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removed 'basestring' Co-authored-by: Dilawar Singh <[email protected]>
* not a bug. * Turned scripts recieved from harsha into a test case. open #402. * Renamed wrapper.Neutral to __Wrapper__. With new API, this functionality can be built in. * closes #401 * Fixed another bug: -DWTIH_BOOST=ON could not override GSL after WITH_GSL was cached by cmake. Ie, if once built with default options, there was no way to use BOOST without cleaning up the old build completely. * check is made if solver has space while reading/writing SBML files,small change to port the code to py3 * Squashed commit of the following: commit b313f8d72537b6d8218857d0f0ef81268bc05f81 Author: Dilawar Singh <[email protected]> Date: Sun Apr 12 19:03:24 2020 +0530 moved __init__.py and moose.py to pybind folder. commit 77afafd49dc6e99b1c00c060b00181d1190e1c7b Author: Dilawar Singh <[email protected]> Date: Sun Apr 12 18:03:28 2020 +0530 Use not gui backend. commit 6ad911c73c5f9d01846c5869263c12ee82e1bdf8 Author: Dilawar Singh <[email protected]> Date: Sun Apr 12 13:23:33 2020 +0530 Variable and Cinfo need not be exposed. commit 5fec8497593a9d77b5ed5832336747c6cd8fb33c Author: Dilawar Singh <[email protected]> Date: Sun Apr 12 12:27:13 2020 +0530 Create moose element from vec and field. commit ab3d85dc0f023a4cda2a9cf7ecfae97d860567b2 Author: Dilawar Singh <[email protected]> Date: Sun Apr 12 11:21:21 2020 +0530 Added support for ["string", double] valueFinfoItem. commit 9c967c02abd565c90d452d200f778e1d2ed78349 Author: Anushree Narjala <[email protected]> Date: Sun Apr 12 10:03:17 2020 +0530 seed is an int and can't be empty. commit cc7ea95 Author: Dilawar Singh <[email protected]> Date: Sat Apr 11 15:46:11 2020 +0530 This is a really good commit. `.num` is supported now. commit 2185c65 Author: Dilawar Singh <[email protected]> Date: Sat Apr 11 12:28:39 2020 +0530 Added doxygen target. commit 32c3fc7 Author: Dilawar Singh <[email protected]> Date: Fri Apr 10 13:09:09 2020 +0530 Finfo is also vectorised. commit d716124 Author: Dilawar Singh <[email protected]> Date: Fri Apr 10 12:03:53 2020 +0530 Negative indexing is allowed. Fixes one more moose-examples neuroml/LIF/twoLIFxml_firing.py commit a2d6a38 Author: Dilawar Singh <[email protected]> Date: Thu Apr 9 21:07:04 2020 +0530 Use old PyRun code. Pybind11 does not have subterpreter support. commit 2587c0d Author: Dilawar Singh <[email protected]> Date: Thu Apr 9 13:58:16 2020 +0530 Added a test for testing pyrun. commit f3a4925 Author: Dilawar Singh <[email protected]> Date: Thu Apr 9 11:25:11 2020 +0530 when `-DWITH_BOOST=ON` is passed to cmake, it now overrides `WITH_GSL` option. Also fixes build failure. commit 2127c3a Author: Dilawar Singh <[email protected]> Date: Thu Apr 9 11:15:01 2020 +0530 Fixes https://gitlab.com/dilawar/moose-core/-/issues/7 commit 31f2b8f Author: Dilawar Singh <[email protected]> Date: Wed Apr 8 23:16:37 2020 +0530 If Function is not valid_, return quietly. commit b91a0ef Author: Dilawar Singh <[email protected]> Date: Wed Apr 8 22:25:06 2020 +0530 All tests are passing now. commit 0ce71ac Author: Dilawar Singh <[email protected]> Date: Wed Apr 8 20:13:39 2020 +0530 genesis and kkit are reverted back to master. commit 6535c46 Author: Dilawar Singh <[email protected]> Date: Wed Apr 8 19:03:13 2020 +0530 isA is working just fine. commit bf118f4 Author: Dilawar Singh <[email protected]> Date: Wed Apr 8 14:18:23 2020 +0530 We can now assign moose.vec to a field which takes Id. refactoring. int -> double, bool -> (int, double) coercing is allowed. Fixed script /home1/dilawars/Work.HG/GITLAB/moose-examples/snippets/interpol2d.py in https://gitlab.com/dilawar/moose-examples/-/issues/1 commit fb57aaf Author: Dilawar Singh <[email protected]> Date: Wed Apr 8 13:21:19 2020 +0530 overloading template function is not so straight-forward when typecasting can happen by itslf e.g. int and unsigned int. commit 22aeb43 Author: Dilawar Singh <[email protected]> Date: Wed Apr 8 09:52:57 2020 +0530 moose.element return single ObjId and not vec as I mistakenly assumed. commit ea81f1c Author: Dilawar Singh <[email protected]> Date: Tue Apr 7 21:45:13 2020 +0530 Vectorize function later. commit 4624651 Author: Dilawar Singh <[email protected]> Date: Tue Apr 7 20:48:47 2020 +0530 name, path, and parent of moose.vec are not vectorised. commit 6126a64 Author: Dilawar Singh <[email protected]> Date: Tue Apr 7 19:20:28 2020 +0530 snippets/savemodel.py is causing problem now. commit 15eae1d Author: Dilawar Singh <[email protected]> Date: Tue Apr 7 18:08:37 2020 +0530 vec values are returned as numpy array. commit cc89202 Author: Dilawar Singh <[email protected]> Date: Tue Apr 7 16:55:00 2020 +0530 Default parameters in connect is now working. First argument is not needed if it is a class member function. commit 8092a8e Author: Dilawar Singh <[email protected]> Date: Tue Apr 7 16:19:16 2020 +0530 If a Shell function retuns Id, wrap it in a MooseVec. The current API has this behaviour. commit 8ca430c Author: Dilawar Singh <[email protected]> Date: Tue Apr 7 13:54:52 2020 +0530 TODO: Id should be wrapped as moose.vec commit d6552e6 Author: Dilawar Singh <[email protected]> Date: Tue Apr 7 12:05:31 2020 +0530 Passes snippets/synapse.py https://gitlab.com/dilawar/moose-examples/-/issues/1 commit 3ea0a66 Author: Dilawar Singh <[email protected]> Date: Tue Apr 7 11:23:27 2020 +0530 Support more return types. commit 0862930 Author: Dilawar Singh <[email protected]> Date: Tue Apr 7 10:44:35 2020 +0530 MooseVec can now handle fieldElement as well. commit 1d40e74 Author: Dilawar Singh <[email protected]> Date: Mon Apr 6 21:03:58 2020 +0530 Needs some major overhaul of API. commit 3116b05 Author: Dilawar Singh <[email protected]> Date: Mon Apr 6 15:04:32 2020 +0530 Removed melement. commit 8baffdc Author: Dilawar Singh <[email protected]> Date: Mon Apr 6 15:00:59 2020 +0530 Support more fieldType. Fixes one more failing script in moose examples. commit b3a3e84 Author: Dilawar Singh <[email protected]> Date: Mon Apr 6 14:01:28 2020 +0530 Time to run examples now. commit 731fc47 Author: Dilawar Singh <[email protected]> Date: Mon Apr 6 13:44:38 2020 +0530 type checking has been moved to C++ code. its bit tricky here and not as readable as it should be. May be I can leave this at the python level. commit 790efdf Author: Dilawar Singh <[email protected]> Date: Mon Apr 6 13:24:30 2020 +0530 Some more progress. Getting a bit more faster than the current API. commit 4e24621 Author: Dilawar Singh <[email protected]> Date: Mon Apr 6 13:17:18 2020 +0530 Overloaded funtions. commit bc95f4d Author: Dilawar Singh <[email protected]> Date: Mon Apr 6 12:25:23 2020 +0530 Enabled helper functions. commit aeecc41 Author: Dilawar Singh <[email protected]> Date: Mon Apr 6 00:17:06 2020 +0530 beat the old api in microbenchmarks as well. commit 6e88eff Author: Dilawar Singh <[email protected]> Date: Sun Apr 5 23:56:00 2020 +0530 minor tweaks. commit 1dd9390 Author: Dilawar Singh <[email protected]> Date: Sun Apr 5 23:46:37 2020 +0530 moose.create is fast but moose.delete is bit slow. commit 0eda1b7 Author: Dilawar Singh <[email protected]> Date: Sun Apr 5 22:39:37 2020 +0530 forward declaration and compile fixes. commit a3bdd69 Author: Dilawar Singh <[email protected]> Date: Sun Apr 5 20:05:43 2020 +0530 Added benchmark file. commit e294eea Author: Dilawar Singh <[email protected]> Date: Sun Apr 5 19:55:01 2020 +0530 added micro benchmarks. commit 5979dc4 Author: Dilawar Singh <[email protected]> Date: Sat Apr 4 23:25:28 2020 +0530 Added documentations. commit 56c12f4 Author: Dilawar Singh <[email protected]> Date: Sat Apr 4 22:21:40 2020 +0530 All tests are passing.. needs to add some tests.. commit f039fad Author: Dilawar Singh <[email protected]> Date: Sat Apr 4 21:58:28 2020 +0530 _cmoose to _moose. commit 9543258 Author: Dilawar Singh <[email protected]> Date: Sat Apr 4 19:57:21 2020 +0530 Needs to fix some more API issues. commit 4d6c147 Author: Dilawar Singh <[email protected]> Date: Sat Apr 4 17:49:15 2020 +0530 Added version 2.5 commit f0efd21 Author: Dilawar Singh <[email protected]> Date: Sat Apr 4 17:41:41 2020 +0530 Removed a broken test and renamed one. The namedvars tests is moved to fixme (not supported). commit cd3dc5a Author: Dilawar Singh <[email protected]> Date: Sat Apr 4 12:11:59 2020 +0530 Needs final touch. commit 5262dc4 Author: Dilawar Singh <[email protected]> Date: Sat Apr 4 12:03:56 2020 +0530 Added one more missing attribute. commit 7757643 Author: Dilawar Singh <[email protected]> Date: Sat Apr 4 11:25:53 2020 +0530 test commit [skip ci] commit cb8a970 Author: Dilawar Singh <[email protected]> Date: Sat Apr 4 10:28:06 2020 +0530 old test is back. commit 06e3357 Author: Dilawar Singh <[email protected]> Date: Sat Apr 4 10:24:53 2020 +0530 Fixed the issue with isinstance(x, moose.CubeMesh). Now it is working fine. commit 685ab75 Author: Dilawar Singh <[email protected]> Date: Sat Apr 4 07:26:24 2020 +0530 One more test is passing. commit 6188e09 Author: Dilawar Singh <[email protected]> Date: Sat Apr 4 07:25:25 2020 +0530 Restored old values in the test. commit 349f8ea Author: Dilawar Singh <[email protected]> Date: Sat Apr 4 05:55:15 2020 +0530 fixes to one more tests. commit c90986a Author: Dilawar Singh <[email protected]> Date: Sat Apr 4 05:42:22 2020 +0530 Now do a local testing. commit e6a6575 Author: Dilawar Singh <[email protected]> Date: Sat Apr 4 05:37:26 2020 +0530 numerical assertion of oscillatory tests are hard. commit 5af49e9 Author: Dilawar Singh <[email protected]> Date: Sat Apr 4 05:26:34 2020 +0530 Almost all tests are passing. commit d7f03bd Author: Dilawar Singh <[email protected]> Date: Sat Apr 4 04:54:44 2020 +0530 remove 'value' attribute from the ObjId, it was conflicting with MString 'value'. commit ce79591 Author: Dilawar Singh <[email protected]> Date: Sat Apr 4 04:43:36 2020 +0530 Needs to fix doc. commit 113dddc Author: Dilawar Singh <[email protected]> Date: Sat Apr 4 04:36:02 2020 +0530 more tests are passing. all test_Xreacs are passing now. commit 29ff41c Author: Dilawar Singh <[email protected]> Date: Sat Apr 4 04:31:33 2020 +0530 Use ObjId instread of Id in buildMeshJunction. commit 33e9591 Author: Dilawar Singh <[email protected]> Date: Sat Apr 4 04:27:38 2020 +0530 Passing ObjId as Id is creating trouble. commit 537779e Author: Dilawar Singh <[email protected]> Date: Sat Apr 4 03:59:30 2020 +0530 one more test passes. commit 650309a Author: Dilawar Singh <[email protected]> Date: Sat Apr 4 03:05:28 2020 +0530 delete works. commit b13e051 Author: Dilawar Singh <[email protected]> Date: Sat Apr 4 02:13:31 2020 +0530 Some more tests [skip ci] commit e518d35 Author: Dilawar Singh <[email protected]> Date: Sat Apr 4 01:42:15 2020 +0530 One more test is passed. commit c783578 Author: Dilawar Singh <[email protected]> Date: Sat Apr 4 01:37:24 2020 +0530 isinstance support is added. commit 2a28f9a Author: Dilawar Singh <[email protected]> Date: Fri Apr 3 22:15:46 2020 +0530 Added tests to normalizepath. commit 4c2086a Author: Dilawar Singh <[email protected]> Date: Fri Apr 3 22:08:30 2020 +0530 Global random number generator is moved from basecode to randnum. commit 6a2b7b7 Author: Dilawar Singh <[email protected]> Date: Fri Apr 3 20:09:21 2020 +0530 Couple of seg-faults to take care of. commit 8a90db2 Author: Dilawar Singh <[email protected]> Date: Fri Apr 3 18:27:52 2020 +0530 Fixed one more test. commit 1798a1e Author: Dilawar Singh <[email protected]> Date: Fri Apr 3 14:18:47 2020 +0530 Need to fix rdesignuer now. commit 0be10c0 Author: Dilawar Singh <[email protected]> Date: Fri Apr 3 12:59:16 2020 +0530 Finfo can also return .vec. commit 226d616 Author: Dilawar Singh <[email protected]> Date: Fri Apr 3 12:35:32 2020 +0530 Function is also fixed. commit b68a97b Author: Dilawar Singh <[email protected]> Date: Fri Apr 3 12:22:29 2020 +0530 SynapseTest is also passing. commit 8f2a039 Author: Dilawar Singh <[email protected]> Date: Fri Apr 3 11:38:20 2020 +0530 Fixes all the c++ tests commit 173b9d2 Author: Dilawar Singh <[email protected]> Date: Fri Apr 3 11:28:47 2020 +0530 ObjId.vec create a vec on the fly. commit e71fea0 Author: Dilawar Singh <[email protected]> Date: Thu Apr 2 22:39:02 2020 +0530 Same problem on OSX. One more test is failing. commit 47e25f9 Author: Dilawar Singh <[email protected]> Date: Thu Apr 2 22:08:41 2020 +0530 Some more fixes. moose.element is not honoring dataIndex. commit 9de507a Author: Dilawar Singh <[email protected]> Date: Thu Apr 2 20:17:29 2020 +0530 bebug vec and connection list. commit d7f0a26 Author: Dilawar Singh <[email protected]> Date: Thu Apr 2 19:22:00 2020 +0530 Refactoring. commit 2221410 Author: Dilawar Singh <[email protected]> Date: Thu Apr 2 16:17:48 2020 +0530 Added .clang-format file. commit 7a8437d Author: Dilawar Singh <[email protected]> Date: Thu Apr 2 12:44:32 2020 +0530 more progress. Lets have lunch first now. commit 0ed8933 Author: Dilawar Singh <[email protected]> Date: Thu Apr 2 12:25:44 2020 +0530 Fix Xreacs later. commit 04d4d2f Author: Dilawar Singh <[email protected]> Date: Thu Apr 2 11:52:19 2020 +0530 Refactoring. If Finfo* is passed, no need to pass rttitype and fname. We can get these values from Finfo. commit 77cc0b1 Author: Dilawar Singh <[email protected]> Date: Wed Apr 1 21:21:06 2020 +0530 refacorted codebase... commit 52cfdf7 Author: Dilawar Singh <[email protected]> Date: Wed Apr 1 21:06:13 2020 +0530 Added extra header for Finfo ... commit b16dd1c Author: Dilawar Singh <[email protected]> Date: Wed Apr 1 19:58:56 2020 +0530 Needs to implement LookupFinfo set. commit 8199fc0 Author: Dilawar Singh <[email protected]> Date: Wed Apr 1 18:48:25 2020 +0530 Disable pybind11. commit 5c25dad Author: Dilawar Singh <[email protected]> Date: Wed Apr 1 18:48:02 2020 +0530 One more tests seem to pass. commit 40a4559 Author: Dilawar Singh <[email protected]> Date: Wed Apr 1 18:22:52 2020 +0530 Some more fixes. commit dd9b50e Author: Dilawar Singh <[email protected]> Date: Wed Apr 1 17:59:50 2020 +0530 Perfect. One more test passes. commit fec019b Author: Dilawar Singh <[email protected]> Date: Wed Apr 1 15:41:22 2020 +0530 Refactoring and some more generic programming. commit 9eb2308 Author: Dilawar Singh <[email protected]> Date: Tue Mar 31 20:48:57 2020 +0530 small fixes. Changes in API requires .id . commit 7de3228 Author: Dilawar Singh <[email protected]> Date: Tue Mar 31 19:13:51 2020 +0530 Minor tweak to a test. commit c541b91 Author: Dilawar Singh <[email protected]> Date: Tue Mar 31 19:08:36 2020 +0530 One more test passed. commit 5cc3d3b Merge: ce579ac 1abb6f1 Author: Dilawar Singh <[email protected]> Date: Tue Mar 31 18:59:23 2020 +0530 Merge branch 'pybind11_shell' into temp commit ce579ac Author: Dilawar Singh <[email protected]> Date: Tue Mar 31 18:58:59 2020 +0530 renmaed. commit 16bbc3e Author: Dilawar Singh <[email protected]> Date: Tue Mar 31 18:20:55 2020 +0530 phew. I made a boo boo before. commit 1abb6f1 Merge: 24df86a fa06c38 Author: Dilawar Singh <[email protected]> Date: Tue Mar 31 02:24:30 2020 +0530 Merge branch 'pybind11_shell' of gitlab.com:dilawar/moose-core