Changeset 949953 for src/Actions

Timestamp:

Nov 7, 2011, 12:23:52 PM (13 years ago)

Author:

Frederik Heber <heber@…>

Branches:

Action_Thermostats, Add_AtomRandomPerturbation, Add_FitFragmentPartialChargesAction, Add_RotateAroundBondAction, Add_SelectAtomByNameAction, Added_ParseSaveFragmentResults, AddingActions_SaveParseParticleParameters, Adding_Graph_to_ChangeBondActions, Adding_MD_integration_tests, Adding_ParticleName_to_Atom, Adding_StructOpt_integration_tests, AtomFragments, Automaking_mpqc_open, AutomationFragmentation_failures, Candidate_v1.5.4, Candidate_v1.6.0, Candidate_v1.6.1, ChangeBugEmailaddress, ChangingTestPorts, ChemicalSpaceEvaluator, CombiningParticlePotentialParsing, Combining_Subpackages, Debian_Package_split, Debian_package_split_molecuildergui_only, Disabling_MemDebug, Docu_Python_wait, EmpiricalPotential_contain_HomologyGraph, EmpiricalPotential_contain_HomologyGraph_documentation, Enable_parallel_make_install, Enhance_userguide, Enhanced_StructuralOptimization, Enhanced_StructuralOptimization_continued, Example_ManyWaysToTranslateAtom, Exclude_Hydrogens_annealWithBondGraph, FitPartialCharges_GlobalError, Fix_BoundInBox_CenterInBox_MoleculeActions, Fix_ChargeSampling_PBC, Fix_ChronosMutex, Fix_FitPartialCharges, Fix_FitPotential_needs_atomicnumbers, Fix_ForceAnnealing, Fix_IndependentFragmentGrids, Fix_ParseParticles, Fix_ParseParticles_split_forward_backward_Actions, Fix_PopActions, Fix_QtFragmentList_sorted_selection, Fix_Restrictedkeyset_FragmentMolecule, Fix_StatusMsg, Fix_StepWorldTime_single_argument, Fix_Verbose_Codepatterns, Fix_fitting_potentials, Fixes, ForceAnnealing_goodresults, ForceAnnealing_oldresults, ForceAnnealing_tocheck, ForceAnnealing_with_BondGraph, ForceAnnealing_with_BondGraph_continued, ForceAnnealing_with_BondGraph_continued_betteresults, ForceAnnealing_with_BondGraph_contraction-expansion, FragmentAction_writes_AtomFragments, FragmentMolecule_checks_bonddegrees, GeometryObjects, Gui_Fixes, Gui_displays_atomic_force_velocity, ImplicitCharges, IndependentFragmentGrids, IndependentFragmentGrids_IndividualZeroInstances, IndependentFragmentGrids_IntegrationTest, IndependentFragmentGrids_Sole_NN_Calculation, JobMarket_RobustOnKillsSegFaults, JobMarket_StableWorkerPool, JobMarket_unresolvable_hostname_fix, MoreRobust_FragmentAutomation, ODR_violation_mpqc_open, PartialCharges_OrthogonalSummation, PdbParser_setsAtomName, PythonUI_with_named_parameters, QtGui_reactivate_TimeChanged_changes, Recreated_GuiChecks, Rewrite_FitPartialCharges, RotateToPrincipalAxisSystem_UndoRedo, SaturateAtoms_findBestMatching, SaturateAtoms_singleDegree, StoppableMakroAction, Subpackage_CodePatterns, Subpackage_JobMarket, Subpackage_LinearAlgebra, Subpackage_levmar, Subpackage_mpqc_open, Subpackage_vmg, Switchable_LogView, ThirdParty_MPQC_rebuilt_buildsystem, TrajectoryDependenant_MaxOrder, TremoloParser_IncreasedPrecision, TremoloParser_MultipleTimesteps, TremoloParser_setsAtomName, Ubuntu_1604_changes, stable

Children:

c20b35

Parents:

071243

git-author:

Frederik Heber <heber@…> (09/26/11 12:59:25)

git-committer:

Frederik Heber <heber@…> (11/07/11 12:23:52)

Message:

pyMoleCuilder now has full functionality.

