Testpatch

.github/workflows/openms_ci_matrix_full.yml

@@ -413,6 +413,7 @@ jobs:
           BUILD_TYPE: "Release"
           OPENMP: "ON"
           BOOST_USE_STATIC: ${{ steps.set-vars.outputs.static_boost }}
+          COMPILE_PXDS: ${{ startsWith(matrix.os, 'ubuntu') && github.event_name == 'pull_request' && github.event.pull_request.base.ref == 'develop' && 'ON' || 'OFF' }} # test generation of pxds
           #  BUILD_FLAGS: "-p:CL_MPCount=2" # For VS Generator and MSBuild
           BUILD_FLAGS: "-j${{ steps.cpu-cores.outputs.count }}" # Ninja will otherwise use all cores (doesn't go well in GHA).
           CMAKE_CCACHE_EXE: "ccache"
@@ -670,7 +671,7 @@ jobs:
       - name: run GHA release action.
         id: create_release
         if: inputs.do_release
-        uses: ncipollo/release-action@v1.14.0
+        uses: ncipollo/release-action@v1.16.0
         with: 
           bodyFile: RELEASE_TEXT_GH.md
           tag: ${{ github.ref_name }}
@@ -941,7 +942,7 @@ jobs:
           mkdir -p ~/.ssh/
           echo "$PASS" > ~/.ssh/private.key
           sudo chmod 600 ~/.ssh/private.key
-          ln -s ./$folder latest  #create link to the release folder
+          ln -s ../$folder latest  #create link to the release folder
           rsync --progress -avz -e "ssh -i ~/.ssh/private.key -p $PORT -o StrictHostKeyChecking=no" latest "$USER@$HOST:/knime-plugin/updateSite/release"
 
   do-release:
@@ -963,36 +964,65 @@ jobs:
         shell: bash
         run: echo "RUN_NAME=${{ github.event.pull_request && github.event.number || github.ref_name }}" >> $GITHUB_ENV
 
-      # NB we create the tag for the OpenMS repo next in a separate action.
+          # We created the draft release during deploy-installer step. Now we want to publish it.
+      - name: Publish OpenMS release
+        id: publish_release
+        if: inputs.do_release
+        uses: ncipollo/release-action@v1.16.0
+        with:
+          tag: ${{ github.ref_name }}
+          draft: false
+          allowUpdates: true
+          artifactErrorsFailBuild: true
+          makeLatest: ${{ inputs.mark_as_latest }}
+          omitBodyDuringUpdate: true
+          omitNameDuringUpdate: true
+          updateOnlyUnreleased: true
+
+
+          # NB we create the tag for the OpenMS repo next in a separate action.
+          # SPW TODO: Move the script here to a file once its stable
       - id: bash_create_tags
         name: create tags for other repos
         shell: bash
         env: 
           GH_TOKEN: ${{ steps.app-token.outputs.token }}
         run: |
-          function createGitTag() {
+          function handleGitTag() {
             REPO=$1
             SHA=$2
-            gh api \
-              --method POST \
+            TAG_NAME="${{ env.RUN_NAME }}"
+
+            # Check if the tag exists
+            TAG_EXISTS=$(gh api \
+              --method GET \
               -H "Accept: application/vnd.github+json" \
               -H "X-GitHub-Api-Version: 2022-11-28" \
-              /repos/${REPO}/git/refs \
-              -f ref="refs/tags/${{ env.RUN_NAME }}" \
-            -f sha="${SHA}"
-          }
-
-          function updateGitTag() {
-            REPO=$1
-            SHA=$2
-
-            gh api \
-              --method PATCH \
-              -H "Accept: application/vnd.github+json" \
-              -H "X-GitHub-Api-Version: 2022-11-28" \
-              /repos/${REPO}/git/refs/tags/${{ env.RUN_NAME }} \
-              -f sha="${SHA}" \
-              -F force=true
+              /repos/${REPO}/git/refs/tags/${TAG_NAME} 2>/dev/null || echo "TAG_NOT_FOUND")
+
+            if [[ "$TAG_EXISTS" == "TAG_NOT_FOUND" ]]; then
+              # Tag doesn't exist, create it
+              echo "Creating tag ${TAG_NAME} in ${REPO} pointing to ${SHA}"
+              gh api \
+                --method POST \
+                -H "Accept: application/vnd.github+json" \
+                -H "X-GitHub-Api-Version: 2022-11-28" \
+                /repos/${REPO}/git/refs \
+                -f ref="refs/tags/${TAG_NAME}" \
+                -f sha="${SHA}"
+            else
+              # Tag exists, check if it points to the same SHA
+              EXISTING_SHA=$(echo $TAG_EXISTS | jq -r '.object.sha')
+
+              if [[ "$EXISTING_SHA" == "$SHA" ]]; then
+                # Tag already points to the correct SHA, do nothing
+                echo "Tag ${TAG_NAME} already exists in ${REPO} and points to the correct SHA: ${SHA}"
+              else
+                # Tag exists but points to a different SHA, throw an error
+                echo "Error: Tag ${TAG_NAME} already exists in ${REPO} but points to ${EXISTING_SHA} instead of ${SHA}. Manual intervention required."
+                exit 1
+              fi
+            fi
           }
           DEOPENMS_SHA=$(curl -s -X GET https://api.github.com/repos/OpenMS/de.openms.knime/git/ref/heads/develop |jq -r '.object.sha')
           GKN_SHA=$(curl -s -X GET https://api.github.com/repos/genericworkflownodes/GenericKnimeNodes/git/ref/heads/develop |jq -r '.object.sha')
@@ -1003,15 +1033,14 @@ jobs:
           TUTORIAL_SHA=$(curl https://api.github.com/repos/OpenMS/Tutorials/git/refs/heads/master | jq -r ".object.sha")
           DOCS_SHA=$(curl https://api.github.com/repos/OpenMS/OpenMS-docs/git/refs/heads/develop | jq -r ".object.sha")
 