into pybind11_shell commit fa06c38 Author: Dilawar Singh <[email protected]> Date: Tue Mar 31 02:14:22 2020 +0530 Id and ObjId are not playing well together... commit 48832b1 Author: Dilawar Singh <[email protected]> Date: Tue Mar 31 01:30:34 2020 +0530 test_synchan is a good example; possible we should return moose.vec there. commit 8667c13 Author: Dilawar Singh <[email protected]> Date: Tue Mar 31 01:28:02 2020 +0530 temp commit. commit 24df86a Author: Dilawar Singh <[email protected]> Date: Mon Mar 30 23:39:46 2020 +0530 Temp commit. Exposing only Id. commit 448b8b5 Author: Dilawar Singh <[email protected]> Date: Mon Mar 30 23:14:51 2020 +0530 more tests are passing... commit d1b4990 Author: Dilawar Singh <[email protected]> Date: Mon Mar 30 20:35:39 2020 +0530 Need to find a solution.. commit 6b5082b Author: Dilawar Singh <[email protected]> Date: Mon Mar 30 19:05:44 2020 +0530 Refactoring and have a working moose.vec API. commit 98d8d34 Author: Dilawar Singh <[email protected]> Date: Mon Mar 30 18:05:07 2020 +0530 [skip ci] needs tweaking in the API. commit 0f7929c Author: Dilawar Singh <[email protected]> Date: Mon Mar 30 14:40:37 2020 +0530 Support vec. But first need a nap. commit 93d6e83 Author: Dilawar Singh <[email protected]> Date: Mon Mar 30 13:33:05 2020 +0530 refactoring. commit fd03015 Author: Dilawar Singh <[email protected]> Date: Mon Mar 30 13:17:31 2020 +0530 random works. commit fc34547 Author: Dilawar Singh <[email protected]> Date: Mon Mar 30 11:49:00 2020 +0530 Need to polish the API. commit 6af0f2c Author: Dilawar Singh <[email protected]> Date: Mon Mar 30 11:00:03 2020 +0530 Lets move to DestFinfo. commit 476d700 Author: Dilawar Singh <[email protected]> Date: Mon Mar 30 07:53:31 2020 +0530 Return type. commit 778208a Merge: dab5af4 dd65791 Author: Dilawar Singh <[email protected]> Date: Mon Mar 30 07:42:04 2020 +0530 Merge branch 'pybind11_shell' of gitlab.com:dilawar/moose-core into pybind11_shell commit dd65791 Author: Dilawar Singh <[email protected]> Date: Mon Mar 30 06:54:42 2020 +0530 Updated [skip ci] commit 76ec2a1 Author: Dilawar Singh <[email protected]> Date: Sun Mar 29 23:00:02 2020 +0530 [skip ci] some more changes. commit c4d7bc6 Author: Dilawar Singh <[email protected]> Date: Sun Mar 29 22:24:57 2020 +0530 We go both API integrated. commit f0ac785 Author: Dilawar Singh <[email protected]> Date: Sun Mar 29 21:48:18 2020 +0530 LookupField is a function. commit aee928e Author: Dilawar Singh <[email protected]> Date: Sun Mar 29 21:11:48 2020 +0530 Do the rest tomorrow. commit e118e12 Author: Dilawar Singh <[email protected]> Date: Sun Mar 29 20:45:21 2020 +0530 Retuning binding to std::function which return the Finfo value. commit dab5af4 Author: Dilawar Singh <[email protected]> Date: Sun Mar 29 18:01:12 2020 +0530 isA is method. Time to make it a subscriptable dictionary. commit c7a7b24 Author: Dilawar Singh <[email protected]> Date: Sun Mar 29 15:34:42 2020 +0530 Lets handle LookupField::set and get. commit a06e478 Author: Dilawar Singh <[email protected]> Date: Sun Mar 29 01:13:46 2020 +0530 Deal with it tomorrow. commit bb1cae5 Author: Dilawar Singh <[email protected]> Date: Sun Mar 29 00:28:22 2020 +0530 Getting there. [skip ci] commit 5cccf8b Author: Dilawar Singh <[email protected]> Date: Sat Mar 28 22:33:21 2020 +0530 Some refactoring. Back to same functionality [skip ci]. commit a979de6 Author: Dilawar Singh <[email protected]> Date: Sat Mar 28 20:46:01 2020 +0530 Updated a bit more .. commit b43c617 Author: Dilawar Singh <[email protected]> Date: Sat Mar 28 19:47:58 2020 +0530 New API works fantastic. commit 0deb291 Author: Dilawar Singh <[email protected]> Date: Sat Mar 28 19:40:19 2020 +0530 Incremental change. Dynamic attributes. commit 7f2539c Author: Dilawar Singh <[email protected]> Date: Sat Mar 28 19:31:31 2020 +0530 Subclassing _ObjId now. commit 0f64cd0 Author: Dilawar Singh <[email protected]> Date: Sat Mar 28 18:12:57 2020 +0530 Dynamic attributes are needed now. commit eff08b2 Author: Dilawar Singh <[email protected]> Date: Sat Mar 28 16:16:13 2020 +0530 All test passes. Needs to work on the API now. commit 8791df7 Author: Dilawar Singh <[email protected]> Date: Sat Mar 28 15:40:35 2020 +0530 Blazingly fast. commit 070f735 Author: Dilawar Singh <[email protected]> Date: Sat Mar 28 14:06:47 2020 +0530 Perfect. The base API works now. Not time to do a profiling. commit 07a1348 Author: Dilawar Singh <[email protected]> Date: Sat Mar 28 00:28:22 2020 +0530 This is for tomorow. commit 72f7b62 Author: Dilawar Singh <[email protected]> Date: Fri Mar 27 21:43:33 2020 +0530 Work from home. commit 4ea29e9 Author: Dilawar Singh <[email protected]> Date: Fri Mar 27 20:32:19 2020 +0530 May be later. commit eff6f90 Author: Dilawar Singh <[email protected]> Date: Fri Mar 27 17:57:40 2020 +0530 Not sure about the testKsolve.cpp tests. commit bef104c Author: Dilawar Singh <[email protected]> Date: Fri Mar 27 17:11:34 2020 +0530 Do testing with master branch. commit 0078af1 Author: Dilawar Singh <[email protected]> Date: Fri Mar 27 14:45:40 2020 +0530 get can not overloaded pretty well. Use different name for getting different value. It is verbose now but we can override later. commit 915e10f Merge: 911bd03 bf2d609 Author: Dilawar Singh <[email protected]> Date: Fri Mar 27 13:56:46 2020 +0530 Merge branch 'pybind11_shell' of gitlab.com:dilawar/moose-core into pybind11_shell commit bf2d609 Author: Dilawar Singh <[email protected]> Date: Fri Mar 27 14:11:18 2020 +0530 add test function. commit 911bd03 Author: Dilawar Singh <[email protected]> Date: Fri Mar 27 13:56:12 2020 +0530 local changes. commit cc7144f Author: Dilawar Singh <[email protected]> Date: Fri Mar 27 13:50:40 2020 +0530 Move to gulgula. commit d41e7eb Author: Dilawar Singh <[email protected]> Date: Fri Mar 27 04:18:44 2020 +0530 Allmost there. commit d913ceb Author: Dilawar Singh <[email protected]> Date: Fri Mar 27 01:50:18 2020 +0530 addMsg -> connect . commit 8793d33 Author: Dilawar Singh <[email protected]> Date: Fri Mar 27 01:10:24 2020 +0530 get/set are on ObjId . commit d99115c Author: Dilawar Singh <[email protected]> Date: Fri Mar 27 00:47:20 2020 +0530 Ok. Vector and numpy are working. commit 2f3bc04 Author: Dilawar Singh <[email protected]> Date: Thu Mar 26 23:02:03 2020 +0530 move to bebinca for fast compilation. commit a94fec9 Author: Dilawar Singh <[email protected]> Date: Thu Mar 26 18:29:50 2020 +0530 children and parent is not working. commit 756ec3a Author: Dilawar Singh <[email protected]> Date: Wed Mar 25 14:53:17 2020 +0530 Some more fixes. It will be too much debugging to get it right. commit 77451f1 Author: Dilawar Singh <[email protected]> Date: Tue Mar 24 15:07:09 2020 +0530 All the learning experience is over. Pybind11 is great. commit 6edda7a Author: Dilawar Singh <[email protected]> Date: Tue Mar 24 00:55:13 2020 +0530 Add a bit more fields. commit e32c468 Author: Dilawar Singh <[email protected]> Date: Mon Mar 23 23:30:19 2020 +0530 I can complete this API tomorrow. commit 7aaddf7 Author: Dilawar Singh <[email protected]> Date: Mon Mar 23 22:54:35 2020 +0530 added more functions [skip ci] commit 7f1b709 Author: Dilawar Singh <[email protected]> Date: Mon Mar 23 16:38:34 2020 +0530 disable build for now on gitlab ci commit ae2739d Author: Dilawar Singh <[email protected]> Date: Mon Mar 23 15:05:22 2020 +0530 pybind11 module is named _cmoose and it different from _moose. commit 0c33684 Author: Dilawar Singh <[email protected]> Date: Mon Mar 23 14:45:32 2020 +0530 I got wildcardFind to function. commit 65b307c Author: Dilawar Singh <[email protected]> Date: Mon Mar 23 13:33:22 2020 +0530 Fixed the bug I caused by using smart pointer. I am so silly... commit fe596e3 Merge: d5d29bb f4070da Author: Dilawar Singh <[email protected]> Date: Mon Mar 23 12:45:01 2020 +0530 Merge branch 'issue_397' of gitlab.com:dilawar/moose-core into pybind11 commit d5d29bb Author: Dilawar Singh <[email protected]> Date: Sun Mar 22 23:12:58 2020 +0530 Time to support / in path. commit 270ea8c Author: Dilawar Singh <[email protected]> Date: Sun Mar 22 22:50:21 2020 +0530 empty element() commit a1eed3a Author: Dilawar Singh <[email protected]> Date: Sun Mar 22 22:39:55 2020 +0530 temp commit. commit a70b5fe Author: Dilawar Singh <[email protected]> Date: Sun Mar 22 15:44:56 2020 +0530 Great. Lets try cython as well. commit 038490f Author: Dilawar Singh <[email protected]> Date: Sun Mar 22 15:44:27 2020 +0530 Try cython now. commit 8bbf900 Author: Dilawar Singh <[email protected]> Date: Sun Mar 22 13:43:02 2020 +0530 _moose goes to python/moose directory. commit 014bde2 Merge: 8f60899 ad58dc5 Author: Dilawar Singh <[email protected]> Date: Sun Mar 22 13:18:20 2020 +0530 Merge branch 'issue_397' into pybind11 commit f4070da Merge: ad58dc5 5e660e9 Author: Dilawar Singh <[email protected]> Date: Sat Mar 21 22:21:16 2020 +0530 Merge branch 'refactoring' into issue_397 commit 5e660e9 Author: dilawars <[email protected]> Date: Sat Mar 21 21:24:21 2020 +0530 include cmath in Pool.cpp as well. Failed compilation with gcc5.3 commit ad58dc5 Author: dilawars <[email protected]> Date: Sat Mar 21 21:24:21 2020 +0530 include cmath in Pool.cpp as well. Failed compilation with gcc5.3 commit c4d55aa Author: Dilawar Singh <[email protected]> Date: Sat Mar 21 15:45:16 2020 +0530 Minor cleanup in macros and loggers. numCores now use thread library to determine number of available threads. commit f8dcb12 Author: Dilawar Singh <[email protected]> Date: Sat Mar 21 15:32:02 2020 +0530 NUMPY is essential dependency; therefore numpy code is no longer included conditionally. USE_NUMPY is implied and have been removed from cmake. commit 9ef658e Author: Dilawar Singh <[email protected]> Date: Sat Mar 21 15:15:43 2020 +0530 Fix to #397 commit 8f60899 Author: Dilawar Singh <[email protected]> Date: Tue Mar 17 18:27:54 2020 +0530 Perfecto. Create works. commit aa95a0c Author: Dilawar Singh <[email protected]> Date: Sun Mar 15 22:10:07 2020 +0530 pybind11 bindings. commit da9d1d9 Merge: 0e85a57 36c0026 Author: Dilawar Singh <[email protected]> Date: Sun Mar 15 15:40:06 2020 +0530 Merge commit '36c0026886c70e39c505f8715e65a7c3cf1e6ade' as 'external/pybind11' commit 36c0026 Author: Dilawar Singh <[email protected]> Date: Sun Mar 15 15:40:06 2020 +0530 Squashed 'external/pybind11/' content from commit 4f72ef846 git-subtree-dir: external/pybind11 git-subtree-split: 4f72ef846fe8453596230ac285eeaa0ce3278bb4 * Minor fixes to pybind11. * Fix #409 When `moose.Function('abc')` is created, set expression to "0". Expression is not empty by default. This is to mimic the old behaviour. Note that at this point, derivative is not defined and is `nan` (old behaviour: derivative is 0.0). * Ready for a draft PR and initial disucssion. * Return numpy array instead of vector. Probably not the most memory efficient way for returning vector<double> but since most pyMOOSE scripts assume that returned data is numpy array, we return the numpy array. TODO: benchmarking. * Fixed: moose.le can caused segfault when used on moose.vec This also fixes script mgblock.py BhallaLab/moose-examples#71 * Fixed: moose.le can caused segfault when used on moose.vec This also fixes script mgblock.py BhallaLab/moose-examples#71 * removed mkdoc.py from pybind11. * Fixed a pylint error as well python2/python3 compatibility * wildcard -> reacSystemPath Stoic::path is depreacted bcause it collides with Neutral::path. * Fixed another set. * Travis fix: Install pytest on OSX as well. * fix gitlab pipeline install pytest * isinstance is replace to isA added to this, validation.py: error msg is sent back, writeKkit.py: while writting genesis file if any object is not written then errorlog is send/printed which is usefull durning command line * fix test py_run. Relax the matching to 90% using difflib (from 95%). * grenerate documentation on the fly. * Work in progress: __doc__ string from cWork in progress: __doc__ string from cWork in progress: __doc__ string from cWork in progress: __doc__ string from c++ * Keeping the C++ type and Python's type name same. * Cleanup * pydoc support moved moose.py content to __init__.py. This way pydoc works great also fixed travis build. * moose.doc is working now. _moose.generateDoc is the underlying function. Needs to cleanup documentation a bit now. Fixed regression. * update to docs Disabled C++ signature in Python documentations. Added docstring to __init__.py * more docstring are added [skip ci] * Added datetime and other string to version_info. * All functions have docstring. * loadmodel docstring is added. * temp commit. * showmsg is ported to c++. * added more docstring and moved some functions to public api. * Merged hrani changes and mine from new bindings. removed 'basestring' * # This is a combination of 2 commits. # This is the 1st commit message: python2 support. Added python2 support as well. It will be easy to remove later. _moose.element is a good way to convert string/objid/id to melement. # This is the commit message #2: writeKkit * python2 support. Added python2 support as well. It will be easy to remove later. _moose.element is a good way to convert string/objid/id to melement. writeKkit python2 support. Added python2 support as well. It will be easy to remove later. python2 support. Added python2 support as well. It will be easy to remove later. _moose.element is a good way to convert string/objid/id to melement. writeKkit python2 support. Added python2 support as well. It will be easy to remove later. * basestring -> str * fixes to `pip install` Added missing folders. * Fixed pylint error. * moose.getField accepts two argument instead of 3. Updated rmogul.py file. * fix: compiles with clang++ typeid(X) when X is an incomplete type is not supported by C++ standard. Suprisingly this was compiling fine with gcc but not with clang++. version is set to 3.2.0.dev$(today) * travis fixes: OSX PyRun tests compares last 50 lines rather than whole text. This way we can ignore lines with different timestamp. * builds on osx locally. * tests passes with 3.8 as well. * On OSX, stream does not flush properly? Using difflib to test the ratio between got and expected string. * flush the streams before calling tests... * Don't run the trvais/osx Not sure why but only on travis+OSX, pyrun test does not pass. It fails because whole buffer is not dumped to the tty. * Fixes to pyrun tests. * Time to post the API. * listmsg has been moved to C++. * docstring to writeNML2 * Fixed typo in docstring. Ready to be reviewed. * showfield and showfields are both supported. `moose.showfield` is an alias for `moose.showfields`. * Added back moose.ce Co-authored-by: Dilawar Singh <[email protected]> Co-authored-by: HarshaRani <[email protected]> Co-authored-by: Anushree Narjala <[email protected]>
… assign value. Unable to build chem model
