Merge branch 'develop' into feature/isobaricWorkflow

CHANGELOG

@@ -36,6 +36,7 @@ Fixes:
 
 Misc:
 - OpenMSInfo reports the ILP solver (CoinOr or glpk) (#7156)
+- add citation information for OpenMS 3.0 (Nat. Methods) (#7383)
 - Add export for Common Workflow Language (CWL) (#6156)
 - Add tool description lib (TDL) dependency (#6156)
 

src/openms/include/OpenMS/APPLICATIONS/TOPPBase.h

@@ -185,7 +185,10 @@ namespace OpenMS
     */
     String getToolPrefix() const;
 
-private:
+    /// Returns a link to the documentation of the tool (accessible on our servers and only after inclusion in the nightly branch or a release).
+    String getDocumentationURL() const;
+
+  private:
     /// Tool name.  This is assigned once and for all in the constructor.
     String const tool_name_;
 
@@ -350,9 +353,6 @@ namespace OpenMS
     */
     String getSubsection_(const String& name) const;
 
-    /// Returns a link to the documentation of the tool (accessible on our servers and only after inclusion in the nightly branch or a release).
-    String getDocumentationURL() const;
-
     /// Returns the default parameters
     Param getDefaultParameters_() const;
 

src/openms/source/APPLICATIONS/TOPPBase.cpp

@@ -69,10 +69,10 @@ namespace OpenMS
   using namespace Exception;
 
   String TOPPBase::topp_ini_file_ = String(QDir::homePath()) + "/.TOPP.ini";
-  const Citation TOPPBase::cite_openms_ = { "Rost HL, Sachsenberg T, Aiche S, Bielow C et al.",
-      "OpenMS: a flexible open-source software platform for mass spectrometry data analysis",
-      "Nat Meth. 2016; 13, 9: 741-748",
-      "10.1038/nmeth.3959" };
+  const Citation TOPPBase::cite_openms_
+    = {"Pfeuffer, J., Bielow, C., Wein, S. et al.", "OpenMS 3 enables reproducible analysis of large-scale mass spectrometry data",
+       "Nat Methods (2024)", "10.1038/s41592-024-02197-7"};
+
 
   void TOPPBase::setMaxNumberOfThreads(int
 #ifdef _OPENMP
@@ -580,7 +580,7 @@ namespace OpenMS
         is << " + " << is.indent(3) << c.toString() << is.indent(0) << "\n";
     }
     is << is.indent(0) << "\n";
-    is << invert("Usage:\n")
+    is << invert("Usage:") << "\n" // line break needs to be separate, to avoid colored trailing whitespaces
        << "  " << bright(tool_name_) << " <options>" << "\n"
        << "\n";
 

src/topp/OpenMSInfo.cpp

@@ -6,13 +6,15 @@
 // $Authors: Marc Sturm, Chris Bielow $
 // --------------------------------------------------------------------------
 
-#include <OpenMS/config.h>
+#include <OpenMS/APPLICATIONS/TOPPBase.h>
+#include <OpenMS/CONCEPT/Colorizer.h>
 #include <OpenMS/CONCEPT/VersionInfo.h>
 #include <OpenMS/DATASTRUCTURES/String.h>
+#include <OpenMS/FORMAT/IndentedStream.h>
 #include <OpenMS/SYSTEM/BuildInfo.h>
 #include <OpenMS/SYSTEM/File.h>
+#include <OpenMS/config.h>
 #include <OpenMS/openms_data_path.h>
-#include <OpenMS/APPLICATIONS/TOPPBase.h>
 
 #ifdef _OPENMP
   #include "omp.h"
@@ -26,46 +28,49 @@ using namespace std;
 /**
 @page TOPP_OpenMSInfo OpenMSInfo
 
-@brief Prints configurations details of %OpenMS (Version, Git hash, SIMD extensions, Multithreading), along with directories where auxilliary data like 
-       modifications (UniMOD), Enzymes etc are taken from.
+@brief Prints configurations details of %OpenMS (Version, Git hash, SIMD extensions, Multithreading), along with directories where auxilliary data
+like modifications (UniMOD), Enzymes etc are taken from.
 
 Some path's can be manipulated by the user by setting environment variables. If not set, the values are taken from the system defaults.
 
