lp:moose-core

Author: Subhasis Ray
Author Date: 2024-04-11 00:24:41 UTC

Updated neuroml2 imports with error messages (#472)

* Fixed showmsg() bug in pybind11 based version.

The newer implementation of showmsg() shows the outgoing messages with
misdirected arrows. Fixed now.

* Added newer version of pybind11

* Swapped clocks for channel and compartment to fix #467

* This actually fixes scheduling for channels and compartments #467

The previous commit only updated the docs. This one modifies the
actual tick assignments.
Now electrical compartments are scheduled on ticks 2 and 3 and
channels (all derived from ChanBase) on 4.

* Minor fix for compiler warning on loop var creating copy from const

* Removed CMake generated compile command.

the compile command file is generated by cmake in each build
environment and should not be part of the repo.

* Added error message at neuroml import error, corrected imports.

* Updated neuroml2 reader. Yet to debug Granule_98 model.

* Updated neuroml2 reader to handle spherical compartment for CaPool

Also created separate test script for Granule98 model.

* Fixed deprecated imp module use in rdesigneur.

- rdesigneur used imp module, now replaced by importlib.
- commented out debug logs from neuroml2 reader
- TODO: tests/support has files which conflict with tests/core. These
  seem to be old test code which may better be removed.

* Updated test script for Granule98 model

---------

Co-authored-by: HarshaRani <ranishashi@gmail.com>

Author: hrani
Author Date: 2024-03-08 18:27:16 UTC

Updating branch 'master' into updateExprTK

Author: Subhasis Ray
Author Date: 2024-02-22 05:40:55 UTC

Merge branch 'master' into hrani-patch-1

Author: HarshaRani
Author Date: 2024-02-19 16:46:10 UTC

Update pymoose.yml

removal of python-tk

Author: HarshaRani
Author Date: 2024-02-19 16:24:31 UTC

Update pymoose.yml

removal of python-tk

Author: HarshaRani
Author Date: 2023-08-04 13:23:15 UTC

Update pymoose.yml

clean and update

Author: HarshaRani
Author Date: 2022-07-18 06:46:12 UTC

Merge branch 'master' into zombie_gone

Author: HarshaRani
Author Date: 2022-07-12 11:23:13 UTC

Merge branch 'master' into jalebi

Author: Dilawar Singh
Author Date: 2020-09-08 17:45:17 UTC

Fixes to Python3.9 build failure (#420)

* Fixes to BhallaLab/moose-core#419

* A better fix to #419

dict `locals_` is not Py_XINCREF anywhere that is why Py_XDECREF caused segfault.
While `globals_` does not have this issue. In the previous fix https://github.com/BhallaLab/moose-core/pull/420/commits/c570f7c057f9c0ca7360c82a8932bcb0df222da9,
I removed the `Py_XINCREF(globals_)` line as well which would cause memory leak.

* Related to #421 | Use wildard in package_data

Instead of using the full name of module, use wildcard `_moose*.so` in the
`package_data` field. On some platforms, platform info is added between the name
and the suffix e.g. `.cpython-39-powerpc64le-linux-gnu.so`. Using `_moose*.so` will take
care of such cases.

Co-authored-by: Dilawar Singh <dilawars@ncbs.res.in>

Author: Dilawar Singh
Author Date: 2020-05-01 11:28:28 UTC

Update to chennapoda branch (#413)

* Fixed boost segfault with dense solver. Also remove GSL specific attrib from the test. (#310)

* hotfix for running Boost, Added NMDAR to rdesigneurProtos.

* Fixes as suggested by PyLint. Added a target pylint in cmake file. (#308)

* Fixes as suggested by PyLint. Added a target pylint in cmake file.

* Do pylint testing on OSX.

* Fixed import statement.

* Fixed pylint errors, removed unneccessary file.

* Test of available attributes in moose.

* Install python-libsbml and pyneuroml on OSX before running pylint.

* Removed temporary attributes from test.

* plot_utils is not so important. It failes when python-tk not found.

* Fixed boost segfault with dense solver.
Also remove GSL specific attrib from the test.

* Tweak to cmake on OSX. New clang-llvm compiler options added to ignore unused pragmas. Import hhfit only when required.

* None of thest depends on matplotlib anymore.
Added one more rdesineur tests from moose-examples scripts.

* Fix travis: Install python-tk and python3-tk on travis.

* Some fixes to Ca-dependent channel prototypes in rdesigneur.

* Build System Tweaks (#309)

* Fixes as suggested by PyLint. Added a target pylint in cmake file.

* Do pylint testing on OSX.

* Fixed import statement.

* Fixed pylint errors, removed unneccessary file.

* Test of available attributes in moose.

* Install python-libsbml and pyneuroml on OSX before running pylint.

* Removed temporary attributes from test.

* plot_utils is not so important. It failes when python-tk not found.

* Fixed boost segfault with dense solver.
Also remove GSL specific attrib from the test.

* Tweak to cmake on OSX. New clang-llvm compiler options added to ignore unused pragmas. Import hhfit only when required.

* None of thest depends on matplotlib anymore.
Added one more rdesineur tests from moose-examples scripts.

* Fix travis: Install python-tk and python3-tk on travis.

* TIDY UP: basecode and benchmarks can be built independantly. [skip ci]

* Compiles as standalone. [skip ci]

* One more directory is standalone.

* Diffusion dir is standalone as well [skip ci]

* hsolve built in isolation as well [skip ci]

* ksolve is now tidied up [skip ci]

* needs local testing now.

* This passes locally with python3.

* include_guard is not in cmake2.8.

* More more fixes identified by clang-check.

* Added Cell.cpp to build system. This class is probably broken but good
to keep it included.

