| deb64f9 | David C Sterratt | 23 February 2021, 18:54:02 UTC | Moved to .sh extension | 23 February 2021, 18:54:02 UTC |
| a326011 | David C Sterratt | 23 February 2021, 18:52:31 UTC | Now working more reliably for Ubuntu 20.04 | 23 February 2021, 18:52:31 UTC |
| fe99f8c | David C. Sterratt | 08 December 2020, 17:30:55 UTC | Issue #13: Allow update bar to output at user-specified intervals This is now achieved be setting the variable KappaNEURON.progress = <progress interval in milliseconds> To turn off the progress bar completely set KappaNEURON.progress = False By default, KappaNEURON.progress = 1.0 | 08 December 2020, 17:30:55 UTC |
| 011f2c7 | David C. Sterratt | 28 October 2020, 17:05:30 UTC | Added PYTHONPATH | 28 October 2020, 17:05:30 UTC |
| da03c5b | David C. Sterratt | 28 October 2020, 14:31:15 UTC | gcc-7 -> gcc-9 | 28 October 2020, 14:31:15 UTC |
| 3e40118 | David C. Sterratt | 28 October 2020, 14:29:48 UTC | Ubuntu 20.04 install instructions | 28 October 2020, 14:29:48 UTC |
| 766769a | David C Sterratt | 30 June 2020, 15:33:09 UTC | Improved description of the simulation procedure | 30 June 2020, 15:33:09 UTC |
| 1cc636f | David C. Sterratt | 30 June 2020, 14:28:16 UTC | README.md file for docs directory | 30 June 2020, 14:28:16 UTC |
| 4370082 | David C. Sterratt | 30 June 2020, 14:18:49 UTC | Converted implementation notes to Markdown | 30 June 2020, 14:18:49 UTC |
| b17af14 | David C Sterratt | 08 June 2020, 17:02:20 UTC | Fixed another egregious error | 08 June 2020, 17:02:20 UTC |
| e8877f8 | David C Sterratt | 08 June 2020, 17:01:27 UTC | Fixed egregious error | 08 June 2020, 17:01:27 UTC |
| 37e20ca | David C Sterratt | 01 July 2019, 10:26:54 UTC | Fix copy and paste typo | 01 July 2019, 10:26:54 UTC |
| cc9de60 | David C Sterratt | 01 July 2019, 10:06:17 UTC | Resize EU flag | 01 July 2019, 10:06:17 UTC |
| 99d861d | David C Sterratt | 01 July 2019, 09:56:16 UTC | Smaller EU flag | 01 July 2019, 09:56:16 UTC |
| afbc96f | David C Sterratt | 01 July 2019, 09:55:11 UTC | EU acknowledgement | 01 July 2019, 09:55:11 UTC |
| 8d5196d | David C Sterratt | 08 May 2019, 10:42:16 UTC | Bumped version to 0.3.2 | 08 May 2019, 10:42:16 UTC |
| d1afad5 | David C Sterratt | 08 May 2019, 09:02:56 UTC | Updated NEURON install instructions | 08 May 2019, 09:02:56 UTC |
| b9350c1 | David C Sterratt | 06 May 2019, 16:25:51 UTC | get_debug_output() | 06 May 2019, 16:25:51 UTC |
| 1e5583b | David C Sterratt | 09 April 2019, 15:41:18 UTC | Fix for Issue #12: Numerical errors with high propensities at long times This just updates the dependency to v2.1.4 of SpatialKappa, making use of this fix: https://github.com/davidcsterratt/SpatialKappa/commit/4ab93fef4194b59e026267bccb95447e3838db32 | 09 April 2019, 15:41:18 UTC |
| 6db7bb9 | David C Sterratt | 22 February 2019, 12:11:59 UTC | Bumped version to 0.3.0 | 22 February 2019, 12:11:59 UTC |
| beea277 | David C Sterratt | 07 January 2019, 17:08:42 UTC | Remove test made redundant by last set of changes Since the initial value of species are no longer changed automatically, it is no longer expected that the species initial value equal to rounded value of concentration converted to number of ions | 07 January 2019, 17:08:42 UTC |
