| a3f8cd7 | David C Sterratt | 12 September 2014, 08:47:26 UTC | KappaNEURON class now working as reaction It uses _get_memb_flux() to determine the membrane current, which is read in rxd._currents(). This has required computation of _db to be changed so that its length corresponds to the number of membrane fluxes. It is only computed for Species in self._sources | 12 September 2014, 08:47:26 UTC |
| 3515871 | David C Sterratt | 08 September 2014, 14:23:02 UTC | Create kappa sims in new function _create_kappa_sims(), not _update_indices() This is _update_indicies is called whenever init() is called. This meant that kappa sims (and any associated variables set with setVariable()) were being overridden, leading to failed tests. | 08 September 2014, 14:23:02 UTC |
| bab7c2a | David C Sterratt | 08 September 2014, 14:14:22 UTC | Increase dt for speed and new assertEqualWithinTol() function | 08 September 2014, 14:14:22 UTC |
| 85654fb | David C. Sterratt | 05 September 2014, 16:27:46 UTC | Merge in updated tests | 05 September 2014, 16:27:46 UTC |
| 1cef29e | David C. Sterratt | 05 September 2014, 16:24:05 UTC | Refactored tests | 05 September 2014, 16:24:05 UTC |
| c685d1c | David C. Sterratt | 05 September 2014, 15:49:25 UTC | Fixed bug in simple Ca pump test due to P existing in caPump1.ka | 05 September 2014, 15:49:25 UTC |
| c9d0581 | David C. Sterratt | 05 September 2014, 15:47:57 UTC | Improved debugging output | 05 September 2014, 15:47:57 UTC |
| 198f6b3 | David C. Sterratt | 05 September 2014, 15:47:14 UTC | Taken out duplicated test | 05 September 2014, 15:47:14 UTC |
| bc5300f | David C. Sterratt | 05 September 2014, 10:15:57 UTC | Used get_mode() function in all tests | 05 September 2014, 10:15:57 UTC |
| 28efe3d | David C. Sterratt | 05 September 2014, 10:02:16 UTC | First steps towards generalising the code to allow kappa mechanisms in arbitrary sections | 05 September 2014, 10:02:16 UTC |
| e6b7cea | David C Sterratt | 03 September 2014, 16:08:04 UTC | Removed some print cruft | 03 September 2014, 16:08:04 UTC |
| e4cabd4 | David C Sterratt | 02 September 2014, 16:00:41 UTC | Nonlinear calcium pump test working | 02 September 2014, 16:00:41 UTC |
| bbe3504 | David C Sterratt | 02 September 2014, 16:00:04 UTC | Updated comment | 02 September 2014, 16:00:04 UTC |
| 33019d5 | David C Sterratt | 02 September 2014, 15:59:18 UTC | Updated comments | 02 September 2014, 15:59:18 UTC |
| fbd8ab3 | David C Sterratt | 02 September 2014, 15:55:41 UTC | Updated comments | 02 September 2014, 15:55:41 UTC |
| 3422cc2 | David C Sterratt | 29 August 2014, 15:29:29 UTC | Run all tests from Makefile | 29 August 2014, 15:29:29 UTC |
| 23c40da | David C Sterratt | 29 August 2014, 14:26:10 UTC | Added test_injectCalciumPumpGHK | 29 August 2014, 14:26:10 UTC |
| 0328298 | David C Sterratt | 29 August 2014, 13:27:59 UTC | Test 2 (Ca accumulation with pump) now working | 29 August 2014, 13:27:59 UTC |
| 7c03453 | David C Sterratt | 29 August 2014, 13:22:18 UTC | Changed suffix to caPump2 | 29 August 2014, 13:22:18 UTC |
| 6e09d76 | David C Sterratt | 29 August 2014, 13:21:30 UTC | Added GHK flag | 29 August 2014, 13:21:30 UTC |
| de3ff5f | David C Sterratt | 29 August 2014, 13:20:49 UTC | Added vclamp argument to functions | 29 August 2014, 13:20:49 UTC |
| 84a44cd | David C Sterratt | 29 August 2014, 13:19:35 UTC | Added the calculations for Calcium pump test | 29 August 2014, 13:19:35 UTC |
| 9c5b636 | David C Sterratt | 28 August 2014, 11:32:14 UTC | Refactored test code | 28 August 2014, 11:32:14 UTC |