* Hotfix: Neuroml2 fixes. (#315)

```AttributeError: 'NML2Reader' object has no attribute 'rate_fn_map'```
This is causing failure of moose-examples: https://travis-ci.org/BhallaLab/moose-examples/jobs/436070992

* Fixes to build failure on OSX because cmake does not MACOSX but APPLE on (#316)

OSX.

* Update CMakeLists.txt

Do not treat warning as errors. It causes headaches with new compiler versions and OSX updates.

* corrected the spell of CyclMesh-->CylMesh, negating the yaxis for kkit is corrected as now saving the value of scene coOrdinates (#313)

* Rdesigneur passiveDistrib modified to handle legacy commands

* Update README.md (#312)

* Update README.md

Updated installation instructions.

- Removed open build service repo.
- Added nightly version.

* Use system python on travis. Using full paths.

* Use xcode 10.0

* Minor typo in warning report for Dsolve

* Hotfix. If self.network not found, sett the temperate to 25 deg C.

* Now user can pass verbose option to mooseReadNML2

* Works after disabling alpha and beta properties.

* CylMesh are written to SBML with annotation field and only zeroth ele… (#318)

* CylMesh are written to SBML with annotation field and only zeroth element/voxel is taken

* originaly volex's volume and volex details are populated, but now cylMesh volume with volex details is populated

* reading info field for channel from kkit file (#321)

* Channel are written back to genesis and zeroth voxel moose object is written for both cubeMesh or CylMesh

* while reading the sbml model validator can be switched off

* cleanup in print statement

* Bugfix for ConcChan to correct scaling for permeability to SI units of millimolar

* Fixed test_Xchan1.py to match bugfix for Dsolve.

* Added dummy CubeMesh as default parent for EndoMesh to avert segvs on several methods

* Fixed numDimentions to 3

* Fixes to EndoMesh (#327)

* Added dummy CubeMesh as default parent for EndoMesh to avert segvs on several methods

* Fixed numDimentions to 3

* Fixes to rdesigneur so that chemProto without chemDistrib will not fail confusingly.

* Got rid of printf debug line

* Fix to rdesigneurProtos so that the classic HH Na and K_DR channels now work properly.

* CylMesh,EndoMesh,NeuroMesh compartment are written to SBML as compartment with annotation field in which surround,isMembraneBound,numDiffCompts

* variable name used in before assignment cleanup

* Squashed commit of the following:

commit 5a789d986838bf53be118ffbfc3034946dd7da83
Author: Dilawar Singh <dilawars@ncbs.res.in>
Date: Thu Nov 8 21:41:11 2018 +0530

    Fixes to NML reader.

commit b17c8badfe9cfb5947b6b9652894ea8f3ec9158e
Author: Dilawar Singh <dilawars@ncbs.res.in>
Date: Thu Nov 8 21:02:00 2018 +0530

    Temp commit. Added a skeleton of function to compute rate from moose
    classes.

commit 68768653eb5722acc1585b5b757bef84a256338b
Author: Dilawar Singh <dilawars@ncbs.res.in>
Date: Thu Nov 8 09:55:27 2018 +0530

    When self.versbose is set, write the flattened file to XML.

* gate with id z is loaded into gateZ in moose now.

* For CylMesh, totLength and diffLength is written to Annotation to get number of voxel

* xfer cross compartment molecules are not written as species and also for Reaction and Enzyme

* Using built in logging library.

* Fixed the bug caused by previous two commits. Now I need to make sure that
ca pool is read at each timepoint.

* Tweaks.

* Reading and creating CylMesh and EndoMesh if specified in the Annotation field

* Added other meshes while searching for groups

* xref pool are not wirtten and cleaned up if part of Reaction/Enzyme or notes,
group are checked under all the mesh

* searching for _xfer_

* Fix to Im calculation in HSolve, to include external channels like receptors. Also fix to Neuron.cpp for setting channelDistribution, to always load Ca_concs first, to ensure that any dependent channels are able to find them.

* groups and subgroups are written to sbml and read from xml files

* reading and writing diff and motor constant for pool

* Fix to CaConc to factor in valence of 2. Update to rdesigneur to handle SBML files

* using existing restoreXreacs function to remove _xfer_ objects before writting into SBML and genesis files

* Continuation to PR #308 (#340)

* Fixed docstrings of some functions.

* Fixed attribute tests.

* Update INSTALL.md

Cleaned up.

- Removed instructions which were no longer valid.
- Removed all `gnu-make` related stuff. `gnu-make` based build system has been long deprecated.
- `pip` is recommented way of installing `pymoose` hence OBS repo informations are removed from this repo.

* Hotfix: Neuroml2 fixes (#343)

* When self.versbose is set, write the flattened file to XML.

* Temp commit. Added a skeleton of function to compute rate from moose
classes.

* Fixes to NML reader.

* Enough fun with spacevim.

* Running fine though not sure if results are correct. Ask Jefferey to
validate.

* Dec 19 | continuation of NML2 fixes (#344)

* When self.versbose is set, write the flattened file to XML.

* Temp commit. Added a skeleton of function to compute rate from moose
classes.

* Fixes to NML reader.

* Enough fun with spacevim.

* Running fine though not sure if results are correct. Ask Jefferey to
validate.

* Good. Now we have concentration dependant HHGates as well.

* Search for a suitable CaConc in /library and use its name in expression. Its a
hack which is likely to work in mose cases. Not sure what would be a better
implementation.

* Corrected the K_AHP z gate and make_Ca y gate

In K_AHP, added the line K_AHP.useConcentration = 1
In K_AHP z gate, corrected the value of zB[i] from 1.0 to 1.0+zA[i]
In make_Ca y gate, corrected the value of yA[i] from 0.0 to 5.0 when the potential is less than EREST_ACT

* Travis build failure (#350)

* Fixes to build failure on travis (OSX).

* Potential fixes to travis.

* Updated xcode10 images.

* Issue 342 | TCP/UD Socket based Table Streamer (#345)

* - Implements TCP socket streamer. Opens on port 31416.
- Added a test case which also shows how to use it.
- The output is in JSON format.

* it is a good idea to zip the data with time for server.

* Temp commit. Needs to make sure that recv socket can read the data.

* Ready for a PR.

* Added moose server.

* This is nice but I don't know what is going on behind the scene. Must implement
from the scratch.

* Using raw sockets from python.

* I can now execute script on server.

* Updated a bit more.

* This works with ghevar [skip ci]

* A working version [skip ci]

* Extra code which saves all images to pdf file.

* A working version [skip ci]
Better path handling and result streaming. Needs to have a protocol for sending
messages.
python -m moose.server run the server.
removed pyflakes reported error [skip ci]
remove default -h (help) which was in conflict with -h (--host). [skip ci]

* Pipeline is complete. Works fine.

* Fixed pylint error.

* Socket works on OSX as well.

* Added logger. Need to test from different network.

* block socket till specified data is received.

Removed old dreprecated scripts. They are part of parent moose repo and
no longer required here.

Some more corner cases are handled.

Don't use fullpath.

Autosetup SocketStreamer when environment variable MOOSE_TCP_STREAMER_ADDRESS is
set to e.g. localhost:31416 .

Try till all data is recieved.

* Squashed commit of the following:

commit 206baccabb1d7c7b5b90accf9961376febcaab47
Author: Dilawar Singh <dilawars@ncbs.res.in>
Date: Tue Feb 5 10:11:27 2019 +0530

    removed the background client. Accept only 1 client.

commit b71dbb3d3f312ca1eec4fb456e8ea758123ad505
Author: Dilawar Singh <dilawars@ncbs.res.in>
Date: Mon Feb 4 15:55:44 2019 +0530

    changed the implementation. Now process function does nothing. We launch a
    thread in the background which monitor connections and stream the data. If no
    environment variable is set then no data is streamed and tables are safe.
    Tables are flushed when data is streamed. Need to change this behaviour.

* Socket streamer are alos available.

* added unix domain socket as well.

* Renamed some tests.

* On OSX, I can't send all the data [skip ci].

* Needs some more work [skip ci].

