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Merged
merged 4 commits into from
Aug 15, 2018
Merged

Fixes to allow tests to pass under Fedora 29 #282

merged 4 commits into from
Aug 15, 2018

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keszybz
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@keszybz keszybz commented Aug 14, 2018

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keszybz added 3 commits August 14, 2018 17:59
@keszybz
Do not try to access position -1 in string
dc8dd21 
This ain't python ;(
@keszybz
Avoid open-coded strdup that cause compilation failure with new gcc
cfd4b5a 
/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,
@keszybz
Avoid open-coded strdup that causes a warning
702f67c 
/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.
@dilawar dilawar requested a review from subhacom August 15, 2018 04:13
dilawar
dilawar approved these changes Aug 15, 2018
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These fixes are required for => python3.7

dilawar
dilawar approved these changes Aug 15, 2018
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Looks good.
Fixes build failure for Python.h (>=python3.7).

@dilawar dilawar merged commit 4c2e7fa into BhallaLab:chamcham Aug 15, 2018
dilawar pushed a commit to dilawar/pymoose-community that referenced this pull request Aug 15, 2018
@keszybz
Fixes to allow tests to pass under Fedora 29 (BhallaLab#282)
68c5e57 
* 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.
dilawar pushed a commit to dilawar/pymoose-community that referenced this pull request Aug 15, 2018
Integrated BhallaLab#282
467eedf
dilawar pushed a commit to dilawar/pymoose-community that referenced this pull request Aug 16, 2018
@keszybz
Fixes to allow tests to pass under Fedora 29 (BhallaLab#282)
1980b72 
* 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.
@hrani hrani mentioned this pull request Aug 18, 2018
Closed
upibhalla pushed a commit that referenced this pull request Aug 21, 2018
@dilawar @upibhalla
Test xreacs (#287)
7a1b0d8 
* 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.
upibhalla pushed a commit that referenced this pull request Sep 7, 2018
@dilawar @upibhalla
Parallel solvers (#293)
d229eba 
* 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.

* Moved utility test to tests directory.

* Enabled parallel KSolve.

* parallel solver and added a test script.

* Default behvaiour is to use serial version of both Gsolve and Ksolve.
Fixes to build system.
Needs benchmarking.

* USE 3 Threads to tests. Travis is failing because threads are not
joining. Strange!

* Added boost::thread also. No performance improvement but no seg-faults
either.

* c++11 version with std::threads. Improved performance equivalent to
boost solver.

* Run test in serial. Travis builds are timedout.

* Similar design pattern in Gsolve.

* Everything looks fine locally. Probably the timeout problem is specific
to travis.

* Very good speedup. Lets go more finescale.

* Some reformatting. Tabs to spaces by vim and tiny tweaks here and there.
Nothing logical changed.

* Faster function. But detaching muparser make everything go gaga.

* Some formatting changes.

* Don't use async even in boost case.

* Minor cleanup.

* Clean up neuroml utilities. Revered back changes which broken nml
support.

* Cleanup: removed debug related statements.

* This compiles with new API. Need benchmarking.

* Thinner wrapper around boost solvers.

* Using lambdas instead of bind. Hopefully it is even thinner.

* Some changes to test script. By default use n//2 threads.

* Great performance with gcc7.

* Disable debug build with python3.

* Prefer c++11 library function if possible.

* Gsolve now also accepts numThreads options.

* Some changes to Gsolve.

* Dsolve is multithreaded as well. It inherits number of threads from
Ksolve or Gsolve.

* Disabled MPI and NUMCORE information.

* Fixes to Parallel build with boost.

* Resolve symbolic path when searching for module in rdesigneur.

* Fixes to rdesignuer when path contains symbolic link and .
for example: /home1/dilawars/Work.SVN/PlayGround/TestMooseParallel/Sep04_check_parallel_speed/proto21.make_K_AHP()

    find('.') -> rfind('.')

* When versbose mode is set, print when a function call has ended.

* Get the GIL in PyRun process function.

* temp commit for testing on bebinca [skip ci].

* Better printing of SWC diagnostic message.

* Replaced some function calls with their faster equivalents.