* not a bug. * Turned scripts recieved from harsha into a test case. open #402. * Renamed wrapper.Neutral to __Wrapper__. With new API, this functionality can be built in. * closes #401 * Fixed another bug: -DWTIH_BOOST=ON could not override GSL after WITH_GSL was cached by cmake. Ie, if once built with default options, there was no way to use BOOST without cleaning up the old build completely. * check is made if solver has space while reading/writing SBML files,small change to port the code to py3 * Squashed commit of the following: commit b313f8d72537b6d8218857d0f0ef81268bc05f81 Author: Dilawar Singh <[email protected]> Date: Sun Apr 12 19:03:24 2020 +0530 moved __init__.py and moose.py to pybind folder. commit 77afafd49dc6e99b1c00c060b00181d1190e1c7b Author: Dilawar Singh <[email protected]> Date: Sun Apr 12 18:03:28 2020 +0530 Use not gui backend. commit 6ad911c73c5f9d01846c5869263c12ee82e1bdf8 Author: Dilawar Singh <[email protected]> Date: Sun Apr 12 13:23:33 2020 +0530 Variable and Cinfo need not be exposed. commit 5fec8497593a9d77b5ed5832336747c6cd8fb33c Author: Dilawar Singh <[email protected]> Date: Sun Apr 12 12:27:13 2020 +0530 Create moose element from vec and field. commit ab3d85dc0f023a4cda2a9cf7ecfae97d860567b2 Author: Dilawar Singh <[email protected]> Date: Sun Apr 12 11:21:21 2020 +0530 Added support for ["string", double] valueFinfoItem. commit 9c967c02abd565c90d452d200f778e1d2ed78349 Author: Dilawar Singh <[email protected]> Date: Sun Apr 12 10:03:17 2020 +0530 seed is an int and can't be empty. commit cc7ea95 Author: Dilawar Singh <[email protected]> Date: Sat Apr 11 15:46:11 2020 +0530 This is a really good commit. `.num` is supported now. commit 2185c65 Author: Dilawar Singh <[email protected]> Date: Sat Apr 11 12:28:39 2020 +0530 Added doxygen target. commit 32c3fc7 Author: Dilawar Singh <[email protected]> Date: Fri Apr 10 13:09:09 2020 +0530 Finfo is also vectorised. commit d716124 Author: Dilawar Singh <[email protected]> Date: Fri Apr 10 12:03:53 2020 +0530 Negative indexing is allowed. Fixes one more moose-examples neuroml/LIF/twoLIFxml_firing.py commit a2d6a38 Author: Dilawar Singh <[email protected]> Date: Thu Apr 9 21:07:04 2020 +0530 Use old PyRun code. Pybind11 does not have subterpreter support. commit 2587c0d Author: Dilawar Singh <[email protected]> Date: Thu Apr 9 13:58:16 2020 +0530 Added a test for testing pyrun. commit f3a4925 Author: Dilawar Singh <[email protected]> Date: Thu Apr 9 11:25:11 2020 +0530 when `-DWITH_BOOST=ON` is passed to cmake, it now overrides `WITH_GSL` option. Also fixes build failure. commit 2127c3a Author: Dilawar Singh <[email protected]> Date: Thu Apr 9 11:15:01 2020 +0530 Fixes https://gitlab.com/dilawar/moose-core/-/issues/7 commit 31f2b8f Author: Dilawar Singh <[email protected]> Date: Wed Apr 8 23:16:37 2020 +0530 If Function is not valid_, return quietly. commit b91a0ef Author: Dilawar Singh <[email protected]> Date: Wed Apr 8 22:25:06 2020 +0530 All tests are passing now. commit 0ce71ac Author: Dilawar Singh <[email protected]> Date: Wed Apr 8 20:13:39 2020 +0530 genesis and kkit are reverted back to master. commit 6535c46 Author: Dilawar Singh <[email protected]> Date: Wed Apr 8 19:03:13 2020 +0530 isA is working just fine. commit bf118f4 Author: Dilawar Singh <[email protected]> Date: Wed Apr 8 14:18:23 2020 +0530 We can now assign moose.vec to a field which takes Id. refactoring. int -> double, bool -> (int, double) coercing is allowed. Fixed script /home1/dilawars/Work.HG/GITLAB/moose-examples/snippets/interpol2d.py in https://gitlab.com/dilawar/moose-examples/-/issues/1 commit fb57aaf Author: Dilawar Singh <[email protected]> Date: Wed Apr 8 13:21:19 2020 +0530 overloading template function is not so straight-forward when typecasting can happen by itslf e.g. int and unsigned int. commit 22aeb43 Author: Dilawar Singh <[email protected]> Date: Wed Apr 8 09:52:57 2020 +0530 moose.element return single ObjId and not vec as I mistakenly assumed. commit ea81f1c Author: Dilawar Singh <[email protected]> Date: Tue Apr 7 21:45:13 2020 +0530 Vectorize function later. commit 4624651 Author: Dilawar Singh <[email protected]> Date: Tue Apr 7 20:48:47 2020 +0530 name, path, and parent of moose.vec are not vectorised. commit 6126a64 Author: Dilawar Singh <[email protected]> Date: Tue Apr 7 19:20:28 2020 +0530 snippets/savemodel.py is causing problem now. commit 15eae1d Author: Dilawar Singh <[email protected]> Date: Tue Apr 7 18:08:37 2020 +0530 vec values are returned as numpy array. commit cc89202 Author: Dilawar Singh <[email protected]> Date: Tue Apr 7 16:55:00 2020 +0530 Default parameters in connect is now working. First argument is not needed if it is a class member function. commit 8092a8e Author: Dilawar Singh <[email protected]> Date: Tue Apr 7 16:19:16 2020 +0530 If a Shell function retuns Id, wrap it in a MooseVec. The current API has this behaviour. commit 8ca430c Author: Dilawar Singh <[email protected]> Date: Tue Apr 7 13:54:52 2020 +0530 TODO: Id should be wrapped as moose.vec commit d6552e6 Author: Dilawar Singh <[email protected]> Date: Tue Apr 7 12:05:31 2020 +0530 Passes snippets/synapse.py https://gitlab.com/dilawar/moose-examples/-/issues/1 commit 3ea0a66 Author: Dilawar Singh <[email protected]> Date: Tue Apr 7 11:23:27 2020 +0530 Support more return types. commit 0862930 Author: Dilawar Singh <[email protected]> Date: Tue Apr 7 10:44:35 2020 +0530 MooseVec can now handle fieldElement as well. commit 1d40e74 Author: Dilawar Singh <[email protected]> Date: Mon Apr 6 21:03:58 2020 +0530 Needs some major overhaul of API. commit 3116b05 Author: Dilawar Singh <[email protected]> Date: Mon Apr 6 15:04:32 2020 +0530 Removed melement. commit 8baffdc Author: Dilawar Singh <[email protected]> Date: Mon Apr 6 15:00:59 2020 +0530 Support more fieldType. Fixes one more failing script in moose examples. commit b3a3e84 Author: Dilawar Singh <[email protected]> Date: Mon Apr 6 14:01:28 2020 +0530 Time to run examples now. commit 731fc47 Author: Dilawar Singh <[email protected]> Date: Mon Apr 6 13:44:38 2020 +0530 type checking has been moved to C++ code. its bit tricky here and not as readable as it should be. May be I can leave this at the python level. commit 790efdf Author: Dilawar Singh <[email protected]> Date: Mon Apr 6 13:24:30 2020 +0530 Some more progress. Getting a bit more faster than the current API. commit 4e24621 Author: Dilawar Singh <[email protected]> Date: Mon Apr 6 13:17:18 2020 +0530 Overloaded funtions. commit bc95f4d Author: Dilawar Singh <[email protected]> Date: Mon Apr 6 12:25:23 2020 +0530 Enabled helper functions. commit aeecc41 Author: Dilawar Singh <[email protected]> Date: Mon Apr 6 00:17:06 2020 +0530 beat the old api in microbenchmarks as well. commit 6e88eff Author: Dilawar Singh <[email protected]> Date: Sun Apr 5 23:56:00 2020 +0530 minor tweaks. commit 1dd9390 Author: Dilawar Singh <[email protected]> Date: Sun Apr 5 23:46:37 2020 +0530 moose.create is fast but moose.delete is bit slow. commit 0eda1b7 Author: Dilawar Singh <[email protected]> Date: Sun Apr 5 22:39:37 2020 +0530 forward declaration and compile fixes. commit a3bdd69 Author: Dilawar Singh <[email protected]> Date: Sun Apr 5 20:05:43 2020 +0530 Added benchmark file. commit e294eea Author: Dilawar Singh <[email protected]> Date: Sun Apr 5 19:55:01 2020 +0530 added micro benchmarks. commit 5979dc4 Author: Dilawar Singh <[email protected]> Date: Sat Apr 4 23:25:28 2020 +0530 Added documentations. commit 56c12f4 Author: Dilawar Singh <[email protected]> Date: Sat Apr 4 22:21:40 2020 +0530 All tests are passing.. needs to add some tests.. commit f039fad Author: Dilawar Singh <[email protected]> Date: Sat Apr 4 21:58:28 2020 +0530 _cmoose to _moose. commit 9543258 Author: Dilawar Singh <[email protected]> Date: Sat Apr 4 19:57:21 2020 +0530 Needs to fix some more API issues. commit 4d6c147 Author: Dilawar Singh <[email protected]> Date: Sat Apr 4 17:49:15 2020 +0530 Added version 2.5 commit f0efd21 Author: Dilawar Singh <[email protected]> Date: Sat Apr 4 17:41:41 2020 +0530 Removed a broken test and renamed one. The namedvars tests is moved to fixme (not supported). commit cd3dc5a Author: Dilawar Singh <[email protected]> Date: Sat Apr 4 12:11:59 2020 +0530 Needs final touch. commit 5262dc4 Author: Dilawar Singh <[email protected]> Date: Sat Apr 4 12:03:56 2020 +0530 Added one more missing attribute. commit 7757643 Author: Dilawar Singh <[email protected]> Date: Sat Apr 4 11:25:53 2020 +0530 test commit [skip ci] commit cb8a970 Author: Dilawar Singh <[email protected]> Date: Sat Apr 4 10:28:06 2020 +0530 old test is back. commit 06e3357 Author: Dilawar Singh <[email protected]> Date: Sat Apr 4 10:24:53 2020 +0530 Fixed the issue with isinstance(x, moose.CubeMesh). Now it is working fine. commit 685ab75 Author: Dilawar Singh <[email protected]> Date: Sat Apr 4 07:26:24 2020 +0530 One more test is passing. commit 6188e09 Author: Dilawar Singh <[email protected]> Date: Sat Apr 4 07:25:25 2020 +0530 Restored old values in the test. commit 349f8ea Author: Dilawar Singh <[email protected]> Date: Sat Apr 4 05:55:15 2020 +0530 fixes to one more tests. commit c90986a Author: Dilawar Singh <[email protected]> Date: Sat Apr 4 05:42:22 2020 +0530 Now do a local testing. commit e6a6575 Author: Dilawar Singh <[email protected]> Date: Sat Apr 4 05:37:26 2020 +0530 numerical assertion of oscillatory tests are hard. commit 5af49e9 Author: Dilawar Singh <[email protected]> Date: Sat Apr 4 05:26:34 2020 +0530 Almost all tests are passing. commit d7f03bd Author: Dilawar Singh <[email protected]> Date: Sat Apr 4 04:54:44 2020 +0530 remove 'value' attribute from the ObjId, it was conflicting with MString 'value'. commit ce79591 Author: Dilawar Singh <[email protected]> Date: Sat Apr 4 04:43:36 2020 +0530 Needs to fix doc. commit 113dddc Author: Dilawar Singh <[email protected]> Date: Sat Apr 4 04:36:02 2020 +0530 more tests are passing. all test_Xreacs are passing now. commit 29ff41c Author: Dilawar Singh <[email protected]> Date: Sat Apr 4 04:31:33 2020 +0530 Use ObjId instread of Id in buildMeshJunction. commit 33e9591 Author: Dilawar Singh <[email protected]> Date: Sat Apr 4 04:27:38 2020 +0530 Passing ObjId as Id is creating trouble. commit 537779e Author: Dilawar Singh <[email protected]> Date: Sat Apr 4 03:59:30 2020 +0530 one more test passes. commit 650309a Author: Dilawar Singh <[email protected]> Date: Sat Apr 4 03:05:28 2020 +0530 delete works. commit b13e051 Author: Dilawar Singh <[email protected]> Date: Sat Apr 4 02:13:31 2020 +0530 Some more tests [skip ci] commit e518d35 Author: Dilawar Singh <[email protected]> Date: Sat Apr 4 01:42:15 2020 +0530 One more test is passed. commit c783578 Author: Dilawar Singh <[email protected]> Date: Sat Apr 4 01:37:24 2020 +0530 isinstance support is added. commit 2a28f9a Author: Dilawar Singh <[email protected]> Date: Fri Apr 3 22:15:46 2020 +0530 Added tests to normalizepath. commit 4c2086a Author: Dilawar Singh <[email protected]> Date: Fri Apr 3 22:08:30 2020 +0530 Global random number generator is moved from basecode to randnum. commit 6a2b7b7 Author: Dilawar Singh <[email protected]> Date: Fri Apr 3 20:09:21 2020 +0530 Couple of seg-faults to take care of. commit 8a90db2 Author: Dilawar Singh <[email protected]> Date: Fri Apr 3 18:27:52 2020 +0530 Fixed one more test. commit 1798a1e Author: Dilawar Singh <[email protected]> Date: Fri Apr 3 14:18:47 2020 +0530 Need to fix rdesignuer now. commit 0be10c0 Author: Dilawar Singh <[email protected]> Date: Fri Apr 3 12:59:16 2020 +0530 Finfo can also return .vec. commit 226d616 Author: Dilawar Singh <[email protected]> Date: Fri Apr 3 12:35:32 2020 +0530 Function is also fixed. commit b68a97b Author: Dilawar Singh <[email protected]> Date: Fri Apr 3 12:22:29 2020 +0530 SynapseTest is also passing. commit 8f2a039 Author: Dilawar Singh <[email protected]> Date: Fri Apr 3 11:38:20 2020 +0530 Fixes all the c++ tests commit 173b9d2 Author: Dilawar Singh <[email protected]> Date: Fri Apr 3 11:28:47 2020 +0530 ObjId.vec create a vec on the fly. commit e71fea0 Author: Dilawar Singh <[email protected]> Date: Thu Apr 2 22:39:02 2020 +0530 Same problem on OSX. One more test is failing. commit 47e25f9 Author: Dilawar Singh <[email protected]> Date: Thu Apr 2 22:08:41 2020 +0530 Some more fixes. moose.element is not honoring dataIndex. commit 9de507a Author: Dilawar Singh <[email protected]> Date: Thu Apr 2 20:17:29 2020 +0530 bebug vec and connection list. commit d7f0a26 Author: Dilawar Singh <[email protected]> Date: Thu Apr 2 19:22:00 2020 +0530 Refactoring. commit 2221410 Author: Dilawar Singh <[email protected]> Date: Thu Apr 2 16:17:48 2020 +0530 Added .clang-format file. commit 7a8437d Author: Dilawar Singh <[email protected]> Date: Thu Apr 2 12:44:32 2020 +0530 more progress. Lets have lunch first now. commit 0ed8933 Author: Dilawar Singh <[email protected]> Date: Thu Apr 2 12:25:44 2020 +0530 Fix Xreacs later. commit 04d4d2f Author: Dilawar Singh <[email protected]> Date: Thu Apr 2 11:52:19 2020 +0530 Refactoring. If Finfo* is passed, no need to pass rttitype and fname. We can get these values from Finfo. commit 77cc0b1 Author: Dilawar Singh <[email protected]> Date: Wed Apr 1 21:21:06 2020 +0530 refacorted codebase... commit 52cfdf7 Author: Dilawar Singh <[email protected]> Date: Wed Apr 1 21:06:13 2020 +0530 Added extra header for Finfo ... commit b16dd1c Author: Dilawar Singh <[email protected]> Date: Wed Apr 1 19:58:56 2020 +0530 Needs to implement LookupFinfo set. commit 8199fc0 Author: Dilawar Singh <[email protected]> Date: Wed Apr 1 18:48:25 2020 +0530 Disable pybind11. commit 5c25dad Author: Dilawar Singh <[email protected]> Date: Wed Apr 1 18:48:02 2020 +0530 One more tests seem to pass. commit 40a4559 Author: Dilawar Singh <[email protected]> Date: Wed Apr 1 18:22:52 2020 +0530 Some more fixes. commit dd9b50e Author: Dilawar Singh <[email protected]> Date: Wed Apr 1 17:59:50 2020 +0530 Perfect. One more test passes. commit fec019b Author: Dilawar Singh <[email protected]> Date: Wed Apr 1 15:41:22 2020 +0530 Refactoring and some more generic programming. commit 9eb2308 Author: Dilawar Singh <[email protected]> Date: Tue Mar 31 20:48:57 2020 +0530 small fixes. Changes in API requires .id . commit 7de3228 Author: Dilawar Singh <[email protected]> Date: Tue Mar 31 19:13:51 2020 +0530 Minor tweak to a test. commit c541b91 Author: Dilawar Singh <[email protected]> Date: Tue Mar 31 19:08:36 2020 +0530 One more test passed. commit 5cc3d3b Merge: ce579ac 1abb6f1 Author: Dilawar Singh <[email protected]> Date: Tue Mar 31 18:59:23 2020 +0530 Merge branch 'pybind11_shell' into temp commit ce579ac Author: Dilawar Singh <[email protected]> Date: Tue Mar 31 18:58:59 2020 +0530 renmaed. commit 16bbc3e Author: Dilawar Singh <[email protected]> Date: Tue Mar 31 18:20:55 2020 +0530 phew. I made a boo boo before. commit 1abb6f1 Merge: 24df86a fa06c38 Author: Dilawar Singh <[email protected]> Date: Tue Mar 31 02:24:30 2020 +0530 Merge branch 'pybind11_shell' of gitlab.com:dilawar/moose-core into pybind11_shell commit fa06c38 Author: Dilawar Singh <[email protected]> Date: Tue Mar 31 02:14:22 2020 +0530 Id and ObjId are not playing well together... commit 48832b1 Author: Dilawar Singh <[email protected]> Date: Tue Mar 31 01:30:34 2020 +0530 test_synchan is a good example; possible we should return moose.vec there. commit 8667c13 Author: Dilawar Singh <[email protected]> Date: Tue Mar 31 01:28:02 2020 +0530 temp commit. commit 24df86a Author: Dilawar Singh <[email protected]> Date: Mon Mar 30 23:39:46 2020 +0530 Temp commit. Exposing only Id. commit 448b8b5 Author: Dilawar Singh <[email protected]> Date: Mon Mar 30 23:14:51 2020 +0530 more tests are passing... commit d1b4990 Author: Dilawar Singh <[email protected]> Date: Mon Mar 30 20:35:39 2020 +0530 Need to find a solution.. commit 6b5082b Author: Dilawar Singh <[email protected]> Date: Mon Mar 30 19:05:44 2020 +0530 Refactoring and have a working moose.vec API. commit 98d8d34 Author: Dilawar Singh <[email protected]> Date: Mon Mar 30 18:05:07 2020 +0530 [skip ci] needs tweaking in the API. commit 0f7929c Author: Dilawar Singh <[email protected]> Date: Mon Mar 30 14:40:37 2020 +0530 Support vec. But first need a nap. commit 93d6e83 Author: Dilawar Singh <[email protected]> Date: Mon Mar 30 13:33:05 2020 +0530 refactoring. commit fd03015 Author: Dilawar Singh <[email protected]> Date: Mon Mar 30 13:17:31 2020 +0530 random works. commit fc34547 Author: Dilawar Singh <[email protected]> Date: Mon Mar 30 11:49:00 2020 +0530 Need to polish the API. commit 6af0f2c Author: Dilawar Singh <[email protected]> Date: Mon Mar 30 11:00:03 2020 +0530 Lets move to DestFinfo. commit 476d700 Author: Dilawar Singh <[email protected]> Date: Mon Mar 30 07:53:31 2020 +0530 Return type. commit 778208a Merge: dab5af4 dd65791 Author: Dilawar Singh <[email protected]> Date: Mon Mar 30 07:42:04 2020 +0530 Merge branch 'pybind11_shell' of gitlab.com:dilawar/moose-core into pybind11_shell commit dd65791 Author: Dilawar Singh <[email protected]> Date: Mon Mar 30 06:54:42 2020 +0530 Updated [skip ci] commit 76ec2a1 Author: Dilawar Singh <[email protected]> Date: Sun Mar 29 23:00:02 2020 +0530 [skip ci] some more changes. commit c4d7bc6 Author: Dilawar Singh <[email protected]> Date: Sun Mar 29 22:24:57 2020 +0530 We go both API integrated. commit f0ac785 Author: Dilawar Singh <[email protected]> Date: Sun Mar 29 21:48:18 2020 +0530 LookupField is a function. commit aee928e Author: Dilawar Singh <[email protected]> Date: Sun Mar 29 21:11:48 2020 +0530 Do the rest tomorrow. commit e118e12 Author: Dilawar Singh <[email protected]> Date: Sun Mar 29 20:45:21 2020 +0530 Retuning binding to std::function which return the Finfo value. commit dab5af4 Author: Dilawar Singh <[email protected]> Date: Sun Mar 29 18:01:12 2020 +0530 isA is method. Time to make it a subscriptable dictionary. commit c7a7b24 Author: Dilawar Singh <[email protected]> Date: Sun Mar 29 15:34:42 2020 +0530 Lets handle LookupField::set and get. commit a06e478 Author: Dilawar Singh <[email protected]> Date: Sun Mar 29 01:13:46 2020 +0530 Deal with it tomorrow. commit bb1cae5 Author: Dilawar Singh <[email protected]> Date: Sun Mar 29 00:28:22 2020 +0530 Getting there. [skip ci] commit 5cccf8b Author: Dilawar Singh <[email protected]> Date: Sat Mar 28 22:33:21 2020 +0530 Some refactoring. Back to same functionality [skip ci]. commit a979de6 Author: Dilawar Singh <[email protected]> Date: Sat Mar 28 20:46:01 2020 +0530 Updated a bit more .. commit b43c617 Author: Dilawar Singh <[email protected]> Date: Sat Mar 28 19:47:58 2020 +0530 New API works fantastic. commit 0deb291 Author: Dilawar Singh <[email protected]> Date: Sat Mar 28 19:40:19 2020 +0530 Incremental change. Dynamic attributes. commit 7f2539c Author: Dilawar Singh <[email protected]> Date: Sat Mar 28 19:31:31 2020 +0530 Subclassing _ObjId now. commit 0f64cd0 Author: Dilawar Singh <[email protected]> Date: Sat Mar 28 18:12:57 2020 +0530 Dynamic attributes are needed now. commit eff08b2 Author: Dilawar Singh <[email protected]> Date: Sat Mar 28 16:16:13 2020 +0530 All test passes. Needs to work on the API now. commit 8791df7 Author: Dilawar Singh <[email protected]> Date: Sat Mar 28 15:40:35 2020 +0530 Blazingly fast. commit 070f735 Author: Dilawar Singh <[email protected]> Date: Sat Mar 28 14:06:47 2020 +0530 Perfect. The base API works now. Not time to do a profiling. commit 07a1348 Author: Dilawar Singh <[email protected]> Date: Sat Mar 28 00:28:22 2020 +0530 This is for tomorow. commit 72f7b62 Author: Dilawar Singh <[email protected]> Date: Fri Mar 27 21:43:33 2020 +0530 Work from home. commit 4ea29e9 Author: Dilawar Singh <[email protected]> Date: Fri Mar 27 20:32:19 2020 +0530 May be later. commit eff6f90 Author: Dilawar Singh <[email protected]> Date: Fri Mar 27 17:57:40 2020 +0530 Not sure about the testKsolve.cpp tests. commit bef104c Author: Dilawar Singh <[email protected]> Date: Fri Mar 27 17:11:34 2020 +0530 Do testing with master branch. commit 0078af1 Author: Dilawar Singh <[email protected]> Date: Fri Mar 27 14:45:40 2020 +0530 get can not overloaded pretty well. Use different name for getting different value. It is verbose now but we can override later. commit 915e10f Merge: 911bd03 bf2d609 Author: Dilawar Singh <[email protected]> Date: Fri Mar 27 13:56:46 2020 +0530 Merge branch 'pybind11_shell' of gitlab.com:dilawar/moose-core into pybind11_shell commit bf2d609 Author: Dilawar Singh <[email protected]> Date: Fri Mar 27 14:11:18 2020 +0530 add test function. commit 911bd03 Author: Dilawar Singh <[email protected]> Date: Fri Mar 27 13:56:12 2020 +0530 local changes. commit cc7144f Author: Dilawar Singh <[email protected]> Date: Fri Mar 27 13:50:40 2020 +0530 Move to gulgula. commit d41e7eb Author: Dilawar Singh <[email protected]> Date: Fri Mar 27 04:18:44 2020 +0530 Allmost there. commit d913ceb Author: Dilawar Singh <[email protected]> Date: Fri Mar 27 01:50:18 2020 +0530 addMsg -> connect . commit 8793d33 Author: Dilawar Singh <[email protected]> Date: Fri Mar 27 01:10:24 2020 +0530 get/set are on ObjId . commit d99115c Author: Dilawar Singh <[email protected]> Date: Fri Mar 27 00:47:20 2020 +0530 Ok. Vector and numpy are working. commit 2f3bc04 Author: Dilawar Singh <[email protected]> Date: Thu Mar 26 23:02:03 2020 +0530 move to bebinca for fast compilation. commit a94fec9 Author: Dilawar Singh <[email protected]> Date: Thu Mar 26 18:29:50 2020 +0530 children and parent is not working. commit 756ec3a Author: Dilawar Singh <[email protected]> Date: Wed Mar 25 14:53:17 2020 +0530 Some more fixes. It will be too much debugging to get it right. commit 77451f1 Author: Dilawar Singh <[email protected]> Date: Tue Mar 24 15:07:09 2020 +0530 All the learning experience is over. Pybind11 is great. commit 6edda7a Author: Dilawar Singh <[email protected]> Date: Tue Mar 24 00:55:13 2020 +0530 Add a bit more fields. commit e32c468 Author: Dilawar Singh <[email protected]> Date: Mon Mar 23 23:30:19 2020 +0530 I can complete this API tomorrow. commit 7aaddf7 Author: Dilawar Singh <[email protected]> Date: Mon Mar 23 22:54:35 2020 +0530 added more functions [skip ci] commit 7f1b709 Author: Dilawar Singh <[email protected]> Date: Mon Mar 23 16:38:34 2020 +0530 disable build for now on gitlab ci commit ae2739d Author: Dilawar Singh <[email protected]> Date: Mon Mar 23 15:05:22 2020 +0530 pybind11 module is named _cmoose and it different from _moose. commit 0c33684 Author: Dilawar Singh <[email protected]> Date: Mon Mar 23 14:45:32 2020 +0530 I got wildcardFind to function. commit 65b307c Author: Dilawar Singh <[email protected]> Date: Mon Mar 23 13:33:22 2020 +0530 Fixed the bug I caused by using smart pointer. I am so silly... commit fe596e3 Merge: d5d29bb f4070da Author: Dilawar Singh <[email protected]> Date: Mon Mar 23 12:45:01 2020 +0530 Merge branch 'issue_397' of gitlab.com:dilawar/moose-core into pybind11 commit d5d29bb Author: Dilawar Singh <[email protected]> Date: Sun Mar 22 23:12:58 2020 +0530 Time to support / in path. commit 270ea8c Author: Dilawar Singh <[email protected]> Date: Sun Mar 22 22:50:21 2020 +0530 empty element() commit a1eed3a Author: Dilawar Singh <[email protected]> Date: Sun Mar 22 22:39:55 2020 +0530 temp commit. commit a70b5fe Author: Dilawar Singh <[email protected]> Date: Sun Mar 22 15:44:56 2020 +0530 Great. Lets try cython as well. commit 038490f Author: Dilawar Singh <[email protected]> Date: Sun Mar 22 15:44:27 2020 +0530 Try cython now. commit 8bbf900 Author: Dilawar Singh <[email protected]> Date: Sun Mar 22 13:43:02 2020 +0530 _moose goes to python/moose directory. commit 014bde2 Merge: 8f60899 ad58dc5 Author: Dilawar Singh <[email protected]> Date: Sun Mar 22 13:18:20 2020 +0530 Merge branch 'issue_397' into pybind11 commit f4070da Merge: ad58dc5 5e660e9 Author: Dilawar Singh <[email protected]> Date: Sat Mar 21 22:21:16 2020 +0530 Merge branch 'refactoring' into issue_397 commit 5e660e9 Author: dilawars <[email protected]> Date: Sat Mar 21 21:24:21 2020 +0530 include cmath in Pool.cpp as well. Failed compilation with gcc5.3 commit ad58dc5 Author: dilawars <[email protected]> Date: Sat Mar 21 21:24:21 2020 +0530 include cmath in Pool.cpp as well. Failed compilation with gcc5.3 commit c4d55aa Author: Dilawar Singh <[email protected]> Date: Sat Mar 21 15:45:16 2020 +0530 Minor cleanup in macros and loggers. numCores now use thread library to determine number of available threads. commit f8dcb12 Author: Dilawar Singh <[email protected]> Date: Sat Mar 21 15:32:02 2020 +0530 NUMPY is essential dependency; therefore numpy code is no longer included conditionally. USE_NUMPY is implied and have been removed from cmake. commit 9ef658e Author: Dilawar Singh <[email protected]> Date: Sat Mar 21 15:15:43 2020 +0530 Fix to #397 commit 8f60899 Author: Dilawar Singh <[email protected]> Date: Tue Mar 17 18:27:54 2020 +0530 Perfecto. Create works. commit aa95a0c Author: Dilawar Singh <[email protected]> Date: Sun Mar 15 22:10:07 2020 +0530 pybind11 bindings. commit da9d1d9 Merge: 0e85a57 36c0026 Author: Dilawar Singh <[email protected]> Date: Sun Mar 15 15:40:06 2020 +0530 Merge commit '36c0026886c70e39c505f8715e65a7c3cf1e6ade' as 'external/pybind11' commit 36c0026 Author: Dilawar Singh <[email protected]> Date: Sun Mar 15 15:40:06 2020 +0530 Squashed 'external/pybind11/' content from commit 4f72ef846 git-subtree-dir: external/pybind11 git-subtree-split: 4f72ef846fe8453596230ac285eeaa0ce3278bb4 * Minor fixes to pybind11. * Fix #409 When `moose.Function('abc')` is created, set expression to "0". Expression is not empty by default. This is to mimic the old behaviour. Note that at this point, derivative is not defined and is `nan` (old behaviour: derivative is 0.0). * Ready for a draft PR and initial disucssion. * Return numpy array instead of vector. Probably not the most memory efficient way for returning vector<double> but since most pyMOOSE scripts assume that returned data is numpy array, we return the numpy array. TODO: benchmarking. * Fixed: moose.le can caused segfault when used on moose.vec This also fixes script mgblock.py BhallaLab/moose-examples#71 * Fixed: moose.le can caused segfault when used on moose.vec This also fixes script mgblock.py BhallaLab/moose-examples#71 * removed mkdoc.py from pybind11. * Fixed a pylint error as well python2/python3 compatibility * wildcard -> reacSystemPath Stoic::path is depreacted bcause it collides with Neutral::path. * Fixed another set. * Travis fix: Install pytest on OSX as well. * fix gitlab pipeline install pytest * isinstance is replace to isA added to this, validation.py: error msg is sent back, writeKkit.py: while writting genesis file if any object is not written then errorlog is send/printed which is usefull durning command line * fix test py_run. Relax the matching to 90% using difflib (from 95%). * grenerate documentation on the fly. * Work in progress: __doc__ string from cWork in progress: __doc__ string from cWork in progress: __doc__ string from cWork in progress: __doc__ string from c++ * Keeping the C++ type and Python's type name same. * Cleanup * pydoc support moved moose.py content to __init__.py. This way pydoc works great also fixed travis build. * moose.doc is working now. _moose.generateDoc is the underlying function. Needs to cleanup documentation a bit now. Fixed regression. * update to docs Disabled C++ signature in Python documentations. Added docstring to __init__.py * more docstring are added [skip ci] * Added datetime and other string to version_info. * All functions have docstring. * loadmodel docstring is added. * temp commit. * showmsg is ported to c++. * added more docstring and moved some functions to public api. * Merged hrani changes and mine from new bindings. removed 'basestring' * # This is a combination of 2 commits. python2 support. Added python2 support as well. It will be easy to remove later. _moose.element is a good way to convert string/objid/id to melement. writeKkit * python2 support. Added python2 support as well. It will be easy to remove later. _moose.element is a good way to convert string/objid/id to melement. writeKkit python2 support. Added python2 support as well. It will be easy to remove later. python2 support. Added python2 support as well. It will be easy to remove later. _moose.element is a good way to convert string/objid/id to melement. writeKkit python2 support. Added python2 support as well. It will be easy to remove later. * basestring -> str * fixes to `pip install` Added missing folders. * Fixed pylint error. * moose.getField accepts two argument instead of 3. Updated rmogul.py file. * fix: compiles with clang++ typeid(X) when X is an incomplete type is not supported by C++ standard. Suprisingly this was compiling fine with gcc but not with clang++. version is set to 3.2.0.dev$(today) * travis fixes: OSX PyRun tests compares last 50 lines rather than whole text. This way we can ignore lines with different timestamp. * builds on osx locally. * tests passes with 3.8 as well. * On OSX, stream does not flush properly? Using difflib to test the ratio between got and expected string. * flush the streams before calling tests... * Don't run the trvais/osx Not sure why but only on travis+OSX, pyrun test does not pass. It fails because whole buffer is not dumped to the tty. * Fixes to pyrun tests. * Time to post the API. * listmsg has been moved to C++. * docstring to writeNML2 * Fixed typo in docstring. Ready to be reviewed. * showfield and showfields are both supported. `moose.showfield` is an alias for `moose.showfields`. * Added back moose.ce Co-authored-by: Dilawar Singh <[email protected]> Co-authored-by: HarshaRani <[email protected]> Co-authored-by: Anushree Narjala <[email protected]>