-          createGitTag OpenMS/contrib $CONTRIB_SHA  || updateGitTag OpenMS/contrib $CONTRIB_SHA 
-          createGitTag OpenMS/pyopenms-docs $PYDOCS_SHA  || updateGitTag OpenMS/pyopenms-docs $PYDOCS_SHA 
-          createGitTag OpenMS/THIRDPARTY $THIRDPARTY_SHA  || updateGitTag OpenMS/THIRDPARTY $THIRDPARTY_SHA 
-          createGitTag OpenMS/Tutorials $TUTORIAL_SHA  || updateGitTag OpenMS/Tutorials $TUTORIAL_SHA 
-          createGitTag OpenMS/OpenMS-docs $DOCS_SHA  || updateGitTag OpenMS/OpenMS-docs $DOCS_SHA 
-          createGitTag OpenMS/de.openms.knime $DEOPENMS_SHA  || updateGitTag OpenMS/de.openms.knime $DEOPENMS_SHA 
-
-          #FIXME reenable these after we get the correct access permissions
-          #createGitTag genericworkflownodes/de.openms.knime.dynamicJSViewers $JSViewer_SHA || updateGitTag genericworkflownodes/de.openms.knime.dynamicJSViewers $GKN_SHA 
+          handleGitTag OpenMS/contrib $CONTRIB_SHA
+          handleGitTag OpenMS/pyopenms-docs $PYDOCS_SHA
+          handleGitTag OpenMS/THIRDPARTY $THIRDPARTY_SHA
+          handleGitTag OpenMS/Tutorials $TUTORIAL_SHA
+          handleGitTag OpenMS/OpenMS-docs $DOCS_SHA
+          handleGitTag OpenMS/de.openms.knime $DEOPENMS_SHA
+          # Uncomment when permissions are fixed
+          # handleGitTag genericworkflownodes/de.openms.knime.dynamicJSViewers $JSViewer_SHA
 
