Test xreacs (#287)
* Merge bhallalab.
* Using std::copysign to get the sign of a number.
* DO NOT use round() method to get to the nearest integer. It violates
mass-conservation in small system. The probabilistic algorithm is better and
does not cause extra molecules in system.
* Force disable round() method. Fixed error message in plotutil import failure.
* Disable rounding off in reinit function.
1.2 1.2 ... 1.2
will be converted to 1.0 1.0 ..2.0... 1.0 etc. Both sequences will have
different sum sometime and will cause mass-conservation error.
* Fixed error in utility function.
* Problem is unresolvable.
* removed test logger.
* Merged upstraems and tweaks to cmake policy. Enforcing NEW by default.
* Absolute path in header.
* Show extra molecule warning when number is significant.
* Fixes to allow tests to pass under Fedora 29 (#282)
* Do not try to access position -1 in string
This ain't python ;(
* Avoid open-coded strdup that cause compilation failure with new gcc
/builddir/build/BUILD/moose-3.1.3/moose-core/pymoose/moosemodule.cpp:2724:32: error: invalid conversion from 'const char*' to 'char*' [-fpermissive]
strncpy(vec[currIndex].name,
* Avoid open-coded strdup that causes a warning
/home/zbyszek/python/moose/moose-core/pymoose/mfield.cpp: In function 'int moose_Field_init(_Field*, PyObject*, PyObject*)':
/home/zbyszek/python/moose/moose-core/pymoose/mfield.cpp:122:12: warning: 'char* strncpy(char*, const char*, size_t)' output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation]
strncpy(name, fieldName, size);
~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~
/home/zbyszek/python/moose/moose-core/pymoose/mfield.cpp:120:25: note: length computed here
size_t size = strlen(fieldName);
~~~~~~^~~~~~~~~~~
Add error handling while at it.
* Use single thread by default unless all benchamarking is done. For small
system, multithreaded version is costly.
* Added test-suite for Xreads from Upi.
* Enabled tests.
* Some cleanup in tests.
DO not position EndoMesh.
* Added new tests from Upi.
* Test each script separately.
* Save the file in all tests.
* Fixes to filenames.
* Added tests.
* Moved utility test to tests directory.
* test_xreacs suite is now passing.
* Removed temp tests.
* Disable matplotlib from tests.
* Test was failing with boost with 5e-5 tolerance. Increased it to 6e-5
and now everything is fine.
loadmodel with add_delete_chemSolver (#288)
* setting up dsolver and by passing loadModel from moosemodule.cpp to moose.py
* ReadKkit.cpp: solver is set in moose.py for genesis and cspace, so warning about setting ee solver is removed, Annotator.cpp: default solver is set as gsl in annotator/info which is changed to ee, moose.py:Bypassed loadModel from mooseModule.cpp to moose.py and for cspace and kinetics model addChemSolver is called if gsl or gssa is passed, add_Delete_ChemicalSolver.py: dsolve is quered if compartment is greater than 1
* Small change checked for dsolve exist to set the buildMeshJunction
* moose.py: bypassed the loadmodel and added solver is passed, add_Delete_ChemSolver.py: if length of compt greater than one then only dsolve is checked for deletion
* Update add_Delete_ChemicalSolver.py
python 3 and 2 sorting list
* Update add_Delete_ChemicalSolver.py
* Update add_Delete_ChemicalSolver.py
* Update add_Delete_ChemicalSolver.py
compartment sorting is done manually and setting of Dsolve is also rearranged
* clean up in add_Delete_chemicalsolver wrt to dsolve, mooseaddChemSolver moosedeleteChemSolver is mooseAddChemSolver mooseDeleteChemSolver, moose.py return is changed value for chemUtil is changed
* mooseaddChemSolver is changed to mooseAddChemSolver and same with moosedeleteChemSolver to mooseDeleteChemSolver
* from moose.py file modelpath is returned
* cleaner way to check the compartment size before setting up the solver
* Update mfield.cpp
This was fixed by subhasis for https://github.com/BhallaLab/moose-core/pull/179 in 658af76a4, this was reverted in b5898ac306 commit
This causes seg fault while accessing while accessing table.vector in some cases. E.g moose-examples/snippets/crossComptSimpleReac.py and crossComptSimpleReacGSSA.py
* moose.py: mooseAddChemSolver is called only for gsl and gssa after loadModel, add_Delete_ChemicalSolver.py: positionCompt() and fixXreacs() for gsl and gssa irrespective of multi-compartment