* Merged hrani changes and mine from new bindings. removed 'basestring' * New python bindings using pybind11 (#410) * not a bug. * Turned scripts recieved from harsha into a test case. open #402. * Renamed wrapper.Neutral to __Wrapper__. With new API, this functionality can be built in. * closes #401 * Fixed another bug: -DWTIH_BOOST=ON could not override GSL after WITH_GSL was cached by cmake. Ie, if once built with default options, there was no way to use BOOST without cleaning up the old build completely. * check is made if solver has space while reading/writing SBML files,small change to port the code to py3 * Squashed commit of the following: commit b313f8d72537b6d8218857d0f0ef81268bc05f81 Author: Dilawar Singh <[email protected]> Date: Sun Apr 12 19:03:24 2020 +0530 moved __init__.py and moose.py to pybind folder. commit 77afafd49dc6e99b1c00c060b00181d1190e1c7b Author: Dilawar Singh <[email protected]> Date: Sun Apr 12 18:03:28 2020 +0530 Use not gui backend. commit 6ad911c73c5f9d01846c5869263c12ee82e1bdf8 Author: Dilawar Singh <[email protected]> Date: Sun Apr 12 13:23:33 2020 +0530 Variable and Cinfo need not be exposed. commit 5fec8497593a9d77b5ed5832336747c6cd8fb33c Author: Dilawar Singh <[email protected]> Date: Sun Apr 12 12:27:13 2020 +0530 Create moose element from vec and field. commit ab3d85dc0f023a4cda2a9cf7ecfae97d860567b2 Author: Dilawar Singh <[email protected]> Date: Sun Apr 12 11:21:21 2020 +0530 Added support for ["string", double] valueFinfoItem. commit 9c967c02abd565c90d452d200f778e1d2ed78349 Author: Anushree Narjala <[email protected]> Date: Sun Apr 12 10:03:17 2020 +0530 seed is an int and can't be empty. commit cc7ea95 Author: Dilawar Singh <[email protected]> Date: Sat Apr 11 15:46:11 2020 +0530 This is a really good commit. `.num` is supported now. commit 2185c65 Author: Dilawar Singh <[email protected]> Date: Sat Apr 11 12:28:39 2020 +0530 Added doxygen target. commit 32c3fc7 Author: Dilawar Singh <[email protected]> Date: Fri Apr 10 13:09:09 2020 +0530 Finfo is also vectorised. commit d716124 Author: Dilawar Singh <[email protected]> Date: Fri Apr 10 12:03:53 2020 +0530 Negative indexing is allowed. Fixes one more moose-examples neuroml/LIF/twoLIFxml_firing.py commit a2d6a38 Author: Dilawar Singh <[email protected]> Date: Thu Apr 9 21:07:04 2020 +0530 Use old PyRun code. Pybind11 does not have subterpreter support. commit 2587c0d Author: Dilawar Singh <[email protected]> Date: Thu Apr 9 13:58:16 2020 +0530 Added a test for testing pyrun. commit f3a4925 Author: Dilawar Singh <[email protected]> Date: Thu Apr 9 11:25:11 2020 +0530 when `-DWITH_BOOST=ON` is passed to cmake, it now overrides `WITH_GSL` option. Also fixes build failure. commit 2127c3a Author: Dilawar Singh <[email protected]> Date: Thu Apr 9 11:15:01 2020 +0530 Fixes https://gitlab.com/dilawar/moose-core/-/issues/7 commit 31f2b8f Author: Dilawar Singh <[email protected]> Date: Wed Apr 8 23:16:37 2020 +0530 If Function is not valid_, return quietly. commit b91a0ef Author: Dilawar Singh <[email protected]> Date: Wed Apr 8 22:25:06 2020 +0530 All tests are passing now. commit 0ce71ac Author: Dilawar Singh <[email protected]> Date: Wed Apr 8 20:13:39 2020 +0530 genesis and kkit are reverted back to master. commit 6535c46 Author: Dilawar Singh <[email protected]> Date: Wed Apr 8 19:03:13 2020 +0530 isA is working just fine. commit bf118f4 Author: Dilawar Singh <[email protected]> Date: Wed Apr 8 14:18:23 2020 +0530 We can now assign moose.vec to a field which takes Id. refactoring. int -> double, bool -> (int, double) coercing is allowed. Fixed script /home1/dilawars/Work.HG/GITLAB/moose-examples/snippets/interpol2d.py in https://gitlab.com/dilawar/moose-examples/-/issues/1 commit fb57aaf Author: Dilawar Singh <[email protected]> Date: Wed Apr 8 13:21:19 2020 +0530 overloading template function is not so straight-forward when typecasting can happen by itslf e.g. int and unsigned int. commit 22aeb43 Author: Dilawar Singh <[email protected]> Date: Wed Apr 8 09:52:57 2020 +0530 moose.element return single ObjId and not vec as I mistakenly assumed. commit ea81f1c Author: Dilawar Singh <[email protected]> Date: Tue Apr 7 21:45:13 2020 +0530 Vectorize function later. commit 4624651 Author: Dilawar Singh <[email protected]> Date: Tue Apr 7 20:48:47 2020 +0530 name, path, and parent of moose.vec are not vectorised. commit 6126a64 Author: Dilawar Singh <[email protected]> Date: Tue Apr 7 19:20:28 2020 +0530 snippets/savemodel.py is causing problem now. commit 15eae1d Author: Dilawar Singh <[email protected]> Date: Tue Apr 7 18:08:37 2020 +0530 vec values are returned as numpy array. commit cc89202 Author: Dilawar Singh <[email protected]> Date: Tue Apr 7 16:55:00 2020 +0530 Default parameters in connect is now working. First argument is not needed if it is a class member function. commit 8092a8e Author: Dilawar Singh <[email protected]> Date: Tue Apr 7 16:19:16 2020 +0530 If a Shell function retuns Id, wrap it in a MooseVec. The current API has this behaviour. commit 8ca430c Author: Dilawar Singh <[email protected]> Date: Tue Apr 7 13:54:52 2020 +0530 TODO: Id should be wrapped as moose.vec commit d6552e6 Author: Dilawar Singh <[email protected]> Date: Tue Apr 7 12:05:31 2020 +0530 Passes snippets/synapse.py https://gitlab.com/dilawar/moose-examples/-/issues/1 commit 3ea0a66 Author: Dilawar Singh <[email protected]> Date: Tue Apr 7 11:23:27 2020 +0530 Support more return types. commit 0862930 Author: Dilawar Singh <[email protected]> Date: Tue Apr 7 10:44:35 2020 +0530 MooseVec can now handle fieldElement as well. commit 1d40e74 Author: Dilawar Singh <[email protected]> Date: Mon Apr 6 21:03:58 2020 +0530 Needs some major overhaul of API. commit 3116b05 Author: Dilawar Singh <[email protected]> Date: Mon Apr 6 15:04:32 2020 +0530 Removed melement. commit 8baffdc Author: Dilawar Singh <[email protected]> Date: Mon Apr 6 15:00:59 2020 +0530 Support more fieldType. Fixes one more failing script in moose examples. commit b3a3e84 Author: Dilawar Singh <[email protected]> Date: Mon Apr 6 14:01:28 2020 +0530 Time to run examples now. commit 731fc47 Author: Dilawar Singh <[email protected]> Date: Mon Apr 6 13:44:38 2020 +0530 type checking has been moved to C++ code. its bit tricky here and not as readable as it should be. May be I can leave this at the python level. commit 790efdf Author: Dilawar Singh <[email protected]> Date: Mon Apr 6 13:24:30 2020 +0530 Some more progress. Getting a bit more faster than the current API. commit 4e24621 Author: Dilawar Singh <[email protected]> Date: Mon Apr 6 13:17:18 2020 +0530 Overloaded funtions. commit bc95f4d Author: Dilawar Singh <[email protected]> Date: Mon Apr 6 12:25:23 2020 +0530 Enabled helper functions. commit aeecc41 Author: Dilawar Singh <[email protected]> Date: Mon Apr 6 00:17:06 2020 +0530 beat the old api in microbenchmarks as well. commit 6e88eff Author: Dilawar Singh <[email protected]> Date: Sun Apr 5 23:56:00 2020 +0530 minor tweaks. commit 1dd9390 Author: Dilawar Singh <[email protected]> Date: Sun Apr 5 23:46:37 2020 +0530 moose.create is fast but moose.delete is bit slow. commit 0eda1b7 Author: Dilawar Singh <[email protected]> Date: Sun Apr 5 22:39:37 2020 +0530 forward declaration and compile fixes. commit a3bdd69 Author: Dilawar Singh <[email protected]> Date: Sun Apr 5 20:05:43 2020 +0530 Added benchmark file. commit e294eea Author: Dilawar Singh <[email protected]> Date: Sun Apr 5 19:55:01 2020 +0530 added micro benchmarks. commit 5979dc4 Author: Dilawar Singh <[email protected]> Date: Sat Apr 4 23:25:28 2020 +0530 Added documentations. commit 56c12f4 Author: Dilawar Singh <[email protected]> Date: Sat Apr 4 22:21:40 2020 +0530 All tests are passing.. needs to add some tests.. commit f039fad Author: Dilawar Singh <[email protected]> Date: Sat Apr 4 21:58:28 2020 +0530 _cmoose to _moose. commit 9543258 Author: Dilawar Singh <[email protected]> Date: Sat Apr 4 19:57:21 2020 +0530 Needs to fix some more API issues. commit 4d6c147 Author: Dilawar Singh <[email protected]> Date: Sat Apr 4 17:49:15 2020 +0530 Added version 2.5 commit f0efd21 Author: Dilawar Singh <[email protected]> Date: Sat Apr 4 17:41:41 2020 +0530 Removed a broken test and renamed one. The namedvars tests is moved to fixme (not supported). commit cd3dc5a Author: Dilawar Singh <[email protected]> Date: Sat Apr 4 12:11:59 2020 +0530 Needs final touch. commit 5262dc4 Author: Dilawar Singh <[email protected]> Date: Sat Apr 4 12:03:56 2020 +0530 Added one more missing attribute. commit 7757643 Author: Dilawar Singh <[email protected]> Date: Sat Apr 4 11:25:53 2020 +0530 test commit [skip ci] commit cb8a970 Author: Dilawar Singh <[email protected]> Date: Sat Apr 4 10:28:06 2020 +0530 old test is back. commit 06e3357 Author: Dilawar Singh <[email protected]> Date: Sat Apr 4 10:24:53 2020 +0530 Fixed the issue with isinstance(x, moose.CubeMesh). Now it is working fine. commit 685ab75 Author: Dilawar Singh <[email protected]> Date: Sat Apr 4 07:26:24 2020 +0530 One more test is passing. commit 6188e09 Author: Dilawar Singh <[email protected]> Date: Sat Apr 4 07:25:25 2020 +0530 Restored old values in the test. commit 349f8ea Author: Dilawar Singh <[email protected]> Date: Sat Apr 4 05:55:15 2020 +0530 fixes to one more tests. commit c90986a Author: Dilawar Singh <[email protected]> Date: Sat Apr 4 05:42:22 2020 +0530 Now do a local testing. commit e6a6575 Author: Dilawar Singh <[email protected]> Date: Sat Apr 4 05:37:26 2020 +0530 numerical assertion of oscillatory tests are hard. commit 5af49e9 Author: Dilawar Singh <[email protected]> Date: Sat Apr 4 05:26:34 2020 +0530 Almost all tests are passing. commit d7f03bd Author: Dilawar Singh <[email protected]> Date: Sat Apr 4 04:54:44 2020 +0530 remove 'value' attribute from the ObjId, it was conflicting with MString 'value'. commit ce79591 Author: Dilawar Singh <[email protected]> Date: Sat Apr 4 04:43:36 2020 +0530 Needs to fix doc. commit 113dddc Author: Dilawar Singh <[email protected]> Date: Sat Apr 4 04:36:02 2020 +0530 more tests are passing. all test_Xreacs are passing now. commit 29ff41c Author: Dilawar Singh <[email protected]> Date: Sat Apr 4 04:31:33 2020 +0530 Use ObjId instread of Id in buildMeshJunction. commit 33e9591 Author: Dilawar Singh <[email protected]> Date: Sat Apr 4 04:27:38 2020 +0530 Passing ObjId as Id is creating trouble. commit 537779e Author: Dilawar Singh <[email protected]> Date: Sat Apr 4 03:59:30 2020 +0530 one more test passes. commit 650309a Author: Dilawar Singh <[email protected]> Date: Sat Apr 4 03:05:28 2020 +0530 delete works. commit b13e051 Author: Dilawar Singh <[email protected]> Date: Sat Apr 4 02:13:31 2020 +0530 Some more tests [skip ci] commit e518d35 Author: Dilawar Singh <[email protected]> Date: Sat Apr 4 01:42:15 2020 +0530 One more test is passed. commit c783578 Author: Dilawar Singh <[email protected]> Date: Sat Apr 4 01:37:24 2020 +0530 isinstance support is added. commit 2a28f9a Author: Dilawar Singh <[email protected]> Date: Fri Apr 3 22:15:46 2020 +0530 Added tests to normalizepath. commit 4c2086a Author: Dilawar Singh <[email protected]> Date: Fri Apr 3 22:08:30 2020 +0530 Global random number generator is moved from basecode to randnum. commit 6a2b7b7 Author: Dilawar Singh <[email protected]> Date: Fri Apr 3 20:09:21 2020 +0530 Couple of seg-faults to take care of. commit 8a90db2 Author: Dilawar Singh <[email protected]> Date: Fri Apr 3 18:27:52 2020 +0530 Fixed one more test. commit 1798a1e Author: Dilawar Singh <[email protected]> Date: Fri Apr 3 14:18:47 2020 +0530 Need to fix rdesignuer now. commit 0be10c0 Author: Dilawar Singh <[email protected]> Date: Fri Apr 3 12:59:16 2020 +0530 Finfo can also return .vec. commit 226d616 Author: Dilawar Singh <[email protected]> Date: Fri Apr 3 12:35:32 2020 +0530 Function is also fixed. commit b68a97b Author: Dilawar Singh <[email protected]> Date: Fri Apr 3 12:22:29 2020 +0530 SynapseTest is also passing. commit 8f2a039 Author: Dilawar Singh <[email protected]> Date: Fri Apr 3 11:38:20 2020 +0530 Fixes all the c++ tests commit 173b9d2 Author: Dilawar Singh <[email protected]> Date: Fri Apr 3 11:28:47 2020 +0530 ObjId.vec create a vec on the fly. commit e71fea0 Author: Dilawar Singh <[email protected]> Date: Thu Apr 2 22:39:02 2020 +0530 Same problem on OSX. One more test is failing. commit 47e25f9 Author: Dilawar Singh <[email protected]> Date: Thu Apr 2 22:08:41 2020 +0530 Some more fixes. moose.element is not honoring dataIndex. commit 9de507a Author: Dilawar Singh <[email protected]> Date: Thu Apr 2 20:17:29 2020 +0530 bebug vec and connection list. commit d7f0a26 Author: Dilawar Singh <[email protected]> Date: Thu Apr 2 19:22:00 2020 +0530 Refactoring. commit 2221410 Author: Dilawar Singh <[email protected]> Date: Thu Apr 2 16:17:48 2020 +0530 Added .clang-format file. commit 7a8437d Author: Dilawar Singh <[email protected]> Date: Thu Apr 2 12:44:32 2020 +0530 more progress. Lets have lunch first now. commit 0ed8933 Author: Dilawar Singh <[email protected]> Date: Thu Apr 2 12:25:44 2020 +0530 Fix Xreacs later. commit 04d4d2f Author: Dilawar Singh <[email protected]> Date: Thu Apr 2 11:52:19 2020 +0530 Refactoring. If Finfo* is passed, no need to pass rttitype and fname. We can get these values from Finfo. commit 77cc0b1 Author: Dilawar Singh <[email protected]> Date: Wed Apr 1 21:21:06 2020 +0530 refacorted codebase... commit 52cfdf7 Author: Dilawar Singh <[email protected]> Date: Wed Apr 1 21:06:13 2020 +0530 Added extra header for Finfo ... commit b16dd1c Author: Dilawar Singh <[email protected]> Date: Wed Apr 1 19:58:56 2020 +0530 Needs to implement LookupFinfo set. commit 8199fc0 Author: Dilawar Singh <[email protected]> Date: Wed Apr 1 18:48:25 2020 +0530 Disable pybind11. commit 5c25dad Author: Dilawar Singh <[email protected]> Date: Wed Apr 1 18:48:02 2020 +0530 One more tests seem to pass. commit 40a4559 Author: Dilawar Singh <[email protected]> Date: Wed Apr 1 18:22:52 2020 +0530 Some more fixes. commit dd9b50e Author: Dilawar Singh <[email protected]> Date: Wed Apr 1 17:59:50 2020 +0530 Perfect. One more test passes. commit fec019b Author: Dilawar Singh <[email protected]> Date: Wed Apr 1 15:41:22 2020 +0530 Refactoring and some more generic programming. commit 9eb2308 Author: Dilawar Singh <[email protected]> Date: Tue Mar 31 20:48:57 2020 +0530 small fixes. Changes in API requires .id . commit 7de3228 Author: Dilawar Singh <[email protected]> Date: Tue Mar 31 19:13:51 2020 +0530 Minor tweak to a test. commit c541b91 Author: Dilawar Singh <[email protected]> Date: Tue Mar 31 19:08:36 2020 +0530 One more test passed. commit 5cc3d3b Merge: ce579ac 1abb6f1 Author: Dilawar Singh <[email protected]> Date: Tue Mar 31 18:59:23 2020 +0530 Merge branch 'pybind11_shell' into temp commit ce579ac Author: Dilawar Singh <[email protected]> Date: Tue Mar 31 18:58:59 2020 +0530 renmaed. commit 16bbc3e Author: Dilawar Singh <[email protected]> Date: Tue Mar 31 18:20:55 2020 +0530 phew. I made a boo boo before. commit 1abb6f1 Merge: 24df86a fa06c38 Author: Dilawar Singh <[email protected]> Date: Tue Mar 31 02:24:30 2020 +0530 Merge branch 'pybind11_shell' of gitlab.com:dilawar/moose-core into pybind11_shell commit fa06c38 Author: Dilawar Singh <[email protected]> Date: Tue Mar 31 02:14:22 2020 +0530 Id and ObjId are not playing well together... commit 48832b1 Author: Dilawar Singh <[email protected]> Date: Tue Mar 31 01:30:34 2020 +0530 test_synchan is a good example; possible we should return moose.vec there. commit 8667c13 Author: Dilawar Singh <[email protected]> Date: Tue Mar 31 01:28:02 2020 +0530 temp commit. commit 24df86a Author: Dilawar Singh <[email protected]> Date: Mon Mar 30 23:39:46 2020 +0530 Temp commit. Exposing only Id. commit 448b8b5 Author: Dilawar Singh <[email protected]> Date: Mon Mar 30 23:14:51 2020 +0530 more tests are passing... commit d1b4990 Author: Dilawar Singh <[email protected]> Date: Mon Mar 30 20:35:39 2020 +0530 Need to find a solution.. commit 6b5082b Author: Dilawar Singh <[email protected]> Date: Mon Mar 30 19:05:44 2020 +0530 Refactoring and have