| 1cb15f3 | Willem Wybo | 05 January 2021, 18:35:27 UTC | Merge pull request #115 from pythonjam/issue81 Issue81 | 05 January 2021, 18:35:27 UTC |
| 58243ed | Willem Wybo | 05 January 2021, 18:22:27 UTC | cleanup ionchannels.py | 05 January 2021, 18:22:27 UTC |
| 25389dd | Willem Wybo | 05 January 2021, 14:49:55 UTC | fix evaluation of exponentials in C code with ad hoc method | 05 January 2021, 14:49:55 UTC |
| 4a8b1a5 | pythonjam | 22 December 2020, 04:08:31 UTC | fixing comment | 22 December 2020, 04:08:31 UTC |
| 909c58c | pythonjam | 22 December 2020, 04:04:26 UTC | issue 81 fix Converting expressions to rational in order to prevent evaluation of Add inside exp and thereby increasing numerical stability | 22 December 2020, 04:04:26 UTC |
| 80cb457 | benelot | 21 December 2020, 16:24:26 UTC | Reenable gallery and add import neuron to trigger the missing import in the examples | 21 December 2020, 16:24:26 UTC |
| a7cd11d | benelot | 21 December 2020, 11:06:55 UTC | Temporarily disable the gallery | 21 December 2020, 11:06:55 UTC |
| 71d775c | benelot | 21 December 2020, 11:02:51 UTC | Add many hacks to make the universal mock object pass | 21 December 2020, 11:02:51 UTC |
| eb02570 | benelot | 21 December 2020, 10:01:21 UTC | Fix import in rst and add the universal iterable mock object for h | 21 December 2020, 10:01:21 UTC |
| 0e254aa | Benjamin Ellenberger | 21 December 2020, 09:05:30 UTC | Remove simtools from sphinx exclude list | 21 December 2020, 09:05:30 UTC |
| 9619cba | Willem Wybo | 18 November 2020, 15:37:15 UTC | Merge pull request #101 from WillemWybo/maint/language-level-3 Change language level cython | 18 November 2020, 15:37:15 UTC |
| a7994b4 | Willem Wybo | 18 November 2020, 15:36:00 UTC | Merge branch 'master' into maint/language-level-3 | 18 November 2020, 15:36:00 UTC |
| a5582f2 | Willem Wybo | 18 November 2020, 13:53:16 UTC | Merge pull request #113 from WillemWybo/fix/compartmentfitter-bugfixes Fix/compartmentfitter bugfixes | 18 November 2020, 13:53:16 UTC |
| 2e18b9c | Willem Wybo | 18 November 2020, 13:43:25 UTC | add option to force membrane time-scale fit | 18 November 2020, 13:43:25 UTC |
| 4a33f2d | Willem Wybo | 18 November 2020, 12:16:25 UTC | remove warnings in checkPassive | 18 November 2020, 12:16:25 UTC |
| ea5fcb8 | Willem Wybo | 18 November 2020, 11:52:47 UTC | allow specification of whether to use all channels for passive fit in checkPassive | 18 November 2020, 11:52:47 UTC |
| 4b7b78b | Willem Wybo | 18 November 2020, 11:46:31 UTC | bugfix in checkPassive + fix in docstring CompartmentFitter | 18 November 2020, 11:46:31 UTC |
| ccfd581 | Willem Wybo | 07 August 2020, 15:13:32 UTC | Merge pull request #111 from WillemWybo/fix/another-correction Another correction | 07 August 2020, 15:13:32 UTC |
| 9916a6d | Willem Wybo | 07 August 2020, 15:12:54 UTC | another correction | 07 August 2020, 15:12:54 UTC |
| 641b087 | Willem Wybo | 07 August 2020, 15:07:47 UTC | Merge pull request #110 from WillemWybo/fix/further-corrections-for-docs Specify explicit location for NEURON classes in trees.rst | 07 August 2020, 15:07:47 UTC |
| c8c1859 | Willem Wybo | 07 August 2020, 15:06:42 UTC | specify explicit location for NEURON classes in trees.rst since there are not imported in __init__ | 07 August 2020, 15:06:42 UTC |