* Set environment variable MOOSE_SHOW_SOLVER_PERF to show the timing info
of ksolve.

* Squashed commit of the following:

commit b6c2fad494ed9addea9ca02f12708ed21ee4d021
Author: Dilawar Singh <dilawars@ncbs.res.in>
Date:   Thu Sep 6 12:05:25 2018 +0530

    Some tweaks in printing information.

commit a7e31db
Author: Dilawar Singh <dilawars@ncbs.res.in>
Date:   Thu Sep 6 11:14:33 2018 +0530

    Tweaks in printing diagnostics.

commit c43b890
Author: Dilawar Singh <dilawars@ncbs.res.in>
Date:   Thu Sep 6 10:24:12 2018 +0530

    Added a map to keep the time and steps taken by Ksolve and Hsolve.

commit c6ee187
Author: Dilawar Singh <dilawars@ncbs.res.in>
Date:   Wed Sep 5 18:34:57 2018 +0530

    HSolve will also show the time taken.

* Rdesigneur fixes from master branch.

* Fixed a macro and removed debug message.

* Dsolve is serial again. updateJunction can not be parallelized since it
both reads and update the value of either side of voxelpool inside a for loop.

* Use fixXreacs from moose. Removed the local copy.

* Added test for dsolve and gsolve together.
dilawar pushed a commit to dilawar/pymoose-community that referenced this pull request May 30, 2019
Squashed commit of the following:
f0466ec 
commit 0da2e75
Merge: 999c563 6addb09
Author: Dilawar Singh <dilawars@ncbs.res.in>
Date:   Tue May 28 11:04:12 2019 +0530

    Merge branch 'master' of github.com:BhallaLab/moose-core into exprtk

commit 999c563
Author: Dilawar Singh <dilawars@ncbs.res.in>
Date:   Mon May 27 16:33:42 2019 +0530

    Fixed table tests.

commit 7d9238e
Author: Dilawar Singh <dilawars@ncbs.res.in>
Date:   Mon May 27 16:11:10 2019 +0530

    Refactoring Ksolve.

commit c3141cb
Author: Dilawar Singh <dilawars@ncbs.res.in>
Date:   Mon May 27 13:52:08 2019 +0530

    IMplemented std::async to launch the thread with given policy. Needs
    profiling.  minor refactoring.
    Since we can not order order in launching thread, setting moose.seed
    would not result in deterministic number BhallaLab#365

commit 421e85a
Author: Dilawar Singh <dilawars@ncbs.res.in>
Date:   Mon May 27 00:14:23 2019 +0530

    Can't force order in multithreaded programs.

commit 569b279
Author: Dilawar Singh <dilawars@ncbs.res.in>
Date:   Sun May 26 18:14:56 2019 +0530

    Removed global call to rng from one more place.

commit 8ce2787
Author: Dilawar Singh <dilawars@ncbs.res.in>
Date:   Sun May 26 11:17:20 2019 +0530

    Invalid chunk size again.
    minor cleanup.
    A bit of refactoring. Need to fix the RNG in Gsolve.cpp

commit 40e146d
Author: Dilawar Singh <dilawars@ncbs.res.in>
Date:   Sun May 26 10:14:19 2019 +0530

    Fixes to CylMesh x0/x1 and diffLength bug.

commit 4f3f191
Author: Dilawar Singh <dilawars@ncbs.res.in>
Date:   Sat May 25 14:32:43 2019 +0530

    Added ASN support.
    Address leak in symbol table.
    No move in copy contructor.

commit 24ae9f9
Author: Dilawar Singh <dilawars@ncbs.res.in>
Date:   Fri May 24 17:38:54 2019 +0530

    We are back to malloc_consolidate error.
    Minor cleanup.

commit 86f46d4
Author: Dilawar Singh <dilawars@ncbs.res.in>
Date:   Fri May 24 13:56:28 2019 +0530

    Debug on arch with debug python.
    FuncTerm uses shared_ptr for MooseParser.
    parser is a shared pointer in FuncTerm as well.

commit f0fb7f3
Author: Dilawar Singh <dilawars@ncbs.res.in>
Date:   Fri May 24 12:06:33 2019 +0530