       - name: Merge to Develop
         if: inputs.mark_as_latest

.github/workflows/update_version_numbers.yml

@@ -21,52 +21,10 @@ jobs:
       # Update files with new package version numbers
       - name: update files
         run: |
-          # setting variables
-          package_version_major="${{ github.event.inputs.major }}"
-          package_version_minor="${{ github.event.inputs.minor }}"
-          package_version_patch="${{ github.event.inputs.patch }}"
-          package_version="${{ github.event.inputs.major }}.${{ github.event.inputs.minor }}.${{ github.event.inputs.patch }}"
-          echo "Setting version $package_version"
-
-          # update main cmakelist
-          sed -i '' "s#.*set(OPENMS_PACKAGE_VERSION_MAJOR.*#set(OPENMS_PACKAGE_VERSION_MAJOR \"$package_version_major\")#" CMakeLists.txt
-          sed -i '' "s#.*set(OPENMS_PACKAGE_VERSION_MINOR.*#set(OPENMS_PACKAGE_VERSION_MINOR \"$package_version_minor\")#" CMakeLists.txt
-          sed -i '' "s#.*set(OPENMS_PACKAGE_VERSION_PATCH.*#set(OPENMS_PACKAGE_VERSION_PATCH \"$package_version_patch\")#" CMakeLists.txt
-
-          # update version info test
-          sed -i '' "s#detail.version_major =.*#detail.version_major = $package_version_major;#" ./src/tests/class_tests/openms/source/VersionInfo_test.cpp
-          sed -i '' "s#detail.version_minor =.*#detail.version_minor = $package_version_minor;#" ./src/tests/class_tests/openms/source/VersionInfo_test.cpp
-          sed -i '' "s#detail.version_patch =.*#detail.version_patch = $package_version_patch;#" ./src/tests/class_tests/openms/source/VersionInfo_test.cpp
-
-          # update vcpkg.json
-          sed -i '' "s/\"version-string\": \".*\"/\"version-string\": \"$package_version\"/" vcpkg.json
-
-          # update test write ini out:
-          sed -i '' "s#<ITEM name=\"version\" value=\".*\" type=\"string\"#<ITEM name=\"version\" value=\"$package_version\" type=\"string\"#g" ./src/tests/topp/WRITE_INI_OUT.ini
-          # update INIUpdater version
-          sed -i '' "s#<ITEM name=\"version\" value=\".*\" type=\"string\"#<ITEM name=\"version\" value=\"$package_version\" type=\"string\"#g" ./src/tests/topp/INIUpdater_1_noupdate.toppas
-
-
-          # 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=\"$package_version\" type=\"string\"#g" {} \;
-          # Update Changelog
-          # Define the new section using a here-doc
-          section_header=$(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 \$. == ${line_num}" CHANGELOG
+          bash tools/update_version_numbers.sh \
+            "${{ github.event.inputs.major }}" \
+            "${{ github.event.inputs.minor }}" \
+            "${{ github.event.inputs.patch }}"
 
       # Check for changes
       - name: check for changed files

CHANGELOG

@@ -10,6 +10,13 @@ Parameters - list of algorithm or TOPP tool parameters that changed in this rele
 PR - Pull Request (on GitHub), i.e. integration of a new feature or bugfix
 #<number>, e.g. #4957 - a reference to an issue or pull request on GitHub, visit e.g. https://github.com/OpenMS/OpenMS/pull/XXXX (replace XXXX with number of interest) for details
 
+
+- Libary:
+  ID information got factored out of MSSpectrum
+
+- removed outdated tools:
+  SpecLibCreator, SpecLibSearch, IDMassAccuracy
+
 ------------------------------------------------------------------------------------------
 ----                                OpenMS 3.5.0     (under development)              ----
 ------------------------------------------------------------------------------------------
@@ -18,21 +25,20 @@ General:
 
 Dependencies:
 
-OpenSwath:
-
 Misc:
+ - show load/store progress for files in all TOPP tools (#8041)
 
 Fixes:
 
 Library:
 - Removed `assignRanks` and `sortByRanks` in PeptideIdentifications and sort and filter by score instead. Also removed `updateHitRanks` in IDFilter (#7991)
 - Remove ranke member in PeptideHit and store ranks as meta value (for backwards compatibility). (#7997)
 
-- removed tools:
+Removed tools:
 
 
 ------------------------------------------------------------------------------------------
-----                                OpenMS 3.4.0     (under development)              ----
+----                                OpenMS 3.4.0     (May 2025)                       ----
 ------------------------------------------------------------------------------------------
 
 General:
@@ -75,7 +81,7 @@ Library:
 - made FASTA file reader more robust in presence of whitespaces (#7960)
 - add 3' cyclophosphate version of RNAse 4, fix handling of cleavage gains (#7928)
 