• For each header file there is a COMMAND_stringargs() function defined.
• boost python module exports all Action's COMMAND_stringargs() that are present in GlobalListOfActions.hpp.
• new source file AllActionPython.hpp is created in Actions/Makefile.am that enlists all the headers.
• New implemenations:
  • Action_impl_python.hpp: defines COMMAND_stringargs() via some boost:: preprocessor magic.
  • Action_impl_undef.hpp: contains undefs to the Action's .def files.
• also docstrings are working, both for module and for each exported function.
• so far, all arguments have a (in NODEFAULT case empty) default value. This is because we cannot perform string comparisons with the preprocessor only numeric ones (i.e. NODEFAULT would have to be 0 or alike).

• Extracted cleanUp() from builder_init.cpp and placed into own module.
• cleanUp() is now also registered atexit() for pyMoleCuilder where it is needed as well.
• AddStaticEntitiestoIgnoreList() has likewise been extracted.

Location:

src/Actions

Files:

• Action_impl_python.hpp (added)
• Action_impl_undef.hpp (added)
• Makefile.am (modified) (2 diffs)
• pyMoleCuilder.cpp (modified) (2 diffs)

src/Actions/Makefile.am ¶

@@ -407 +407 @@
 libMolecuilderActionPrototypes_la_includedir = $(includedir)/MoleCuilder/Actions/
 
-BUILT_SOURCES += AllActionHeaders.hpp
+BUILT_SOURCES += AllActionHeaders.hpp AllActionPython.hpp
 
 #       UIElements/libMolecuilderUI.la
@@ -459 +459 @@
         echo "#endif /* ALLACTIONHEADERS_HPP_ */" >>$@;
 
+AllActionPython.hpp: $(ACTIONPROTOTYPESHEADER)
+        echo "#ifndef ALLACTIONPYTHON_HPP_" >$@; \
+        echo "#define ALLACTIONPYTHON_HPP_" >>$@; \
+        for file in $(ACTIONPROTOTYPESHEADER); do \
+                echo "#include \"`echo $$file | sed -e 's/hpp/def/'`\"" >>$@; \
+                echo "#include \"Actions/Action_impl_python.hpp\"" >>$@; \
+                echo "#include \"Actions/Action_impl_undef.hpp\"" >>$@; \
+        done; \
+        echo "#endif /* ALLACTIONPYTHON_HPP_ */" >>$@;
+
+
 MOSTLYCLEANFILES += \
-        AllActionHeaders.hpp
+        AllActionHeaders.hpp \
+        AllActionPython.hpp

src/Actions/pyMoleCuilder.cpp ¶

@@ -18 +18 @@
 #endif
 
-#include <boost/python/def.hpp>
+#include <boost/python.hpp>
 #include <boost/python/module.hpp>
 #include <boost/python/args.hpp>
@@ -24 +24 @@
 #include "CodePatterns/MemDebug.hpp"
 
-#include "Actions/CommandAction/HelpAction.hpp"
+//!> define all present actions
+#include "GlobalListOfActions.hpp"
+
+//!> python wrapping for all of these actions
+#include "AllActionPython.hpp"
+
+#include "cleanUp.hpp"
+#include "Actions/ActionHistory.hpp"
+
 
 BOOST_PYTHON_MODULE(pyMoleCuilder)
 {
-  boost::python::def(
-      "CommandHelp",
-      MoleCuilder::CommandHelp,
-      boost::python::args("actionname"),
-      "this gives a list of all Actions."
-      );
+  // need to init the history before any action is created
+  MoleCuilder::ActionHistory::init();
+
+  // from this moment on, we need to be sure to deeinitialize in the correct order
+  // this is handled by the cleanup function
+  atexit(cleanUp);
+
+  // set the docstring of the current module scope
+  boost::python::scope().attr("__doc__") = "pyMolecuilder are the python bindings to all Actions of the program suite MoleCuilder.\n\nMoleCuilder is a program to build molecular (dynamics) worlds, allowing you indefinite manipulation, control and analysis over the atoms and molecules within a simulation domain.";
+
+#define export_print(z,n,list) \
+        BOOST_PP_CAT(export_, BOOST_PP_SEQ_ELEM(n, list))();
+#define BOOST_PP_LOCAL_MACRO(n) export_print(~, n, GLOBALLISTOFACTIONS)
+#define BOOST_PP_LOCAL_LIMITS  (0, BOOST_PP_DEC(BOOST_PP_SEQ_SIZE(GLOBALLISTOFACTIONS)))
+#include BOOST_PP_LOCAL_ITERATE()
+#undef instance_print  
 }