    Compiles successfully after merge.

commit e2b1eec
Merge: 4a747ba 58292d6
Author: Dilawar Singh <dilawars@ncbs.res.in>
Date:   Fri May 24 11:52:31 2019 +0530

    Merge branch 'master' into exprtk

commit 4a747ba
Author: Dilawar Singh <dilawars@ncbs.res.in>
Date:   Fri May 24 11:41:43 2019 +0530

    Time to merge master.

commit 14bb0d1
Author: Dilawar Singh <dilawars@ncbs.res.in>
Date:   Fri May 24 10:48:45 2019 +0530

    Getting rid of debug code.

commit d1b422a
Author: Dilawar Singh <dilawars@ncbs.res.in>
Date:   Thu May 23 22:54:30 2019 +0530

    needs to cleanup API.

commit 66a839f
Author: Dilawar Singh <dilawars@ncbs.res.in>
Date:   Thu May 23 18:33:54 2019 +0530

    Some testing and we are good to go.

commit 6a51b7d
Author: Dilawar Singh <dilawars@ncbs.res.in>
Date:   Thu May 23 18:27:03 2019 +0530

    Memory leak at the end but API is functional now.

commit b1fa3e4
Author: Dilawar Singh <dilawars@ncbs.res.in>
Date:   Thu May 23 17:36:15 2019 +0530

    Refactoring. Regex to find the variables x\d+ and y\d+ .

commit 6a795f2
Author: Dilawar Singh <dilawars@ncbs.res.in>
Date:   Thu May 23 16:25:25 2019 +0530

    error in cleanup.

commit ef13819
Author: Dilawar Singh <dilawars@ncbs.res.in>
Date:   Thu May 23 16:25:14 2019 +0530

    Somewhere error in cleaup.

commit d64e5c7
Author: Dilawar Singh <dilawars@ncbs.res.in>
Date:   Thu May 23 11:40:48 2019 +0530

    Allright. Need to redo the API.

commit 22825c4
Author: Dilawar Singh <dilawars@ncbs.res.in>
Date:   Thu May 23 10:57:13 2019 +0530

    Refactoring in Function and ZombieFunction

commit 9f4257d
Author: Dilawar Singh <dilawars@ncbs.res.in>
Date:   Wed May 22 20:36:56 2019 +0530

    temp commit. Need to cleanup Function.

commit 943c5c9
Author: Dilawar Singh <dilawars@ncbs.res.in>
Date:   Wed May 22 19:06:27 2019 +0530

    need to fix test_expr_parser.py script.

commit abd1466
Author: Dilawar Singh <dilawars@ncbs.res.in>
Date:   Wed May 22 16:29:28 2019 +0530

    Fixed parser issue. No mofification to variables address should be
    allowed after variable table has been registered.

commit b22c95e
Merge: b5dbbe9 fad1ded
Author: Dilawar Singh <dilawars@ncbs.res.in>
Date:   Tue May 21 21:16:23 2019 +0530

    Merge branch 'exprtk' of https://github.com/dilawar/moose-core into exprtk

commit b5dbbe9
Author: Dilawar Singh <dilawars@ncbs.res.in>
Date:   Tue May 21 21:15:51 2019 +0530

    Debug later.

commit fad1ded
Author: Dilawar Singh <dilawars@ncbs.res.in>
Date:   Tue May 21 17:52:34 2019 +0530

    CDASH location.

commit add6844
Author: Dilawar Singh <dilawars@ncbs.res.in>
Date:   Mon Aug 27 12:35:08 2018 +0530

    test_muparser.py is still failing.

commit af797e7
Author: Dilawar Singh <dilawars@ncbs.res.in>
Date:   Mon Aug 27 00:35:29 2018 +0530

    Something is wrong in FuncTer.

commit de08cbd
Author: Dilawar Singh <dilawars@ncbs.res.in>
Date:   Sun Aug 26 23:26:03 2018 +0530

    Function rand, srand and rand2 and srand2 function. Needs to modify
    documentations.

