MSSimulator Erweiterung

.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/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

@@ -6,7 +6,7 @@ ARG DEBIAN_FRONTEND=noninteractive
 ARG CLANGDVER=12.0.1
 
 # Install tools for VSCode, Intellisense, JRE for Thirdparties, etc. using apt-get
-RUN apt-get -q update && apt-get install -yq gdb unzip wget php openjdk-11-jre clang-tidy python3-pip && rm -rf /var/lib/apt/lists/*
+RUN apt-get -q update && apt-get install -yq gdb unzip wget php openjdk-11-jre python3-pip && rm -rf /var/lib/apt/lists/*
 RUN wget https://github.com/clangd/clangd/releases/download/$CLANGDVER/clangd-linux-$CLANGDVER.zip && unzip clangd-linux-$CLANGDVER.zip -d /opt/ && mv /opt/clangd_$CLANGDVER /opt/clangd/ && rm clangd-linux-$CLANGDVER.zip 
 #
 # More information: https://www.gitpod.io/docs/42_config_docker/

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
@@ -56,8 +57,10 @@ the authors tag in the respective file header.
  - Knut Reinert
  - Lars Nilse
  - Leon Bichmann
+ - Leon Kuchenbecker
  - Lucia Espona
  - Lukas Mueller
+ - Lucas Rieckert
  - Lukas Zimmermann
  - Marcel Schilling
  - Marc Sturm

CHANGELOG

@@ -16,6 +16,9 @@ UTIL - An executable, just like a TOPP tool, but usually experimental or of less
 ------------------------------------------------------------------------------------------
 
 - Deisotoping algorithm using KL
+- Resolve compatibility issues between IDRipper and IDMerger #4957
+- Basic MzTabM support for AccurateMassSearch
+- Changed default parameter keep_unidentified_masses to "true" (AccurateMassSearch/AccurateMassSearchEngine)
 
 ------------------------------------------------------------------------------------------
 ----                                OpenMS 2.7                                        ----

PULL_REQUEST_TEMPLATE.md

@@ -12,6 +12,12 @@ Please include a summary of the change and which issue is fixed.
 # How can I get additional information on failed tests during CI:
 If your PR is failing you can check out 
 - http://cdash.openms.de/index.php?project=OpenMS and look for your PR. If you click in the column that lists the failed tests you will get detailed error messages.
+- Or click on the action: e.g., for clang-format linting
 
 # Note:
 - Once you opened a PR try to minimize the number of *pushes* to it as every push will trigger CI (automated builds and test) and is rather heavy on our infrastructure (e.g., if several pushes per day are performed).
+
+# Advanced commands (admins / reviewer only):
+- /rebase will try to rebase the PR on the current develop branch.
+- /reformat (experimental) applies the clang-format style changes as additional commit
+- setting the label NoJenkins will skip tests for this PR on jenkins (saves resources e.g., on edits that do not affect tests)

cmake/compiler_flags.cmake

@@ -42,6 +42,11 @@ if (MY_CXX_FLAGS)
   add_compile_options(${MY_CXX_FLAGS})
 endif()
 
+if (${CMAKE_SYSTEM_NAME} MATCHES "Darwin")
+  # workaround for MacOS 10.13 and below which does not support std::visit
+  # see https://github.com/OpenMS/OpenMS/issues/5714
+  add_definitions(-D_LIBCPP_DISABLE_AVAILABILITY)  
+endif()
 
 if (CMAKE_COMPILER_IS_GNUCXX)
 

cmake/package_general.cmake

@@ -63,7 +63,7 @@ set(CPACK_RESOURCE_FILE_README ${PROJECT_SOURCE_DIR}/cmake/OpenMSPackageResource
 #  " COMPONENT applications)
 
 if(APPLE OR WIN32) ## On Linux we require Qt to be installed from the package manager system-wide (e.g. via dependencies)
-  set(PACKAGE_QT_COMPONENTS "${OpenMS_QT_COMPONENTS};${OpenMS_GUI_QT_COMPONENTS}")
+  set(PACKAGE_QT_COMPONENTS "${OpenMS_QT_COMPONENTS};${OpenMS_GUI_QT_COMPONENTS};${OpenMS_GUI_QT_COMPONENTS_OPT}")
   find_package(Qt5 COMPONENTS ${PACKAGE_QT_COMPONENTS}) ## we have to find again so the target variables are reloaded
   install_qt5_libs("${PACKAGE_QT_COMPONENTS}" ${INSTALL_LIB_DIR} "QTLibs")
 endif()