* Squashed commit of the following:

commit ff2b989659fdeb34ff5095177e17325286bd6746
Author: Dilawar Singh <dilawars@ncbs.res.in>
Date: Wed Feb 6 21:26:03 2019 +0530

    Test passes on linux.

commit 8ca89dc7b6a6d2bbad68cc2b696cbc871ed12107
Author: Dilawar Singh <dilawars@ncbs.res.in>
Date: Wed Feb 6 19:27:05 2019 +0530

    Latency in TCP socket is bad.

commit c3e15d8d3c92c51720823fb75d229be1c141dae4
Author: Dilawar Singh <dilawars@ncbs.res.in>
Date: Wed Feb 6 18:56:36 2019 +0530

    Fixed both tests. Now test on OSX.

commit c731328cdb38fe433d57d986fa070818ca793803
Author: Dilawar Singh <dilawars@ncbs.res.in>
Date: Wed Feb 6 18:52:08 2019 +0530

    Time is handled by table.

commit 701ea554eaa58320a4c0473f24c352eb1821afd8
Author: Dilawar Singh <dilawars@ncbs.res.in>
Date: Wed Feb 6 16:26:35 2019 +0530

    Fixed frame size helped.

commit b1686810a2e3c6496b08ad1b0196932a490debc6
Author: Dilawar Singh <dilawars@ncbs.res.in>
Date: Wed Feb 6 15:59:38 2019 +0530

    Test on osx [skip ci].

* Squashed commit of the following:

commit c3e15d8d3c92c51720823fb75d229be1c141dae4
Author: Dilawar Singh <dilawars@ncbs.res.in>
Date: Wed Feb 6 18:56:36 2019 +0530

    Fixed both tests. Now test on OSX.

commit c731328cdb38fe433d57d986fa070818ca793803
Author: Dilawar Singh <dilawars@ncbs.res.in>
Date: Wed Feb 6 18:52:08 2019 +0530

    Time is handled by table.

commit 701ea554eaa58320a4c0473f24c352eb1821afd8
Author: Dilawar Singh <dilawars@ncbs.res.in>
Date: Wed Feb 6 16:26:35 2019 +0530

    Fixed frame size helped.

commit b1686810a2e3c6496b08ad1b0196932a490debc6
Author: Dilawar Singh <dilawars@ncbs.res.in>
Date: Wed Feb 6 15:59:38 2019 +0530

    Test on osx [skip ci].

* TCP socket latency is high for small simulations.

* TCP socket works with latency but OK to use.

* Environment variable is working file. Time to merge.

* SO_REUSEPORT is not always defined. The build fails on centos-5 (#351)

(manylinux1) which is used to build python wheel. This manylinux1 is
ported to cento6, keep is option.

* Efficient Network Streamer for MOOSE (#352)

* This version shows images perfectly well. do not use timestamp since their value
will not compare with timestamp of artifacts on different machines.

* Temp commit.

* CTRL+C is still not behaving well.

* Socket information is separated and stored in one class.

* os.file.isfile does not work with UNIX_DOMAIN_SOCKET. use os.path.exists.

* Working version. Good for demo.

* Updated a little.

* Streaming is now flawless.

* passes.

* Local tests passes.

* Good for demo.

* Squashed commit of the following:

commit 33fd75bf051e4799d2c37d3dc6cd59d3bbd73f42
Author: Dilawar Singh <dilawars@ncbs.res.in>
Date: Sat Feb 9 17:48:43 2019 +0530

    Working fantastically with multiprocessing.

commit 3fd5a8724e7b9cc0c681f44f4019ecb3844129eb
Author: Dilawar Singh <dilawars@ncbs.res.in>
Date: Sat Feb 9 16:29:59 2019 +0530

    Split connect and stream function into two.

* A decent working version.

* updated a little bit more.

* Small simulation do not steam all the data. Large simulations are
working fine.

* Working version. May be SocketStreamer is ticking too fast.

* faster tests; non-blocking client.

* use absolute import | python3 error in build.

* folder name changed for reflect if PYTHON3 is being used.

* Added some delay after start()

* Fixes for OSX.

* The last table is allowed to have slightly fewer elements.

* Some more improvement.

* Travis Fix | Don't run streamer multitab tests on OSX/Travis. (#354)

* Don't run streamer multitab tests on OSX/Travis.

* Disable all socket streamer tests.

* readKkit.cpp : create annotator field for kinetic, readSBML.py: validator flag is set to on from true,groupname and groupid is passed, if both are missing then its not a valid sbml file, textcolor is set now, validator.py: added errormsg at validator, writeSBML.py: from chemconnectUtil getcolor is called and also group width and height is written if it comes from GUI, chemConnectUtil.py: getColor,validcolorcheck,getRandcolor moved from gui to core, writeKkit.py: text color might be a rgb which should go as string in kkit file, moose/utils.py: cleaned mooseaddchemsolver to mooseAddChemSolver, moose.py: solver is set if passed with moose.mooseReadSBML(), Annotator.h,cpp: added field height and width for group, rainbow.pkl added file

* cleanedup for python3 as well while loading pickle file

* syntax cleanup

* adding pickle file rainbow2.pkl for mapping colors from genesis

* travis complaining of same function name

* converting dictionary compatible to python3

* HOTFIX #357 | Cleaning up HDF5 related macros in cmake. (#358)

* Cleaning up HDF5 related macros in cmake.

* Update to OSX build. Use xcode10.1

* getCordColor is unused function removing

* function import was missing

* clean up with color conversion to hex values

* Fix for typo in socket implementation. (#359)

HOTFIX | Fix for typo in socket implementation.

* Fixes to issue #360. Regression caused by #352 . (#361)

* More tests and some rearrangements (#363)

* Rearranged tests. Any tests which is in alpha has been moved to
tests/alpha directory. To run these tests, use configuration Devel with
ctest.

* Added this script in regression tests. Seems to be passing https://github.com/BhallaLab/moose-core/issues/239
Reopen it if this is not a fix.

* Issue #47 is WONTFIX.

* Refactoring script related to #93 .

* Fixed return statement outside function error. So silly!

* bumped xcode version to 10.2

* On OSX, use python3 only.

* Fix #364 .

* Fixed boost include paths.

* Reverting xcode to default on travis.

* Also test with xcode image 10.2 but allow failure.
Removed insource odeint library since centos7 has the required version
of boost. CentOS6 is EOL.

* moose.test() is python3 compatible.

10.2 seems to be buggy on travis. making failure non-strict on it. Must
build with xcode9.4

Added xcode10.2 image.

* Hotfixes | diffLength and max compartments, rdesigneur+py3 etc, build system (#368)

* Don't run streamer multitab tests on OSX/Travis.

* Disable all socket streamer tests.

* 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 https://github.com/BhallaLab/moose-core/issues/365

* temp commit.

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

* Fixes to CylMesh x0/x1 and diffLength bug.

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

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

* Build is passing.

* Fixes to travis file.

* Fixes to tests.

* Fixed test_gsolve_parallel.

* NSDF related fixes.

* Fixed boost compile flags.

* More tests (#369)

* Got tests from exprtk_ new branch.

* Added new function rnd which honors global seed.

* Fixed derivative tests. muParser Derivative is not very precise.

* More tests and cleanup in muParser interface.

* muParser is bit less precise on OSX.

* Examples fixes (#370)

* cherrypick this to apply onto master. TODO: Cherrypick.

* Added another tests: moose.Function controls reaction rates.

* Using MooseParser as a interface class.

* Use moose.element instead of moose.Clock.

* When x1 is set to hight, rescale diffLength. When diffLength is set too
low, rescale x1.

* Don't print time to initialize info in release.

* honour limit set by SparseMatrix. Max number of entries allowed is 20k.

* neuroml: do not use "is" with strings

This works, but only because of an implementation detail: short
strings are interned as part of module code. But the rules are complicated
and we should not rely on this.

See http://guilload.com/python-string-interning/ for a nice writeup.

Python3.8 now warns about this.

* readSBML:compartment name and id is mapped, in Assignment rule a check made for integer in the expression,writeSBML:added autlayout which was required for writting cspace model while writting from command line, for cplxpool's x-y coordinates and motor/diff constant are added,fixXreac: check to see if object exist before _moose.connect, case where object is deleted but _xref_ annotation info field still hold the reference

* writekkit: cleanup

* upi commit dec 2019 (#380)

* Fixed Ca channel proto, thanks to Harshavardan

* Fix to vclamp in rdesigneur. Fix to ConcChan handling involving many files