commit 14a7543
Author: Dilawar Singh <dilawars@ncbs.res.in>
Date:   Sun Aug 26 22:45:00 2018 +0530

    Needs final tweaking before raising a PR. Some tests are failing.

commit bb5fb2c
Author: Dilawar Singh <dilawars@ncbs.res.in>
Date:   Sun Aug 26 21:31:52 2018 +0530

    ExprTK module.

commit aa72a46
Author: Dilawar Singh <dilawars@ncbs.res.in>
Date:   Sun Aug 26 19:33:22 2018 +0530

    Removed debug messages.

commit 12b86d4
Author: Dilawar Singh <dilawars@ncbs.res.in>
Date:   Sun Aug 26 19:32:21 2018 +0530

    Using smart pointers to manage memory.

commit ddfc9bc
Author: Dilawar Singh <dilawars@ncbs.res.in>
Date:   Sun Aug 26 19:09:39 2018 +0530

    All test passing.

commit d7465c8
Merge: 87959cd 7a7072a
Author: Dilawar Singh <dilawars@ncbs.res.in>
Date:   Sun Aug 26 17:54:04 2018 +0530

    Merge commit '7a7072ae7245de5be61372e54e76468f00d5df30' into tiny_expr

commit 7a7072a
Author: Dilawar Singh <dilawars@ncbs.res.in>
Date:   Sun Aug 26 17:53:12 2018 +0530

    Squashed 'external/tinyexpr/' changes from 4dfb202cc..d689465d3

    d689465d3 Looks OK for integration into moose.
    89bd8a363 Support uppercase letters as well. See codeplea/tinyexpr#41 for upstream status and other information. TODO: Support numbers in scientific notation such as 1e-13 etc.
    6c884356e Got rid of makefiles.
    360be8da9 update cmake build system.
    f26faa3ba Local use cases.

    git-subtree-dir: external/tinyexpr
    git-subtree-split: d689465d360687eac4ffbc70253708148563660a

commit 87959cd
Author: Dilawar Singh <dilawars@ncbs.res.in>
Date:   Sun Aug 26 17:48:05 2018 +0530

    Pulling in new tinyexpr customized for moose.

commit 4ca4abd
Author: Dilawar Singh <dilawars@ncbs.res.in>
Date:   Sun Aug 26 17:01:11 2018 +0530

    Make tinyexpr to support uppercase characters as well
    codeplea/tinyexpr#41

commit 53b20a3
Author: Dilawar Singh <dilawars@ncbs.res.in>
Date:   Sun Aug 26 05:22:17 2018 +0530

    One more test passed.

commit a07ca1c
Author: Dilawar Singh <dilawars@ncbs.res.in>
Date:   Sun Aug 26 05:10:24 2018 +0530

    One more test is passed.

commit 7cbef8e
Author: Dilawar Singh <dilawars@ncbs.res.in>
Date:   Sun Aug 26 03:46:54 2018 +0530

    testKsolve is still have segfaults.

commit b986eb7
Author: Dilawar Singh <dilawars@ncbs.res.in>
Date:   Sun Aug 26 03:25:42 2018 +0530

    Few more changes. Python tests are passing. Some c++ tests are failing.

commit 7d0d132
Author: Dilawar Singh <dilawars@ncbs.res.in>
Date:   Sat Aug 25 23:52:39 2018 +0530

    Everything seems to be fine now. Lets check the Neuron class now.

commit 58bdd9c
Author: Dilawar Singh <dilawars@ncbs.res.in>
Date:   Sat Aug 25 22:30:46 2018 +0530

    Equivalent implementations.

commit c5fded8
Author: Dilawar Singh <dilawars@ncbs.res.in>
Date:   Sat Aug 25 21:00:21 2018 +0530

    removed npy support. On large files, it was not working properly. Only
    csv format is supported in Streamer.

commit f6f00d3
Author: Dilawar Singh <dilawars@ncbs.res.in>
Date:   Sat Aug 25 19:54:45 2018 +0530

    Partially correct. Now let see if 't' wroks.

commit 57536c0
Author: Dilawar Singh <dilawars@ncbs.res.in>
Date:   Sat Aug 25 18:58:58 2018 +0530

    values are being passed to parser ok. Still it could not evaluate.