doc/CMakeLists.txt

@@ -80,11 +80,12 @@ if(ENABLE_DOCS)
   if(WITH_GUI)
     #------------------------------------------------------------------------------
     # QT dependencies
-    find_package(Qt5 COMPONENTS Core Network Svg OpenGL REQUIRED)
+    find_package(Qt5 COMPONENTS Core Network Sql Svg OpenGL REQUIRED)
+    find_package(Qt5 COMPONENTS WebEngineWidgets)
     set(_doc_progs_include ${OpenMS_GUI_INCLUDE_DIRECTORIES})
     set(_doc_progs_link_libraries ${OpenMS_GUI_LIBRARIES})
   else()
-    find_package(Qt5 COMPONENTS Core Network REQUIRED)
+    find_package(Qt5 COMPONENTS Core Network Sql REQUIRED)
     set(_doc_progs_include ${OpenMS_INCLUDE_DIRECTORIES})
     set(_doc_progs_link_libraries ${OpenMS_LIBRARIES})
   endif()

doc/code_examples/CMakeLists.txt

@@ -50,7 +50,7 @@ include_directories(SYSTEM ${OpenMS_INCLUDE_DIRECTORIES})
 
 #------------------------------------------------------------------------------
 # QT dependencies
-find_package(Qt5 COMPONENTS Core Network REQUIRED)
+find_package(Qt5 COMPONENTS Core Network Sql REQUIRED)
 
 # add the targets
 foreach(i ${EXAMPLES_executables})
@@ -70,6 +70,7 @@ add_dependencies(Tutorials_build ${EXAMPLES_executables})
 
 if(WITH_GUI)
   find_package(Qt5 COMPONENTS Core Network OpenGL Svg REQUIRED)
+  find_package(Qt5 COMPONENTS WebEngineWidgets)
   # add OpenMS GUI includes
   include_directories(SYSTEM ${OpenMS_GUI_INCLUDE_DIRECTORIES})
 

doc/code_examples/Tutorial_FeatureMap.cpp

@@ -57,9 +57,9 @@ int main()
 
   // Calculate and output the ranges
   map.updateRanges();
-  cout << "Int: " << map.getMinInt() << " - " << map.getMaxInt() << endl;
-  cout << "RT:  " << map.getMin()[0] << " - " << map.getMax()[0] << endl;
-  cout << "m/z: " << map.getMin()[1] << " - " << map.getMax()[1] << endl;
+  cout << "Int: " << map.getMinIntensity() << " - " << map.getMaxIntensity() << endl;
+  cout << "RT:  " << map.getMinRT() << " - " << map.getMaxRT() << endl;
+  cout << "m/z: " << map.getMinMZ() << " - " << map.getMaxMZ() << endl;
 
   // ... and many more
   return 0;

doc/code_examples/Tutorial_GUI_ParamEditor.cpp

@@ -58,6 +58,6 @@ Int main(int argc, const char** argv)
 
   editor->store();
   paramFile.store("Tutorial_ParamEditor_out.ini", param);
-
+  delete editor;
   return 0;
 } //end of main

doc/code_examples/Tutorial_GUI_Plot1D.cpp

@@ -33,7 +33,7 @@
 #include <OpenMS/FORMAT/DTAFile.h>
 #include <OpenMS/KERNEL/StandardTypes.h>
 #include <OpenMS/KERNEL/OnDiscMSExperiment.h>
-#include <OpenMS/VISUAL/LayerData.h>
+#include <OpenMS/VISUAL/LayerDataBase.h>
 