-- removed tools:
+Removed tools:
   - XTandemAdapter
   - MascotAdapter (note: MascotAdapterOnline still exists) (#7927)
 

CMakeLists.txt

@@ -49,7 +49,6 @@ set(CMAKE_AUTOMOC_COMPILER_PREDEFINES OFF)
 # General CMake definitions & helper
 #------------------------------------------------------------------------------
 SET(CMAKE_ALLOW_LOOSE_LOOP_CONSTRUCTS true)
-
 #------------------------------------------------------------------------------
 ## CMake sanity check: sometimes CMAKE_SIZEOF_VOID_P just vanishes when
 ## updating CMake.
@@ -83,7 +82,13 @@ option(ENABLE_DOCS "Indicates whether documentation should be built." ON)
 option(WITH_GUI "Build GUI parts of OpenMS (TOPPView&Co). This requires QtGui." ON)
 option(NO_WEBENGINE_WIDGETS "Do not use QtWebengineWidgets. Disables Javascript views in TOPPView." OFF)
 option(WITH_HDF5 "Build HDF5 parts of OpenMS." OFF)
-option(ENABLE_CWL "Build and validate the CWL description files for all TOPP tools." OFF)
+option(ENABLE_TDL "Load dependency and compile against TDL (required for CWL file support)." ON)
+option(ENABLE_CWL_GENERATION "Build and validate the CWL description files for all TOPP tools (Requires ENABLE_TDL=ON)." OFF)
+
+if(ENABLE_CWL_GENERATION AND NOT ENABLE_TDL)
+    message(FATAL_ERROR "ENABLE_CWL_GENERATION requires ENABLE_TDL to be ON.")
+endif()
+
 
 if(MSVC)
   option(MT_ENABLE_NESTED_OPENMP "Enable nested parallelism." OFF)
@@ -476,7 +481,7 @@ endif()
 #------------------------------------------------------------------------------
 # CWL generation (updates openms/share/commonwl/*.cwl files for all TOPP tools)
 #------------------------------------------------------------------------------
-if (ENABLE_CWL)
+if (ENABLE_CWL_GENERATION)
   include(${OPENMS_HOST_DIRECTORY}/cmake/cwl_generation.cmake)
 endif()
 

doc/code_examples/Tutorial_GUI_Plot1D.cpp

@@ -11,6 +11,8 @@
 #include <OpenMS/openms_data_path.h> // exotic header for path to tutorial data
 #include <QApplication>
 
+#include <boost/make_shared.hpp>
+
 using namespace OpenMS;
 using namespace std;
 
@@ -20,13 +22,13 @@ Int main(int argc, const char** argv)
 
   QApplication app(argc, const_cast<char**>(argv));
 
-  PeakMap exp;
+  AnnotatedMSRun exp;
+  auto exp_sptr = boost::make_shared<AnnotatedMSRun>();
   MSSpectrum spec;
   // demonstrating how to load a single spectrum from file formats which only contain a single spec
   // alternatively: use FileHandler().loadExperiment() if you need an experiment anyway
   FileHandler().loadSpectrum(tutorial_data_path, spec, {FileTypes::DTA});
-  exp.addSpectrum(spec);
-  LayerDataBase::ExperimentSharedPtrType exp_sptr(new PeakMap(exp));
+  exp_sptr->getMSExperiment().addSpectrum(spec);
   LayerDataBase::ODExperimentSharedPtrType on_disc_exp_sptr(new OnDiscMSExperiment());
   Plot1DWidget widget(Param(), DIM::Y, nullptr);
   widget.canvas()->addPeakLayer(exp_sptr, on_disc_exp_sptr);