commit 6875fe8
Author: Dilawar Singh <dilawars@ncbs.res.in>
Date:   Sat Aug 25 17:30:34 2018 +0530

    Some more progress. Now needs to link the variables correctly.

commit f3a1f13
Author: Dilawar Singh <dilawars@ncbs.res.in>
Date:   Sat Aug 25 14:39:35 2018 +0530

    Compiles but seg-fault.

commit 82b0ddb
Author: Dilawar Singh <dilawars@ncbs.res.in>
Date:   Fri Aug 24 14:01:58 2018 +0530

    This compiles fine. Now need to integrate tiny expression.

commit 2c3bdf1
Author: Dilawar Singh <dilawars@ncbs.res.in>
Date:   Fri Aug 24 11:45:41 2018 +0530

    Some modification; but replacing muParser is not easy.

commit 23e0b64
Author: Dilawar Singh <dilawars@ncbs.res.in>
Date:   Fri Aug 24 11:07:42 2018 +0530

    Squashed 'external/tinyexpr/' changes from ffb0d41b1..4dfb202cc

    4dfb202cc Merge pull request BhallaLab#38 from cschreib/master
    9de3ed238 Fixed right-to-left interpreter and repeated unary operators
    4cdeb9150 Added equality tests
    c1b01d879 Added comparison and logical operators
    aecac8226 Added missing install target for include file
    2f664da4d Added GUI options for library compilation options
    a0fe4fa91 Allow customizing library options TE_NAT_LOG and TE_POW_FROM_RIGHT
    57cd1fd4a Added missing install target
    da52ce22b Fixed tests not built with the right preprocessos options
    c95c36b83 Tweak build
    c62727052 Add CMake build system support

    git-subtree-dir: external/tinyexpr
    git-subtree-split: 4dfb202cc9f8324dcf78bc568637628324c4d357

commit 0874771
Merge: 2b9e94b 23e0b64
Author: Dilawar Singh <dilawars@ncbs.res.in>
Date:   Fri Aug 24 11:07:42 2018 +0530

    Merge commit '23e0b64ade6b4586a2b6303bba9b2a033a857f16' into tiny_expr

commit e456bcc
Author: Dilawar Singh <dilawars@ncbs.res.in>
Date:   Fri Aug 24 11:05:38 2018 +0530

    Squashed 'external/tinyexpr/' content from commit ffb0d41b1

    git-subtree-dir: external/tinyexpr
    git-subtree-split: ffb0d41b13e5f8d318db95feb071c220c134fe70

commit 2b9e94b
Merge: e742c40 e456bcc
Author: Dilawar Singh <dilawars@ncbs.res.in>
Date:   Fri Aug 24 11:05:38 2018 +0530

    Merge commit 'e456bccf0b5bef7d52aabca5c1e39cc41a66810e' as 'external/tinyexpr'

commit e742c40
Author: Dilawar Singh <dilawars@ncbs.res.in>
Date:   Fri Aug 24 11:05:23 2018 +0530

    Removed muparser.

commit cccb839
Merge: c37069b 3790376
Author: Dilawar Singh <dilawars@ncbs.res.in>
Date:   Thu Aug 23 12:54:42 2018 +0530

    Merge branch 'master' of github.com:BhallaLab/moose-core

commit c37069b
Author: Dilawar Singh <dilawars@ncbs.res.in>
Date:   Tue Aug 21 18:49:33 2018 +0530

    Moved utility test to tests directory.

commit 8f5fcd3
Merge: 09eb207 637d223
Author: Dilawar Singh <dilawar@users.noreply.github.com>
Date:   Tue Aug 21 12:28:19 2018 +0530

    Merge branch 'master' into master

commit 09eb207
Merge: 3d7a843 3a8489c
Author: Dilawar Singh <dilawar@users.noreply.github.com>
Date:   Tue Aug 21 10:05:40 2018 +0530

    Merge branch 'master' into master

commit 3d7a843
Merge: 08e3114 7c321bf
Author: Dilawar Singh <dilawar@users.noreply.github.com>
Date:   Fri Aug 17 10:28:18 2018 +0530

