false
 ObjCSpaceBeforeProtocolList: true
 PointerAlignment: Left
-ReflowComments: false
-SpaceAfterCStyleCast: true
+ReflowComments: true
+SortIncludes: true
+SortUsingDeclarations: true
+SpaceAfterCStyleCast: false
 SpaceAfterLogicalNot: false
 SpaceAfterTemplateKeyword: false
 SpaceBeforeAssignmentOperators: true
-SpaceBeforeCpp11BracedList: false
+SpaceBeforeCpp11BracedList: true
 SpaceBeforeCtorInitializerColon: true
 SpaceBeforeInheritanceColon: true
 SpaceBeforeParens: ControlStatements
 SpaceBeforeRangeBasedForLoopColon: true
 SpaceInEmptyParentheses: false
-SpacesBeforeTrailingComments: 0
+SpacesBeforeTrailingComments: 1
 SpacesInAngles: false
 SpacesInCStyleCastParentheses: false
 SpacesInContainerLiterals: false
 SpacesInParentheses: false
 SpacesInSquareBrackets: false
+Standard: Cpp11
 TabWidth: 2
 UseTab: Never

.github/workflows/cppcheck.yml

@@ -0,0 +1,20 @@
+name: cppcheck-action-test
+on: [push]
+
+jobs:
+  build:
+    name: cppcheck-test
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v2
+
+      - name: cppcheck
+        uses: deep5050/cppcheck-action@main
+        with:
+          github_token: ${{ secrets.GITHUB_TOKEN}}
+          exclude_check: ./src/openms/thirdparty
+          inconclusive: disable
+          other_options: -i./cmake -i./doc -i./src/tests
+
+      - name: show report    
+        run: cat cppcheck_report.txt

.github/workflows/dockerdeploy.yml

@@ -0,0 +1,71 @@
+name: deploy-docker-images
+on:
+  workflow_dispatch:
+  push:
+    branches:        
+      - nightly
+      - 'release/**'
+
+jobs:
+  Deploy:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Extract branch name
+        shell: bash
+        run: echo "##[set-output name=branch;]$(echo ${GITHUB_REF#refs/heads/})"
+        id: extract_branch
+      - name: Define tag name
+        shell: bash
+        run: |
+            BRANCH=${{ steps.extract_branch.outputs.branch }}
+            ## use latest to follow docker conventions
+            if [[ "$BRANCH" == "develop" ]]
+            then 
+              BRANCH="latest"
+            fi
+            if [[ "$BRANCH" == "nightly" ]]
+            then 
+              BRANCH="latest"
+            fi
+            ## Remove release/ from release branch name
+            echo "##[set-output name=tag;]$(echo ${BRANCH#release/})"
+        id: tag_name
+      - name: Downcase REPO
+        run: echo "##[set-output name=repo;]$(echo ${GITHUB_REPOSITORY,,})"
+        id: downcase_repo
+      - name: Checkout Dockerfiles
+        shell: bash # uses git bash on windows
+        run: |
+            git clone https://github.com/OpenMS/dockerfiles
+            cd dockerfiles
+            ## for release, try to checkout the specific release branch in the dockerfiles repo first
+            if [[ "${{ steps.extract_branch.outputs.branch }}" == "release/"* ]]
+            then
+              git checkout ${{ steps.extract_branch.outputs.branch }} || git checkout master
+            fi
+      - name: Login to GitHub Container Registry
+        uses: docker/login-action@v1
+        with:
+          registry: ghcr.io
+          username: jpfeuffer
+          password: ${{ secrets.GH_REGISTRY_TOKEN }}
+      - name: Build and Push Docker Library Image
+        uses: docker/build-push-action@v2
+        with:
+          push: true # Will only build if this is not here
+          context: dockerfiles/library
+          build-args: |
+            OPENMS_TAG=latest
+            OPENMS_BRANCH=${{ steps.extract_branch.outputs.branch }}
+          tags: |
+            ghcr.io/${{ steps.downcase_repo.outputs.repo }}-library:${{ steps.tag_name.outputs.tag }}
+      - name: Build and Push Docker Tools Image
+        uses: docker/build-push-action@v2
+        with:
+          push: true # Will only build if this is not here
+          context: dockerfiles/executables
+          build-args: |
+            OPENMS_TAG=latest
+            OPENMS_BRANCH=${{ steps.extract_branch.outputs.branch }}
+          tags: |
+            ghcr.io/${{ steps.downcase_repo.outputs.repo }}-executables:${{ steps.tag_name.outputs.tag }}

.github/workflows/openms-ci.yml

@@ -12,15 +12,15 @@ on:
 jobs:
 
   build-win:
-    runs-on: windows-latest
+    runs-on: windows-2022
     continue-on-error: true
     steps:
     - uses: actions/checkout@v2
       with:
         path: OpenMS
 
     - 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
+      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\2022\\Enterprise\Common7\IDE\CommonExtensions\Microsoft\CMake\CMake\bin" | Out-File -FilePath $env:GITHUB_ENV -Encoding utf8 -Append
 
     - name: Install Qt
       uses: jurplel/install-qt-action@v2
@@ -43,7 +43,7 @@ jobs:
       uses: actions/cache@v2
       with:
         path: ${{ github.workspace }}/OpenMS/contrib
-        key: ${{ runner.os }}-contrib
+        key: ${{ runner.os }}-contrib2
 
     - name: Load contrib build
       if: steps.cache-contrib-win.outputs.cache-hit != 'true'
@@ -71,9 +71,9 @@ jobs:
       id: extract_pr
 
     - name: Setup cmake
-      uses: jwlawson/actions-setup-cmake@v1.8
+      uses: jwlawson/actions-setup-cmake@v1.12
       with:
-        cmake-version: '3.20.x'
+        cmake-version: 'latest'
 