| a1478ff | David C Sterratt | 27 August 2014, 10:58:13 UTC | Work on GHK test case including factoring out shared code | 27 August 2014, 10:58:13 UTC |
| a7f316c | David C Sterratt | 26 August 2014, 15:11:41 UTC | Completed tests of simple calcium injection | 26 August 2014, 15:11:41 UTC |
| 24e77b6 | David C Sterratt | 26 August 2014, 12:23:31 UTC | Added comment and numpy->np | 26 August 2014, 12:23:31 UTC |
| 1038f44 | David C Sterratt | 21 August 2014, 16:35:54 UTC | Intermediate stage in which it looks as though calcium accumulation is working | 21 August 2014, 16:35:54 UTC |
| 1a2751b | David C Sterratt | 19 August 2014, 15:10:19 UTC | Graphs plotted to help debug | 19 August 2014, 15:10:19 UTC |
| cd2d472 | David C Sterratt | 12 August 2014, 16:00:34 UTC | Merged simple Ca accumulation test from master | 12 August 2014, 16:00:34 UTC |
| b0b200d | David C Sterratt | 12 August 2014, 15:57:43 UTC | Test of simple Ca accumulation added | 12 August 2014, 15:57:43 UTC |
| 5101bbd | David C Sterratt | 12 August 2014, 15:53:29 UTC | Commented out _kn_currents callback | 12 August 2014, 15:53:29 UTC |
| c956327 | David C Sterratt | 08 August 2014, 16:21:24 UTC | Shorter simulations for faster tests | 08 August 2014, 16:21:24 UTC |
| 3cb3638 | David C Sterratt | 08 August 2014, 16:11:38 UTC | Merge branch 'master' into continuous_influx_currents2_db | 08 August 2014, 16:11:38 UTC |
| 26b9c39 | David C Sterratt | 08 August 2014, 14:04:49 UTC | Moved boilerplate code to class to allow for multiple runs | 08 August 2014, 14:04:49 UTC |
| f8501f1 | David C Sterratt | 08 August 2014, 14:04:15 UTC | More informative error message when failure to set initial concentration | 08 August 2014, 14:04:15 UTC |
| 7fb57b6 | David C Sterratt | 08 August 2014, 14:03:18 UTC | Fixed error in file which caused test to fail | 08 August 2014, 14:03:18 UTC |
| 64e9bd6 | David C Sterratt | 06 August 2014, 16:25:20 UTC | Basis for multiple tests now working | 06 August 2014, 16:25:20 UTC |
| 3494e48 | David C Sterratt | 06 August 2014, 16:24:52 UTC | Clean up output and make progress reporting optional | 06 August 2014, 16:24:52 UTC |
| ff6729c | David C Sterratt | 06 August 2014, 16:21:49 UTC | Fix loss of gateway if Kappa object deleted | 06 August 2014, 16:21:49 UTC |
| ac52f65 | David C Sterratt | 06 August 2014, 14:14:04 UTC | Got test running by reducing compartment volume | 06 August 2014, 14:14:04 UTC |
| 8aadd47 | David C Sterratt | 06 August 2014, 14:12:22 UTC | Added exception in python for if too many ions are being added | 06 August 2014, 14:12:22 UTC |
| 2a27fe5 | David C Sterratt | 06 August 2014, 13:41:05 UTC | Merge branch 'master' into continuous_influx_currents2_db | 06 August 2014, 13:41:05 UTC |
| 05b760d | David C Sterratt | 06 August 2014, 13:10:36 UTC | Comment out broken print statement | 06 August 2014, 13:10:36 UTC |
| 7381139 | David C. Sterratt | 06 August 2014, 09:41:28 UTC | nrnivmodl now called from Makefile so binaries ready for test suite | 06 August 2014, 09:41:28 UTC |
| d6bb7ce | David C Sterratt | 05 August 2014, 16:22:33 UTC | Get setUp() to compile mod files | 05 August 2014, 16:22:33 UTC |
| e9b2399 | David C Sterratt | 05 August 2014, 15:27:01 UTC | Added backtraces from exceptions | 05 August 2014, 15:27:01 UTC |
| 3b74cae | David C Sterratt | 05 August 2014, 15:24:39 UTC | Cleanup properly when last _kappa_scheme closed | 05 August 2014, 15:24:39 UTC |
| 03b6668 | David C Sterratt | 05 August 2014, 09:35:08 UTC | Start of unittest framework | 05 August 2014, 09:35:08 UTC |