* Fix to HSolve so that assignment of passive properties Em, Cm and Rm reflects in the solver calculations without having to rebuild the entire solver.

* Fix conversion for ConcChan in ReadKkit, corresponding fix to calculations in Dsolve

* Fixed test_Xchan1.py to work with fixed ConcChan permeability units

* readsbml: compartment name & Id is mapped to the values in comptSbmlidMooseIdMap,writesbml: added annotation for cplxpool, autolayout for cspaccemodels (#374)

* while writting genesis file compartment is added as a group

* kkit: channel's permeability converted from uM to mM, writeSBML: channel is written as MMenz and Km in kinetics law updated based on no. substrate

* Hotfix | Packaging issues on OSX (#383)

* Don't run streamer multitab tests on OSX/Travis.

* Disable all socket streamer tests.

* - Make python3 default python.
- cmake 3.12 is minimum required.
- Fixes to Python API. strncpy can not write to `const char*`. Instead initialize with value.
- Build system fixes.

* Fixes for gcc5 series. It is not smart enough to figure out which field is being updated. These needs to be ported to branch chamcham as well.

* Create cmake.yml

* Updated commands.

* removing github actions.

* Create build.yml

* Added sudo ...

* Run sudo apt-update ...

* Fixed the name of package...

* Fixed make and test targets.

* Added workflow file.

* Update build.yml

* Add pip support to build system | `pip install pymoose` will work on all platforms (#385)

* Don't run streamer multitab tests on OSX/Travis.

* Disable all socket streamer tests.

* added moose.about(). Show essential information about moose project

* Add .gitlab-ci.yml

* Update .gitlab-ci.yml

* - Make python3 default python.
- cmake 3.12 is minimum required.
- Fixes to Python API. strncpy can not write to `const char*`. Instead initialize with value.
- Build system fixes.

* Fixes for gcc5 series. It is not smart enough to figure out which field is being updated. These needs to be ported to branch chamcham as well.

* Create cmake.yml

* Updated commands.

* removing github actions.

* Create build.yml

* Added sudo ...

* Run sudo apt-update ...

* Fixed the name of package...

* Fixed make and test targets.

* Added workflow file.

* Update build.yml

* Using python setup.py to build the module.

* Not yet complete because we still don't have static linking to gsl .

* Temp commit: Build locally.

* Run in inside a docker image to tweak.

* Some more tweaks.

* Added centos build docker file.

* Docker build was successful. Needs to improve test function...

* Added centos build docker file.
Docker build was successful. Needs to improve test function...
setup.py is working just fine.
CMake and python's setup.py can use each other. Time to remove pymoose/setup.cmake.py file.
Removed the cmake helper script. It has been moved to topmost directory where it can be used on its own.

Squashed commit of the following:

commit 374bf500cf4ad7c43f22004a1e3c04047d3b6c4f
Author: Dilawar Singh <dilawars@ncbs.res.in>
Date: Tue Feb 4 14:22:29 2020 +0530

    This seems to work just fine.

commit 4746ec40edea16b0d1b047da4e9a08035fdf8143
Author: Dilawar Singh <dilawars@ncbs.res.in>
Date: Mon Feb 3 21:54:25 2020 +0530

    testing is required.

commit d2ddaf7a073f36a0e3ac7f5138ccd0f9054a8d52
Author: Dilawar Singh <dilawars@ncbs.res.in>
Date: Mon Feb 3 21:34:59 2020 +0530

    Seems to be just fine now.

commit 63dceb42ed29e38e31412b640f093f75b50ef1cc
Merge: c743aed1b 549935359
Author: Dilawar <dilawar.s.rajput@gmail.com>
Date: Mon Feb 3 15:32:41 2020 +0000

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

commit c743aed1bf6f55a6aeef4016f1f8806dc9282b9d
Author: Dilawar <dilawar.s.rajput@gmail.com>
Date: Mon Feb 3 15:32:05 2020 +0000

    Some more changes.

commit 5499353592e5f0259184d1fa94f32ce074a42993
Author: Dilawar Singh <dilawars@ncbs.res.in>
Date: Mon Feb 3 20:52:43 2020 +0530

    Use cmake2.8

commit c8b365ab8ab78b6a6202e4104c141d24e117d09d
Author: Dilawar Singh <dilawars@ncbs.res.in>
Date: Mon Feb 3 20:37:54 2020 +0530

    Lets test it in fresh docker image.

removed uninstall target, use pip to uninstall moose.

Added path in target_link_directories macro for target moose.bin.

MOOSE's python module.

* Minor tweaks...

* Some more tweaks.

* Added command test to setup.py which calls ctest.

* Temp commit.

* Removed the target_link_directories command which is available only in
very recent cmake.

* Added docker-file for suse.

* Updated cmake file; build directory is now part of directories to
search.

* Update build.yml

Fixed the test command in github actions.

* Use latest xcode.

* Squashed commit of the following:

commit ecdc1a8596708ca76b6e230da0643dd57a7bd504
Author: Dilawar Singh <dilawar.s.rajput@gmail.com>
Date: Wed Feb 5 14:15:46 2020 +0530

    Use latest xcode.

commit 2a81096d64b6a115c62ff4bf21a560c6c6b926b1
Merge: a4a23382f e7cd7c0ec
Author: Dilawar Singh <dilawar.s.rajput@gmail.com>
Date: Wed Feb 5 14:14:24 2020 +0530

    Merge remote-tracking branch 'bhallalab/master'

commit a4a23382f3f861c13e0e695854745beb30b298a5
Author: Dilawar Singh <dilawar@users.noreply.github.com>
Date: Wed Feb 5 13:42:26 2020 +0530

    Update build.yml

    Fixed the test command in github actions.

commit cb0095f4a833859fd13cf3b191bcffbe39e37ebb
Merge: 4408bee41 71c9756f1
Author: Dilawar Singh <dilawar.s.rajput@gmail.com>
Date: Wed Feb 5 14:10:24 2020 +0530

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

commit 71c9756f1bf448b20dad267f4db5f67f9dbd27b0
Author: Dilawar Singh <dilawars@ncbs.res.in>
Date: Tue Feb 4 23:20:11 2020 +0530

    Updated cmake file; build directory is now part of directories to
    search.

commit 2f0d93ab93db433cfea31512f655688fd800aac7
Author: Dilawar Singh <dilawars@ncbs.res.in>
Date: Tue Feb 4 23:00:55 2020 +0530

    Added docker-file for suse.

commit 82adc1ce999449309c08b4c118c66689e07ac1f0
Author: Dilawar Singh <dilawars@ncbs.res.in>
Date: Tue Feb 4 22:43:53 2020 +0530

    Removed the target_link_directories command which is available only in
    very recent cmake.

commit 36055662501ac60d2878ac679dbc3b665729230a
Author: Dilawar Singh <dilawars@ncbs.res.in>
Date: Tue Feb 4 17:46:22 2020 +0530

    Temp commit.

commit 6248e129aca21e9a9539ca2d9948fa9b1e64900c
Author: Dilawar Singh <dilawars@ncbs.res.in>
Date: Tue Feb 4 17:43:14 2020 +0530

    Added command test to setup.py which calls ctest.

commit a3d25aa0796d8e65f8040a46cc37263beffae0a9
Author: Dilawar Singh <dilawars@ncbs.res.in>
Date: Tue Feb 4 16:49:40 2020 +0530

    Some more tweaks.

commit 9a14b5c74a587c8f079c764a1cd128335a6a2b7d
Author: Dilawar Singh <dilawars@ncbs.res.in>
Date: Tue Feb 4 15:35:58 2020 +0530

    Minor tweaks...

commit 9f475b35f6603f5ee2af2e65819c4dc6a92c5f20
Author: Dilawar Singh <dilawar.s.rajput@gmail.com>
Date: Mon Feb 3 14:01:12 2020 +0530

    Added centos build docker file.
    Docker build was successful. Needs to improve test function...
    setup.py is working just fine.
    CMake and python's setup.py can use each other. Time to remove pymoose/setup.cmake.py file.
    Removed the cmake helper script. It has been moved to topmost directory where it can be used on its own.

    Squashed commit of the following:

    commit 374bf500cf4ad7c43f22004a1e3c04047d3b6c4f
    Author: Dilawar Singh <dilawars@ncbs.res.in>
    Date: Tue Feb 4 14:22:29 2020 +0530

        This seems to work just fine.

    commit 4746ec40edea16b0d1b047da4e9a08035fdf8143
    Author: Dilawar Singh <dilawars@ncbs.res.in>
    Date: Mon Feb 3 21:54:25 2020 +0530

        testing is required.

    commit d2ddaf7a073f36a0e3ac7f5138ccd0f9054a8d52
    Author: Dilawar Singh <dilawars@ncbs.res.in>
    Date: Mon Feb 3 21:34:59 2020 +0530

        Seems to be just fine now.

    commit 63dceb42ed29e38e31412b640f093f75b50ef1cc
    Merge: c743aed1b 549935359
    Author: Dilawar <dilawar.s.rajput@gmail.com>
    Date: Mon Feb 3 15:32:41 2020 +0000

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

    commit c743aed1bf6f55a6aeef4016f1f8806dc9282b9d
    Author: Dilawar <dilawar.s.rajput@gmail.com>
    Date: Mon Feb 3 15:32:05 2020 +0000

        Some more changes.

    commit 5499353592e5f0259184d1fa94f32ce074a42993