 using namespace OpenMS;
 using namespace std;
@@ -49,11 +49,11 @@ Int main(int argc, const char ** argv)
   PeakMap exp;
   exp.resize(1);
   DTAFile().load(tutorial_data_path + "/data/Tutorial_Spectrum1D.dta", exp[0]);
-  LayerData::ExperimentSharedPtrType exp_sptr(new PeakMap(exp));
-  LayerData::ODExperimentSharedPtrType on_disc_exp_sptr(new OnDiscMSExperiment());
+  LayerDataBase::ExperimentSharedPtrType exp_sptr(new PeakMap(exp));
+  LayerDataBase::ODExperimentSharedPtrType on_disc_exp_sptr(new OnDiscMSExperiment());
   Plot1DWidget * widget = new Plot1DWidget(Param(), nullptr);
   widget->canvas()->addLayer(exp_sptr, on_disc_exp_sptr);
   widget->show();
-
+  delete widget;
   return app.exec();
 } //end of main

doc/code_examples/Tutorial_RangeManager.cpp

@@ -51,9 +51,9 @@ Int main()
   //calculate the ranges
   map.updateRanges();
 
-  cout << "Int: " << map.getMinInt() << " - " << map.getMaxInt() << endl;
-  cout << "RT:  " << map.getMin()[0] << " - " << map.getMax()[0] << endl;
-  cout << "m/z: " << map.getMin()[1] << " - " << map.getMax()[1] << endl;
+  cout << "Int: " << map.getMinIntensity() << " - " << map.getMaxIntensity() << endl;
+  cout << "RT:  " << map.getMinRT() << " - " << map.getMaxRT() << endl;
+  cout << "m/z: " << map.getMinMZ() << " - " << map.getMaxMZ() << endl;
 
   return 0;
 } //end of main

doc/doxygen/install/install-linux.doxygen

@@ -113,12 +113,12 @@
     sudo apt-get install qtbase5-dev libqt5svg5-dev libqt5opengl5-dev
     sudo apt-get install libboost-regex-dev libboost-iostreams-dev \
       libboost-date-time-dev libboost-math-dev libboost-random-dev libsvm-dev \
-      libglpk-dev zlib1g-dev libxerces-c-dev seqan-dev libbz2-dev coinor-libcoinmp-dev libhdf5-dev
+      libglpk-dev zlib1g-dev libxerces-c-dev libbz2-dev coinor-libcoinmp-dev libhdf5-dev
       # Use from contrib: EIGEN; SQLITE; WILDMAGIC (since libwildmagic-dev is buggy)
     </pre></td>
   </tr>
   <tr>
-      <td><B>Ubuntu/Debian <br/>(>= 17.04)</B></td>
+      <td><B>Ubuntu/Debian <br/>(17.04 and 18.04)</B></td>
       <td><pre>
     # include the ubuntu universe repository and update
     sudo add-apt-repository universe
@@ -127,7 +127,7 @@
     sudo apt-get install qtbase5-dev libqt5svg5-dev libqt5opengl5-dev
     sudo apt-get install libeigen3-dev libsqlite3-dev libwildmagic-dev libboost-random1.62-dev \
       libboost-regex1.62-dev libboost-iostreams1.62-dev libboost-date-time1.62-dev libboost-math1.62-dev \
-      libxerces-c-dev libglpk-dev zlib1g-dev libsvm-dev libbz2-dev seqan-dev coinor-libcoinmp-dev libhdf5-dev
+      libxerces-c-dev libglpk-dev zlib1g-dev libsvm-dev libbz2-dev coinor-libcoinmp-dev libhdf5-dev
       # this should eliminate the need for building contrib libraries.
       </pre></td>
   </tr>
@@ -141,7 +141,7 @@
     sudo apt-get install qtbase5-dev libqt5svg5-dev libqt5opengl5-dev
     sudo apt-get install libeigen3-dev libsqlite3-dev libwildmagic-dev libboost-random1.67-dev \
       libboost-regex1.67-dev libboost-iostreams1.67-dev libboost-date-time1.67-dev libboost-math1.67-dev \
-      libxerces-c-dev libglpk-dev zlib1g-dev libsvm-dev libbz2-dev seqan-dev coinor-libcoinmp-dev libhdf5-dev
+      libxerces-c-dev libglpk-dev zlib1g-dev libsvm-dev libbz2-dev coinor-libcoinmp-dev libhdf5-dev
       # this should eliminate the need for building contrib libraries.
       </pre></td>
   </tr>