| 82fb296 | David C. Sterratt | 24 July 2014, 04:11:03 UTC | Put continous running code into _run_kappa_continuous() | 24 July 2014, 04:11:03 UTC |
| af01073 | David C. Sterratt | 24 July 2014, 04:04:08 UTC | Almost working continuous influx version | 24 July 2014, 04:04:08 UTC |
| b07de74 | David C. Sterratt | 24 July 2014, 03:59:48 UTC | Added setSeed() function | 24 July 2014, 03:59:48 UTC |
| 37c202a | David C. Sterratt | 11 July 2014, 09:39:30 UTC | Communication of current changes via global variable db | 11 July 2014, 09:39:30 UTC |
| c2c22ba | David C. Sterratt | 11 July 2014, 04:38:25 UTC | Updated to comment | 11 July 2014, 04:38:25 UTC |
| b95a216 | David C Sterratt | 08 July 2014, 15:20:26 UTC | Demonstration of noise being added to currents, but not feeding into voltag | 08 July 2014, 15:20:26 UTC |
| b43deaf | David C Sterratt | 08 July 2014, 13:11:45 UTC | Tidying of code and plotting | 08 July 2014, 13:11:45 UTC |
| 07e280d | David C Sterratt | 08 July 2014, 13:06:13 UTC | Make adding voltage clamp optional | 08 July 2014, 13:06:13 UTC |
| 771791f | David C Sterratt | 08 July 2014, 13:04:00 UTC | Make current flow during time window, not dependent on voltage | 08 July 2014, 13:04:00 UTC |
| 0d8e2c4 | David C Sterratt | 08 July 2014, 12:58:50 UTC | Corrected comments | 08 July 2014, 12:58:50 UTC |
| 4be79c3 | David C Sterratt | 04 July 2014, 17:34:39 UTC | Apparently working version of continous influx | 04 July 2014, 17:34:39 UTC |
| ce2b215 | David C Sterratt | 04 July 2014, 17:31:58 UTC | Improvements to INSTALL instructions | 04 July 2014, 17:31:58 UTC |
| eac4745 | David C Sterratt | 04 July 2014, 17:30:59 UTC | Improvements in formatting of graph | 04 July 2014, 17:30:59 UTC |
| 8f4ed40 | David C Sterratt | 20 June 2014, 13:55:22 UTC | Fixed bug in run_free() which used runUntilTime() instead of runForTime() | 20 June 2014, 13:55:22 UTC |
| fbe2a1f | David C Sterratt | 20 June 2014, 13:53:40 UTC | Fixed the printing of newlines at the end of a simulation | 20 June 2014, 13:54:34 UTC |
| f9b2d68 | David C Sterratt | 20 June 2014, 13:49:30 UTC | Comment on commented-out discrepancy detection code | 20 June 2014, 13:49:30 UTC |
| 341cda7 | David C Sterratt | 20 June 2014, 13:29:10 UTC | Attempt to print newline at end of run() command | 20 June 2014, 13:29:10 UTC |
| 155f866 | David C Sterratt | 19 June 2014, 16:00:47 UTC | Textual progress indicator, using the new SpatialKappa functionality | 19 June 2014, 16:00:47 UTC |
| 20c0a2d | David C Sterratt | 16 June 2014, 15:42:55 UTC | Fix #7: When setting initial values in Kappa.re_init(), check the species name is an observable | 16 June 2014, 15:42:55 UTC |
| ba23ccb | David C Sterratt | 16 June 2014, 15:16:07 UTC | Fix #6: Set initial concentration of species to zero if not set | 16 June 2014, 15:16:07 UTC |
| 7cf4b72 | David C Sterratt | 01 April 2014, 15:04:04 UTC | Removed cruft | 01 April 2014, 15:04:04 UTC |
| b48ece7 | David C. Sterratt | 01 April 2014, 09:33:18 UTC | Added comment | 01 April 2014, 09:33:18 UTC |
| f668502 | David C Sterratt | 07 February 2014, 20:38:36 UTC | Got rid of print cruft | 07 February 2014, 20:38:36 UTC |
| f7143b7 | David C Sterratt | 07 February 2014, 18:45:13 UTC | Updated with location of default SpatialKappa archive | 07 February 2014, 18:45:13 UTC |
| cd0e52e | David C Sterratt | 05 February 2014, 12:08:05 UTC | Added stargazin, though not full pathway | 05 February 2014, 12:08:05 UTC |
| 55e0f3f | David C Sterratt | 05 February 2014, 12:05:33 UTC | Fixed printing figure to file | 05 February 2014, 12:05:33 UTC |