| 5ca1273 | Willem Wybo | 07 August 2020, 14:56:43 UTC | Merge pull request #109 from WillemWybo/fix/further-correction-to-fakeh Further correction fo fake h | 07 August 2020, 14:56:43 UTC |
| 84667b6 | Willem Wybo | 07 August 2020, 14:55:54 UTC | correction fo fake h | 07 August 2020, 14:55:54 UTC |
| 7039c3d | Willem Wybo | 07 August 2020, 14:50:34 UTC | Merge pull request #108 from WillemWybo/enh/attempt-docbuild-wo-neuron Add non-functional h module for attempt at doc compilation | 07 August 2020, 14:50:34 UTC |
| c5c58a6 | Willem Wybo | 07 August 2020, 14:48:12 UTC | add non-functional h module for doc compilation | 07 August 2020, 14:48:12 UTC |
| 9101648 | Willem Wybo | 07 August 2020, 14:29:15 UTC | Merge pull request #107 from WillemWybo/enh/further-doc-correction Further correction for NeuronSimTree docs | 07 August 2020, 14:29:15 UTC |
| 89767b4 | Willem Wybo | 07 August 2020, 14:28:21 UTC | further correction | 07 August 2020, 14:28:21 UTC |
| 90766bd | Willem Wybo | 07 August 2020, 14:22:56 UTC | Merge pull request #106 from WillemWybo/enh/wrap-neuron-import Wrap neuron import in `neuronmodel.py` in try statement for sphinx | 07 August 2020, 14:22:56 UTC |
| 7cc1a36 | Willem Wybo | 07 August 2020, 14:20:01 UTC | wrap neuron import in neuronmodel.py in try statement for sphinx | 07 August 2020, 14:20:01 UTC |
| 73a6320 | Willem Wybo | 07 August 2020, 14:16:59 UTC | Merge pull request #105 from WillemWybo/enh/neuronsimtree-correction Addition correction for `NeuronSimTree` reference | 07 August 2020, 14:16:59 UTC |
| d36656e | Willem Wybo | 07 August 2020, 14:16:15 UTC | reference correction | 07 August 2020, 14:16:15 UTC |
| 8977c05 | Willem Wybo | 07 August 2020, 14:12:12 UTC | Merge pull request #104 from WillemWybo/enh/neuronsimtree-docs Try adding NEURON components to website reference | 07 August 2020, 14:12:12 UTC |
| 81a71c0 | Willem Wybo | 07 August 2020, 14:11:43 UTC | correction to reference | 07 August 2020, 14:11:43 UTC |
| bd7dd35 | Willem Wybo | 07 August 2020, 14:09:39 UTC | try adding neuronsimtree to online docs | 07 August 2020, 14:09:39 UTC |
| 422fc31 | Willem Wybo | 07 August 2020, 14:08:28 UTC | improve neuronsimtree docstrings | 07 August 2020, 14:08:28 UTC |
| fc08b61 | Willem Wybo | 07 August 2020, 13:00:13 UTC | Merge pull request #103 from WillemWybo/enh/sov_tree-tutorial Tutorial for `neat.SOVTree` | 07 August 2020, 13:00:13 UTC |
| 9037ed0 | Willem Wybo | 07 August 2020, 12:56:29 UTC | try adding SOV tutorial to website | 07 August 2020, 12:56:29 UTC |
| 0312ba2 | Willem Wybo | 07 August 2020, 12:54:43 UTC | add units to number of docstrings for GreensTree and SOVTree | 07 August 2020, 12:54:43 UTC |
| 49a1f05 | Willem Wybo | 07 August 2020, 12:54:07 UTC | update tutorials morphologies | 07 August 2020, 12:54:07 UTC |
| 24593d2 | Willem Wybo | 07 August 2020, 12:53:07 UTC | update other tutorials | 07 August 2020, 12:53:07 UTC |
| 69076cf | Willem Wybo | 07 August 2020, 12:51:58 UTC | add tutorial on SOVTree | 07 August 2020, 12:51:58 UTC |
| 99389d5 | Willem Wybo | 07 August 2020, 12:11:41 UTC | add tolerance to .swc three-point convention check | 07 August 2020, 12:11:41 UTC |
| 4a9580a | Benjamin Ellenberger | 29 July 2020, 13:55:17 UTC | Update all code blocks | 29 July 2020, 13:55:17 UTC |
