Merge branch 'feature/oswSpeedUp' of github.com:jcharkow/OpenMS into …

…feature/oswSpeedUp

.github/workflows/openms_ci_matrix_full.yml

@@ -191,7 +191,7 @@ jobs:
           brew install --quiet ccache autoconf automake libtool ninja && brew link --overwrite ccache
 
           if [[ "${{ steps.set-vars.outputs.pkg_type }}" != "none" ]]; then
-            brew install python@3.11 --force --overwrite
+            brew install python@3.12 --force --overwrite
             brew install --quiet doxygen ghostscript graphviz
           fi
         fi

CHANGELOG

@@ -27,6 +27,7 @@ Fixes:
 - more robust parsing of mzIdentML (#7153)
 - more robust FileConverter (#7176)
 - MSFragger: allow relative path to database (#7155)
+- MSGFPlusAdapter: allow concurrent creation of indexed database (#7272)
 - ParamEditor: fixed error for the subsection parameter (ParamNode) to go through store function (#7180)
 - TOPPAS: open files in TOPPView (#7213)
 

share/OpenMS/examples/TOPPAS/QualityControl.toppas

@@ -1,15 +1,14 @@
 <?xml version="1.0" encoding="ISO-8859-1"?>
 <PARAMETERS version="1.7.0" xsi:noNamespaceSchemaLocation="https://raw.githubusercontent.com/OpenMS/OpenMS/develop/share/OpenMS/SCHEMAS/Param_1_7_0.xsd" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance">
   <NODE name="info" description="">
-    <ITEM name="version" value="3.1.0-pre-disabled-20231206" type="string" description="" required="false" advanced="false" />
+    <ITEM name="version" value="3.1.0-pre-disabled-20231216" type="string" description="" required="false" advanced="false" />
     <ITEM name="num_vertices" value="24" type="int" description="" required="false" advanced="false" />
     <ITEM name="num_edges" value="30" type="int" description="" required="false" advanced="false" />
     <ITEM name="description" value="&lt;![CDATA[&lt;!DOCTYPE HTML PUBLIC &quot;-//W3C//DTD HTML 4.0//EN&quot; &quot;http://www.w3.org/TR/REC-html40/strict.dtd&quot;&gt;
 &lt;html&gt;&lt;head&gt;&lt;meta name=&quot;qrichtext&quot; content=&quot;1&quot; /&gt;&lt;style type=&quot;text/css&quot;&gt;
 p, li { white-space: pre-wrap; }
 &lt;/style&gt;&lt;/head&gt;&lt;body style=&quot; font-family:&apos;Arial&apos;; font-size:12pt; font-weight:400; font-style:normal;&quot;&gt;
-&lt;p style=&quot; margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;&lt;span style=&quot; color:#000000;&quot;&gt;note: do not run this workflow with multiple jobs in parallel, otherwise you will encounter this issue with MSGF+: https://github.com/OpenMS/OpenMS/issues/7255&lt;/span&gt;&lt;/p&gt;
-&lt;p style=&quot;-qt-paragraph-type:empty; margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px; color:#000000;&quot;&gt;&lt;br /&gt;&lt;/p&gt;&lt;/body&gt;&lt;/html&gt;]]&gt;" type="string" description="" required="false" advanced="false" />
+&lt;p style=&quot;-qt-paragraph-type:empty; margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;&lt;br /&gt;&lt;/p&gt;&lt;/body&gt;&lt;/html&gt;]]&gt;" type="string" description="" required="false" advanced="false" />
   </NODE>
   <NODE name="vertices" description="">
     <NODE name="0" description="">

src/openms/CMakeLists.txt

@@ -59,11 +59,11 @@ set(CF_OPENMS_ASSERTIONS ${CF_OPENMS_ASSERTIONS} CACHE INTERNAL "Enables debug m
 
 
 #------------------------------------------------------------------------------
-# third party libs shipped with OpenMS directly
+# external third-party libs statically linked to OpenMS
 #------------------------------------------------------------------------------
 # The following library is in our public API, so create export targets
 #install(EXPORT EvergreenTarget DESTINATION ${INSTALL_LIB_DIR}/cmake/OpenMS FILE OpenMSTargets.cmake COMPONENT cmake)
-add_subdirectory(thirdparty)
+add_subdirectory(extern)
 
 #------------------------------------------------------------------------------
 # external libs (contrib or system)