     - name: Add THIRDPARTY
       shell: bash
@@ -109,7 +109,7 @@ jobs:
           fi
 
       env:
-          CMAKE_GENERATOR: "Visual Studio 16 2019"
+          CMAKE_GENERATOR: "Visual Studio 17 2022"
           CONTRIB_BUILD_DIRECTORY: "${{ github.workspace }}/OpenMS/contrib"
           CI_PROVIDER: "GitHub-Actions"
           SOURCE_DIRECTORY: "${{ github.workspace }}/OpenMS"
@@ -151,7 +151,7 @@ jobs:
       uses: actions/cache@v2
       with:
         path: ${{ github.workspace }}/OpenMS/contrib
-        key: ${{ runner.os }}-contrib
+        key: ${{ runner.os }}-contrib2
 
     - name: Load contrib build
       if: steps.cache-contrib-os.outputs.cache-hit != 'true'

.github/workflows/openms_clang_format.yml

@@ -0,0 +1,33 @@
+# Action to allow clang format linting at the files changed in the PR
+
+on:
+  pull_request:
+    branches:
+    - develop
+
+name: Clang format linting
+jobs:
+
+# Checkout OpenMS
+  lint:
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v2
+
+# Get files changed in the PR
+    - name: Get changed files
+      id: changed_files
+      uses: tj-actions/changed-files@v12
+      with:
+          path: .
+          files: |
+            \.h$
+            \.cpp$
+
+# Perform linting
+    - name: Use clang format linting
+      if: steps.changed_files.outputs.any_modified == 'true'
+      uses: DoozyX/clang-format-lint-action@v0.13
+      with:
+        source: ${{ steps.changed_files.outputs.all_modified_files }}
+        clangFormatVersion: 13

.github/workflows/openms_clang_format_add_and_commit.yml

@@ -0,0 +1,39 @@
+# Action to allow clang format linting at the files changed in the PR
+
+on:
+  issue_comment:
+    types: [created]
+
+jobs:
+  lint:
+    name: Automatic clang format linting
+    runs-on: ubuntu-latest
+    if: github.event.issue.pull_request != '' && contains(github.event.comment.body, '/reformat')
+    steps:
+      - uses: actions/checkout@v2
+        with:
+          ref: ${{ github.event.pull_request.head.sha }}
+          fetch-depth: 0
+
+# Get files changed in the PR
+      - name: Get changed files
+        id: changed-files
+        uses: tj-actions/changed-files@v10.1
+        with:
+            path: .
+            files: |
+              \.h$
+              \.cpp$
+
+# Perform linting
+      - name: Use clang format linting
+        uses: DoozyX/clang-format-lint-action@v0.13
+        with:
+          source: ${{ steps.changed-files.outputs.all_modified_files }}
+          clangFormatVersion: 13
+          inplace: True
+      - uses: EndBug/add-and-commit@v4
+        with:
+          message: 'Committing clang-format changes'
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}

.github/workflows/pyopenms-wheels.yml

@@ -212,10 +212,13 @@ jobs:
               ln -s $f $lnknm
             done
             for f in $Qt5_Dir/lib/*.framework/Versions/5/Qt*
+            do
+              install_name_tool -id $Qt5_Dir/lib/$(basename $f).framework/Versions/Current/$(basename $f) $f
+            done
+            for f in $Qt5_Dir/lib/*.framework/Versions/Current/Qt*
             do
               install_name_tool -id $f $f
             done
-            otool -L /Users/runner/work/OpenMS/Qt/5.12.7/clang_64/lib/QtCore.framework/Versions/5/QtCore
           popd
           mkdir bld
           pushd bld
@@ -254,6 +257,7 @@ jobs:
             # build pyopenms distribution (macOS)
             cmake -DPYTHON_EXECUTABLE:FILEPATH=$CURRENT_PYTHON_EXECUTABLE -DPYOPENMS=ON .
             make -j4 pyopenms
+            ls -la pyOpenMS/pyopenms/QtCore.framework/Versions/*
 
             # copy to directory
             cp pyOpenMS/dist/*.whl pyopenms_whls/

.github/workflows/rebase.yml

@@ -13,6 +13,6 @@ jobs:
       with:
         fetch-depth: 0
     - name: Automatic Rebase
-      uses: cirrus-actions/rebase@1.3.1
+      uses: cirrus-actions/rebase@1.5
       env:
         GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}

.gitmodules

@@ -5,3 +5,6 @@
 	path = THIRDPARTY
 	url = https://github.com/OpenMS/THIRDPARTY
 	shallow = true
+[submodule "src/pyOpenMS/pyopenms-extra"]
+	path = src/pyOpenMS/pyopenms-extra
+	url = https://github.com/OpenMS/pyopenms-extra.git

.gitpod.Dockerfile

@@ -1,4 +1,4 @@
-FROM openms/contrib:latest
+FROM ghcr.io/openms/contrib:latest
 
 #USER gitpod
 # Avoid user input

AUTHORS

@@ -23,6 +23,7 @@ the authors tag in the respective file header.
  - Darren Kessner
  - David Wojnar
  - David Voigt
+ - Dhanmoni Nath
  - Dilek Dere
  - Dimitri Schachmann
  - Dominik Schmitz
@@ -53,9 +54,11 @@ the authors tag in the respective file header.
  - Juliane Schmachtenberg
  - Julianus Pfeuffer
  - Katharina Albers
+ - Khue Nguyen
  - Knut Reinert
  - Lars Nilse
  - Leon Bichmann
+ - Leon Kuchenbecker
  - Lucia Espona
  - Lukas Mueller
  - Lukas Zimmermann