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Merged
upibhalla merged 139 commits into from
May 1, 2020
Merged

Update to chennapoda branch #413

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eb4e836
Fixed boost segfault with dense solver. Also remove GSL specific att…
dilawar Sep 23, 2018
79e2d65
hotfix for running Boost, Added NMDAR to rdesigneurProtos.
upibhalla Sep 24, 2018
cdbf917
Merge branch 'master' of https://github.com/BhallaLab/moose-core
upibhalla Sep 24, 2018
0909ceb
Fixes as suggested by PyLint. Added a target pylint in cmake file. (#…
dilawar Sep 24, 2018
aaf589a
Merge branch 'master' of https://github.com/BhallaLab/moose-core
upibhalla Sep 24, 2018
88bcf07
Merge pull request #311 from upibhalla/master
dilawar Sep 24, 2018
293d441
Some fixes to Ca-dependent channel prototypes in rdesigneur.
upibhalla Oct 2, 2018
d274993
Build System Tweaks (#309)
dilawar Oct 2, 2018
b57a6d0
Merge branch 'master' into master
dilawar Oct 2, 2018
e464295
Merge pull request #314 from upibhalla/master
dilawar Oct 2, 2018
2fb51c9
Hotfix: Neuroml2 fixes. (#315)
dilawar Oct 3, 2018
f0e4db0
Fixes to build failure on OSX because cmake does not MACOSX but APPLE…
dilawar Oct 5, 2018
a8769f2
Update CMakeLists.txt
dilawar Oct 5, 2018
5d20e04
corrected the spell of CyclMesh-->CylMesh, negating the yaxis for kki…
hrani Oct 5, 2018
51dd776
Rdesigneur passiveDistrib modified to handle legacy commands
upibhalla Oct 10, 2018
f66ba90
Merge branch 'master' of https://github.com/BhallaLab/moose-core
upibhalla Oct 10, 2018
ecfca84
Update README.md (#312)
dilawar Oct 11, 2018
d6e35de
Merge branch 'master' into master
dilawar Oct 11, 2018
b4637b2
Merge pull request #317 from upibhalla/master
dilawar Oct 11, 2018
3a655cd
Minor typo in warning report for Dsolve
upibhalla Oct 12, 2018
7c86d4e
Merge branch 'master' of https://github.com/BhallaLab/moose-core
upibhalla Oct 12, 2018
556ebef
Hotfix. If self.network not found, sett the temperate to 25 deg C.
Oct 17, 2018
0b208c8
Now user can pass verbose option to mooseReadNML2
Oct 18, 2018
6375834
Works after disabling alpha and beta properties.
Oct 18, 2018
f917df1
Merge pull request #319 from dilawar/master
dilawar Oct 18, 2018
ba88932
CylMesh are written to SBML with annotation field and only zeroth ele…
hrani Oct 18, 2018
53cbe36
reading info field for channel from kkit file (#321)
hrani Oct 23, 2018
05eba8f
Channel are written back to genesis and zeroth voxel moose object is …
hrani Oct 23, 2018
5b0bbe1
Merge pull request #322 from hrani/master
upibhalla Oct 26, 2018
9b0569b
while reading the sbml model validator can be switched off
hrani Oct 26, 2018
83afd0f
Merge branch 'master' into master
hrani Oct 26, 2018
70f116a
cleanup in print statement
hrani Oct 26, 2018
865e99d
Merge branch 'master' of https://github.com/hrani/moose-core
hrani Oct 26, 2018
182e95c
Bugfix for ConcChan to correct scaling for permeability to SI units o…
upibhalla Oct 28, 2018
2e22276
Merge branch 'master' of https://github.com/BhallaLab/moose-core
upibhalla Oct 28, 2018
0327eb9
Fixed test_Xchan1.py to match bugfix for Dsolve.