| c1ab1ea | David C Sterratt | 05 February 2014, 12:02:39 UTC | Fixed printing figure to file | 05 February 2014, 12:02:39 UTC |
| d074f50 | David C Sterratt | 05 February 2014, 12:01:36 UTC | Converted to KappaNEURON module | 05 February 2014, 12:01:36 UTC |
| 66e1473 | David C Sterratt | 05 February 2014, 11:52:24 UTC | Tidy up import statements | 05 February 2014, 11:52:24 UTC |
| c0fb6fd | David C Sterratt | 05 February 2014, 11:49:35 UTC | More meaningful error messages in case of faulty kappa file | 05 February 2014, 11:49:35 UTC |
| 208d852 | David C Sterratt | 04 February 2014, 16:47:23 UTC | Makefile fixes | 04 February 2014, 16:47:23 UTC |
| 034c0ff | David C Sterratt | 04 February 2014, 16:47:00 UTC | One last runByTime2 -> runForTime | 04 February 2014, 16:47:00 UTC |
| 6a90207 | David C Sterratt | 29 January 2014, 13:18:35 UTC | Updated install instructions | 29 January 2014, 13:18:35 UTC |
| 9a8e224 | David C Sterratt | 29 January 2014, 13:11:19 UTC | Reflect change in SpatialKappa API: runForDt -> runForTime | 29 January 2014, 13:11:19 UTC |
| 6b76e68 | David C. Sterratt | 25 January 2014, 09:18:00 UTC | Moved Makefile to correct test directory | 25 January 2014, 09:29:54 UTC |
| b9f0da6 | David C. Sterratt | 25 January 2014, 09:16:23 UTC | Updated to reflect current test_ca_pulse | 25 January 2014, 09:29:54 UTC |
| 05fd418 | David C. Sterratt | 25 January 2014, 09:11:22 UTC | Removed redundant python testing files | 25 January 2014, 09:29:54 UTC |
| 1b1b928 | David C. Sterratt | 25 January 2014, 09:07:34 UTC | Removed stray comma | 25 January 2014, 09:29:54 UTC |
| f3784d0 | David C. Sterratt | 25 January 2014, 09:07:07 UTC | Added setup.py file | 25 January 2014, 09:29:54 UTC |
| 1f6a4ee | David C. Sterratt | 25 January 2014, 08:57:46 UTC | Corrected install instructions | 25 January 2014, 09:29:54 UTC |
| bcbcfcb | David C. Sterratt | 25 January 2014, 08:53:30 UTC | Converted to use the SpatialKappa python interface rather than interfacing py4j directly | 25 January 2014, 09:29:49 UTC |
| 3260a6d | David C. Sterratt | 24 January 2014, 14:45:52 UTC | Merge branch 'master' into py4j-auto-launch | 24 January 2014, 14:45:52 UTC |
| 8ff07f8 | David C. Sterratt | 24 January 2014, 14:45:26 UTC | Rename directory to more logical name | 24 January 2014, 14:45:26 UTC |
| df6887e | David C. Sterratt | 24 January 2014, 14:44:32 UTC | Removed redundant files in test directory | 24 January 2014, 14:44:32 UTC |
| 6dc3cc2 | David C. Sterratt | 24 January 2014, 14:25:17 UTC | Changes to INSTALL instructions | 24 January 2014, 14:25:17 UTC |
| 2b20894 | David C. Sterratt | 24 January 2014, 14:18:45 UTC | Moved INSTALL to python directory | 24 January 2014, 14:18:45 UTC |
| 05ef91e | David C. Sterratt | 24 January 2014, 14:17:30 UTC | Stripped out unneeded bits before pushing to SpatialKappa repo | 24 January 2014, 14:17:30 UTC |
| 9c1d380 | David C. Sterratt | 24 January 2014, 13:01:40 UTC | Moved SpatialKappa code to python directory | 24 January 2014, 13:01:40 UTC |
| 6d4f8d0 | David C Sterratt | 23 January 2014, 17:36:32 UTC | Initial version of setup file | 23 January 2014, 17:36:32 UTC |
| f31aa67 | David C Sterratt | 23 January 2014, 16:59:55 UTC | Test now runs Kappa file | 23 January 2014, 16:59:55 UTC |
| 8b4cc4e | David C Sterratt | 23 January 2014, 16:59:10 UTC | Added classpath argument to constructor | 23 January 2014, 16:59:10 UTC |
| f84d921 | David C Sterratt | 23 January 2014, 15:53:03 UTC | Reference to installing py4j via easy_install | 23 January 2014, 15:53:03 UTC |