a working moose.vec API. commit 98d8d34 Author: Dilawar Singh <[email protected]> Date: Mon Mar 30 18:05:07 2020 +0530 [skip ci] needs tweaking in the API. commit 0f7929c Author: Dilawar Singh <[email protected]> Date: Mon Mar 30 14:40:37 2020 +0530 Support vec. But first need a nap. commit 93d6e83 Author: Dilawar Singh <[email protected]> Date: Mon Mar 30 13:33:05 2020 +0530 refactoring. commit fd03015 Author: Dilawar Singh <[email protected]> Date: Mon Mar 30 13:17:31 2020 +0530 random works. commit fc34547 Author: Dilawar Singh <[email protected]> Date: Mon Mar 30 11:49:00 2020 +0530 Need to polish the API. commit 6af0f2c Author: Dilawar Singh <[email protected]> Date: Mon Mar 30 11:00:03 2020 +0530 Lets move to DestFinfo. commit 476d700 Author: Dilawar Singh <[email protected]> Date: Mon Mar 30 07:53:31 2020 +0530 Return type. commit 778208a Merge: dab5af4 dd65791 Author: Dilawar Singh <[email protected]> Date: Mon Mar 30 07:42:04 2020 +0530 Merge branch 'pybind11_shell' of gitlab.com:dilawar/moose-core into pybind11_shell commit dd65791 Author: Dilawar Singh <[email protected]> Date: Mon Mar 30 06:54:42 2020 +0530 Updated [skip ci] commit 76ec2a1 Author: Dilawar Singh <[email protected]> Date: Sun Mar 29 23:00:02 2020 +0530 [skip ci] some more changes. commit c4d7bc6 Author: Dilawar Singh <[email protected]> Date: Sun Mar 29 22:24:57 2020 +0530 We go both API integrated. commit f0ac785 Author: Dilawar Singh <[email protected]> Date: Sun Mar 29 21:48:18 2020 +0530 LookupField is a function. commit aee928e Author: Dilawar Singh <[email protected]> Date: Sun Mar 29 21:11:48 2020 +0530 Do the rest tomorrow. commit e118e12 Author: Dilawar Singh <[email protected]> Date: Sun Mar 29 20:45:21 2020 +0530 Retuning binding to std::function which return the Finfo value. commit dab5af4 Author: Dilawar Singh <[email protected]> Date: Sun Mar 29 18:01:12 2020 +0530 isA is method. Time to make it a subscriptable dictionary. commit c7a7b24 Author: Dilawar Singh <[email protected]> Date: Sun Mar 29 15:34:42 2020 +0530 Lets handle LookupField::set and get. commit a06e478 Author: Dilawar Singh <[email protected]> Date: Sun Mar 29 01:13:46 2020 +0530 Deal with it tomorrow. commit bb1cae5 Author: Dilawar Singh <[email protected]> Date: Sun Mar 29 00:28:22 2020 +0530 Getting there. [skip ci] commit 5cccf8b Author: Dilawar Singh <[email protected]> Date: Sat Mar 28 22:33:21 2020 +0530 Some refactoring. Back to same functionality [skip ci]. commit a979de6 Author: Dilawar Singh <[email protected]> Date: Sat Mar 28 20:46:01 2020 +0530 Updated a bit more .. commit b43c617 Author: Dilawar Singh <[email protected]> Date: Sat Mar 28 19:47:58 2020 +0530 New API works fantastic. commit 0deb291 Author: Dilawar Singh <[email protected]> Date: Sat Mar 28 19:40:19 2020 +0530 Incremental change. Dynamic attributes. commit 7f2539c Author: Dilawar Singh <[email protected]> Date: Sat Mar 28 19:31:31 2020 +0530 Subclassing _ObjId now. commit 0f64cd0 Author: Dilawar Singh <[email protected]> Date: Sat Mar 28 18:12:57 2020 +0530 Dynamic attributes are needed now. commit eff08b2 Author: Dilawar Singh <[email protected]> Date: Sat Mar 28 16:16:13 2020 +0530 All test passes. Needs to work on the API now. commit 8791df7 Author: Dilawar Singh <[email protected]> Date: Sat Mar 28 15:40:35 2020 +0530 Blazingly fast. commit 070f735 Author: Dilawar Singh <[email protected]> Date: Sat Mar 28 14:06:47 2020 +0530 Perfect. The base API works now. Not time to do a profiling. commit 07a1348 Author: Dilawar Singh <[email protected]> Date: Sat Mar 28 00:28:22 2020 +0530 This is for tomorow. commit 72f7b62 Author: Dilawar Singh <[email protected]> Date: Fri Mar 27 21:43:33 2020 +0530 Work from home. commit 4ea29e9 Author: Dilawar Singh <[email protected]> Date: Fri Mar 27 20:32:19 2020 +0530 May be later. commit eff6f90 Author: Dilawar Singh <[email protected]> Date: Fri Mar 27 17:57:40 2020 +0530 Not sure about the testKsolve.cpp tests. commit bef104c Author: Dilawar Singh <[email protected]> Date: Fri Mar 27 17:11:34 2020 +0530 Do testing with master branch. commit 0078af1 Author: Dilawar Singh <[email protected]> Date: Fri Mar 27 14:45:40 2020 +0530 get can not overloaded pretty well. Use different name for getting different value. It is verbose now but we can override later. commit 915e10f Merge: 911bd03 bf2d609 Author: Dilawar Singh <[email protected]> Date: Fri Mar 27 13:56:46 2020 +0530 Merge branch 'pybind11_shell' of gitlab.com:dilawar/moose-core into pybind11_shell commit bf2d609 Author: Dilawar Singh <[email protected]> Date: Fri Mar 27 14:11:18 2020 +0530 add test function. commit 911bd03 Author: Dilawar Singh <[email protected]> Date: Fri Mar 27 13:56:12 2020 +0530 local changes. commit cc7144f Author: Dilawar Singh <[email protected]> Date: Fri Mar 27 13:50:40 2020 +0530 Move to gulgula. commit d41e7eb Author: Dilawar Singh <[email protected]> Date: Fri Mar 27 04:18:44 2020 +0530 Allmost there. commit d913ceb Author: Dilawar Singh <[email protected]> Date: Fri Mar 27 01:50:18 2020 +0530 addMsg -> connect . commit 8793d33 Author: Dilawar Singh <[email protected]> Date: Fri Mar 27 01:10:24 2020 +0530 get/set are on ObjId . commit d99115c Author: Dilawar Singh <[email protected]> Date: Fri Mar 27 00:47:20 2020 +0530 Ok. Vector and numpy are working. commit 2f3bc04 Author: Dilawar Singh <[email protected]> Date: Thu Mar 26 23:02:03 2020 +0530 move to bebinca for fast compilation. commit a94fec9 Author: Dilawar Singh <[email protected]> Date: Thu Mar 26 18:29:50 2020 +0530 children and parent is not working. commit 756ec3a Author: Dilawar Singh <[email protected]> Date: Wed Mar 25 14:53:17 2020 +0530 Some more fixes. It will be too much debugging to get it right. commit 77451f1 Author: Dilawar Singh <[email protected]> Date: Tue Mar 24 15:07:09 2020 +0530 All the learning experience is over. Pybind11 is great. commit 6edda7a Author: Dilawar Singh <[email protected]> Date: Tue Mar 24 00:55:13 2020 +0530 Add a bit more fields. commit e32c468 Author: Dilawar Singh <[email protected]> Date: Mon Mar 23 23:30:19 2020 +0530 I can complete this API tomorrow. commit 7aaddf7 Author: Dilawar Singh <[email protected]> Date: Mon Mar 23 22:54:35 2020 +0530 added more functions [skip ci] commit 7f1b709 Author: Dilawar Singh <[email protected]> Date: Mon Mar 23 16:38:34 2020 +0530 disable build for now on gitlab ci commit ae2739d Author: Dilawar Singh <[email protected]> Date: Mon Mar 23 15:05:22 2020 +0530 pybind11 module is named _cmoose and it different from _moose. commit 0c33684 Author: Dilawar Singh <[email protected]> Date: Mon Mar 23 14:45:32 2020 +0530 I got wildcardFind to function. commit 65b307c Author: Dilawar Singh <[email protected]> Date: Mon Mar 23 13:33:22 2020 +0530 Fixed the bug I caused by using smart pointer. I am so silly... commit fe596e3 Merge: d5d29bb f4070da Author: Dilawar Singh <[email protected]> Date: Mon Mar 23 12:45:01 2020 +0530 Merge branch 'issue_397' of gitlab.com:dilawar/moose-core into pybind11 commit d5d29bb Author: Dilawar Singh <[email protected]> Date: Sun Mar 22 23:12:58 2020 +0530 Time to support / in path. commit 270ea8c Author: Dilawar Singh <[email protected]> Date: Sun Mar 22 22:50:21 2020 +0530 empty element() commit a1eed3a Author: Dilawar Singh <[email protected]> Date: Sun Mar 22 22:39:55 2020 +0530 temp commit. commit a70b5fe Author: Dilawar Singh <[email protected]> Date: Sun Mar 22 15:44:56 2020 +0530 Great. Lets try cython as well. commit 038490f Author: Dilawar Singh <[email protected]> Date: Sun Mar 22 15:44:27 2020 +0530 Try cython now. commit 8bbf900 Author: Dilawar Singh <[email protected]> Date: Sun Mar 22 13:43:02 2020 +0530 _moose goes to python/moose directory. commit 014bde2 Merge: 8f60899 ad58dc5 Author: Dilawar Singh <[email protected]> Date: Sun Mar 22 13:18:20 2020 +0530 Merge branch 'issue_397' into pybind11 commit f4070da Merge: ad58dc5 5e660e9 Author: Dilawar Singh <[email protected]> Date: Sat Mar 21 22:21:16 2020 +0530 Merge branch 'refactoring' into issue_397 commit 5e660e9 Author: dilawars <[email protected]> Date: Sat Mar 21 21:24:21 2020 +0530 include cmath in Pool.cpp as well. Failed compilation with gcc5.3 commit ad58dc5 Author: dilawars <[email protected]> Date: Sat Mar 21 21:24:21 2020 +0530 include cmath in Pool.cpp as well. Failed compilation with gcc5.3 commit c4d55aa Author: Dilawar Singh <[email protected]> Date: Sat Mar 21 15:45:16 2020 +0530 Minor cleanup in macros and loggers. numCores now use thread library to determine number of available threads. commit f8dcb12 Author: Dilawar Singh <[email protected]> Date: Sat Mar 21 15:32:02 2020 +0530 NUMPY is essential dependency; therefore numpy code is no longer included conditionally. USE_NUMPY is implied and have been removed from cmake. commit 9ef658e Author: Dilawar Singh <[email protected]> Date: Sat Mar 21 15:15:43 2020 +0530 Fix to #397 commit 8f60899 Author: Dilawar Singh <[email protected]> Date: Tue Mar 17 18:27:54 2020 +0530 Perfecto. Create works. commit aa95a0c Author: Dilawar Singh <[email protected]> Date: Sun Mar 15 22:10:07 2020 +0530 pybind11 bindings. commit da9d1d9 Merge: 0e85a57 36c0026 Author: Dilawar Singh <[email protected]> Date: Sun Mar 15 15:40:06 2020 +0530 Merge commit '36c0026886c70e39c505f8715e65a7c3cf1e6ade' as 'external/pybind11' commit 36c0026 Author: Dilawar Singh <[email protected]> Date: Sun Mar 15 15:40:06 2020 +0530 Squashed 'external/pybind11/' content from commit 4f72ef846 git-subtree-dir: external/pybind11 git-subtree-split: 4f72ef846fe8453596230ac285eeaa0ce3278bb4 * Minor fixes to pybind11. * Fix #409 When `moose.Function('abc')` is created, set expression to "0". Expression is not empty by default. This is to mimic the old behaviour. Note that at this point, derivative is not defined and is `nan` (old behaviour: derivative is 0.0). * Ready for a draft PR and initial disucssion. * Return numpy array instead of vector. Probably not the most memory efficient way for returning vector<double> but since most pyMOOSE scripts assume that returned data is numpy array, we return the numpy array. TODO: benchmarking. * Fixed: moose.le can caused segfault when used on moose.vec This also fixes script mgblock.py BhallaLab/moose-examples#71 * Fixed: moose.le can caused segfault when used on moose.vec This also fixes script mgblock.py BhallaLab/moose-examples#71 * removed mkdoc.py from pybind11. * Fixed a pylint error as well python2/python3 compatibility * wildcard -> reacSystemPath Stoic::path is depreacted bcause it collides with Neutral::path. * Fixed another set. * Travis fix: Install pytest on OSX as well. * fix gitlab pipeline install pytest * isinstance is replace to isA added to this, validation.py: error msg is sent back, writeKkit.py: while writting genesis file if any object is not written then errorlog is send/printed which is usefull durning command line * fix test py_run. Relax the matching to 90% using difflib (from 95%). * grenerate documentation on the fly. * Work in progress: __doc__ string from cWork in progress: __doc__ string from cWork in progress: __doc__ string from cWork in progress: __doc__ string from c++ * Keeping the C++ type and Python's type name same. * Cleanup * pydoc support moved moose.py content to __init__.py. This way pydoc works great also fixed travis build. * moose.doc is working now. _moose.generateDoc is the underlying function. Needs to cleanup documentation a bit now. Fixed regression. * update to docs Disabled C++ signature in Python documentations. Added docstring to __init__.py * more docstring are added [skip ci] * Added datetime and other string to version_info. * All functions have docstring. * loadmodel docstring is added. * temp commit. * showmsg is ported to c++. * added more docstring and moved some functions to public api. * Merged hrani changes and mine from new bindings. removed 'basestring' * # This is a combination of 2 commits. # This is the 1st commit message: python2 support. Added python2 support as well. It will be easy to remove later. _moose.element is a good way to convert string/objid/id to melement. # This is the commit message #2: writeKkit * python2 support. Added python2 support as well. It will be easy to remove later. _moose.element is a good way to convert string/objid/id to melement. writeKkit python2 support. Added python2 support as well. It will be easy to remove later. python2 support. Added python2 support as well. It will be easy to remove later. _moose.element is a good way to convert string/objid/id to melement. writeKkit python2 support. Added python2 support as well. It will be easy to remove later. * basestring -> str * fixes to `pip install` Added missing folders. * Fixed pylint error. * moose.getField accepts two argument instead of 3. Updated rmogul.py file. * fix: compiles with clang++ typeid(X) when X is an incomplete type is not supported by C++ standard. Suprisingly this was compiling fine with gcc but not with clang++. version is set to 3.2.0.dev$(today) * travis fixes: OSX PyRun tests compares last 50 lines rather than whole text. This way we can ignore lines with different timestamp. * builds on osx locally. * tests passes with 3.8 as well. * On OSX, stream does not flush properly? Using difflib to test the ratio between got and expected string. * flush the streams before calling tests... * Don't run the trvais/osx Not sure why but only on travis+OSX, pyrun test does not pass. It fails because whole buffer is not dumped to the tty. * Fixes to pyrun tests. * Time to post the API. * listmsg has been moved to C++. * docstring to writeNML2 * Fixed typo in docstring. Ready to be reviewed. * showfield and showfields are both supported. `moose.showfield` is an alias for `moose.showfields`. * Added back moose.ce Co-authored-by: Dilawar Singh <[email protected]> Co-authored-by: HarshaRani <[email protected]> Co-authored-by: Anushree Narjala <[email protected]> * loadModel does not return a tuple anymore. Not sure when this changes were made but someplace loadModel assumes a tuple is returned and other place it does not. * Fixes to issue #414 - Tweaks to rdesigneur - Added missing function overloads in the python API. * Added missing __version__, version() still works. * Integrated fixes #419, #420 Co-authored-by: Dilawar Singh <[email protected]> Co-authored-by: Dilawar Singh <[email protected]> Co-authored-by: HarshaRani <[email protected]> Co-authored-by: Anushree Narjala <[email protected]>
* replace getId->id, getId().value,getDataIndex->dataIndex isnstance->isA due to changes in new python binding commit * replace isinstance to isA * missing of closing brackets * missing of closing brackets