    Author: Dilawar Singh <dilawars@ncbs.res.in>
    Date: Mon Feb 3 20:52:43 2020 +0530

        Use cmake2.8

    commit c8b365ab8ab78b6a6202e4104c141d24e117d09d
    Author: Dilawar Singh <dilawars@ncbs.res.in>
    Date: Mon Feb 3 20:37:54 2020 +0530

        Lets test it in fresh docker image.

    removed uninstall target, use pip to uninstall moose.

    Added path in target_link_directories macro for target moose.bin.

    MOOSE's python module.

commit 4408bee419480de5ca1214021fe273f64e08ec25
Author: Dilawar Singh <dilawar.s.rajput@gmail.com>
Date: Mon Feb 3 16:00:45 2020 +0530

    Docker build was successful. Needs to improve test function...

commit 892b9c373d0532ffbd8bffd4021f76581a7205ea
Author: Dilawar Singh <dilawar.s.rajput@gmail.com>
Date: Mon Feb 3 14:01:12 2020 +0530

    Added centos build docker file.

commit 5777ede1c9c1be93d393f56eb5b36cccb3dd8d43
Author: Dilawar Singh <dilawar.s.rajput@gmail.com>
Date: Mon Feb 3 08:05:43 2020 +0000

    Some more tweaks.

commit ac301424e1a4eb20478898f2433e53d7321aa6af
Author: Dilawar Singh <dilawar.s.rajput@gmail.com>
Date: Mon Feb 3 13:08:53 2020 +0530

    Run in inside a docker image to tweak.

commit 8bee4d0a3c529f51e98b9df55df414302fbd4281
Author: Dilawar Singh <dilawars@ncbs.res.in>
Date: Sun Feb 2 04:03:40 2020 +0530

    Temp commit: Build locally.

commit 4d8342e7f5c559c1c87a4364bc2eff614570858b
Author: Dilawar Singh <dilawars@ncbs.res.in>
Date: Sun Feb 2 03:54:14 2020 +0530

    Not yet complete because we still don't have static linking to gsl .

commit 18e65d511ee02562b5fc8abd4a6deedad616c6a7
Author: Dilawar Singh <dilawars@ncbs.res.in>
Date: Sun Feb 2 03:47:38 2020 +0530

    Using python setup.py to build the module.

commit 7a8f52d9ec9e58b5b97344cdd154c9794a2ee498
Merge: 6a7de616d 1bbbc2d9c
Author: Dilawar Singh <dilawars@ncbs.res.in>
Date: Sun Feb 2 03:12:45 2020 +0530

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

commit 6a7de616d24acaa1e4ec5d83716e05aeb9bfdce8
Merge: 27f62f585 749f1b8cf
Author: Dilawar Singh <dilawars@ncbs.res.in>
Date: Sun Feb 2 02:30:13 2020 +0530

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

commit 749f1b8cfd4bb3ee72ca1056ff63cf1983e4a8f8
Author: Dilawar Singh <dilawar@users.noreply.github.com>
Date: Sun Feb 2 00:18:52 2020 +0530

    Update build.yml

commit f089c1c17618c56f8035e9f7531c96827f3990e6
Author: Dilawar Singh <dilawar.s.rajput@gmail.com>
Date: Sat Feb 1 22:49:27 2020 +0530

    Added workflow file.

commit 3502f138dd42b959e43f4a2bc3ea216bceecaa98
Author: Dilawar Singh <dilawar.s.rajput@gmail.com>
Date: Sat Feb 1 22:46:39 2020 +0530

    Fixed make and test targets.

commit 0768916236ade6c344195acddfc5ef44aeab711d
Author: Dilawar Singh <dilawar.s.rajput@gmail.com>
Date: Sat Feb 1 22:43:40 2020 +0530

    Fixed the name of package...

commit 1998950a9bfd7bb840ee26905903be8a53da95df
Author: Dilawar Singh <dilawar.s.rajput@gmail.com>
Date: Sat Feb 1 22:42:04 2020 +0530

    Run sudo apt-update ...

commit 2cf32944b15a1d5fcbf059edf79310ebe3359882
Author: Dilawar Singh <dilawar.s.rajput@gmail.com>
Date: Sat Feb 1 22:40:20 2020 +0530

    Added sudo ...

commit 06aa508c732f62674c19cc6352d64cec4814e3bf
Author: Dilawar Singh <dilawar@users.noreply.github.com>
Date: Sat Feb 1 22:38:24 2020 +0530

    Create build.yml

commit 08950de44037bcaf3b03f765751bd9f46040ce52
Author: Dilawar Singh <dilawar.s.rajput@gmail.com>
Date: Sat Feb 1 22:03:15 2020 +0530

    removing github actions.

commit f471483925c85db8f982e12077f6ba3309a9a18c
Author: Dilawar Singh <dilawar.s.rajput@gmail.com>
Date: Sat Feb 1 21:50:33 2020 +0530

    Updated commands.

commit 7453901989a6fde28b488157766a62b998196b19
Author: Dilawar Singh <dilawar@users.noreply.github.com>
Date: Sat Feb 1 21:39:29 2020 +0530

    Create cmake.yml

commit 69a3aaeb423e98074da0e98680c59937de65d241
Author: Dilawar Singh <dilawar.s.rajput@gmail.com>
Date: Fri Jan 31 09:28:14 2020 +0000

    Fixes for gcc5 series. It is not smart enough to figure out which field is being updated. These needs to be ported to branch chamcham as well.

commit 9e0b0d1adc126b2d4784cb8966a2ecf302059f63
Author: Dilawar Singh <dilawars@ncbs.res.in>
Date: Fri Jan 31 13:02:32 2020 +0530

    - Make python3 default python.
    - cmake 3.12 is minimum required.
    - Fixes to Python API. strncpy can not write to `const char*`. Instead initialize with value.
    - Build system fixes.

commit 27f62f5853555aa1b54685a4493a2a11c9a192cd
Merge: 2062ab231 ebfb5dc4c
Author: Dilawar Singh <dilawars@ncbs.res.in>
Date: Mon Jun 3 12:06:58 2019 +0530

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

commit ebfb5dc4c43e356f30f981bdda06c2ec4480a95b
Merge: 45216b3de 526c5b091
Author: Dilawar Singh <dilawars@ncbs.res.in>
Date: Sun Jun 2 19:22:16 2019 +0530

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

commit 1bbbc2d9cd09ede27e5d2ac6e7f880fb300630fb
Author: Dilawar Singh <dilawar.s.rajput@gmail.com>
Date: Fri Apr 19 14:45:57 2019 +0530

    added moose.about(). Show essential information about moose project

commit c319cb400ecc42441f619e23f07147109625b63e
Merge: 45216b3de 1b38d64f4
Author: Dilawar Singh <dilawar.s.rajput@gmail.com>
Date: Fri Apr 19 14:36:14 2019 +0530

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

commit 45216b3de2e7e7f349eb323de6cc5b2ad8e6c93e
Merge: 740fb440d 58292d606
Author: Dilawar Singh <dilawar.s.rajput@gmail.com>
Date: Fri Apr 19 14:35:14 2019 +0530

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

commit 740fb440dd964efde30de2a46637380ed8cb8daa
Merge: 352012076 f227bb07c
Author: Dilawar Singh <dilawar.s.rajput@gmail.com>
Date: Thu Mar 7 11:18:57 2019 +0530

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

commit 3520120767f9ca84eefc3f21ebec216291e66414
Author: Dilawar Singh <dilawars@ncbs.res.in>
Date: Wed Feb 13 14:12:53 2019 +0530

    Disable all socket streamer tests.

commit 2dd9688a45a6be8eae59019d31fadeab3beed53d
Author: Dilawar Singh <dilawars@ncbs.res.in>
Date: Wed Feb 13 13:11:50 2019 +0530

    Don't run streamer multitab tests on OSX/Travis.

* Setup.py works with both python2 and python3.

* Using timer to timeout the test. This removes a very old bug..

* Removing old tests; move them to moose-examples.

* matplotlib is always optional for tests.

* setup.py seems to be building just fine. Needs tweaking in the tests.

* Using setup.py file to build and install pymoose.

* Fixes to github actions..

* Fixes to YAML file.

* Create pymoose.yml

Build with different version of python.

* Some more fixes to github workflows.

* Install dependencies...

* Updated a bit more ...

* make debian fronend non-interactive...

* Added missing dependencies.

* Use pip to install numpy/matplotlib before build.

* Remove build tests here. [skip ci]

* Update .gitlab-ci.yml

* Squashed commit of the following:

commit 287a26a99e1fb4b72a1ca8d15622cadbcfa4eb96
Author: Dilawar Singh <dilawars@ncbs.res.in>
Date: Wed Feb 5 21:51:22 2020 +0530

    Remove build tests here. [skip ci]

commit af3b1ec8755f0a8f0a0eb64c537b3239b0fe23f7
Author: Dilawar Singh <dilawars@ncbs.res.in>
Date: Wed Feb 5 21:41:07 2020 +0530

    Use pip to install numpy/matplotlib before build.

commit ddebb11bd9b1ad8f648f133cfd8b31531ebf14c1
Author: Dilawar Singh <dilawars@ncbs.res.in>
Date: Wed Feb 5 21:39:05 2020 +0530

    Added missing dependencies.

commit 347353b7df2a2f3d40c0d83eb256cc13cfecc0cf
Author: Dilawar Singh <dilawars@ncbs.res.in>
Date: Wed Feb 5 21:37:18 2020 +0530

    make debian fronend non-interactive...

commit 3e69fe7308eff2a21a85ad6df7491d9c961de0e7
Author: Dilawar Singh <dilawars@ncbs.res.in>
Date: Wed Feb 5 21:30:11 2020 +0530

    Updated a bit more ...

commit 7da6a986b02c124a883e3945f6504d0b136d6e75
Author: Dilawar Singh <dilawars@ncbs.res.in>
Date: Wed Feb 5 21:27:21 2020 +0530

    Install dependencies...

commit 5d4c5ecbfb9f0ad62625517b3b9bc5d366e6e740
Author: Dilawar Singh <dilawars@ncbs.res.in>
Date: Wed Feb 5 21:22:54 2020 +0530

    Some more fixes to github workflows.

commit 6dd377ce9011d0e55618b3acaaa913158053da24
Author: Dilawar Singh <dilawars@ncbs.res.in>
Date: Wed Feb 5 21:12:31 2020 +0530

    Fixes to YAML file.

commit 14529cace16d1e4db9366937a6b5f4b652e87ab1