| 764ed26 | David C Sterratt | 20 December 2018, 19:26:47 UTC | Initialise from observables | 20 December 2018, 19:26:47 UTC |
| 93ccd9a | David C Sterratt | 20 December 2018, 14:45:46 UTC | Better separation of model and initialisation, using SpatialKappa v.2.1.3 | 20 December 2018, 14:45:46 UTC |
| ba84326 | David C Sterratt | 04 December 2018, 17:43:22 UTC | matplotlib dependency is <3.0 to allow python2 compatibility | 04 December 2018, 17:43:22 UTC |
| fa6e03b | David C Sterratt | 04 December 2018, 15:09:43 UTC | Some changes to get NEURON compiling from git repository | 04 December 2018, 15:09:43 UTC |
| 9e7763b | David C Sterratt | 04 December 2018, 15:04:38 UTC | Communicate voltage to SpatialKappa | 04 December 2018, 15:05:58 UTC |
| d967c42 | David C Sterratt | 04 December 2018, 14:51:24 UTC | Improved structure and comments in constructor | 04 December 2018, 14:51:24 UTC |
| 719092c | David C Sterratt | 04 December 2018, 10:57:24 UTC | Updated interface to match API changes in SpatialKappa 2.1.2 | 04 December 2018, 14:49:52 UTC |
| 488daf9 | David C Sterratt | 01 October 2018, 16:04:33 UTC | Fix #10: Initial value changes only after first timestep In Kappa.re_init() the initial value of the species concentraion is set to the value of concentration once the concentration has been converted in to numbers and back again. | 01 October 2018, 16:04:33 UTC |
| 8749d0e | David C Sterratt | 14 September 2018, 17:19:42 UTC | README file for PSD simulation | 14 September 2018, 17:19:42 UTC |
| ba3d47c | David C Sterratt | 14 September 2018, 17:13:36 UTC | Moved simplx simulations into separate directory | 14 September 2018, 17:13:36 UTC |
| 04dbb75 | David C Sterratt | 14 September 2018, 17:08:16 UTC | Improved documentation of basic example, and fit mod-ka comparison | 14 September 2018, 17:08:16 UTC |
| 32bd0b6 | David C Sterratt | 14 September 2018, 14:28:35 UTC | Basic Ca accumulation example added | 14 September 2018, 14:28:35 UTC |
| ba31022 | David C Sterratt | 12 September 2018, 16:46:08 UTC | Virtual environment instructions | 12 September 2018, 16:46:08 UTC |
| 433f451 | David C Sterratt | 12 September 2018, 16:33:08 UTC | Fixed formatting | 12 September 2018, 16:33:08 UTC |
| 10be5de | David C Sterratt | 12 September 2018, 16:32:19 UTC | Added test step | 12 September 2018, 16:32:19 UTC |
| ab97b3d | David C Sterratt | 12 September 2018, 16:23:35 UTC | Various fixes | 12 September 2018, 16:23:35 UTC |
| beb6b7e | David C Sterratt | 12 September 2018, 16:04:44 UTC | Update INSTALL-neuron.md | 12 September 2018, 16:04:44 UTC |
| 117f973 | David C Sterratt | 12 September 2018, 16:04:28 UTC | Update INSTALL-neuron.md | 12 September 2018, 16:04:28 UTC |
| 86835bb | David C Sterratt | 12 September 2018, 16:02:58 UTC | Fixed link | 12 September 2018, 16:02:58 UTC |
| 5b6662c | David C Sterratt | 12 September 2018, 16:01:39 UTC | Issue #9: Neuron 7.4 install instructions | 12 September 2018, 16:01:39 UTC |
| 647ce75 | David C Sterratt | 12 September 2018, 15:41:58 UTC | Fixed broken tests with pump molecules The tests with pump molecules were not matching because the Kappa setup code was no longer setting the intial concentration of P. The commit fixes that problem, and also makes tests save the figures to PNG files in a directory test_figs. | 12 September 2018, 15:41:58 UTC |