doc/code_examples/Tutorial_MSExperiment.cpp

@@ -52,12 +52,23 @@ int main()
     }
   }
 
-  // update the data ranges for all dimensions (RT, m/z, int, IM) and print them:
+  // updateRanges provides a fast way to update the ranges of all spectra and chromatograms in the experiment.
+  // Once updated, the data ranges for all dimensions (RT, m/z, int, IM) can be printed.
   exp.updateRanges();
   std::cout << "Data ranges:\n";
-  exp.printRange(std::cout);
-  std::cout << "\nGet maximum intensity on its own: " << exp.getMaxIntensity() << '\n';
-  exp.getMinRT();
+  exp.spectrumRanges().printRange(std::cout);
+  std::cout << "\nGet maximum intensity on its own: " << exp.spectrumRanges().getMaxIntensity() << '\n';
+  std::cout << "Get minimum RT on its own: " << exp.spectrumRanges().getMinRT() << '\n';
+  std::cout << "Get maximum RT on its own: " << exp.spectrumRanges().getMaxRT() << '\n';
+  std::cout << "Get minimum m/z on its own: " << exp.spectrumRanges().getMinMZ() << '\n';
+  std::cout << "Get maximum m/z on its own: " << exp.spectrumRanges().getMaxMZ() << '\n';
+
+  // Printing the IM ranges is only possible if the spectra contain IM data (would throw an exception otherwise)  
+  if (!exp.spectrumRanges().RangeMobility::isEmpty())  
+  {  
+    std::cout << "Get minimum IM on its own: " << exp.spectrumRanges().getMinMobility() << '\n';  
+    std::cout << "Get maximum IM on its own: " << exp.spectrumRanges().getMaxMobility() << '\n';  
+  }  
 
   // Store the spectra to a mzML file with:
   FileHandler fh;

doc/doxygen/public/TOPP.doxygen

@@ -103,7 +103,6 @@
   - @subpage TOPP_NovorAdapter - De novo sequencing from tandem mass spectrometry data.
   - @subpage TOPP_SageAdapter - Identifies MS/MS spectra using Sage (external).
   - @subpage TOPP_SimpleSearchEngine - A simple database search engine for annotating MS/MS spectra.
-  - @subpage TOPP_SpecLibSearcher - Identifies peptide MS/MS spectra by spectral matching with a searchable spectral library.
   - @subpage TOPP_SpectraSTSearchAdapter - An interface to the 'SEARCH' mode of the SpectraST program (external, beta).
 
 
@@ -117,7 +116,6 @@
   - @subpage TOPP_IDDecoyProbability - Estimates peptide probabilities using a decoy search strategy. WARNING: This utility is deprecated.
   - @subpage TOPP_IDExtractor - Extracts n peptides randomly or best n from idXML files.
   - @subpage TOPP_IDMapper - Assigns protein/peptide identifications to feature or consensus features.
-  - @subpage TOPP_IDMassAccuracy - Calculates a distribution of the mass error from given mass spectra and IDs.
   - @subpage TOPP_IDPosteriorErrorProbability - Estimates posterior error probabilities using a mixture model.
   - @subpage TOPP_IDScoreSwitcher - Switches between different scores of peptide or protein hits in identification data.
   - @subpage TOPP_PeptideIndexer - Refreshes the protein references for all peptide hits.
@@ -126,7 +124,6 @@
   - @subpage TOPP_ProteinInference - Infer proteins from a list of (high-confidence) peptides.
   - @subpage TOPP_PSMFeatureExtractor - Creates search engine specific features for PercolatorAdapter input.
   - @subpage TOPP_SequenceCoverageCalculator - Prints information about idXML files.
-  - @subpage TOPP_SpecLibCreator - Creates an MSP-formatted spectral library.
   - @subpage TOPP_StaticModification - Allows to attach a set of fixed modifications to an idXML file (MS/MS search results), e.g. to add 15N (N15) labeling post-hoc.
 
 

doc/doxygen/public/developer_tutorial.doxygen

@@ -160,8 +160,6 @@ The extensible %OpenMS library implements common mass spectrometric data process
         - Database search:
             - Peptides (Tool %SimpleSearchEngine and its classes - started simple but is, by now, rather complete peptide identification engine)
             - Protein-Protein cross-links (Tool OpenPepXL)
-        - Spectral library search:
-            - Tool SpecLibSearcher and its classes
         - DeNovo:
             - Tool CompNovoCID and its classes
     - Quantification:

dockerfiles/Dockerfile

@@ -89,7 +89,7 @@ RUN <<-EOF
 
     # copying only the binaries that are relevant to Linux
     cp -r THIRDPARTY/All/* ${THIRDPARTY_DIR}
-    cp -r THIRDPARTY/Linux/64bit/* ${THIRDPARTY_DIR}
+    cp -r THIRDPARTY/Linux/x86_64/* ${THIRDPARTY_DIR}
 
     rm -rf THIRDPARTY
 EOF