Author: Dilawar Singh <dilawars@ncbs.res.in>
Date: Wed Feb 5 21:08:05 2020 +0530

    Fixes to github actions..

commit 7be23ed154426b98a8cf65277937ca7be9df3dad
Author: Dilawar Singh <dilawars@ncbs.res.in>
Date: Wed Feb 5 21:06:58 2020 +0530

    Using setup.py file to build and install pymoose.

commit 0c3f7438a2e37489e78ba6948a3a1d5e908a4932
Author: Dilawar Singh <dilawars@ncbs.res.in>
Date: Wed Feb 5 18:44:20 2020 +0530

    setup.py seems to be building just fine. Needs tweaking in the tests.

commit 3667a0093e2ff3d7d254755e2ffa9847e234f4be
Author: Dilawar Singh <dilawars@ncbs.res.in>
Date: Wed Feb 5 17:41:12 2020 +0530

    matplotlib is always optional for tests.

commit f26d0ccd95f56f95e2001159fc7aa8e080109ec5
Author: Dilawar Singh <dilawars@ncbs.res.in>
Date: Wed Feb 5 17:35:17 2020 +0530

    Removing old tests; move them to moose-examples.

commit 8058ede2efa37b5531ad4a2c88b06654b87815b7
Author: Dilawar Singh <dilawars@ncbs.res.in>
Date: Wed Feb 5 17:23:47 2020 +0530

    Using timer to timeout the test. This removes a very old bug..

commit 6b873960b343346f5563af1504ee15598ab42224
Author: Dilawar Singh <dilawars@ncbs.res.in>
Date: Wed Feb 5 16:01:16 2020 +0530

    Setup.py works with both python2 and python3.

commit ecdc1a8596708ca76b6e230da0643dd57a7bd504
Author: Dilawar Singh <dilawar.s.rajput@gmail.com>
Date: Wed Feb 5 14:15:46 2020 +0530

    Use latest xcode.

commit 2a81096d64b6a115c62ff4bf21a560c6c6b926b1
Merge: a4a23382f e7cd7c0ec
Author: Dilawar Singh <dilawar.s.rajput@gmail.com>
Date: Wed Feb 5 14:14:24 2020 +0530

    Merge remote-tracking branch 'bhallalab/master'

commit a4a23382f3f861c13e0e695854745beb30b298a5
Author: Dilawar Singh <dilawar@users.noreply.github.com>
Date: Wed Feb 5 13:42:26 2020 +0530

    Update build.yml

    Fixed the test command in github actions.

commit cb0095f4a833859fd13cf3b191bcffbe39e37ebb
Merge: 4408bee41 71c9756f1
Author: Dilawar Singh <dilawar.s.rajput@gmail.com>
Date: Wed Feb 5 14:10:24 2020 +0530

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

commit 71c9756f1bf448b20dad267f4db5f67f9dbd27b0
Author: Dilawar Singh <dilawars@ncbs.res.in>
Date: Tue Feb 4 23:20:11 2020 +0530

    Updated cmake file; build directory is now part of directories to
    search.

commit 2f0d93ab93db433cfea31512f655688fd800aac7
Author: Dilawar Singh <dilawars@ncbs.res.in>
Date: Tue Feb 4 23:00:55 2020 +0530

    Added docker-file for suse.

commit e7cd7c0ec9d5eb47edfd4d0095e55e5ee93cb835
Author: Dilawar Singh <dilawar@users.noreply.github.com>
Date: Tue Feb 4 22:47:27 2020 +0530

    Hotfix | Packaging issues on OSX (#383)

    * Don't run streamer multitab tests on OSX/Travis.

    * Disable all socket streamer tests.

    * - Make python3 default python.
    - cmake 3.12 is minimum required.
    - Fixes to Python API. strncpy can not write to `const char*`. Instead initialize with value.
    - Build system fixes.

    * Fixes for gcc5 series. It is not smart enough to figure out which field is being updated. These needs to be ported to branch chamcham as well.

    * Create cmake.yml

    * Updated commands.

    * removing github actions.

    * Create build.yml

    * Added sudo ...

    * Run sudo apt-update ...

    * Fixed the name of package...

    * Fixed make and test targets.

    * Added workflow file.

    * Update build.yml

commit 82adc1ce999449309c08b4c118c66689e07ac1f0
Author: Dilawar Singh <dilawars@ncbs.res.in>
Date: Tue Feb 4 22:43:53 2020 +0530

    Removed the target_link_directories command which is available only in
    very recent cmake.

commit 36055662501ac60d2878ac679dbc3b665729230a
Author: Dilawar Singh <dilawars@ncbs.res.in>
Date: Tue Feb 4 17:46:22 2020 +0530

    Temp commit.

commit 6248e129aca21e9a9539ca2d9948fa9b1e64900c
Author: Dilawar Singh <dilawars@ncbs.res.in>
Date: Tue Feb 4 17:43:14 2020 +0530

    Added command test to setup.py which calls ctest.

commit a3d25aa0796d8e65f8040a46cc37263beffae0a9
Author: Dilawar Singh <dilawars@ncbs.res.in>
Date: Tue Feb 4 16:49:40 2020 +0530

    Some more tweaks.

commit 9a14b5c74a587c8f079c764a1cd128335a6a2b7d
Author: Dilawar Singh <dilawars@ncbs.res.in>
Date: Tue Feb 4 15:35:58 2020 +0530

    Minor tweaks...

commit 9f475b35f6603f5ee2af2e65819c4dc6a92c5f20
Author: Dilawar Singh <dilawar.s.rajput@gmail.com>
Date: Mon Feb 3 14:01:12 2020 +0530

    Added centos build docker file.
    Docker build was successful. Needs to improve test function...
    setup.py is working just fine.
    CMake and python's setup.py can use each other. Time to remove pymoose/setup.cmake.py file.
    Removed the cmake helper script. It has been moved to topmost directory where it can be used on its own.

    Squashed commit of the following:

    commit 374bf500cf4ad7c43f22004a1e3c04047d3b6c4f
    Author: Dilawar Singh <dilawars@ncbs.res.in>
    Date: Tue Feb 4 14:22:29 2020 +0530

        This seems to work just fine.

    commit 4746ec40edea16b0d1b047da4e9a08035fdf8143
    Author: Dilawar Singh <dilawars@ncbs.res.in>
    Date: Mon Feb 3 21:54:25 2020 +0530

        testing is required.

    commit d2ddaf7a073f36a0e3ac7f5138ccd0f9054a8d52
    Author: Dilawar Singh <dilawars@ncbs.res.in>
    Date: Mon Feb 3 21:34:59 2020 +0530

        Seems to be just fine now.

    commit 63dceb42ed29e38e31412b640f093f75b50ef1cc
    Merge: c743aed1b 549935359
    Author: Dilawar <dilawar.s.rajput@gmail.com>
    Date: Mon Feb 3 15:32:41 2020 +0000

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

    commit c743aed1bf6f55a6aeef4016f1f8806dc9282b9d
    Author: Dilawar <dilawar.s.rajput@gmail.com>
    Date: Mon Feb 3 15:32:05 2020 +0000

        Some more changes.

    commit 5499353592e5f0259184d1fa94f32ce074a42993
    Author: Dilawar Singh <dilawars@ncbs.res.in>
    Date: Mon Feb 3 20:52:43 2020 +0530

        Use cmake2.8

    commit c8b365ab8ab78b6a6202e4104c141d24e117d09d
    Author: Dilawar Singh <dilawars@ncbs.res.in>
    Date: Mon Feb 3 20:37:54 2020 +0530

        Lets test it in fresh docker image.

    removed uninstall target, use pip to uninstall moose.

    Added path in target_link_directories macro for target moose.bin.

    MOOSE's python module.

commit 4408bee419480de5ca1214021fe273f64e08ec25
Author: Dilawar Singh <dilawar.s.rajput@gmail.com>
Date: Mon Feb 3 16:00:45 2020 +0530

    Docker build was successful. Needs to improve test function...

commit 892b9c373d0532ffbd8bffd4021f76581a7205ea
Author: Dilawar Singh <dilawar.s.rajput@gmail.com>
Date: Mon Feb 3 14:01:12 2020 +0530

    Added centos build docker file.

commit 5777ede1c9c1be93d393f56eb5b36cccb3dd8d43
Author: Dilawar Singh <dilawar.s.rajput@gmail.com>
Date: Mon Feb 3 08:05:43 2020 +0000

    Some more tweaks.

commit ac301424e1a4eb20478898f2433e53d7321aa6af
Author: Dilawar Singh <dilawar.s.rajput@gmail.com>
Date: Mon Feb 3 13:08:53 2020 +0530

    Run in inside a docker image to tweak.

commit 8bee4d0a3c529f51e98b9df55df414302fbd4281
Author: Dilawar Singh <dilawars@ncbs.res.in>
Date: Sun Feb 2 04:03:40 2020 +0530

    Temp commit: Build locally.

commit 4d8342e7f5c559c1c87a4364bc2eff614570858b
Author: Dilawar Singh <dilawars@ncbs.res.in>
Date: Sun Feb 2 03:54:14 2020 +0530

    Not yet complete because we still don't have static linking to gsl .

commit 18e65d511ee02562b5fc8abd4a6deedad616c6a7
Author: Dilawar Singh <dilawars@ncbs.res.in>
Date: Sun Feb 2 03:47:38 2020 +0530

    Using python setup.py to build the module.

commit 7a8f52d9ec9e58b5b97344cdd154c9794a2ee498
Merge: 6a7de616d 1bbbc2d9c
Author: Dilawar Singh <dilawars@ncbs.res.in>
Date: Sun Feb 2 03:12:45 2020 +0530

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

commit 1bbbc2d9cd09ede27e5d2ac6e7f880fb300630fb
Author: Dilawar Singh <dilawar.s.rajput@gmail.com>
Date: Fri Apr 19 14:45:57 2019 +0530

    added moose.about(). Show essential information about moose project

commit c319cb400ecc42441f619e23f07147109625b63e
Merge: 45216b3de 1b38d64f4
Author: Dilawar Singh <dilawar.s.rajput@gmail.com>
Date: Fri Apr 19 14:36:14 2019 +0530

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

* Added pipeline.

* Added missing setuptools. Update setuptools before building.

* Install python-dev in dependencies...

* Non-zero cpu count...

* Updated gitlab CI.