#405) * closes #401 * Fixed another bug: -DWTIH_BOOST=ON could not override GSL after WITH_GSL was cached by cmake. Ie, if once built with default options, there was no way to use BOOST without cleaning up the old build completely. * Fix #409 When `moose.Function('abc')` is created, set expression to "0". Expression is not empty by default. This is to mimic the old behaviour. Note that at this point, derivative is not defined and is `nan` (old behaviour: derivative is 0.0). * New python bindings using pybind11 (#410) * not a bug. * Turned scripts recieved from harsha into a test case. open #402. * Renamed wrapper.Neutral to __Wrapper__. With new API, this functionality can be built in. * closes #401 * Fixed another bug: -DWTIH_BOOST=ON could not override GSL after WITH_GSL was cached by cmake. Ie, if once built with default options, there was no way to use BOOST without cleaning up the old build completely. * check is made if solver has space while reading/writing SBML files,small change to port the code to py3 * Squashed commit of the following: commit b313f8d72537b6d8218857d0f0ef81268bc05f81 Author: Dilawar Singh <[email protected]> Date: Sun Apr 12 19:03:24 2020 +0530 moved __init__.py and moose.py to pybind folder. commit 77afafd49dc6e99b1c00c060b00181d1190e1c7b Author: Dilawar Singh <[email protected]> Date: Sun Apr 12 18:03:28 2020 +0530 Use not gui backend. commit 6ad911c73c5f9d01846c5869263c12ee82e1bdf8 Author: Dilawar Singh <[email protected]> Date: Sun Apr 12 13:23:33 2020 +0530 Variable and Cinfo need not be exposed. commit 5fec8497593a9d77b5ed5832336747c6cd8fb33c Author: Dilawar Singh <[email protected]> Date: Sun Apr 12 12:27:13 2020 +0530 Create moose element from vec and field. commit ab3d85dc0f023a4cda2a9cf7ecfae97d860567b2 Author: Dilawar Singh <[email protected]> Date: Sun Apr 12 11:21:21 2020 +0530 Added support for ["string", double] valueFinfoItem. commit 9c967c02abd565c90d452d200f778e1d2ed78349 Author: Anushree Narjala <[email protected]> Date: Sun Apr 12 10:03:17 2020 +0530 seed is an int and can't be empty. commit cc7ea95 Author: Dilawar Singh <[email protected]> Date: Sat Apr 11 15:46:11 2020 +0530 This is a really good commit. `.num` is supported now. commit 2185c65 Author: Dilawar Singh <[email protected]> Date: Sat Apr 11 12:28:39 2020 +0530 Added doxygen target. commit 32c3fc7 Author: Dilawar Singh <[email protected]> Date: Fri Apr 10 13:09:09 2020 +0530 Finfo is also vectorised. commit d716124 Author: Dilawar Singh <[email protected]> Date: Fri Apr 10 12:03:53 2020 +0530 Negative indexing is allowed. Fixes one more moose-examples neuroml/LIF/twoLIFxml_firing.py commit a2d6a38 Author: Dilawar Singh <[email protected]> Date: Thu Apr 9 21:07:04 2020 +0530 Use old PyRun code. Pybind11 does not have subterpreter support. commit 2587c0d Author: Dilawar Singh <[email protected]> Date: Thu Apr 9 13:58:16 2020 +0530 Added a test for testing pyrun. commit f3a4925 Author: Dilawar Singh <[email protected]> Date: Thu Apr 9 11:25:11 2020 +0530 when `-DWITH_BOOST=ON` is passed to cmake, it now overrides `WITH_GSL` option. Also fixes build failure. commit 2127c3a Author: Dilawar Singh <[email protected]> Date: Thu Apr 9 11:15:01 2020 +0530 Fixes https://gitlab.com/dilawar/moose-core/-/issues/7 commit 31f2b8f Author: Dilawar Singh <[email protected]> Date: Wed Apr 8 23:16:37 2020 +0530 If Function is not valid_, return quietly. commit b91a0ef Author: Dilawar Singh <[email protected]> Date: Wed Apr 8 22:25:06 2020 +0530 All tests are passing now. commit 0ce71ac Author: Dilawar Singh <[email protected]> Date: Wed Apr 8 20:13:39 2020 +0530 genesis and kkit are reverted back to master. commit 6535c46 Author: Dilawar Singh <[email protected]> Date: Wed Apr 8 19:03:13 2020 +0530 isA is working just fine. commit bf118f4 Author: Dilawar Singh <[email protected]> Date: Wed Apr 8 14:18:23 2020 +0530 We can now assign moose.vec to a field which takes Id. refactoring. int -> double, bool -> (int, double) coercing is allowed. Fixed script /home1/dilawars/Work.HG/GITLAB/moose-examples/snippets/interpol2d.py in https://gitlab.com/dilawar/moose-examples/-/issues/1 commit fb57aaf Author: Dilawar Singh <[email protected]> Date: Wed Apr 8 13:21:19 2020 +0530 overloading template function is not so straight-forward when typecasting can happen by itslf e.g. int and unsigned int. commit 22aeb43 Author: Dilawar Singh <[email protected]> Date: Wed Apr 8 09:52:57 2020 +0530 moose.element return single ObjId and not vec as I mistakenly assumed. commit ea81f1c Author: Dilawar Singh <[email protected]> Date: Tue Apr 7 21:45:13 2020 +0530 Vectorize function later. commit 4624651 Author: Dilawar Singh <[email protected]> Date: Tue Apr 7 20:48:47 2020 +0530 name, path, and parent of moose.vec are not vectorised. commit 6126a64 Author: Dilawar Singh <[email protected]> Date: Tue Apr 7 19:20:28 2020 +0530 snippets/savemodel.py is causing problem now. commit 15eae1d Author: Dilawar Singh <[email protected]> Date: Tue Apr 7 18:08:37 2020 +0530 vec values are returned as numpy array. commit cc89202 Author: Dilawar Singh <[email protected]> Date: Tue Apr 7 16:55:00 2020 +0530 Default parameters in connect is now working. First argument is not needed if it is a class member function. commit 8092a8e Author: Dilawar Singh <[email protected]> Date: Tue Apr 7 16:19:16 2020 +0530 If a Shell function retuns Id, wrap it in a MooseVec. The current API has this behaviour. commit 8ca430c Author: Dilawar Singh <[email protected]> Date: Tue Apr 7 13:54:52 2020 +0530 TODO: Id should be wrapped as moose.vec commit d6552e6 Author: Dilawar Singh <[email protected]> Date: Tue Apr 7 12:05:31 2020 +0530 Passes snippets/synapse.py https://gitlab.com/dilawar/moose-examples/-/issues/1 commit 3ea0a66 Author: Dilawar Singh <[email protected]> Date: Tue Apr 7 11:23:27 2020 +0530 Support more return types. commit 0862930 Author: Dilawar Singh <[email protected]> Date: Tue Apr 7 10:44:35 2020 +0530 MooseVec can now handle fieldElement as well. commit 1d40e74 Author: Dilawar Singh <[email protected]> Date: Mon Apr 6 21:03:58 2020 +0530 Needs some major overhaul of API. commit 3116b05 Author: Dilawar Singh <[email protected]> Date: Mon Apr 6 15:04:32 2020 +0530 Removed melement. commit 8baffdc Author: Dilawar Singh <[email protected]> Date: Mon Apr 6 15:00:59 2020 +0530 Support more fieldType. Fixes one more failing script in moose examples. commit b3a3e84 Author: Dilawar Singh <[email protected]> Date: Mon Apr 6 14:01:28 2020 +0530 Time to run examples now. commit 731fc47 Author: Dilawar Singh <[email protected]> Date: Mon Apr 6 13:44:38 2020 +0530 type checking has been moved to C++ code. its bit tricky here and not as readable as it should be. May be I can leave this at the python level. commit 790efdf Author: Dilawar Singh <[email protected]> Date: Mon Apr 6 13:24:30 2020 +0530 Some more progress. Getting a bit more faster than the current API. commit 4e24621 Author: Dilawar Singh <[email protected]> Date: Mon Apr 6 13:17:18 2020 +0530 Overloaded funtions. commit bc95f4d Author: Dilawar Singh <[email protected]> Date: Mon Apr 6 12:25:23 2020 +0530 Enabled helper functions. commit aeecc41 Author: Dilawar Singh <[email protected]> Date: Mon Apr 6 00:17:06 2020 +0530 beat the old api in microbenchmarks as well. commit 6e88eff Author: Dilawar Singh <[email protected]> Date: Sun Apr 5 23:56:00 2020 +0530 minor tweaks. commit 1dd9390 Author: Dilawar Singh <[email protected]> Date: Sun Apr 5 23:46:37 2020 +0530 moose.create is fast but moose.delete is bit slow. commit 0eda1b7 Author: Dilawar Singh <[email protected]> Date: Sun Apr 5 22:39:37 2020 +0530 forward declaration and compile fixes. commit a3bdd69 Author: Dilawar Singh <[email protected]> Date: Sun Apr 5 20:05:43 2020 +0530 Added benchmark file. commit e294eea Author: Dilawar Singh <[email protected]> Date: Sun Apr 5 19:55:01 2020 +0530 added micro benchmarks. commit 5979dc4 Author: Dilawar Singh <[email protected]> Date: Sat Apr 4 23:25:28 2020 +0530 Added documentations. commit 56c12f4 Author: Dilawar Singh <[email protected]> Date: Sat Apr 4 22:21:40 2020 +0530 All tests are passing.. needs to add some tests.. commit f039fad Author: Dilawar Singh <[email protected]> Date: Sat Apr 4 21:58:28 2020 +0530 _cmoose to _moose. commit 9543258 Author: Dilawar Singh <[email protected]> Date: Sat Apr 4 19:57:21 2020 +0530 Needs to fix some more API issues. commit 4d6c147 Author: Dilawar Singh <[email protected]> Date: Sat Apr 4 17:49:15 2020 +0530 Added version 2.5 commit f0efd21 Author: Dilawar Singh <[email protected]> Date: Sat Apr 4 17:41:41 2020 +0530 Removed a broken test and renamed one. The namedvars tests is moved to fixme (not supported). commit cd3dc5a Author: Dilawar Singh <[email protected]> Date: Sat Apr 4 12:11:59 2020 +0530 Needs final touch. commit 5262dc4 Author: Dilawar Singh <[email protected]> Date: Sat Apr 4 12:03:56 2020 +0530 Added one more missing attribute. commit 7757643 Author: Dilawar Singh <[email protected]> Date: Sat Apr 4 11:25:53 2020 +0530 test commit [skip ci] commit cb8a970 Author: Dilawar Singh <[email protected]> Date: Sat Apr 4 10:28:06 2020 +0530 old test is back. commit 06e3357 Author: Dilawar Singh <[email protected]> Date: Sat Apr 4 10:24:53 2020 +0530 Fixed the issue with isinstance(x, moose.CubeMesh). Now it is working fine. commit 685ab75 Author: Dilawar Singh <[email protected]> Date: Sat Apr 4 07:26:24 2020 +0530 One more test is passing. commit 6188e09 Author: Dilawar Singh <[email protected]> Date: Sat Apr 4 07:25:25 2020 +0530 Restored old values in the test. commit 349f8ea Author: Dilawar Singh <[email protected]> Date: Sat Apr 4 05:55:15 2020 +0530 fixes to one more tests. commit c90986a Author: Dilawar Singh <[email protected]> Date: Sat Apr 4 05:42:22 2020 +0530 Now do a local testing. commit e6a6575 Author: Dilawar Singh <[email protected]> Date: Sat Apr 4 05:37:26 2020 +0530 numerical assertion of oscillatory tests are hard. commit 5af49e9 Author: Dilawar Singh <[email protected]> Date: Sat Apr 4 05:26:34 2020 +0530 Almost all tests are passing. commit d7f03bd Author: Dilawar Singh <[email protected]> Date: Sat Apr 4 04:54:44 2020 +0530 remove 'value' attribute from the ObjId, it was conflicting with MString 'value'. commit ce79591 Author: Dilawar Singh <[email protected]> Date: Sat Apr 4 04:43:36 2020 +0530 Needs to fix doc. commit 113dddc Author: Dilawar Singh <[email protected]> Date: Sat Apr 4 04:36:02 2020 +0530 more tests are passing. all test_Xreacs are passing now. commit 29ff41c Author: Dilawar Singh <[email protected]> Date: Sat Apr 4 04:31:33 2020 +0530 Use ObjId instread of Id in buildMeshJunction. commit 33e9591 Author: Dilawar Singh <[email protected]> Date: Sat Apr 4 04:27:38 2020 +0530 Passing ObjId as Id is creating trouble. commit 537779e Author: Dilawar Singh <[email protected]> Date: Sat Apr 4 03:59:30 2020 +0530 one more test passes. commit 650309a Author: Dilawar Singh <[email protected]> Date: Sat Apr 4 03:05:28 2020 +0530 delete works. commit b13e051 Author: Dilawar Singh <[email protected]> Date: Sat Apr 4 02:13:31 2020 +0530 Some more tests [skip ci] commit e518d35 Author: Dilawar Singh <[email protected]> Date: Sat Apr 4 01:42:15 2020 +0530 One more test is passed. commit c783578 Author: Dilawar Singh <[email protected]> Date: Sat Apr 4 01:37:24 2020 +0530 isinstance support is added. commit 2a28f9a Author: Dilawar Singh <[email protected]> Date: Fri Apr 3 22:15:46 2020 +0530 Added tests to normalizepath. commit 4c2086a Author: Dilawar Singh <[email protected]> Date: Fri Apr 3 22:08:30 2020 +0530 Global random number generator is moved from basecode to randnum. commit 6a2b7b7 Author: Dilawar Singh <[email protected]> Date: Fri Apr 3 20:09:21 2020 +0530 Couple of seg-faults to take care of. commit 8a90db2 Author: Dilawar Singh <[email protected]> Date: Fri Apr 3 18:27:52 2020 +0530 Fixed one more test. commit 1798a1e Author: Dilawar Singh <[email protected]> Date: Fri Apr 3 14:18:47 2020 +0530 Need to fix rdesignuer now. commit 0be10c0 Author: Dilawar Singh <[email protected]> Date: Fri Apr 3 12:59:16 2020 +0530 Finfo can also return .vec. commit 226d616 Author: Dilawar Singh <[email protected]> Date: Fri Apr 3 12:35:32 2020 +0530 Function is also fixed. commit b68a97b Author: Dilawar Singh <[email protected]> Date: Fri Apr 3 12:22:29 2020 +0530 SynapseTest is also passing. commit 8f2a039 Author: Dilawar Singh <[email protected]> Date: Fri Apr 3 11:38:20 2020 +0530 Fixes all the c++ tests commit 173b9d2 Author: Dilawar Singh <[email protected]> Date: Fri Apr 3 11:28:47 2020 +0530 ObjId.vec create a vec on the fly. commit e71fea0 Author: Dilawar Singh <[email protected]> Date: Thu Apr 2 22:39:02 2020 +0530 Same problem on OSX. One more test is failing. commit 47e25f9 Author: Dilawar Singh <[email protected]> Date: Thu Apr 2 22:08:41 2020 +0530 Some more fixes. moose.element is not honoring dataIndex. commit 9de507a Author: Dilawar Singh <[email protected]> Date: Thu Apr 2 20:17:29 2020 +0530 bebug vec and connection list. commit d7f0a26 Author: Dilawar Singh <[email protected]> Date: Thu Apr 2 19:22:00 2020 +0530 Refactoring. commit 2221410 Author: Dilawar Singh <[email protected]> Date: Thu Apr 2 16:17:48 2020 +0530 Added .clang-format file. commit 7a8437d Author: Dilawar Singh <[email protected]> Date: Thu Apr 2 12:44:32 2020 +0530 more progress. Lets have lunch first now. commit 0ed8933 Author: Dilawar Singh <[email protected]> Date: Thu Apr 2 12:25:44 2020 +0530 Fix Xreacs later. commit 04d4d2f Author: Dilawar Singh <[email protected]> Date: Thu Apr 2 11:52:19 2020 +0530 Refactoring. If Finfo* is passed, no need to pass rttitype and fname. We can get these values from Finfo. commit 77cc0b1 Author: Dilawar Singh <[email protected]> Date: Wed Apr 1 21:21:06 2020 +0530 refacorted codebase... commit 52cfdf7 Author: Dilawar Singh <[email protected]> Date: Wed Apr 1 21:06:13 2020 +0530 Added extra header for Finfo ... commit b16dd1c Author: Dilawar Singh <[email protected]> Date: Wed Apr 1 19:58:56 2020 +0530 Needs to implement LookupFinfo set. commit 8199fc0 Author: Dilawar Singh <[email protected]> Date: Wed Apr 1 18:48:25 2020 +0530 Disable pybind11. commit 5c25dad Author: Dilawar Singh <[email protected]> Date: Wed Apr 1 18:48:02 2020 +0530 One more tests seem to pass. commit 40a4559 Author: Dilawar Singh <[email protected]> Date: Wed Apr 1 18:22:52 2020 +0530 Some more fixes. commit dd9b50e Author: Dilawar Singh <[email protected]> Date: Wed Apr 1 17:59:50 2020 +0530 Perfect. One more test passes. commit fec019b Author: Dilawar Singh <[email protected]> Date: Wed Apr 1 15:41:22 2020 +0530 Refactoring and some more generic programming. commit 9eb2308 Author: Dilawar Singh <[email protected]> Date: Tue Mar 31 20:48:57 2020 +0530 small fixes. Changes in API requires .id . commit 7de3228 Author: Dilawar Singh <[email protected]> Date: Tue Mar 31 19:13:51 2020 +0530 Minor tweak to a test. commit c541b91 Author: Dilawar Singh <[email protected]> Date: Tue Mar 31 19:08:36 2020 +0530 One more test passed. commit 5cc3d3b Merge: ce579ac 1abb6f1 Author: Dilawar Singh <[email protected]> Date: Tue Mar 31 18:59:23 2020 +0530 Merge branch 'pybind11_shell' into temp commit ce579ac Author: Dilawar Singh <[email protected]> Date: Tue Mar 31 18:58:59 2020 +0530 renmaed. commit 16bbc3e Author: Dilawar Singh <[email protected]> Date: Tue Mar 31 18:20:55 2020 +0530 phew. I made a boo boo before. commit 1abb6f1 Merge: 24df86a fa06c38 Author: Dilawar Singh <[email protected]> Date: Tue Mar 31 02:24:30 2020 +0530 Merge branch 'pybind11_shell' of gitlab.com:dilawar/moose-core into pybind11_shell commit fa06c38 Author: Dilawar Singh <[email protected]> Date: Tue Mar 31 02:14:22 2020 +0530 Id and ObjId are not playing well