upibhalla Oct 28, 2018
e4c1993
Merge pull request #324 from upibhalla/master
dilawar Oct 29, 2018
5a8ec04
Merge branch 'master' into master
hrani Oct 30, 2018
1f91c76
Added dummy CubeMesh as default parent for EndoMesh to avert segvs on…
upibhalla Nov 3, 2018
12e429d
Merge branch 'master' of https://github.com/BhallaLab/moose-core
upibhalla Nov 3, 2018
aca01be
Fixed numDimentions to 3
upibhalla Nov 3, 2018
905c983
Merge pull request #323 from hrani/master
upibhalla Nov 3, 2018
552ca01
Merge branch 'master' into master
hrani Nov 3, 2018
50f03b8
Fixes to EndoMesh (#327)
upibhalla Nov 3, 2018
47ee21c
Fixes to rdesigneur so that chemProto without chemDistrib will not fa…
upibhalla Nov 4, 2018
b8eeb9d
Merge branch 'master' of https://github.com/BhallaLab/moose-core
upibhalla Nov 4, 2018
788bce9
Merge branch 'master' of https://github.com/upibhalla/moose-core
upibhalla Nov 4, 2018
bc3ff9c
Got rid of printf debug line
upibhalla Nov 4, 2018
0bdebdf
Merge pull request #328 from upibhalla/master
dilawar Nov 5, 2018
a56b7e8
Fix to rdesigneurProtos so that the classic HH Na and K_DR channels n…
upibhalla Nov 5, 2018
e5868be
Merge pull request #329 from upibhalla/master
dilawar Nov 6, 2018
740a7a6
CylMesh,EndoMesh,NeuroMesh compartment are written to SBML as compart…
hrani Nov 7, 2018
ef8e54a
variable name used in before assignment cleanup
hrani Nov 7, 2018
b38a440
Squashed commit of the following:
Nov 8, 2018
d569f56
gate with id z is loaded into gateZ in moose now.
Nov 9, 2018
e5fbf8c
For CylMesh, totLength and diffLength is written to Annotation to get…
hrani Nov 9, 2018
b327ec7
xfer cross compartment molecules are not written as species and also …
hrani Nov 12, 2018
86522d3
Using built in logging library.
Nov 13, 2018
90c97b6
Fixed the bug caused by previous two commits. Now I need to make sure…
Nov 13, 2018
26e9662
Tweaks.
Nov 13, 2018
f6c4ab3
Merge pull request #330 from hrani/master
upibhalla Nov 14, 2018
4d1337a
Merge branch 'master' of github.com:dilawar/moose-core
Nov 16, 2018
9791322
Reading and creating CylMesh and EndoMesh if specified in the Annotat…
hrani Nov 19, 2018
2189993
Merge branch 'master' into master
hrani Nov 19, 2018
0cd028c
Added other meshes while searching for groups
hrani Nov 20, 2018
d72ad63
Merge branch 'master' of https://github.com/hrani/moose-core
hrani Nov 20, 2018
01ebb84
Merge pull request #333 from hrani/master
upibhalla Nov 21, 2018
c40c622
xref pool are not wirtten and cleaned up if part of Reaction/Enzyme o…
hrani Nov 22, 2018
23906e5
searching for _xfer_
hrani Nov 22, 2018
1a9b0f5
Merge branch 'master' into master
hrani Nov 22, 2018
7423c39
Merge branch 'master' into master
dilawar Nov 24, 2018
189778c
Merge pull request #331 from dilawar/master
dilawar Nov 24, 2018
6868716
Merge branch 'master' into master
dilawar Nov 24, 2018
b9a5113
Fix to Im calculation in HSolve, to include external channels like re…
upibhalla Nov 24, 2018
d57fa1d
Merge branch 'master' of https://github.com/BhallaLab/moose-core
upibhalla Nov 24, 2018
169d0c8
Merge pull request #336 from upibhalla/master
dilawar Nov 24, 2018
69f9f33
Merge branch 'master' into master
dilawar Nov 24, 2018
fac76ad
groups and subgroups are written to sbml and read from xml files
hrani Nov 30, 2018
d6e5711
Merge pull request #335 from hrani/master
upibhalla Dec 1, 2018
356f43c
reading and writing diff and motor constant for pool
hrani Dec 4, 2018
3aa66d4
Merge pull request #338 from hrani/master
upibhalla Dec 4, 2018
1b48ce7
Fix to CaConc to factor in valence of 2. Update to rdesigneur to hand…
upibhalla Dec 4, 2018
ed7c4d5
Merge pull request #339 from upibhalla/master
dilawar Dec 4, 2018
4dfac33
using existing restoreXreacs function to remove _xfer_ objects before…
hrani Dec 10, 2018
0997a46
Merge pull request #341 from hrani/master
upibhalla Dec 11, 2018
2624d4b
Continuation to PR #308 (#340)
dilawar Dec 11, 2018
1e426a2
Update INSTALL.md
dilawar Dec 18, 2018
e93d391
Hotfix: Neuroml2 fixes (#343)