 <ul>
-  <li> <b>Data path:</b> controlled by the environment variable 'OPENMS_DATA_PATH'; the value should point to a %OpenMS share directory, e.g. 'c:/program files/OpenMS3.1/share/OpenMS'
-  <li> <b>Temp path:</b> controlled by the environment variable 'OPENMS_TMPDIR'; the value should point to where you want %OpenMS to store temporary data.
-  <li> <b>Userdata path:</b> controlled by the environment variable 'OPENMS_HOME_PATH'; the value should point to where you want %OpenMS to store user-realted data, e.g. the .OpenMS.ini.
+  <li> <b>Data path:</b> controlled by the environment variable 'OPENMS_DATA_PATH'; the value should point to a %OpenMS share directory, e.g.
+'c:/program files/OpenMS3.1/share/OpenMS' <li> <b>Temp path:</b> controlled by the environment variable 'OPENMS_TMPDIR'; the value should point to
+where you want %OpenMS to store temporary data. <li> <b>Userdata path:</b> controlled by the environment variable 'OPENMS_HOME_PATH'; the value should
+point to where you want %OpenMS to store user-realted data, e.g. the .OpenMS.ini.
 </ul>
 
 <B>This tool does not need/use any command line parameters.</B>
 
 Example output:
 @code
-OpenMS Version:
-==================
-Version      : 3.1.0-pre-disabled-20230914
-Build time   : Sep 14 2023, 12:02:03
+
+Full documentation: http://www.openms.de/doxygen/nightly/html/TOPP_OpenMSInfo.html
+To cite OpenMS:
+ + Pfeuffer, J., Bielow, C., Wein, S. et al.. OpenMS 3 enables reproducible analysis of large-scale mass spectrometry
+   data. Nat Methods (2024). doi:10.1038/s41592-024-02197-7.
+
+<< OpenMS Version >>
+Version      : 3.1.0
+Build time   : Mar  4 2024, 10:42:53
 Git sha1     : disabled
 Git branch   : disabled
 
-Installation information:
-==================
-Data path    : C:/dev/openms/share/OpenMS
+<< Installation information >>
+Data path    : C:/dev/openms2/share/OpenMS
 Temp path    : C:/Users/bielow/AppData/Local/Temp
 Userdata path: C:/Users/bielow/
 
-Build information:
-==================
+<< Build information >>
 Source path  : C:/dev/openms/src/openms
 Binary path  : C:/dev/openms_build/src/openms
 Binary arch  : 64 bit
-Build type   : Release
+Build type   : Debug
 LP-Solver    : COIN-OR
 OpenMP       : enabled (maxThreads = 32)
-SIMD extensions : SSE, SSE2, SSE3, SSE4.1, AVX
+SIMD extensions : SSE, SSE2, SSE3, SSE4.1, SSE4.2, AVX
 
-OS Information:
-==================
+<< OS Information >>
 Name: Windows
 Version: 10
 Architecture: 64 bit
@@ -82,7 +87,7 @@ const auto max_threads = Internal::OpenMSBuildInfo::getOpenMPMaxNumThreads();
 class TOPPOpenMSInfo : public TOPPBase
 {
 public:
-  TOPPOpenMSInfo() : TOPPBase("OpenMSInfo", "Prints configurations details of OpenMS.")
+  TOPPOpenMSInfo(): TOPPBase("OpenMSInfo", "Prints configurations details of OpenMS.")
   {
   }
 
@@ -93,54 +98,62 @@ class TOPPOpenMSInfo : public TOPPBase
     registerInputFile_("dummy", "<ignored>", "", "A fake input file, which is needed for some workflow systems to call this tool", false, true);
   }
 
-  //Param getSubsectionDefaults_(const String& /*section*/) const override
+  // Param getSubsectionDefaults_(const String& /*section*/) const override
   //{
-  //  return SpectraMerger().getParameters();
-  //}
+  //   return SpectraMerger().getParameters();
+  // }
 
