moose-packages.

build fails.

95fe1a7 Force --install-layout=deb when on debian/ubuntu.

git-subtree-dir: moose-core
git-subtree-split: 95fe1a7b8f24b50d600d5e7c3a1d0171a809b9aa

7ab9e3c Let static page generation fail.
c26d7c7 Build using travis and deploy onto github pages.
feeaf6b Added theme for static pages.
ae1fecb Merge branch 'dirty' of github.com:BhallaLab/moose-examples
c25e57e Passing locally.
2a2db61 Moved the integration to branch 'dirty'
83a516c Test the dirty branch with jekyll.
9667dee Added jekyll to create static page.
742362a Testing Jekyll and travis integration.
9aa4a3d Prepare index.md  file post test.
e885ea5 Modified shell script so it does not hang.
828464a Code to update README.md file with broken scripts.
9a6b3b1 Deploy keys are added. Testing...
74fb0ae Set theme jekyll-theme-minimal
a4e7ce1 Deploy to github pages. Testing.
e3f9a41 Added code to deploy on moose-examples static page.
ab45904 Default timeout is 30 secs [ skip ci ]
3e30131 Added python-pygraphviz to dependencies.
b825107 Added python-scipy on travis.
73d8bff Merge branch 'master' into traub_2005
60a9f7d Update README.md
4d30457 Updated VClamp commandIn destFinfo name in test_tcr
8846ae5 Fixes for nonexistent NRN data
03735e8 Fixed syntax error
24c349d Multiple workarounds to directory paths and data files from neuron
ccc1039 Fixed typo with data directory creation in traub 2005
a15893b Fixed issue where new ZombieCompartment breaks old code using Compartment
024aa0e Added attempt to automatic data directory creation
96a815c updated ref to old table API
78dcbb1 Merge branch 'traub_2005' of https://github.com/BhallaLab/moose-examples into traub_2005
bc5c37d Added fix for #28 (metaclass portability)
b347fa4 Fixes to load-sbml script.
202bb51 Merge branch 'master' of git://github.com/malav4994/moose-examples into PR-25
a20f451 On this branch, making traub_2005 test with recent release. Added subha on this branch. Removed everyone else.
ac68f92 Ignore the traub_2015 directory on travis BhallaLab/moose-examples#28.
caaa45e Removed a png file [skip ci]
cf27b12 Added python-h5py on travis. The hdf5 related scripts needs this module to run on travis.
afbb591 Merge remote-tracking branch 'origin/traub_2005'
dc92ae8 Include traub_2005 in scripts to be tested on travis.
ee70916 If a script is timedout after 30sec, dont consider it a failure. Fixed the result status of timeout command on 14.04 as indicated in manual http://git.savannah.gnu.org/cgit/coreutils.git/tree/src/timeout.c
9f70d7f Fixes to import in loadSbmlmodel file. Read SBML fails.
bbb3fe0 Increased timeout to 3m and using 4 parallel process.
b5a856e Using backend agg to overcome build failure on travis. This way we will not launch the graphics on travis.
450b3da Removed debug print
d34a833 Fix to issue 28
41f5c8b modified some of the snippets files for documentation

git-subtree-dir: moose-examples
git-subtree-split: 7ab9e3cfd8d74f79a73282572d4df4301b6df976

a13dbd9 Better formatted output on running tests. These tests are moose-examples scripts which are known to pass.
1409792 Fixes to debian related python install. When --prefix=/usr is given, its installs in site-packages rather than dist-pacakges.
4f3e773 If for some reason matplotlib is not imported successfully, disable kkit import.
4f6f8b1 Fixes to debian related python install. When --prefix=/usr is given, its installs in site-packages rather than dist-pacakges.
7771173 Merge branch 'master' of github.com:BhallaLab/moose-core
8fff67d Refactoring in cmake file.
3e1e043 Minor changes to test script: Dont wait till test is over to print which test is being executed.

git-subtree-dir: moose-core
git-subtree-split: a13dbd9f31f93d915faee59f440cfe6bbc8ce428

1cbe2f063 __version__ = version( ) is both python2 and python3 compatible.

git-subtree-dir: moose-core
git-subtree-split: 1cbe2f06372d760333681952d6f81e2087c90aac

