Merge branch 'develop' into feature/FLASHDeconv

CHANGELOG

@@ -9,6 +9,62 @@ 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
 UTIL - An executable, just like a TOPP tool, but usually experimental or of lesser importance to common pipelines
 
+------------------------------------------------------------------------------------------
+----                                OpenMS 2.6                                        ----
+------------------------------------------------------------------------------------------
+
+We now create nightly pyopenms wheels
+
+Adapters/Third-party support:
+- LuciphorAdapter now stores which modifications were used for localization (#4771) and localization scores are reported in mzTab #4772 
+- Added Percolator3.0 support, fixed ConsensusID reading from wrong (Percolator-overwritten) meta data (#4829), and adapted the Regex parsing of XTandem Percolator output files #4849 
+- Added options introduced in new MSGF versions #4713 
+- Updated IsoSpec fine structure isotopic calculator sources to v 2.1.0 #4733 
+- Updated other third-party tools
+
+What's new:
+- Introduced a Wizard for Swath data (#4647 #4706 #4758 #4769 #4773 #4837), which also reports summary statistics about Swath TargetedExperiments #4788 #4790
+- Added a new Database Suitability TOPP Tool (#4791 #4781) and FDR filtering support for it #4814 
+- Added support for QC of labeled experiments (iTRAQ/TMT)
+- Added automated QC computations for MRM (#4637)
+- Adapted consensusXML and mzTab to support protein groups (#4630)
+- Consensus/IDMerger: Introduced use of merge idx to ensure keeping track of primaryRuns
+- Epifany: Added calculation of protein group FDR, ID filtering for protein group scores (#4802) and support for inference on not just individual samples but also consensusXML files
+- FeatureFinderCentroided/FeatureFinderAlgorithmPicked: Improved runtime performance #4652 #4701 
+- FeatureFinderIdentification: Improved SLIM-labeling experiment support
+- FileConverter: Improved runtime performance when producing mzML output #4750
+- FLQT: Introduced Fibonacci heaps for large runtime optimization (#4721) and fixed related preconditions/segfaults #4756 #4760 #4778 
+- IDFilter: added support for consensusXMLs #4798 #4799
+- MapAlignerIdentification: New option to use an "identity" transformation when data is too sparse to determine alignment model #4628
+- MzTabExporter: changed to only export one main score, and to derive nativeIDs from data (#4767). Now ensures that all output rows contain the same number of columns #4801 
+- ProteomicsLFQ: Added spectral counting as quantification method (#4726). Introduced performance improvements for AASequence and string parsing, especially for modified sequences. Various further improvements (e.g. #4669)
+- SimpleSearchEngine (multithreaded), TheoreticalSpectrumGenerator, MSSpectrum: Runtime optimization #4709
+- Further introduction of more file streaming to address possible memory consumption issues #4682 #4694
+
+Further fixes:
+- We now limit double precision to 17 digits during file writes #4636 
+- Ensure that CometAdapter always writes indexed mzML fixes for CometAdapter (#4653), fixed the writing of terminal modifications with specific origin in Comet (#4742), the writing of protein terminal mods in Comet and MSGF adapter #4710, and the Comet pepXML modification parsing #4755 
+- Removed secondary search engine settings duplication in mzTab MTD section. #4720 
+- Improved XTandem output protein parsing #4789 to fix Issue #4770
+- Increased (partial) support for parsing mzid with nonstandard, non-CV-term scores, fixes #4859
+- Fixes to NucleicAcidSearchEngine mzTab output #4692
+- ConsensusID now passes spectrum reference meta values along #4703
+- Fix to LFQ requantification #4633
+- Improved MapAlignerTreeGuided memory usage (#4704) and fixed segfault when featureXML contains no IDs #4665 
+- TOPPAS fixes #4780 
+
+Various:
+- OMMSAAdapter now writes out native ids and spectrum references #4852 
+- FileInfo: Report more charge distribution and MS2 activation-method information for Raw files #4836 
+- Added sum formula output in RNAMassCalculator #4677 
+- Added automatic OpenMS tool reporting of peak memory usage #4712 
+- Some extra tools documentation outputs #4822 #4823
+- Extended mapping of filetypes and mimetypes for knime output formats documentation #4839
+- RTEvaluation: fixed output formats #4533 
+- Some further clarifications, standardization/consolidation of outputs formats/consistency
+- Continued fixes/improvement of documentation
+
+
 ------------------------------------------------------------------------------------------
 ----                                OpenMS 2.5                                        ----
 ------------------------------------------------------------------------------------------

PULL_REQUEST_TEMPLATE.md

@@ -0,0 +1,12 @@
+# Description
+
+Please include a summary of the change and which issue is fixed.
+
+Also please:
+- Make sure that you are listed in the AUTHORS file
+- Add relevant changes and new features to the CHANGELOG file
+
+# Checklist:
+- [ ] I have commented my code, particularly in hard-to-understand areas
+- [ ] New and existing unit tests pass locally with my changes
+- [ ] Updated or added python bindings for changed or new classes

cmake/knime/mime.types

@@ -39,3 +39,15 @@ application/x-paramxml paramXML
 application/x-percolatortab tab
 application/x-pqp pqp
 application/x-ms ms
+application/x-splib splib
+application/x-novor novor
+application/x-obo obo
+application/x-analysisxml analysisXML
+application/x-sqmass sqMass
+application/x-osw osw
+application/x-psms psms
+application/x-pin pin
+application/x-pin pout
+application/x-paramxml paramXML
+application/x-xquestxml xml
+application/x-specxml xml