| 2c7f668 | David C Sterratt | 12 September 2018, 14:22:57 UTC | Fix for Issue #9: Get KappaNEURON working with NEURON 7.4 This workaround makes KappaNEURON work with the production version of NEURON from 2015-11-09, as well as the latest version of NEURON in the 7.4 branch of the former mercurial repository (Release 7.4 (1470:0f4526b127ae) 2016-10-31) | 12 September 2018, 14:22:57 UTC |
| 108ba23 | David C Sterratt | 12 September 2018, 13:12:11 UTC | Fix copying of files to temporary directory Now working reliably with NEURON Release 7.4 (1470:0f4526b127ae) 2016-10-31 | 12 September 2018, 13:12:11 UTC |
| 999c1b8 | David C. Sterratt | 07 September 2018, 13:49:57 UTC | Fixed test compilation from source tree on Linux Tested on Ubuntu 18.04 so far | 07 September 2018, 13:49:57 UTC |
| d711511 | David C Sterratt | 05 September 2018, 13:46:36 UTC | Updated instructions | 05 September 2018, 13:46:36 UTC |
| c01fdfc | David C Sterratt | 05 September 2018, 13:45:19 UTC | Unsuccessful attempt at running test suite in one go | 05 September 2018, 13:46:09 UTC |
| 541e329 | David C Sterratt | 05 September 2018, 13:44:31 UTC | Attempt correct destruction | 05 September 2018, 13:44:31 UTC |
| 1148808 | David C Sterratt | 13 August 2018, 13:21:36 UTC | Automated compilation of .mod files | 13 August 2018, 13:21:36 UTC |
| f170a33 | David C Sterratt | 10 August 2018, 16:08:03 UTC | Reorganisation for packaging with pip | 10 August 2018, 16:08:03 UTC |
| 1e715b3 | David C Sterratt | 10 August 2018, 13:23:43 UTC | Updated NEURON install script | 10 August 2018, 13:23:43 UTC |
| 45bfc0c | David C Sterratt | 10 August 2018, 13:22:47 UTC | Removed redudnant scale_by_area | 10 August 2018, 13:22:47 UTC |
| 54f776a | David C Sterratt | 08 June 2017, 15:49:19 UTC | Merge branch 'master' of github.com:davidcsterratt/KappaNEURON | 08 June 2017, 15:49:19 UTC |
| 30e958c | David C Sterratt | 08 June 2017, 15:49:05 UTC | Update to match NEURON 7.4 | 08 June 2017, 15:49:05 UTC |
| 874eb3a | David C Sterratt | 07 June 2017, 14:57:03 UTC | Documentation tweaks | 07 June 2017, 14:57:03 UTC |
| 853ece9 | David C Sterratt | 07 June 2017, 14:21:39 UTC | Removed lumped input function, which was no longer used | 07 June 2017, 14:21:39 UTC |
| 0ebb08e | David C Sterratt | 02 March 2017, 10:57:21 UTC | Update README.md Corrected version of Ubuntu 16.04 | 02 March 2017, 10:57:21 UTC |
| 2761c8c | David C Sterratt | 13 January 2017, 15:40:56 UTC | Brief documentation of PSD model | 13 January 2017, 15:40:56 UTC |
| f77beae | David C Sterratt | 13 January 2017, 15:30:00 UTC | Merge branch 'master' of github.com:davidcsterratt/KappaNEURON | 13 January 2017, 15:30:00 UTC |
| 95a1a30 | David C Sterratt | 13 January 2017, 15:29:10 UTC | Updated information of software versions | 13 January 2017, 15:29:10 UTC |
| 3b94735 | David C Sterratt | 13 January 2017, 14:46:02 UTC | Bumped version number to 0.2.0 | 13 January 2017, 14:46:02 UTC |