| a3f56c1 | Benjamin Ellenberger | 29 July 2020, 13:50:53 UTC | Add missing newlines | 29 July 2020, 13:50:53 UTC |
| 4bbd425 | Benjamin Ellenberger | 29 July 2020, 13:44:23 UTC | Check code block formatting | 29 July 2020, 13:44:23 UTC |
| db949b8 | Willem Wybo | 29 July 2020, 12:41:05 UTC | Merge pull request #94 from jakobj/maint/update-install-instructions Adapt package name, fix README to render on pypi, update installation instructions | 29 July 2020, 12:41:05 UTC |
| f99dee5 | Willem Wybo | 29 July 2020, 11:47:09 UTC | another docstring update | 29 July 2020, 11:47:09 UTC |
| 555cf5b | Willem Wybo | 29 July 2020, 10:40:05 UTC | docstring update for MorphTree._convertLocArgsToLocs | 29 July 2020, 10:40:05 UTC |
| fdf66ba | Willem Wybo | 29 July 2020, 10:33:10 UTC | another docstring update | 29 July 2020, 10:33:10 UTC |
| 04cb6cc | Willem Wybo | 29 July 2020, 10:20:23 UTC | update docstring MorphTree | 29 July 2020, 10:20:23 UTC |
| ea5ea87 | Willem Wybo | 29 July 2020, 10:05:49 UTC | update docstrings | 29 July 2020, 10:05:49 UTC |
| 1e45cf1 | Willem Wybo | 27 July 2020, 11:12:30 UTC | fix ionchannel docstring | 27 July 2020, 11:12:30 UTC |
| c6a1004 | Willem Wybo | 27 July 2020, 11:09:10 UTC | Merge pull request #98 from WillemWybo/fix/soma-reader So there were some bugs that should now be corrected. However, there is also an issue with your morphology: ``` 1 3 1066.38 399.67 157.0 4.9215 -1 2 3 1071.3 399.67 157.0 4.9215 1 3 3 1076.22 399.67 157.0 4.9215 2 4 1 1066.5 402.83 157.0 11.494 2 5 1 1062.4 405.5 157.0 15.308 4 6 1 1056.6 410.25 158.0 20.536 5 7 1 1056.6 410.25 158.0 20.536 6 8 1 1070.0 427.75 161.0 2.305 7 9 3 1070.0 427.75 161.0 0.886 8 ... ``` In `neat`, the first soma node (whose coordinates indicate the center of the soma) should always be the root node, and should occur first in your file. Hence, the following loads correctly: ``` 1 1 1066.38 399.67 157.0 4.9215 -1 2 1 1071.3 399.67 157.0 4.9215 1 3 1 1076.22 399.67 157.0 4.9215 2 4 1 1066.5 402.83 157.0 11.494 2 5 1 1062.4 405.5 157.0 15.308 4 6 1 1056.6 410.25 158.0 20.536 5 7 1 1056.6 410.25 158.0 20.536 6 8 1 1070.0 427.75 161.0 2.305 7 9 3 1070.0 427.75 161.0 0.886 8 ... ``` Note that internally, `neat` has the three-point representation, with as center of the soma the average `x,y,z` coordinates of all soma points defined in the SWC file. Nevertheless, as `neat` represents the soma as a sphere, the three-point representation is redundant, and we only retain the node with index `1` in the standard iterators, the coordinates of which can be acces through `MorphTree.root.xyz` and the spherical radius as `MorphTree.root.R`. Note that the two other nodes of the three point representation can also be accessed explicitly by `MorphTree.__getitem__(2)` or `MorphTree.__getitem__(3)`. Finally, I have modified the docstring of the function `MorphTree.readSWCTreeFromFile()` and it should also show up on the documentation website now. It describes the accepted soma formats. | 27 July 2020, 11:09:10 UTC |
| d0721cf | Willem Wybo | 27 July 2020, 11:00:35 UTC | determine center of soma as average of cylinder endpoints in multicylinder case | 27 July 2020, 11:00:35 UTC |
