From bd6c9d24c0af42687e1db11a1fbf324b5b640c73 Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Mon, 26 Feb 2024 22:54:03 +0000 Subject: [PATCH 1/5] Bump src/pyOpenMS/pyopenms-docs from `6a0aab2` to `e75ffd0` Bumps [src/pyOpenMS/pyopenms-docs](https://github.com/OpenMS/pyopenms-docs) from `6a0aab2` to `e75ffd0`. - [Release notes](https://github.com/OpenMS/pyopenms-docs/releases) - [Commits](https://github.com/OpenMS/pyopenms-docs/compare/6a0aab29763f4ca9cb90625b2671857595342114...e75ffd03616a35c9764c6c9a3954aabebe42a3a3) --- updated-dependencies: - dependency-name: src/pyOpenMS/pyopenms-docs dependency-type: direct:production ... Signed-off-by: dependabot[bot] --- src/pyOpenMS/pyopenms-docs | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/pyOpenMS/pyopenms-docs b/src/pyOpenMS/pyopenms-docs index 6a0aab29763..e75ffd03616 160000 --- a/src/pyOpenMS/pyopenms-docs +++ b/src/pyOpenMS/pyopenms-docs @@ -1 +1 @@ -Subproject commit 6a0aab29763f4ca9cb90625b2671857595342114 +Subproject commit e75ffd03616a35c9764c6c9a3954aabebe42a3a3 From 39a414dd33c9c78cd68c5865c6c9351389a01825 Mon Sep 17 00:00:00 2001 From: Chris Bielow Date: Mon, 4 Mar 2024 12:12:27 +0100 Subject: [PATCH 2/5] update citation to OpenMS 3.0 --- src/openms/source/APPLICATIONS/TOPPBase.cpp | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/src/openms/source/APPLICATIONS/TOPPBase.cpp b/src/openms/source/APPLICATIONS/TOPPBase.cpp index 86e4ff71075..13728ac837b 100755 --- a/src/openms/source/APPLICATIONS/TOPPBase.cpp +++ b/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_) << " " << "\n" << "\n"; From cb913933287749036f1773b53f9af19a818a9855 Mon Sep 17 00:00:00 2001 From: Chris Bielow Date: Mon, 4 Mar 2024 13:10:04 +0100 Subject: [PATCH 3/5] add citiation for OpenMS3.0 to 'OpenMSInfo' tool and beautify output a little --- .../include/OpenMS/APPLICATIONS/TOPPBase.h | 8 +- src/topp/OpenMSInfo.cpp | 129 ++++++++++-------- 2 files changed, 75 insertions(+), 62 deletions(-) diff --git a/src/openms/include/OpenMS/APPLICATIONS/TOPPBase.h b/src/openms/include/OpenMS/APPLICATIONS/TOPPBase.h index d4fba96ffaa..b93aa7a4de8 100644 --- a/src/openms/include/OpenMS/APPLICATIONS/TOPPBase.h +++ b/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; diff --git a/src/topp/OpenMSInfo.cpp b/src/topp/OpenMSInfo.cpp index 2abdbed8750..e5b0f3acf5c 100644 --- a/src/topp/OpenMSInfo.cpp +++ b/src/topp/OpenMSInfo.cpp @@ -6,13 +6,15 @@ // $Authors: Marc Sturm, Chris Bielow $ // -------------------------------------------------------------------------- -#include +#include +#include #include #include +#include #include #include +#include #include -#include #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.
    -
  • Data path: 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' -
  • Temp path: controlled by the environment variable 'OPENMS_TMPDIR'; the value should point to where you want %OpenMS to store temporary data. -
  • Userdata path: 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. +
  • Data path: 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'
  • Temp path: controlled by the environment variable 'OPENMS_TMPDIR'; the value should point to +where you want %OpenMS to store temporary data.
  • Userdata path: 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.
This tool does not need/use any command line parameters. 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", "", "", "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; } From b70742f82c53ba6b4e84aa69568203b288d1d3d2 Mon Sep 17 00:00:00 2001 From: Chris Bielow Date: Mon, 4 Mar 2024 13:15:26 +0100 Subject: [PATCH 4/5] update changelog --- CHANGELOG | 1 + 1 file changed, 1 insertion(+) diff --git a/CHANGELOG b/CHANGELOG index b4b26e57612..7f21c23788a 100644 --- a/CHANGELOG +++ b/CHANGELOG @@ -36,6 +36,7 @@ Fixes: Misc: - OpenMSInfo reports the ILP solver (CoinOr or glpk) (#7156) +- add citation information for OpenMS 3.0 (NatMethods) (#7383) - Add export for Common Workflow Language (CWL) (#6156) - Add tool description lib (TDL) dependency (#6156) From b146ea40041ae92e87340022caacfa6aba750e0f Mon Sep 17 00:00:00 2001 From: Chris Bielow Date: Mon, 4 Mar 2024 14:53:45 +0100 Subject: [PATCH 5/5] Update CHANGELOG Co-authored-by: Timo Sachsenberg --- CHANGELOG | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/CHANGELOG b/CHANGELOG index 7f21c23788a..edfe8d529f1 100644 --- a/CHANGELOG +++ b/CHANGELOG @@ -36,7 +36,7 @@ Fixes: Misc: - OpenMSInfo reports the ILP solver (CoinOr or glpk) (#7156) -- add citation information for OpenMS 3.0 (NatMethods) (#7383) +- 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)