   ExitCodes main_(int, const char**) override
   {
-    cout << "OpenMS Version:" << "\n";
-    cout << "==================" << "\n";
-    cout << "Version      : " << VersionInfo::getVersion() << "\n";
-    cout << "Build time   : " << VersionInfo::getTime() << "\n";
-    cout << "Git sha1     : " << VersionInfo::getRevision() << "\n";
-    cout << "Git branch   : " << VersionInfo::getBranch() << "\n";
-    cout << "\n";
-    cout << "Installation information:" << "\n";
-    cout << "==================" << "\n";
-    cout << "Data path    : " << File::getOpenMSDataPath() << "\n";
-    cout << "Temp path    : " << File::getTempDirectory() << "\n";
-    cout << "Userdata path: " << File::getUserDirectory() << "\n";
-
-    cout << "\n";
-    cout << "Build information:" << "\n";
-    cout << "==================" << "\n";
-    cout << "Source path  : " << OPENMS_SOURCE_PATH << "\n";
-    cout << "Binary path  : " << OPENMS_BINARY_PATH << "\n";
-    cout << "Binary arch  : " << Internal::OpenMSOSInfo::getBinaryArchitecture() << "\n";
-    cout << "Build type   : " << Internal::OpenMSBuildInfo::getBuildType() << "\n";
+    IndentedStream is(cout, 0, 10);
+    is << '\n'
+       << bright("Full documentation: ") // the space is needed, otherwise the remaining line will be underlined on Windows..
+       << underline(TOPPBase::getDocumentationURL()) << " " // the space is needed ...
+       << '\n'
+       << bright("To cite OpenMS:\n") << " + "
+       << is.indent(3) << cite_openms_.toString() << is.indent(0);
+
+    is << "\n\n"
+       << green("<< OpenMS Version >>\n")
+       << "Version      : " << VersionInfo::getVersion() << "\n"
+       << "Build time   : " << VersionInfo::getTime() << "\n"
+       << "Git sha1     : " << VersionInfo::getRevision() << "\n"
+       << "Git branch   : " << VersionInfo::getBranch() << "\n"
+       << "\n"
+       << green("<< Installation information >>\n")
+       << "Data path    : " << File::getOpenMSDataPath() << "\n"
+       << "Temp path    : " << File::getTempDirectory() << "\n"
+       << "Userdata path: " << File::getUserDirectory() << "\n"
+       << "\n"
+       << green("<< Build information >>\n") 
+       << "Source path  : " << OPENMS_SOURCE_PATH << "\n"
+       << "Binary path  : " << OPENMS_BINARY_PATH << "\n"
+       << "Binary arch  : " << Internal::OpenMSOSInfo::getBinaryArchitecture() << "\n"
+       << "Build type   : " << Internal::OpenMSBuildInfo::getBuildType() << "\n";
 #if COINOR_SOLVER == 1
-    cout << "LP-Solver    : COIN-OR\n";
+    is << "LP-Solver    : COIN-OR\n";
 #else
     cout << "LP-Solver    : GLPK\n";
 #endif
-    #ifdef _OPENMP
-    cout << "OpenMP       : " << "enabled (maxThreads = " << max_threads << ")" << "\n";
-    #else
-    cout << "OpenMP       : " << "disabled" << "\n";
-    #endif
-    cout << "SIMD extensions : " << Internal::OpenMSOSInfo::getActiveSIMDExtensions() << "\n";
-    cout << "\n";
+#ifdef _OPENMP
+    is << "OpenMP       : "
+       << "enabled (maxThreads = " << max_threads << ")"
+       << "\n";
+#else
+    is << "OpenMP       : "
+       << "disabled"
+       << "\n";
+#endif
+    is << "SIMD extensions : " << Internal::OpenMSOSInfo::getActiveSIMDExtensions() << "\n"
+       << "\n";
 
     Internal::OpenMSOSInfo info = Internal::OpenMSOSInfo::getOSInfo();
 
-    cout << "OS Information:" << "\n";
-    cout << "==================" << "\n";
-    cout << "Name: " << info.getOSAsString() << "\n";
-    cout << "Version: " << info.getOSVersionAsString() << "\n";
-    cout << "Architecture: " << info.getArchAsString() << "\n";
-    cout << "\n";
+    is << green("<< OS Information >>\n")
+       << "Name: " << info.getOSAsString() << "\n"
+       << "Version: " << info.getOSVersionAsString() << "\n"
+       << "Architecture: " << info.getArchAsString() << "\n"
+       << "\n";
 
     return EXECUTION_OK;
   }