| 60871b0 | Willem Wybo | 27 July 2020, 10:46:46 UTC | corrected example morphology | 27 July 2020, 10:46:46 UTC |
| 1db12ea | Willem Wybo | 27 July 2020, 10:45:59 UTC | corrected test morphologies | 27 July 2020, 10:45:59 UTC |
| c6cf676 | Willem Wybo | 27 July 2020, 10:36:01 UTC | raise error when three-point soma format is not following convention | 27 July 2020, 10:36:01 UTC |
| dff6ab2 | Willem Wybo | 27 July 2020, 09:49:40 UTC | added multicylinder soma test | 27 July 2020, 09:49:40 UTC |
| 2471df9 | Willem Wybo | 27 July 2020, 09:38:42 UTC | remove print statements | 27 July 2020, 09:38:42 UTC |
| ea39ff2 | Willem Wybo | 27 July 2020, 09:33:04 UTC | add multicylinder test morphology, bugfix in multicylinder soma reading | 27 July 2020, 09:33:04 UTC |
| a923de8 | Willem Wybo | 27 July 2020, 09:32:09 UTC | update web documentation | 27 July 2020, 09:32:09 UTC |
| c9823ec | Benjamin Ellenberger | 23 July 2020, 07:59:12 UTC | Ignore .*util.py from neat gallery | 23 July 2020, 07:59:12 UTC |
| c300486 | Willem Wybo | 23 July 2020, 06:54:32 UTC | update example README | 23 July 2020, 06:54:32 UTC |
| 344192b | Benjamin Ellenberger | 22 July 2020, 22:14:33 UTC | Move class into plot function | 22 July 2020, 22:14:33 UTC |
| a7c4405 | Benjamin Ellenberger | 22 July 2020, 22:07:35 UTC | Update sequence_discrimination.py | 22 July 2020, 22:07:35 UTC |
| 32f849f | Benjamin Ellenberger | 22 July 2020, 19:31:51 UTC | Stop script gracefully | 22 July 2020, 19:31:51 UTC |
| 28fe98e | Benjamin Ellenberger | 22 July 2020, 19:17:17 UTC | Plot on ImportError without continuing | 22 July 2020, 19:17:17 UTC |
| 166549a | Benjamin Ellenberger | 22 July 2020, 18:42:41 UTC | Add missing warnings import | 22 July 2020, 18:42:41 UTC |
| 5ec6627 | Benjamin Ellenberger | 22 July 2020, 18:42:21 UTC | Add missing warnings import | 22 July 2020, 18:42:21 UTC |
| aec008c | Benjamin Ellenberger | 22 July 2020, 18:41:53 UTC | Add missing warnings import | 22 July 2020, 18:41:53 UTC |
| 219efe4 | Benjamin Ellenberger | 22 July 2020, 18:35:55 UTC | Catch ImportError instead of ModuleNotFoundError | 22 July 2020, 18:35:55 UTC |
| 8f017d0 | Benjamin Ellenberger | 22 July 2020, 18:35:10 UTC | Catch ImportError instead of ModuleNotFoundError for all neuron imports | 22 July 2020, 18:35:10 UTC |
| 602b318 | Benjamin Ellenberger | 22 July 2020, 18:32:58 UTC | Catch ImportError instead of ModuleNotFoundError | 22 July 2020, 18:32:58 UTC |
| 9412840 | Benjamin Ellenberger | 22 July 2020, 18:23:05 UTC | Change gallery execution pattern | 22 July 2020, 18:23:05 UTC |
| 0e9782b | Benjamin Ellenberger | 22 July 2020, 18:15:29 UTC | Merge pull request #100 from WillemWybo/fix/example-images Plot saved .png for examples scripts if NEURON import fails | 22 July 2020, 18:15:29 UTC |
| d5b7020 | Willem Wybo | 22 July 2020, 08:25:28 UTC | change language level cython | 22 July 2020, 08:25:28 UTC |
| 48fd9ef | Willem Wybo | 22 July 2020, 07:51:51 UTC | plot saved .png if NEURON import fails | 22 July 2020, 07:51:51 UTC |
| 14070fa | Jakob Jordan | 21 July 2020, 09:30:43 UTC | Add MANIFEST.in to include requirements.txt and LICENCE in source dist | 21 July 2020, 09:30:43 UTC |
| 8f16077 | Jakob Jordan | 21 July 2020, 09:30:24 UTC | Fix setup.py to include headers | 21 July 2020, 09:30:24 UTC |
