Merge branch 'dev-vge' into dev

.github/workflows/cmake_tool.yml

@@ -47,7 +47,6 @@ jobs:
         conan export ../app
         conan export ../python_binding
         conan export ../ui
-        conan export tools/mdprep/external/gromacs
         conan export tools/mdprep
         conan create . --build=missing --settings=compiler.cppstd=20
     

dev/conanfile.py

@@ -120,6 +120,9 @@ def generate(self):
 
         copy(self, "*.dll", self.dependencies["qt"].cpp_info.bindir, os.path.join(self.build_folder, self.cpp.build.libdirs[0]))
         copy(self, "*.dll", os.path.join(self.dependencies["qt"].package_folder, "res/archdatadir/plugins"), os.path.join(self.build_folder, self.cpp.build.libdirs[0]))    
+
+        copy(self, "*", os.path.join(self.dependencies["gromacs"].package_folder, "external"), os.path.join(self.build_folder, "external"))        
+        copy(self, "*", os.path.join(self.dependencies["gromacs"].package_folder, "data", "tools","mdprep","gromacs","top"), os.path.join(self.build_folder, "data", "tools", "mdprep", "gromacs", "top" ))        
 
     def layout(self):
         cmake_layout(self)

lib/python_binding/CMakeLists.txt

@@ -10,6 +10,9 @@ find_package(vtx_io CONFIG REQUIRED)
 find_package(pybind11 REQUIRED)
 
 set(_VTX_PYTHON_BINDING_CONAN " ") # So the right target name can be linked
+
+file(GLOB_RECURSE _VTX_PYTHON_BINDING_CMAKE_DIR_CONTENT "${CMAKE_CURRENT_LIST_DIR}/cmake/*")
+message("VTX - _VTX_PYTHON_BINDING_CMAKE_DIR_CONTENT : <${_VTX_PYTHON_BINDING_CMAKE_DIR_CONTENT}>")
 include(cmake/library.cmake)
 
 install(TARGETS vtx_python_binding FILE_SET public_headers DESTINATION include)

lib/python_binding/conanfile.py

@@ -16,7 +16,7 @@ class VTXPythonBindingRecipe(ConanFile):
 
     generators = "CMakeDeps", "CMakeToolchain"
 
-    exports_sources = "CMakeLists.txt", "src/*", "include/*", "cmake/*", "python_script/*"
+    exports_sources = "CMakeLists.txt", "src/*", "include/*", "cmake/library.cmake", "cmake/vtx_python_binding_copy_files.cmake", "python_script/*"
 
     def _generated_cmake_prefix(self):
         return "pybind11-"

lib/tool/tools/mdprep/conanfile.py

@@ -26,7 +26,6 @@ def requirements(self):
         self.requires("vtx_app/1.0")
         self.requires("vtx_ui/1.0")
         self.requires("gromacs/2024.0")
-        self.requires("dylib/2.2.1")
 
     def generate(self):
         copy(self, "*.dll", self.dependencies["vtx_ui"].cpp_info.bindir, os.path.join(self.build_folder, self.cpp.build.libdirs[0]))
@@ -45,16 +44,9 @@ def build(self):
         cmake.configure()
         cmake.build()
 
-        gmx_bin_dir = os.path.join(self.dependencies["vtx-gromacs"].cpp_info.bindir, "bin")
-        gmx_bin_dest = os.path.join(self.build_folder, self.cpp.build.libdirs[0], "external", "tools", "mdprep", "gromacs")
-        for ext in ("*.exe", "*.dll", "*.a", "*.so", "*.dylib", "^[^.]$"): # No extension for executable in linux, right ? TODO !!!
-            copy(self, ext, gmx_bin_dir, gmx_bin_dest)
-
-
     def package(self):
         cmake = CMake(self)
         cmake.install()
-        copy(self, "*.dll", (self.dependencies["vtx-gromacs"].build_folder), os.path.join(self.package_folder, "bin"))
 
     def package_info(self):
         self.cpp_info.libs = ["vtx_tool_mdprep"]