| 4b7750d | David C Sterratt | 13 January 2017, 12:39:42 UTC | Issue #9: Set ion_style() after init() The 7.4 API seems to set the ion_style during species init; thus if we wish to set it, we have to do so after init(). This needs more investigation. | 13 January 2017, 12:43:36 UTC |
| cc7af34 | David C Sterratt | 13 January 2017, 12:39:22 UTC | Use python API for setting section style | 13 January 2017, 12:39:22 UTC |
| c303787 | David C Sterratt | 13 January 2017, 12:25:19 UTC | Issue #9: Update initialisation to NEURON 7.4 rxd API KappaNEURON has been working with a version of NEURON from the trunk of its mercurial repo checked out on 23/9/2014. This was a development version of NEURON 7.4. There have been a number of changes in the API meaning that KappaNEURON does not work with the stable NEURON 7.4 release. One is that initialisation is now carried out using initializer._do_init(), which calls _do_init() functions of region, species and reaction objects. Therefore we need to create a _do_init() function in the KappaNEURON class (which inherits from GeneralizedReaction), which calls _kn_init(), which was previously the neuron.h.FInitializeHandler. _kn_init() no longer needs to call neuron.rxd.rxd.init(). | 13 January 2017, 12:25:19 UTC |
| 6b7b263 | David C Sterratt | 13 January 2017, 12:10:29 UTC | Issue #9: nrr.region._sim_dimension -> nrr.species._has_3d KappaNEURON has been working with a version of NEURON from the trunk of its mercurial repo checked out on 23/9/2014. This was a development version of NEURON 7.4. There have been a number of changes in the API meaning that KappaNEURON does not work with the stable NEURON 7.4 release. The previous method of noting if we are in a 3D section was neuron.rxd.rxd.region._sim_dimension. It is replaced by neuron.rxd.rxd.species._has_3d. | 13 January 2017, 12:10:29 UTC |
| 35eae72 | David C Sterratt | 13 January 2017, 11:39:33 UTC | Improved print statements | 13 January 2017, 11:39:33 UTC |
| 9b51132 | David C Sterratt | 13 January 2017, 11:37:29 UTC | Labelling of plots | 13 January 2017, 11:37:29 UTC |
| ab29baa | David C Sterratt | 13 January 2017, 11:36:32 UTC | Set initial kappa section cai to 0.00005mM | 13 January 2017, 11:36:32 UTC |
| e1a09e1 | David C Sterratt | 10 January 2017, 14:45:20 UTC | Improved output from tests | 10 January 2017, 14:45:20 UTC |
| fbbb95d | David C Sterratt | 09 January 2017, 14:35:42 UTC | Fixed typo in matplotlib package name | 09 January 2017, 14:35:42 UTC |
| 6dd0511 | David C Sterratt | 09 January 2017, 14:23:08 UTC | Fixed escape typo | 09 January 2017, 14:23:08 UTC |
| 3ed3129 | David C Sterratt | 09 January 2017, 14:08:02 UTC | Set VERSION to semantic version format | 09 January 2017, 14:08:02 UTC |
| c629021 | David C Sterratt | 09 January 2017, 13:55:27 UTC | Merged change in INSTALL.md | 09 January 2017, 13:55:27 UTC |
| c025d6b | David C Sterratt | 09 January 2017, 13:53:31 UTC | Added documentation of rxd._curr_indices | 09 January 2017, 13:53:31 UTC |
| 21d123f | David C Sterratt | 09 January 2017, 12:13:13 UTC | Clarified installation instructions, including versions of software used | 09 January 2017, 12:13:13 UTC |
| d11f3e3 | David C Sterratt | 09 January 2017, 12:10:45 UTC | Add matplotlib as dependency | 09 January 2017, 12:10:45 UTC |