| c65e23d | Willem Wybo | 21 July 2020, 08:04:37 UTC | change radius name to R | 21 July 2020, 08:04:37 UTC |
| 8bdd159 | Willem Wybo | 21 July 2020, 07:52:41 UTC | change time measurement to time.process_time() in netsim.pyx and neuronmodel.pyx | 21 July 2020, 07:52:41 UTC |
| febfe6a | Willem Wybo | 21 July 2020, 07:40:18 UTC | bugfix in MorphTree._makeSomaFromCylinders | 21 July 2020, 07:40:18 UTC |
| e70cf9c | Willem Wybo | 21 July 2020, 07:17:22 UTC | Merge pull request #96 from sunzhenyang2018/new_branch changed 'and' and 'or' to '&&' and '||' in NETC.cc | 21 July 2020, 07:17:22 UTC |
| 675472a | Jack Sun | 20 July 2020, 17:40:12 UTC | mised one 'and' on line 804, now changed to '&&' | 20 July 2020, 17:40:12 UTC |
| 8b5c2e4 | Jack Sun | 20 July 2020, 17:10:56 UTC | changed 'and' and 'or' to '&&' and '||' in NETC.cc | 20 July 2020, 17:10:56 UTC |
| 5341b92 | Jakob Jordan | 20 July 2020, 15:13:31 UTC | Fix reading of version number, ship __version__.py with package | 20 July 2020, 15:20:35 UTC |
| d70e9df | Jakob Jordan | 20 July 2020, 10:41:20 UTC | Adapt package name, fix README to render on pypi, update installation instructions | 20 July 2020, 10:43:54 UTC |
| 3a7fab0 | Willem Wybo | 20 July 2020, 08:28:15 UTC | Merge pull request #92 from WillemWybo/fix/compile-issue-virtual-function-declarations Fix return type of virtual functions | 20 July 2020, 08:28:15 UTC |
| df5bc1f | Willem Wybo | 20 July 2020, 08:26:58 UTC | Merge pull request #93 from WillemWybo/enh/copy-mod-files-compilechannels Modify compilechannels to *also* copy mod files in target directory to install location | 20 July 2020, 08:26:58 UTC |
| 7b91392 | Willem Wybo | 20 July 2020, 08:22:39 UTC | fix return type of virtual functions | 20 July 2020, 08:22:39 UTC |
| 5bf70da | Willem Wybo | 20 July 2020, 08:11:58 UTC | remove empty lines | 20 July 2020, 08:11:58 UTC |
| aec950c | Benjamin Ellenberger | 16 July 2020, 14:00:52 UTC | Copy documentation from wrapped function | 16 July 2020, 14:00:52 UTC |
| a2dee21 | Willem Wybo | 14 July 2020, 10:36:23 UTC | Merge pull request #90 from WillemWybo/enh/copy-mod-files-compilechannels Enh/copy mod files compilechannels | 14 July 2020, 10:36:23 UTC |
| 1b55e4c | Willem Wybo | 14 July 2020, 10:35:03 UTC | add functionality to copy mod-files in target dir to install location with compilechannels | 14 July 2020, 10:35:03 UTC |
| 32a8f09 | Willem Wybo | 14 July 2020, 10:26:30 UTC | bugfix to also compile default mech when compilechannels argument is not 'default' | 14 July 2020, 10:26:30 UTC |
| e951f1a | Willem Wybo | 09 June 2020, 08:55:24 UTC | Merge pull request #88 from jakobj/enh/install-without-req-numpy Do not require numpy prior to installation | 09 June 2020, 08:55:24 UTC |
| 4e32d7a | Willem Wybo | 09 June 2020, 08:42:37 UTC | fix setup.py | 09 June 2020, 08:42:37 UTC |
| 995e44c | Jakob Jordan | 05 June 2020, 14:50:51 UTC | Do not require numpy prior to installation | 05 June 2020, 14:50:51 UTC |
| be791e9 | Willem Wybo | 04 June 2020, 09:04:49 UTC | Merge pull request #77 from unibe-cns/fix/setuppy-authors Update authors and add fields in setup.py | 04 June 2020, 09:04:49 UTC |
| e0e7a73 | Willem Wybo | 04 June 2020, 08:59:38 UTC | Merge branch 'master' into fix/setuppy-authors | 04 June 2020, 08:59:38 UTC |