lib/tool/tools/mdprep/include/tools/mdprep/gromacs/gromacs.hpp

@@ -17,19 +17,39 @@ namespace VTX::Tool::Mdprep::Gromacs
 		std::string stdout_;
 		std::string stderr_;
 	};
-	struct GromacsCommandArgs
+	struct JobReport
 	{
-		std::vector<std::string>		arguments;
+		bool					 finished	  = false;
+		bool					 errorOccured = false;
+		std::vector<std::string> errors;
+	};
+	struct GromacsJobData
+	{
+		std::vector<std::string> arguments;
+		std::vector<size_t> expectedOutputFilesIndexes; // Meant to point toward specific argument indexes that hold
+														// path of output files to check
 		VTX::Util::DataLocker<Channels> channelsLocker;
+		JobReport						report;
 		std::optional<Inputs>
 			 interactiveSettings; // If the Inputs class is instanciated, the process is expected to be interactive.
-		bool operator==( const GromacsCommandArgs & ) const noexcept = default;
+		bool operator==( const GromacsJobData & ) const noexcept = default;
+	};
+
+	// The idea is to list output files from all previous job, in reverse chronological order. So we can access last
+	// files first. This is usefull because some job might need some files from a couple of jobs ago, but the last file
+	// of a given extension is always the right file. Therefore we can identify the right file to use for the job by
+	// taking the first one that matches the required extension.
+	struct CumulativeOuputFiles
+	{
+		std::vector<const std::string *> fileStringPtrs;
 	};
 
-	// Blindly execute gromacs with input arguments.
+	// Execute gromacs with input arguments then check if job issued and error
 	//   Assumes relevant arguments have been provided and checked beforehand.
 	//   Assumes gromacs have been instructed on where to find data files (env. var. GMXLIB) as well.
-	void submitGromacsCommand( const fs::path & p_gmx_exe, GromacsCommandArgs & p_args );
+	//   Error issued by the job can be a specific string in output channels or if expected output files doesn't exists
+	//   or are empty.
+	void submitGromacsJob( const fs::path & p_gmx_exe, GromacsJobData & p_args );
 } // namespace VTX::Tool::Mdprep::Gromacs
 
 #endif

lib/tool/tools/mdprep/include/tools/mdprep/gromacs/util.hpp

@@ -1,7 +1,6 @@
 #ifndef __VTX_TOOL_TOOLS_MDPREP_GROMACS_UTIL__
 #define __VTX_TOOL_TOOLS_MDPREP_GROMACS_UTIL__
 
-#include <array>
 #include <filesystem>
 namespace fs = std::filesystem;
 
@@ -23,28 +22,10 @@ namespace VTX::Tool::Mdprep::Gromacs
 	// Show gromacs where to look for forcefields
 	void declareFfDirectory( const fs::path & ) noexcept;
 
-} // namespace VTX::Tool::Mdprep::Gromacs
+	// Fill the job report with results on the job data. Aims to indentify if all expected output files are here and if
+	// there is no error message in any of the chanels.
+	void checkJobResults( GromacsJobData & ) noexcept;
 
-namespace VTX::Tool::Mdprep::Gromacs
-{
-	struct GromacsCommandArgs;
-	struct solvateInstructions // WIP // TODO : move it in appropriate location
-	{
-		fs::path				 inputGro;
-		fs::path				 outputGro;
-		std::array<double, 3ull> box { 0., 0., 0. };
-		double					 radius = 0.105;
-		double					 scale	= 0.57;
-		double					 shell	= 0.;
-		int						 maxsol = 0;
-		bool					 vel	= false;
-	};
-
-	// Write gromacs command arguments using input instructions
-	//    Does nothing if the instructions have default values.
-	//    Does not perform filesystem check on input gro
-	//    If the output_gro is empty, will use the input filename root and append "solv"
-	void convert( const solvateInstructions &, GromacsCommandArgs & ) noexcept;
 } // namespace VTX::Tool::Mdprep::Gromacs
 