* Added scripts to build wheels.

* Create dockerimage.yml

Added action for building wheels.

* Fixes the build failure on CentOS6.

* Squashed commit of the following:

commit f191857e90d7455c2709f4b703cd0be57891f818
Merge: 0401d1000 27f3f6e75
Author: Dilawar Singh <dilawars@ncbs.res.in>
Date: Fri Feb 7 13:49:21 2020 +0530

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

commit 0401d10006bedd47414e1d02b7cbfaacd38106be
Author: Dilawar Singh <dilawars@ncbs.res.in>
Date: Fri Feb 7 13:48:15 2020 +0530

    added travis+pypi token

commit bce6dfee675381d156096f33eb93896c8b1b91ab
Author: Dilawar Singh <dilawars@ncbs.res.in>
Date: Fri Feb 7 13:37:45 2020 +0530

    build wheels on all platform.

commit 27f3f6e75bacbee9aa1257561f94787cf0f88825
Author: Dilawar Singh <dilawar.s.rajput@gmail.com>
Date: Fri Feb 7 06:54:37 2020 +0000

    Let go back to manylinux1 image

commit 9f93811d8201006cfe1a918a010ff00713434eae
Author: Dilawar Singh <dilawar.s.rajput@gmail.com>
Date: Fri Feb 7 05:47:51 2020 +0000

    Added a dummy target.

commit 6fa716cae6d55f7d7f0eeedf676c82003d266680
Merge: 4dc5c3e50 2b4bd1d68
Author: Dilawar Singh <dilawar.s.rajput@gmail.com>
Date: Thu Feb 6 13:41:31 2020 +0000

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

commit 4dc5c3e50fa25f7dc23c410d128d28a581d48ac7
Author: Dilawar Singh <dilawars@ncbs.res.in>
Date: Thu Feb 6 19:07:22 2020 +0530

    Changes to buidl script [skip ci]

commit 15532cb97233febe14e3ab6dcf365fd7a2518302
Author: Dilawar Singh <dilawar.s.rajput@gmail.com>
Date: Thu Feb 6 12:58:24 2020 +0000

    Make the dummy extension optional.

commit 725282a9d9db30c3b7d31eb553b3da5cc648c044
Author: Dilawar Singh <dilawars@ncbs.res.in>
Date: Thu Feb 6 17:55:44 2020 +0530

    Install required tools as well.

commit 22fde7d09d3ad6d27ff8ed998c446a7cc0f1b1d7
Author: Dilawar Singh <dilawars@ncbs.res.in>
Date: Thu Feb 6 16:13:01 2020 +0530

    Dockerfile is added to build wheels in this repo itself.

commit c08fb728fb5edc1fdc7228663f5c1ed9b31b955b
Author: Dilawar Singh <dilawars@ncbs.res.in>
Date: Thu Feb 6 15:56:32 2020 +0530

    renamed build script and fixes to some paths.

* Removed dockerimage workflow for now [skip ci]

* Minor tweaks to test on travis. Fixes FindGSL.cmake script. if(expr1
`OR` expr2) is fixed to if((expr1) OR (expr2)). Fixes to travis build
script. sudo is not required to run this script. Fixes to the travis
build. NSDF support is disabled. CLeanup in OSX build as well. Don't
deploy to pypi. OSX build is passed locally.

* Use a temp build directory.

* Need a better way to create sdist.
Added three targets.
- make sdist
    create a source distribution for PyPi.

- make upload_test

upload the source distribution to TestPyPi. The command reads
environment variable for user and password.

    export PYMOOSE_PYPI_USER=bhallalab
    export PYMOOSE_PYPI_PASSWORD=mypassword
    make upload_test

- make upload

Upload the source distribution to PyPI.

    export PYMOOSE_PYPI_USER=bhallalab
    export PYMOOSE_PYPI_PASSWORD=mypassword
    make upload

Using date and rc tag to create a version for nightly release.
Use twine to upload to test.pypi.org

* Create stale.yml

* Update to install instructions... (#386)

Point release 3.2.1. The version bump is due to using new manylinux2010 images.

* Thread-safe and more performant parser based on ExprTK (#387)

* Update to install instructions...
Point release 3.2.1. The version bump is due to using new manylinux2010 images.

* - Added ExprTK based parser and removed muParser. EXPRTK is faster than
  muParser (see labnotes).
- All tests have been passing.
- Tweaks are made to exprtk operators/functions to make sure old
  expressions used scripts remains valid.

* Added function ln(double v) to EXPRTK. Compatibility with muParser. All tests are passing.

* It is working fine now with Vinu model. Needs to fix the sbmlParserReader which uses numVars_.

* Some more cleanup. Testing on travis. Removed moose.Func(); user should
use `moose.Function`. moose.Func was disabled long back.

* GSolve also honors MOOSE_NUM_THREADS ...

* Local tests are passing. Fixed memory leak issue. A little refactoring and memory segv at the end of the test is now clean.
Removed unneeded/outdated tests and other scripts.
Added new tests based on Vinu model. It is very comprehensive which
tests multithreaded Ksolve/Gsolve, SBML, and moose.Function
Update to install instructions... (#386)
Point release 3.2.1. The version bump is due to using new manylinux2010 images.

* Thanks to clang++; caught another memory related bug. If this passes, do
a memory profiling.

* Minor cleanup. Removed memory allocation and copying at couple of places.
Still memory leaks in exprtk. I think I can't get rid of them.
Parser is a member object rather than member pointer; still some leak but better version than before.

* Renamed test folder for regular tests. Added custom test which uses 4 threads to run Ksolve.
Modified atol and rtol in assertion in one of the tests. Using parallel version of Ksolve/Gsolve everywhere by setting MOOSE_NUM_THREADS=$(nproc)
Increased `rtol` value to make sure tests passes with BOOST solver as well. When the boost's ode solvers are used, the number generated are slightly different.

* - Added a docker file to run travis pipeline locally.
- Fixed python2 seg-fault in new tests. The segv was because / means int division in python2.

* Converting some rdesigneur scripts to tests; since we need to be able to
plot in nonblocking mode, I've added `block` option in `rdes.display`
function.
Multiple tests using pydoc. They are based on rdesigneur tutorials.
install requires matplotlib for rdesigneur.

* - The seg-fault in rdesigneur tests are due to #388.

* In the ksolve, we partition the interval beforehand now. The
single-threaded and multi-threaded numbers are not the same. Fixed
tests to accomodate slightly different values resulted n multi-threaded
mode.

* Categorised tests. Also turned all doctest to normal assertion tests.
Moved alpha tests to fixme tests.

* All tests passing locally with both GSL and BOOST.

* Compilation fixes for the OSX build.
One test marked as python3 only. The pyrun expression uses python3
specific division and print function. Causes segfault with python2
(wontfix)

* Fixes regression caused by #387 (#389)

* The default values changed in the commit (ba1065c) breaks example such
as
https://github.com/BhallaLab/moose-examples/blob/09ca09e68f163a0920653a9400214aff10b6ba16/snippets/rxdFuncDiffusion.py
. The sparse matrix has upper limit of number of rows and columns to
20,000. In the example linked, new values makes it impossible to run the
example as is.

To overcome this, we notify the user whenever this limit is reached and
ask them to set `diffLength` before setting up the `x1`.

On top of this, we can also revert default values to original larger
values. Not sure why these values were changed to the scale of 1e-6?
Unless the reason is known, I am not going to change current values. The
above linked example now works with this commit.

* Script which switches solver is now working fine. Forgot to uncomment `unzombifyModel` in `~Stoich` in previous PR #387.

* switch solver script is working fine now. Added to the test suite.

* During zombiefication, deepcopy of parser is expected. Added more tests
and fixed the deepcopy of parser issue. In Zombiefication, the parser
was not deep copied resulting in erronous values in couple of tests. There
is some memory leak now.

* Prepare a PR now. Test on travis. Some tests might fail with BOOST.
Memory leak is still there.

* 1. Removed copy constructor from moose::Function. It was not used anywhere.
Increased rtol value for a test. Multithreaded solvers gives different
results.
2. Fixed all memory leaks. Probably I don't understand how EXPRTK really
works. using smart pointers with EXPRTK caused memory leak.
3. Log memory leak on travis using valgrind. Install valgrind in docker images as well.

* During zombiefication, deepcopy of parser is expected. Added fix and a
test case.

* Added more tests and fixed the deepcopy of parser issue.
In Zombiefication, the parser was not deep coped resulting in erronous