| 319601d | David C Sterratt | 06 January 2017, 16:34:54 UTC | Update INSTALL.md Link to SpatialKappa install instructions and description of INSTALL-neuron as a script | 06 January 2017, 16:34:54 UTC |
| d212c03 | David C Sterratt | 06 January 2017, 16:28:31 UTC | Added instructions to test for python link working | 06 January 2017, 16:30:30 UTC |
| 6cf327c | David C Sterratt | 06 January 2017, 15:34:41 UTC | Added scipy depdendency | 06 January 2017, 15:34:41 UTC |
| 4835be2 | David C Sterratt | 06 January 2017, 15:21:02 UTC | Added requirement on flex | 06 January 2017, 15:21:02 UTC |
| 9ce72fb | David C Sterratt | 06 January 2017, 15:17:10 UTC | Added libxext-dev | 06 January 2017, 15:17:10 UTC |
| 16fd56f | David C Sterratt | 06 January 2017, 15:13:51 UTC | Added ncurses-dev | 06 January 2017, 15:13:51 UTC |
| ebec8c3 | David C Sterratt | 06 January 2017, 15:10:27 UTC | Added libpython2.7-dev as dependency | 06 January 2017, 15:10:27 UTC |
| b04a4cb | David C Sterratt | 06 January 2017, 15:03:43 UTC | Give correct argument to apt-get | 06 January 2017, 15:03:43 UTC |
| 44bcc01 | David C Sterratt | 06 January 2017, 15:01:39 UTC | Test for file rather than command and require libx11-dev | 06 January 2017, 15:02:36 UTC |
| 9c67122 | David C Sterratt | 06 January 2017, 14:53:06 UTC | Move back to starting directory | 06 January 2017, 14:53:06 UTC |
| 92c12f6 | David C Sterratt | 06 January 2017, 14:52:20 UTC | Change name of neuron-build directory | 06 January 2017, 14:52:20 UTC |
| df6f3f9 | David C Sterratt | 06 January 2017, 14:51:29 UTC | Make installpkg function | 06 January 2017, 14:51:29 UTC |
| ed88422 | David C Sterratt | 06 January 2017, 14:40:34 UTC | Install libtool | 06 January 2017, 14:40:34 UTC |
| 75516c7 | David C Sterratt | 06 January 2017, 14:38:22 UTC | Corrected package name | 06 January 2017, 14:38:22 UTC |
| 6a88c93 | David C Sterratt | 06 January 2017, 14:37:31 UTC | Added pulling of aclocal | 06 January 2017, 14:37:31 UTC |
| 9aa8f57 | David C Sterratt | 06 January 2017, 14:21:12 UTC | Merge branch 'master' of github.com:davidcsterratt/KappaNEURON | 06 January 2017, 14:21:12 UTC |
| 07d9253 | David C Sterratt | 06 January 2017, 14:19:28 UTC | Customise which version of NEURON is installed | 06 January 2017, 14:19:28 UTC |
| 352799b | David C Sterratt | 05 January 2017, 14:32:13 UTC | Update INSTALL.md Link to INSTALL-neuron | 05 January 2017, 14:32:13 UTC |
| d23e6ad | David C Sterratt | 04 February 2016, 11:20:58 UTC | Corrected DOI | 04 February 2016, 11:20:58 UTC |
| 73fd22f | David C Sterratt | 04 February 2016, 11:18:52 UTC | Updated publication details | 04 February 2016, 11:18:52 UTC |
| 5385240 | David C Sterratt | 07 January 2016, 13:30:56 UTC | Updated publication details | 07 January 2016, 13:30:56 UTC |
| 11afed9 | David C. Sterratt | 16 November 2014, 23:04:45 UTC | Font size now 7pt - looks better | 16 November 2014, 23:04:45 UTC |
| 8b25d93 | David C. Sterratt | 16 November 2014, 22:21:32 UTC | Plotting tweaks | 16 November 2014, 22:21:32 UTC |
| e6aa676 | David C. Sterratt | 16 November 2014, 22:21:19 UTC | Made stimulation protocol more like Markram et al (1998) | 16 November 2014, 22:21:19 UTC |