dilawar Dec 18, 2018
c38c643
Dec 19 | continuation of NML2 fixes (#344)
dilawar Dec 19, 2018
a165432
Corrected the K_AHP z gate and make_Ca y gate
analkumar2 Jan 12, 2019
053e256
Merge pull request #348 from analkumar2/master
dilawar Jan 13, 2019
c67f8c0
Travis build failure (#350)
dilawar Jan 13, 2019
441a66b
Issue 342 | TCP/UD Socket based Table Streamer (#345)
dilawar Feb 7, 2019
0f34490
SO_REUSEPORT is not always defined. The build fails on centos-5 (#351)
dilawar Feb 8, 2019
a1a256b
Efficient Network Streamer for MOOSE (#352)
dilawar Feb 13, 2019
f227bb0
Travis Fix | Don't run streamer multitab tests on OSX/Travis. (#354)
dilawar Feb 13, 2019
09d5239
readKkit.cpp : create annotator field for kinetic, readSBML.py: valid…
hrani Mar 6, 2019
d9d36b8
cleanedup for python3 as well while loading pickle file
hrani Mar 6, 2019
2ea935b
syntax cleanup
hrani Mar 7, 2019
ddcbd4d
adding pickle file rainbow2.pkl for mapping colors from genesis
hrani Mar 7, 2019
bfde5cc
travis complaining of same function name
hrani Mar 7, 2019
9b8f038
converting dictionary compatible to python3
hrani Mar 7, 2019
9c4458f
HOTFIX #357 | Cleaning up HDF5 related macros in cmake. (#358)
dilawar Mar 7, 2019
1dfbbeb
Merge branch 'master' into master
dilawar Mar 7, 2019
f723a63
getCordColor is unused function removing
hrani Mar 8, 2019
a812045
Merge branch 'master' of https://github.com/hrani/moose-core
hrani Mar 8, 2019
473e29d
function import was missing
hrani Mar 8, 2019
d3c2c5f
clean up with color conversion to hex values
hrani Mar 11, 2019
58292d6
Fix for typo in socket implementation. (#359)
dilawar Mar 20, 2019
a5e0e95
Fixes to issue #360. Regression caused by #352 . (#361)
dilawar Mar 28, 2019
1b38d64
Merge pull request #356 from hrani/master
upibhalla Mar 29, 2019
6addb09
More tests and some rearrangements (#363)
dilawar May 20, 2019
aec42e2
Hotfixes | diffLength and max compartments, rdesigneur+py3 etc, build…
dilawar May 30, 2019
526c5b0
More tests (#369)
dilawar May 31, 2019
2062ab2
Examples fixes (#370)
dilawar Jun 3, 2019
137e348
neuroml: do not use "is" with strings
keszybz Sep 27, 2019
660c91d
Merge pull request #375 from keszybz/string-comparison
dilawar Sep 27, 2019
eb88a23
readSBML:compartment name and id is mapped, in Assignment rule a chec…
hrani Oct 24, 2019
3d2d554
writekkit: cleanup
hrani Oct 24, 2019
8d68b6d
upi commit dec 2019 (#380)
upibhalla Jan 6, 2020
770ab53
readsbml: compartment name & Id is mapped to the values in comptSbmli…
hrani Jan 7, 2020
60fd143
while writting genesis file compartment is added as a group
hrani Jan 8, 2020
e08492b
kkit: channel's permeability converted from uM to mM, writeSBML: chan…
hrani Jan 8, 2020
16cd0d6
Merge pull request #381 from hrani/master
upibhalla Jan 9, 2020
e7cd7c0
Hotfix | Packaging issues on OSX (#383)
dilawar Feb 4, 2020
ea443fe
Add pip support to build system | `pip install pymoose` will work on …
dilawar Feb 9, 2020
dd2a902
Update to install instructions... (#386)
dilawar Feb 16, 2020
d3fe5e9
Thread-safe and more performant parser based on ExprTK (#387)
dilawar Feb 25, 2020
ec9e209
Fixes regression caused by #387 (#389)
dilawar Feb 27, 2020
9489bbd
Named variables in Function expression (#390)
dilawar Mar 3, 2020
4de9cc7
Combined 391+386+337+281 (#392)
upibhalla Mar 5, 2020
280dfa5
Adds Test Coverage (#394)
dilawar Mar 10, 2020
0e85a57
Bugfix | moose.Streamer streams to numpy format correctly (#395)
dilawar Mar 11, 2020
868fce7
HOTFIX | Fix to https://github.com/BhallaLab/moose-core/issues/397 (#…
dilawar Mar 30, 2020
d845fec
writeSBML: channel's annotation is cleaned up and channel's are writt…
hrani Mar 31, 2020
0ee20b3
color are now hex colors (#403)
hrani Apr 6, 2020
d0e5a45
Merged hrani changes and mine from new bindings.
Apr 18, 2020
17e1dd1
Merged hrani changes and mine from new bindings. (#412)
dilawar Apr 19, 2020
6fb344c
Merge branch 'master' of https://github.com/dilawar/moose-core
Apr 20, 2020
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