values in couple of tets. There is some memory leak now (not very large,
8 bytes per variable per expression).

* Prepare a PR now. Test on travis. Some tests might fail with BOOST.
Memory leak is still there.

* removed copy constructor; it was not used anywhere. [skip ci]
Increased rtol value for a test. Multithreaded solvers gives different
results.

* Fixed all memory leaks. Probably I don't understand how EXPRTK really
works. using smart pointers with EXPRTK caused memory leak. Log memory
leak on travis using valgrind. Fixed tests. Let the EXPRK object manage
its memory.

* BOOST/GSL are only needed in ksolve directory: tweaked cmake to change
compilation flags on ksolve directory only. Build will be faster for various configurations.
Moved one test to fixme (Vinu's model).

* Updated gitlab pipeline. On a single threaded virtual machine, numThreads was set to 0 in couple
of tests. Fixed that. Install pyneuroml to the pipeline. Small leeway in a test.

* std can be close to zero. np.allclose may not handle it properly all the
time.

* boost solver with GSSA may have large variation.

* boost solver with GSSA may have large variation. Test for the sum of all errors.

* Increased the tolerance a bit more.

* Named variables in Function expression (#390)

* - Tests are passing locally.
- MooseParser is a pointer in Function. Simplifies header include.
- Added wrapper.py which generates a derived class moose.A for each
  _moose.A. `moose.A` provides `connect` function. Instead of,
        moose.connect(a, 'f1', b, 'f2')
    One can do,
        a.connect('f1', b, 'f2')

* Developers emails are back in travis config file.

* If a symbol already exists, do not add it again. Fixed typo.

* If sympy not found, allow failure. Added sympy on travis but not on OSX. Don't install sympy with python2.

* removed custom OrderedDict. Python2.6 is not needed to be supported.
Centos6 is EOL.

* Combined 391+386+337+281 (#392)

* Hotfix | some old scripts in moose-examples failed because of regression caused by #390.

* Added graph utility.
Renamed to network_utils. Imported by default when moose.utils is imported. Renamed functions.

* Added Boost ODE based solvers of MarkovChannel. Now GSL is optional.
Renamed MarkovGslSolver class to MarkovOdeSolver. It compiles with both boost and gsl.

* This is squashed version of BhallaLab/moose-core#281

- Added new solver based on 'LSODA' method.

This is a CPP version of the LSODA library for integration into MOOSE simulator. These source code are released under MIT license which is compatible with MOOSE. See Credit below.
Adds three tests (1 python). Results are equivalent to scipy's lsoda solver.
Following changes are made to this version:

Used <array> and <vector> instead of raw array where-ever possible.
Craeted a class LSODA and added a function to integrate it smoothly with moose.
Various tweaks in various functions especially initialization.
Core computing functions starts with index 1 rather than 0; this is hidden away from MOOSE api.
The performance of this solver is really good. In debug mode, on a small model, I got 6.7x speedup without any multi-threading. The solver is not recommended for stiff systems. Once it is integrated we do more profiling vis-a-vis standard RK5 solver.

- Licensing

Work by Heng Li was released under MIT Incense which is less restrictive than GNU-GPLv3. See here. The LSODA class is released under the same license.

- Logs

https://docs.google.com/document/d/e/2PACX-1vQ3wU9xiMSMVcluDrNSzuSGHsttOqAqc8xN4a9qo7wFfYjwl-0KhKyY1LlM5XkQ_5CqJd3eFnUCYiAb/pub

- Credit

The original was aquired from http://www.ccl.net/cca/software/SOURCES/C/kinetics2/index.shtml and modified by Heng Li lh3lh3@gmail.com. Heng merged several C files into one and added a simpler interface. His version can be found http://lh3lh3.users.sourceforge.net/download/lsoda.c .

* Adds Test Coverage (#394)

* Don't run streamer multitab tests on OSX/Travis.

* Disable all socket streamer tests.

* no way to setup proxy yet.

* Temp commit.

* Some more changes but not complete.

* local tests.

* build was successful.

* Added pytest compatible tests. Generates test report at the end.

* Fixed hhfit tests.

* test commit [seg fault] skip ci

* Removed benchamark code.

* Added dependencies to requirements.txt file. Set verbosity to 0. Minor
cleanup. local tests are passing... Added test: rdesineur loads chan
proto from a given file.

* Fixed hhfit test. Added scipy to run hhfit test.

* Fixed one more test.

* test it on xcode10.3

* Some fixes to test_hhfit. The module selects a best function
'fuzzingly'.

* - Removed getopt in pymoose code. It was causing segfault on OSX. Not sure why. `getopt` is no longer needed there.
- Use scipy in tests as well. hhfit requires scipy.
- Added target coverage for make.
- Enabled coverage on travis.
- Fixes to unicode/str issues b/w python2 and 3.

* - Fixes to issue https://github.com/BhallaLab/moose-core/issues/393
- Don't let user use buggy gcc 4.8.x which does not proper regex support. See https://stackoverflow.com/questions/12530406/is-gcc-4-8-or-earlier-buggy-about-regular-expressions

* updated docker file for centos:7 . Install devtoolset-8.

* Some more tweak to test_hhfit.py file. THe hhfit function does not
always return the demanded function but could also return a function
which is a better fit (it is designed this way). Without this fix, the
test could fail on a separte run or on a separte platform.

* Update writeKkit.py

Fixed email id.

Co-authored-by: Dilawar Singh <dilawars@ncbs.res.in>

* Bugfix | moose.Streamer streams to numpy format correctly (#395)

* saving data to npy format in streamer is now bug free. Added three tests: 2 python and 1 at cpp level.

* boost::filesystem is no longer used even when boost is used.

* Default tick for Streamer is 10s.

* Able to run nml2 example with python3 (BhallaLab/moose#253).

Co-authored-by: Dilawar Singh <dilawars@ncbs.res.in>

* HOTFIX | Fix to https://github.com/BhallaLab/moose-core/issues/397 (#399)

* Fix to https://github.com/BhallaLab/moose-core/issues/397

* NUMPY is essential dependency; therefore numpy code is no longer
included conditionally. USE_NUMPY is implied and have been removed from
cmake.

* Minor cleanup in macros and loggers.
numCores now use thread library to determine number of available
threads.

* include cmath in Pool.cpp as well. Failed compilation with gcc5.3

* include cmath in Pool.cpp as well. Failed compilation with gcc5.3

Co-authored-by: Dilawar Singh <dilawars@ncbs.res.in>
Co-authored-by: dilawars <dilawars@nargis.ncbs.res.in>

* writeSBML: channel's annotation is cleaned up and channel's are written in MMenz form,readSBML:Enzyme-cplx connection of reactant/product's are done based on stoichiometry number and reading back channel from MMenz, connected input pool with msg as 'in' and output pool msg as 'out' (#400)

Co-authored-by: HarshaRani <hrani@ncbs.res.in>

* color are now hex colors (#403)

* writeSBML: channel's annotation is cleaned up and channel's are written in MMenz form,readSBML:Enzyme-cplx connection of reactant/product's are done based on stoichiometry number and reading back channel from MMenz, connected input pool with msg as 'in' and output pool msg as 'out'

* rgba color converted to hex color

Co-authored-by: HarshaRani <hrani@ncbs.res.in>

* Merged hrani changes and mine from new bindings.

removed 'basestring'

* Merged hrani changes and mine from new bindings. (#412)

removed 'basestring'

Co-authored-by: Dilawar Singh <dilawars@ncbs.res.in>

Co-authored-by: bhalla <bhalla@ncbs.res.in>
Co-authored-by: HarshaRani <ranishashi@gmail.com>
Co-authored-by: Dilawar Singh <dilawars@ncbs.res.in>
Co-authored-by: Anal Kumar <analkumar2@gmail.com>
Co-authored-by: Zbigniew Jędrzejewski-Szmek <zbyszek@in.waw.pl>
Co-authored-by: dilawars <dilawars@nargis.ncbs.res.in>
Co-authored-by: HarshaRani <hrani@ncbs.res.in>

Author: Dilawar Singh
Author Date: 2019-09-27 09:41:50 UTC

Merge branch 'master' into windows_msys2

Author: Dilawar Singh
Author Date: 2018-09-11 10:11:02 UTC

Merge branch 'master' into gpu

Author: Dilawar Singh
Author Date: 2018-08-29 12:58:42 UTC

Merged master and fixed compilation issues.