    Merge branch 'master' into master

commit 08e3114
Author: Dilawar Singh <dilawars@ncbs.res.in>
Date:   Thu Aug 16 11:35:47 2018 +0530

    Use single thread by default unless all benchamarking is done. For small
    system, multithreaded version is costly.

commit 1980b72
Author: Zbigniew Jędrzejewski-Szmek <zbyszek@in.waw.pl>
Date:   Wed Aug 15 11:06:24 2018 +0200

    Fixes to allow tests to pass under Fedora 29 (BhallaLab#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.

commit cd21147
Merge: 3f37852 1271dcd
Author: Dilawar Singh <dilawars@ncbs.res.in>
Date:   Thu Aug 9 10:33:25 2018 +0530

    Merge branch 'master' of github.com:BhallaLab/moose-core

commit 3f37852
Merge: 4897de3 0445da5
Author: Dilawar Singh <dilawars@ncbs.res.in>
Date:   Tue Jul 24 20:51:16 2018 +0530

    Merge branch 'master' of https://github.com/BhallaLab/moose-core

commit 4897de3
Author: Dilawar Singh <dilawars@ncbs.res.in>
Date:   Fri Jun 22 11:22:53 2018 +0530

    Show extra molecule warning when number is significant.

commit 0376f78
Author: Dilawar Singh <dilawars@ncbs.res.in>
Date:   Fri Jun 22 09:55:12 2018 +0530

    Absolute path in header.

commit 50ccb80
Author: Dilawar Singh <dilawars@ncbs.res.in>
Date:   Fri Jun 22 09:53:06 2018 +0530

    Merged upstraems and tweaks to cmake policy. Enforcing NEW by default.

commit 6e38a09
Merge: f554f45 cddc3bd
Author: Dilawar Singh <dilawars@ncbs.res.in>
Date:   Fri Jun 22 09:27:43 2018 +0530

    Merge branch 'master' of github.com:BhallaLab/moose-core

commit f554f45
Author: Dilawar Singh <dilawars@ncbs.res.in>
Date:   Thu May 17 15:18:18 2018 +0530

    removed test logger.

commit 37ad2a0
Merge: 3aae44b edc3b04
Author: Dilawar Singh <dilawars@ncbs.res.in>
Date:   Mon Apr 23 18:18:29 2018 +0530

    Merge branch 'master' of github.com:dilawar/moose-core

commit edc3b04
Author: Dilawar Singh <dilawars@ncbs.res.in>
Date:   Mon Apr 23 18:16:43 2018 +0530

    Problem is unresolvable.

commit 50fbc9b
Author: Dilawar Singh <dilawars@ncbs.res.in>
Date:   Mon Apr 23 16:13:35 2018 +0530

    Fixed error in utility function.

commit 3aae44b
Merge: 9845862 c3223c9
Author: Dilawar Singh <dilawars@ncbs.res.in>
Date:   Mon Apr 23 14:54:26 2018 +0530

    Merge branch 'master' of github.com:dilawar/moose-core

commit c3223c9
Author: Dilawar Singh <dilawars@ncbs.res.in>
Date:   Mon Apr 23 14:51:24 2018 +0530

    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.

commit 9845862
Author: Dilawar Singh <dilawars@ncbs.res.in>
Date:   Mon Apr 23 14:31:09 2018 +0530

    Force disable round() method. Fixed error message in plotutil import failure.

commit 2b72ade
Author: Dilawar Singh <dilawars@ncbs.res.in>
Date:   Mon Apr 23 13:24:14 2018 +0530

    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.

commit a3c2557
Author: Dilawar Singh <dilawars@ncbs.res.in>
Date:   Sun Apr 22 18:55:57 2018 +0530

    Using std::copysign to get the sign of a number.

commit 06057ed
Author: Dilawar Singh <dilawars@ncbs.res.in>
Date:   Sun Apr 22 18:37:21 2018 +0530

    Merge bhallalab.
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@dilawar dilawar dilawar approved these changes

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@keszybz @dilawar