 #endif

lib/tool/tools/mdprep/src/gromacs/gromacs.cpp

@@ -22,7 +22,7 @@ namespace VTX::Tool::Mdprep::Gromacs
 			out.clear();
 		}
 
-		void interactiveProcessManagement( QProcess & p_proc, bool & p_finished, GromacsCommandArgs & p_args ) noexcept
+		void interactiveProcessManagement( QProcess & p_proc, bool & p_finished, GromacsJobData & p_args ) noexcept
 		{
 			std::string unsentBuf, // Used when the stdout is not ready to be sent
 				bufErr, bufOut;
@@ -83,7 +83,7 @@ namespace VTX::Tool::Mdprep::Gromacs
 			fillMissingString( p_proc.readAllStandardOutput(), bufOut );
 			fillMissingString( *channels, bufErr, bufOut );
 		}
-		void simpleProcessManagement( QProcess & p_proc, bool & p_finished, GromacsCommandArgs & p_args ) noexcept
+		void simpleProcessManagement( QProcess & p_proc, bool & p_finished, GromacsJobData & p_args ) noexcept
 		{
 			QByteArray bufErr, bufOut;
 
@@ -101,7 +101,7 @@ namespace VTX::Tool::Mdprep::Gromacs
 		}
 	} // namespace
 
-	void submitGromacsCommand( const fs::path & p_gmxExe, GromacsCommandArgs & p_args )
+	void submitGromacsJob( const fs::path & p_gmxExe, GromacsJobData & p_args )
 	{
 		QString		pgm { p_gmxExe.string().data() };
 		QStringList qtArgs;

lib/tool/tools/mdprep/src/gromacs/util.cpp

@@ -1,3 +1,5 @@
+#include <regex>
+//
 #include "tools/mdprep/gromacs/inputs.hpp"
 //
 #include "tools/mdprep/gromacs/gromacs.hpp"
@@ -46,6 +48,48 @@ namespace VTX::Tool::Mdprep::Gromacs
 		qputenv( "GMXLIB", env_arg );
 	}
 
-	void convert( const solvateInstructions &, GromacsCommandArgs & ) noexcept {}
+	namespace
+	{
+		void checkErrMsg( JobReport & p_report, const std::string & p_text ) noexcept
+		{
+			const std::regex errRegex { "^[ \t]*Error (.|[\r\n])*?\n\n" };
+			for ( auto it = std::sregex_iterator( p_text.begin(), p_text.end(), errRegex );
+				  it != std::sregex_iterator();
+				  ++it )
+			{
+				p_report.errors.push_back( it->operator[]( 0 ).str() );
+			}
+		}
+	} // namespace
+
+	void checkJobResults( GromacsJobData & p_in ) noexcept
+	{
+		{
+			auto channels = p_in.channelsLocker.open();
+			checkErrMsg( p_in.report, channels->stderr_ );
+			checkErrMsg( p_in.report, channels->stdout_ );
+		}
+
+		for ( auto & it : p_in.expectedOutputFilesIndexes )
+		{
+			fs::path f { p_in.arguments[ it ] };
+			if ( f.empty() )
+				continue;
+			if ( fs::exists( f ) == false || fs::is_regular_file( f ) == false )
+			{
+				p_in.report.errors.push_back(
+					fmt::format( "Expected output file <{}> not found.", p_in.arguments[ it ] )
+				);
+				break;
+			}
+			if ( fs::file_size( f ) == 0 )
+			{
+				p_in.report.errors.push_back( fmt::format( "Expected output file <{}> is empty.", p_in.arguments[ it ] )
+				);
+				break;
+			}
+		}
+		p_in.report.errorOccured = ( p_in.report.errors.empty() == false );
+	}
 
 } // namespace VTX::Tool::Mdprep::Gromacs

lib/tool/tools/mdprep/test/conanfile.py

@@ -24,27 +24,20 @@ def requirements(self):
         self.requires("qt/6.6.1", transitive_headers=True)
         self.requires("vtx_tool_mdprep/1.0")
         self.requires("catch2/3.4.0")        
+        self.requires("gromacs/2024.0")        
 
     def generate(self):
-        copy(self, "*.dll", self.dependencies["vtx_tool_mdprep"].cpp_info.bindir, os.path.join(self.build_folder, self.cpp.build.libdirs[0]))
+        copy(self, "*", os.path.join(self.dependencies["gromacs"].package_folder, "external"), os.path.join(self.build_folder, "external"))        
+        copy(self, "*", os.path.join(self.dependencies["gromacs"].package_folder, "data", "tools","mdprep","gromacs","top"), os.path.join(self.build_folder, "data", "tools", "mdprep", "gromacs", "top" ))    
 
     def layout(self):
         cmake_layout(self)
 