37bf0cc This might pass with upcoming release 3.1.3.
feef205 Merge branch 'master' of github.com:BhallaLab/moose-examples
c41af29 import fix to another file.
2d30a30 Output comparision of GPU & CPU (#26)
7295a8f numpy.array changed to np.array
664f843 Maximum timeout is 1m for all script.
0458697 Fixes to one more script. Error due to merge conflicts.
27fddec Updated script.
0694972 Run scripts now launches 8 process in parallel.
15d3aa7 Merge branch 'master' of github.com:BhallaLab/moose-examples
62d6c58 Enabled trap in bash script. Kill running test when user presses ctrl+c.
65fb8a8 Added beta cmake based test flow.
987c3fb Moved CMakeLists.txt to _travis folder. Old bash style build system is sufficient.
d4a081f Removed one more duplicate file.
9b13403 Removed duplicate files.
98b5eb0 Fixes to script. Runs fine now.
c42aa93 One more fix.
626221e Removed merge conflict.
f1b0bc4 Fixed one more script to make it work.
09ca09e Merge branch 'master' of github.com:BhallaLab/moose-examples
204d5e4 This is removed b'cos Rdesignuer does the job
8c7c00c can pass command line arguments also
70f83d0 cleanup in return type from None to moose.shell
fe4238b indentation for python3
3e81764 indentation fixes for python3
66f1bb0 Removed <<<<, ===  and >>> from improper merge.
0719a5d Merge commit '349abe7e'
7054325 mooseaddChemSolver is needed in loadSbmlModel file
6116c7e Indentation cleanup
9fd501a conflict cleanups
fe297f6 indentation correction
2b24c64 indentation correction
0e329d5 Merge branch 'master' of http://github.com/BhallaLab/moose-examples
7ce262e corrected indentation
864776c added deleted files
87a6963 temp deleted
0f1e722 Resolved merge conflict
0ff3b05 temp deletion
69062d9 For crossComptSimpleReac a temp fix so that segfault doesn't occur, rest cleanup
729f216 deleted unwanted files and added new files
7318878 cleanups
045aa11 Fixed assert by Upi
2b16c59 Deleted temp files.
3881f8a khali khali
97599aa Fixed docstring on example.

git-subtree-dir: moose-examples
git-subtree-split: 37bf0cc0a733d5b4c61659f9eb6e747f57530273

d1130b7 Merge branch 'master' of github.com:BhallaLab/moose-core
967ac3b Added VERSION info moose.version( ) or moose.__version__ returns the version. It was lost somewhere in rrefactoring the code.
457850e Added version( ) and __version__ string.
2625fd0 Added `moose.test` to test `moose-examples` online (#189)
2a822a2 Added assertion in test case and remove import of matplotlib. BhallaLab/moose#221.
2484214 absolute imports are forced with python2 as well.
6c92901 All tests passes locally with python3.
bd78e14 Fixes to import statements.
5c3811e Print time information as well.
a7e715c Inbuilt moose.test( ) functions to run moose-examples. BhallaLab/moose-core#184.
c424e0d Fixes to chemUtil import.
f29e35e Merge branch 'master' of github.com:BhallaLab/moose-core
087aad0 moose.Compartment -> moose.element( ) in couple of more place. One more (#187)
d618fe6 Merge branch 'master' into master
4aca08a Merge branch 'master' of github.com:BhallaLab/moose-core
b8266b3 Fixes to test failure. Not sure if it is correct.  BhallaLab/moose#218 .
56870e8 Merge branch 'master' of github.com:BhallaLab/moose-core
d1e37cb Changed the assert statement. Not sure if this is correct to do BhallaLab/moose-core#218. Need to ask developer for confirmation.
cf44570 We are no longer testing Makefile base flow. Only cmake will be tested from now on.
cf7ff18 moose.Compartment -> moose.element( ) in couple of more place. One more scripts passes the test now.

git-subtree-dir: moose-core
git-subtree-split: d1130b78bd744e01d045459adb20d5bcebdb34a0

ba97d4cc0 Merge commit '0014d826'
6aac85bad Follow up fixes to calcium-hsolve  (#221)

git-subtree-dir: moose-core
git-subtree-split: ba97d4cc05425dc8b8b42ee6f8976989e229a144

git-subtree-dir: moose-examples
git-subtree-split: cd2a2b99b4aff3a581bfbfc5786ff9504f0f2cb8

git subtree.

052318cb4 [skip ci] Moved git precommit script into script. if someone wants to activate it in her repo, rename it to .pre-commit-config.yaml and enable it
d15e77649 Removed legacy makefile #180. These appeared again because of push from subtree in moose repo. Sigh!
ed708e01b No-longer supporting Makefile based old flow on travis.
bea1f4a9d Integrated test script from PR BhallaLab/moose#218 . I need to confirm if results are correct.

git-subtree-dir: moose-core
git-subtree-split: 052318cb48027ca0c401a13be9fddd2b0d5a66b7

* Fix broken assertion

* Add volume calculation of DifShells and DifBuffers

Volume needs to be calculated before a diffusion message with calcium concentration or buffer concentration is obtained. Volume is calculated at reinit and sometimes a diffusion message is received before the reinit resulting in a division by volume of zero. Due to that initial concentration in some difshells and difbuffers is not correct.

* Add sending current message at reinit of channels

In HHChannel change access of functions inherited from ChanCommon.

git-subtree-dir: moose-examples
git-subtree-split: 3a960983fe23dad8e0b34883e61510d05a2f3b2a