cmake/knime/mimetypes.xml

@@ -37,6 +37,21 @@
  <mimetype name="QCML" binary="false" description="qcML (will undergo standardisation maybe) (.qcml)" ext="qcml"/>
  <mimetype name="PARAMXML" binary="false" description="paramXML (subset of the general %OpenMS ini parameter files)" ext="paramXML"/>
  <mimetype name="PERCOLATORTAB" binary="false" description="Percolator tab seperated in/output" ext="tab"/>
- <mimetype name="PQP" binary="true" description="The PQP files are SQLite databases consisting of several tables representing the data contained in TraML files." ext="pqp"/>
+ <mimetype name="PQP" binary="true" description="Peptide query parameter files are SQLite databases consisting of several tables representing the data contained in TraML files." ext="pqp"/>
  <mimetype name="MS" binary="false" description="SIRIUS file format" ext="ms"/  >
+ <mimetype name="SPLIB" binary="false" description="SpectraST spectral library format" ext="splib"/  >
+ <mimetype name="OBO" binary="false" description="Open Biomedical Ontologies format" ext="obo"/  >
+ <mimetype name="HTML" binary="false" description="Hypertext markup language" ext="html"/  >
+ <mimetype name="PIN" binary="false" description="Percolator input format" ext="pin"/  >
+ <mimetype name="POUT" binary="false" description="Percolator output format" ext="pout"/  >
+ <mimetype name="OSW" binary="false" description="OpenSWATH format" ext="osw"/  >
+ <mimetype name="SQMASS" binary="false" description="SQL based mass-spec format" ext="sqmass"/  >
+ <mimetype name="NOVOR" binary="false" description="novoR deNovo search engine output format" ext="novor"/  >
+ <mimetype name="SPECXML" binary="false" description="XQuest spectrum matches format" ext="xml"/  >
+ <mimetype name="XQUESTXML" binary="false" description="XQuest results format" ext="xml"/  >
+ <mimetype name="MRM" binary="false" description="Multiple reaction monitoring format" ext="mrm"/  >
+ <mimetype name="PSQ" binary="false" description="Blast database index for protein database needed for OMSSA" ext="psq"/  >
+ <mimetype name="PSMS" binary="false" description="Simple file format for peptide-spectrum matches" ext="psms"/  >
+ <mimetype name="JSON" binary="false" description="JSON" ext="json"/  >
+ <mimetype name="XSD" binary="false" description="XML schema definitions" ext="xsd"/  >
 </mimetypes>

doc/CMakeLists.txt

@@ -319,7 +319,20 @@ if(ENABLE_DOCS)
 
     #------------------------------------------------------------------------------
     # Install documentation
-    install_directory(${PROJECT_BINARY_DIR}/html ${INSTALL_DOC_DIR} doc)
+    install(DIRECTORY ${PROJECT_BINARY_DIR}/html
+      DESTINATION ${INSTALL_DOC_DIR}
+      COMPONENT doc
+      FILE_PERMISSIONS      OWNER_WRITE OWNER_READ
+                            GROUP_READ
+                            WORLD_READ
+      DIRECTORY_PERMISSIONS OWNER_EXECUTE OWNER_WRITE OWNER_READ
+                            GROUP_EXECUTE GROUP_READ
+                            WORLD_EXECUTE WORLD_READ
+      REGEX "^\\..*" EXCLUDE ## Exclude hidden files (svn, git, DSStore)
+      REGEX ".*\\/\\..*" EXCLUDE ## Exclude hidden files in subdirectories
+      REGEX ".*\\.map\$" EXCLUDE ## Exclude temporary map files
+      REGEX ".*\\.md5\$" EXCLUDE ## Exclude temporary md5 files
+    )
     install_file(${PROJECT_BINARY_DIR}/index.html ${INSTALL_DOC_DIR} doc)
 
     #------------------------------------------------------------------------------

doc/doxygen/Doxyfile.in

@@ -2439,7 +2439,7 @@ DIRECTORY_GRAPH        = YES
 # The default value is: png.
 # This tag requires that the tag HAVE_DOT is set to YES.
 
-DOT_IMAGE_FORMAT       = png
+DOT_IMAGE_FORMAT       = svg
 
 # If DOT_IMAGE_FORMAT is set to svg, then this option can be set to YES to
 # enable generation of interactive SVG images that allow zooming and panning.
@@ -2451,7 +2451,7 @@ DOT_IMAGE_FORMAT       = png
 # The default value is: NO.
 # This tag requires that the tag HAVE_DOT is set to YES.
 
-INTERACTIVE_SVG        = NO
+INTERACTIVE_SVG        = YES
 
 # The DOT_PATH tag can be used to specify the path where the dot tool can be
 # found. If left blank, it is assumed the dot tool can be found in the path.
@@ -2518,7 +2518,7 @@ DOT_GRAPH_MAX_NODES    = 50
 # Minimum value: 0, maximum value: 1000, default value: 0.
 # This tag requires that the tag HAVE_DOT is set to YES.
 
-MAX_DOT_GRAPH_DEPTH    = 1000
+MAX_DOT_GRAPH_DEPTH    = 5
 
 # Set the DOT_TRANSPARENT tag to YES to generate images with a transparent
 # background. This is disabled by default, because dot on Windows does not seem

doc/doxygen/public/TOPP.doxygen

@@ -44,6 +44,7 @@
   - @subpage TOPP_TOPPView - A viewer for mass spectrometry data.
   - @subpage TOPP_TOPPAS - An assistant for GUI-driven TOPP workflow design.
   - @subpage TOPP_INIFileEditor - An editor for %OpenMS configuration files.
+  - @subpage TOPP_SwathWizard - A user-friendly step-by-step wizard for SWATH data analysis
 
   <b>File Handling</b>
   - @subpage TOPP_DTAExtractor - Extracts spectra of an MS run file to several files in DTA format.