     def build(self):
-        """
-        vtx_gromacs_shared = os.path.join(self.dependencies["vtx_tool_mdprep"].folders.build_folder, "vtx_gromacs")
-        ext = ".dll"
-        if self.settings.os == "iOS" :
-            ext = ".dylib"
-        if self.settings.os == "Linux" :
-            ext = ".so"
-        vtx_gromacs_shared += ext
-        """
         cmake = CMake(self)
         cmake.configure()
         cmake.build()
-        #self.run("ctest --rerun-failed --output-on-failure") # TODO uncomment this when build is stable
+        self.run("ctest --rerun-failed --output-on-failure") # TODO uncomment this when build is stable
 
     def package(self):
         cmake = CMake(self)

lib/tool/tools/mdprep/test/data/1ubq_out_pdb2gmx/#1ubq.index.ndx.1#

@@ -0,0 +1,42 @@
+[ prot_sort ]
+   1    2    5    6    7    8    3    4    9   10   13   14   15   16   17
+  11   12   18   19   22   24   23   25   20   21   26   27   30   31   32
+  34   36   35   33   28   29   37   38   41   42   43   39   40   44   45
+  48   49   50   51   52   46   47   53   54   57   59   58   55   56   60
+  61   64   65   66   67   62   63   68   69   72   74   73   70   71   75
+  76   77   78   79   80   83   84   85   86   87   81   82   88   89   92
+  94   93   90   91   95   96   99  101  100  102   97   98  103  104  107
+ 109  108  105  106  110  111  114  115  116  117  112  113  118  119  122
+ 123  124  125  126  120  121  127  128  131  132  133  129  130  134  135
+ 138  139  140  141  142  136  137  143  149  148  147  144  145  146  150
+ 151  154  155  152  153  156  157  160  161  162  163  158  159  164  165
+ 168  170  169  166  167  171  172  175  177  176  178  173  174  179  180
+ 183  184  185  186  187  181  182  188  189  192  193  194  195  190  191
+ 196  197  200  201  202  198  199  203  204  207  208  209  210  211  205
+ 206  212  213  216  214  215  217  218  221  222  223  224  225  219  220
+ 226  227  230  232  231  233  228  229  234  235  238  239  240  241  242
+ 236  237  243  244  247  248  249  250  245  246  251  252  255  256  257
+ 258  259  253  254  260  261  264  265  266  267  268  262  263  269  270
+ 271  272  273  274  277  279  278  280  275  276  281  287  286  285  282
+ 283  284  288  294  293  292  289  290  291  295  296  299  300  301  302
+ 297  298  303  304  307  308  309  310  311  305  306  312  313  316  317
+ 318  319  320  314  315  321  322  325  326  327  328  329  330  331  323
+ 324  332  333  336  337  338  339  334  335  340  341  344  346  345  347
+ 342  343  348  349  352  353  354  356  358  357  355  350  351  359  360
+ 363  361  362  364  365  366  367  368  369  372  373  374  375  376  370
+ 371  377  378  381  382  383  384  385  379  380  386  387  390  391  392
+ 393  388  389  394  395  398  399  400  401  402  396  397  403  404  407
+ 408  409  410  405  406  411  412  413  414  415  416  419  420  421  422
+ 423  424  425  417  418  426  427  430  432  431  428  429  433  434  437
+ 438  439  440  435  436  441  442  445  446  443  444  447  448  451  452
+ 453  454  449  450  455  456  459  460  461  463  465  466  464  462  457
+ 458  467  468  471  472  473  474  469  470  475  476  479  481  480  482
+ 477  478  483  484  487  488  489  490  491  485  486  492  493  496  497
+ 498  499  500  494  495  501  502  505  506  507  508  509  503  504  510
+ 511  514  515  512  513  516  517  520  522  521  518  519  523  524  527
+ 528  529  530  525  526  531  532  535  536  537  539  540  538  533  534
+ 541  542  545  546  547  548  543  544  549  550  553  554  555  551  552
+ 556  557  560  561  562  563  558  559  564  565  568  569  570  571  572
+ 573  574  566  567  575  576  579  580  581  582  577  578  583  584  587
+ 588  589  590  591  592  593  585  586  594  595  596  597  598  599  600
+ 602  601