together... commit 48832b1 Author: Dilawar Singh <[email protected]> Date: Tue Mar 31 01:30:34 2020 +0530 test_synchan is a good example; possible we should return moose.vec there. commit 8667c13 Author: Dilawar Singh <[email protected]> Date: Tue Mar 31 01:28:02 2020 +0530 temp commit. commit 24df86a Author: Dilawar Singh <[email protected]> Date: Mon Mar 30 23:39:46 2020 +0530 Temp commit. Exposing only Id. commit 448b8b5 Author: Dilawar Singh <[email protected]> Date: Mon Mar 30 23:14:51 2020 +0530 more tests are passing... commit d1b4990 Author: Dilawar Singh <[email protected]> Date: Mon Mar 30 20:35:39 2020 +0530 Need to find a solution.. commit 6b5082b Author: Dilawar Singh <[email protected]> Date: Mon Mar 30 19:05:44 2020 +0530 Refactoring and have a working moose.vec API. commit 98d8d34 Author: Dilawar Singh <[email protected]> Date: Mon Mar 30 18:05:07 2020 +0530 [skip ci] needs tweaking in the API. commit 0f7929c Author: Dilawar Singh <[email protected]> Date: Mon Mar 30 14:40:37 2020 +0530 Support vec. But first need a nap. commit 93d6e83 Author: Dilawar Singh <[email protected]> Date: Mon Mar 30 13:33:05 2020 +0530 refactoring. commit fd03015 Author: Dilawar Singh <[email protected]> Date: Mon Mar 30 13:17:31 2020 +0530 random works. commit fc34547 Author: Dilawar Singh <[email protected]> Date: Mon Mar 30 11:49:00 2020 +0530 Need to polish the API. commit 6af0f2c Author: Dilawar Singh <[email protected]> Date: Mon Mar 30 11:00:03 2020 +0530 Lets move to DestFinfo. commit 476d700 Author: Dilawar Singh <[email protected]> Date: Mon Mar 30 07:53:31 2020 +0530 Return type. commit 778208a Merge: dab5af4 dd65791 Author: Dilawar Singh <[email protected]> Date: Mon Mar 30 07:42:04 2020 +0530 Merge branch 'pybind11_shell' of gitlab.com:dilawar/moose-core into pybind11_shell commit dd65791 Author: Dilawar Singh <[email protected]> Date: Mon Mar 30 06:54:42 2020 +0530 Updated [skip ci] commit 76ec2a1 Author: Dilawar Singh <[email protected]> Date: Sun Mar 29 23:00:02 2020 +0530 [skip ci] some more changes. commit c4d7bc6 Author: Dilawar Singh <[email protected]> Date: Sun Mar 29 22:24:57 2020 +0530 We go both API integrated. commit f0ac785 Author: Dilawar Singh <[email protected]> Date: Sun Mar 29 21:48:18 2020 +0530 LookupField is a function. commit aee928e Author: Dilawar Singh <[email protected]> Date: Sun Mar 29 21:11:48 2020 +0530 Do the rest tomorrow. commit e118e12 Author: Dilawar Singh <[email protected]> Date: Sun Mar 29 20:45:21 2020 +0530 Retuning binding to std::function which return the Finfo value. commit dab5af4 Author: Dilawar Singh <[email protected]> Date: Sun Mar 29 18:01:12 2020 +0530 isA is method. Time to make it a subscriptable dictionary. commit c7a7b24 Author: Dilawar Singh <[email protected]> Date: Sun Mar 29 15:34:42 2020 +0530 Lets handle LookupField::set and get. commit a06e478 Author: Dilawar Singh <[email protected]> Date: Sun Mar 29 01:13:46 2020 +0530 Deal with it tomorrow. commit bb1cae5 Author: Dilawar Singh <[email protected]> Date: Sun Mar 29 00:28:22 2020 +0530 Getting there. [skip ci] commit 5cccf8b Author: Dilawar Singh <[email protected]> Date: Sat Mar 28 22:33:21 2020 +0530 Some refactoring. Back to same functionality [skip ci]. commit a979de6 Author: Dilawar Singh <[email protected]> Date: Sat Mar 28 20:46:01 2020 +0530 Updated a bit more .. commit b43c617 Author: Dilawar Singh <[email protected]> Date: Sat Mar 28 19:47:58 2020 +0530 New API works fantastic. commit 0deb291 Author: Dilawar Singh <[email protected]> Date: Sat Mar 28 19:40:19 2020 +0530 Incremental change. Dynamic attributes. commit 7f2539c Author: Dilawar Singh <[email protected]> Date: Sat Mar 28 19:31:31 2020 +0530 Subclassing _ObjId now. commit 0f64cd0 Author: Dilawar Singh <[email protected]> Date: Sat Mar 28 18:12:57 2020 +0530 Dynamic attributes are needed now. commit eff08b2 Author: Dilawar Singh <[email protected]> Date: Sat Mar 28 16:16:13 2020 +0530 All test passes. Needs to work on the API now. commit 8791df7 Author: Dilawar Singh <[email protected]> Date: Sat Mar 28 15:40:35 2020 +0530 Blazingly fast. commit 070f735 Author: Dilawar Singh <[email protected]> Date: Sat Mar 28 14:06:47 2020 +0530 Perfect. The base API works now. Not time to do a profiling. commit 07a1348 Author: Dilawar Singh <[email protected]> Date: Sat Mar 28 00:28:22 2020 +0530 This is for tomorow. commit 72f7b62 Author: Dilawar Singh <[email protected]> Date: Fri Mar 27 21:43:33 2020 +0530 Work from home. commit 4ea29e9 Author: Dilawar Singh <[email protected]> Date: Fri Mar 27 20:32:19 2020 +0530 May be later. commit eff6f90 Author: Dilawar Singh <[email protected]> Date: Fri Mar 27 17:57:40 2020 +0530 Not sure about the testKsolve.cpp tests. commit bef104c Author: Dilawar Singh <[email protected]> Date: Fri Mar 27 17:11:34 2020 +0530 Do testing with master branch. commit 0078af1 Author: Dilawar Singh <[email protected]> Date: Fri Mar 27 14:45:40 2020 +0530 get can not overloaded pretty well. Use different name for getting different value. It is verbose now but we can override later. commit 915e10f Merge: 911bd03 bf2d609 Author: Dilawar Singh <[email protected]> Date: Fri Mar 27 13:56:46 2020 +0530 Merge branch 'pybind11_shell' of gitlab.com:dilawar/moose-core into pybind11_shell commit bf2d609 Author: Dilawar Singh <[email protected]> Date: Fri Mar 27 14:11:18 2020 +0530 add test function. commit 911bd03 Author: Dilawar Singh <[email protected]> Date: Fri Mar 27 13:56:12 2020 +0530 local changes. commit cc7144f Author: Dilawar Singh <[email protected]> Date: Fri Mar 27 13:50:40 2020 +0530 Move to gulgula. commit d41e7eb Author: Dilawar Singh <[email protected]> Date: Fri Mar 27 04:18:44 2020 +0530 Allmost there. commit d913ceb Author: Dilawar Singh <[email protected]> Date: Fri Mar 27 01:50:18 2020 +0530 addMsg -> connect . commit 8793d33 Author: Dilawar Singh <[email protected]> Date: Fri Mar 27 01:10:24 2020 +0530 get/set are on ObjId . commit d99115c Author: Dilawar Singh <[email protected]> Date: Fri Mar 27 00:47:20 2020 +0530 Ok. Vector and numpy are working. commit 2f3bc04 Author: Dilawar Singh <[email protected]> Date: Thu Mar 26 23:02:03 2020 +0530 move to bebinca for fast compilation. commit a94fec9 Author: Dilawar Singh <[email protected]> Date: Thu Mar 26 18:29:50 2020 +0530 children and parent is not working. commit 756ec3a Author: Dilawar Singh <[email protected]> Date: Wed Mar 25 14:53:17 2020 +0530 Some more fixes. It will be too much debugging to get it right. commit 77451f1 Author: Dilawar Singh <[email protected]> Date: Tue Mar 24 15:07:09 2020 +0530 All the learning experience is over. Pybind11 is great. commit 6edda7a Author: Dilawar Singh <[email protected]> Date: Tue Mar 24 00:55:13 2020 +0530 Add a bit more fields. commit e32c468 Author: Dilawar Singh <[email protected]> Date: Mon Mar 23 23:30:19 2020 +0530 I can complete this API tomorrow. commit 7aaddf7 Author: Dilawar Singh <[email protected]> Date: Mon Mar 23 22:54:35 2020 +0530 added more functions [skip ci] commit 7f1b709 Author: Dilawar Singh <[email protected]> Date: Mon Mar 23 16:38:34 2020 +0530 disable build for now on gitlab ci commit ae2739d Author: Dilawar Singh <[email protected]> Date: Mon Mar 23 15:05:22 2020 +0530 pybind11 module is named _cmoose and it different from _moose. commit 0c33684 Author: Dilawar Singh <[email protected]> Date: Mon Mar 23 14:45:32 2020 +0530 I got wildcardFind to function. commit 65b307c Author: Dilawar Singh <[email protected]> Date: Mon Mar 23 13:33:22 2020 +0530 Fixed the bug I caused by using smart pointer. I am so silly... commit fe596e3 Merge: d5d29bb f4070da Author: Dilawar Singh <[email protected]> Date: Mon Mar 23 12:45:01 2020 +0530 Merge branch 'issue_397' of gitlab.com:dilawar/moose-core into pybind11 commit d5d29bb Author: Dilawar Singh <[email protected]> Date: Sun Mar 22 23:12:58 2020 +0530 Time to support / in path. commit 270ea8c Author: Dilawar Singh <[email protected]> Date: Sun Mar 22 22:50:21 2020 +0530 empty element() commit a1eed3a Author: Dilawar Singh <[email protected]> Date: Sun Mar 22 22:39:55 2020 +0530 temp commit. commit a70b5fe Author: Dilawar Singh <[email protected]> Date: Sun Mar 22 15:44:56 2020 +0530 Great. Lets try cython as well. commit 038490f Author: Dilawar Singh <[email protected]> Date: Sun Mar 22 15:44:27 2020 +0530 Try cython now. commit 8bbf900 Author: Dilawar Singh <[email protected]> Date: Sun Mar 22 13:43:02 2020 +0530 _moose goes to python/moose directory. commit 014bde2 Merge: 8f60899 ad58dc5 Author: Dilawar Singh <[email protected]> Date: Sun Mar 22 13:18:20 2020 +0530 Merge branch 'issue_397' into pybind11 commit f4070da Merge: ad58dc5 5e660e9 Author: Dilawar Singh <[email protected]> Date: Sat Mar 21 22:21:16 2020 +0530 Merge branch 'refactoring' into issue_397 commit 5e660e9 Author: dilawars <[email protected]> Date: Sat Mar 21 21:24:21 2020 +0530 include cmath in Pool.cpp as well. Failed compilation with gcc5.3 commit ad58dc5 Author: dilawars <[email protected]> Date: Sat Mar 21 21:24:21 2020 +0530 include cmath in Pool.cpp as well. Failed compilation with gcc5.3 commit c4d55aa Author: Dilawar Singh <[email protected]> Date: Sat Mar 21 15:45:16 2020 +0530 Minor cleanup in macros and loggers. numCores now use thread library to determine number of available threads. commit f8dcb12 Author: Dilawar Singh <[email protected]> Date: Sat Mar 21 15:32:02 2020 +0530 NUMPY is essential dependency; therefore numpy code is no longer included conditionally. USE_NUMPY is implied and have been removed from cmake. commit 9ef658e Author: Dilawar Singh <[email protected]> Date: Sat Mar 21 15:15:43 2020 +0530 Fix to #397 commit 8f60899 Author: Dilawar Singh <[email protected]> Date: Tue Mar 17 18:27:54 2020 +0530 Perfecto. Create works. commit aa95a0c Author: Dilawar Singh <[email protected]> Date: Sun Mar 15 22:10:07 2020 +0530 pybind11 bindings. commit da9d1d9 Merge: 0e85a57 36c0026 Author: Dilawar Singh <[email protected]> Date: Sun Mar 15 15:40:06 2020 +0530 Merge commit '36c0026886c70e39c505f8715e65a7c3cf1e6ade' as 'external/pybind11' commit 36c0026 Author: Dilawar Singh <[email protected]> Date: Sun Mar 15 15:40:06 2020 +0530 Squashed 'external/pybind11/' content from commit 4f72ef846 git-subtree-dir: external/pybind11 git-subtree-split: 4f72ef846fe8453596230ac285eeaa0ce3278bb4 * Minor fixes to pybind11. * Fix #409 When `moose.Function('abc')` is created, set expression to "0". Expression is not empty by default. This is to mimic the old behaviour. Note that at this point, derivative is not defined and is `nan` (old behaviour: derivative is 0.0). * Ready for a draft PR and initial disucssion. * Return numpy array instead of vector. Probably not the most memory efficient way for returning vector<double> but since most pyMOOSE scripts assume that returned data is numpy array, we return the numpy array. TODO: benchmarking. * Fixed: moose.le can caused segfault when used on moose.vec This also fixes script mgblock.py BhallaLab/moose-examples#71 * Fixed: moose.le can caused segfault when used on moose.vec This also fixes script mgblock.py BhallaLab/moose-examples#71 * removed mkdoc.py from pybind11. * Fixed a pylint error as well python2/python3 compatibility * wildcard -> reacSystemPath Stoic::path is depreacted bcause it collides with Neutral::path. * Fixed another set. * Travis fix: Install pytest on OSX as well. * fix gitlab pipeline install pytest * isinstance is replace to isA added to this, validation.py: error msg is sent back, writeKkit.py: while writting genesis file if any object is not written then errorlog is send/printed which is usefull durning command line * fix test py_run. Relax the matching to 90% using difflib (from 95%). * grenerate documentation on the fly. * Work in progress: __doc__ string from cWork in progress: __doc__ string from cWork in progress: __doc__ string from cWork in progress: __doc__ string from c++ * Keeping the C++ type and Python's type name same. * Cleanup * pydoc support moved moose.py content to __init__.py. This way pydoc works great also fixed travis build. * moose.doc is working now. _moose.generateDoc is the underlying function. Needs to cleanup documentation a bit now. Fixed regression. * update to docs Disabled C++ signature in Python documentations. Added docstring to __init__.py * more docstring are added [skip ci] * Added datetime and other string to version_info. * All functions have docstring. * loadmodel docstring is added. * temp commit. * showmsg is ported to c++. * added more docstring and moved some functions to public api. * Merged hrani changes and mine from new bindings. removed 'basestring' * # This is a combination of 2 commits. # This is the 1st commit message: python2 support. Added python2 support as well. It will be easy to remove later. _moose.element is a good way to convert string/objid/id to melement. # This is the commit message #2: writeKkit * python2 support. Added python2 support as well. It will be easy to remove later. _moose.element is a good way to convert string/objid/id to melement. writeKkit python2 support. Added python2 support as well. It will be easy to remove later. python2 support. Added python2 support as well. It will be easy to remove later. _moose.element is a good way to convert string/objid/id to melement. writeKkit python2 support. Added python2 support as well. It will be easy to remove later. * basestring -> str * fixes to `pip install` Added missing folders. * Fixed pylint error. * moose.getField accepts two argument instead of 3. Updated rmogul.py file. * fix: compiles with clang++ typeid(X) when X is an incomplete type is not supported by C++ standard. Suprisingly this was compiling fine with gcc but not with clang++. version is set to 3.2.0.dev$(today) * travis fixes: OSX PyRun tests compares last 50 lines rather than whole text. This way we can ignore lines with different timestamp. * builds on osx locally. * tests passes with 3.8 as well. * On OSX, stream does not flush properly? Using difflib to test the ratio between got and expected string. * flush the streams before calling tests... * Don't run the trvais/osx Not sure why but only on travis+OSX, pyrun test does not pass. It fails because whole buffer is not dumped to the tty. * Fixes to pyrun tests. * Time to post the API. * listmsg has been moved to C++. * docstring to writeNML2 * Fixed typo in docstring. Ready to be reviewed. * showfield and showfields are both supported. `moose.showfield` is an alias for `moose.showfields`. * Added back moose.ce Co-authored-by: Dilawar Singh <[email protected]> Co-authored-by: HarshaRani <[email protected]> Co-authored-by: Anushree Narjala <[email protected]> * Use isclose instread of == * removed duplicate test which was causing build failure. Co-authored-by: Dilawar Singh <[email protected]> Co-authored-by: Dilawar Singh <[email protected]> Co-authored-by: HarshaRani <[email protected]> Co-authored-by: Anushree Narjala <[email protected]>
* Merged hrani changes and mine from new bindings. removed 'basestring' * New python bindings using pybind11 (#410) * not a bug. * Turned scripts recieved from harsha into a test case. open #402. * Renamed wrapper.Neutral to __Wrapper__. With new API, this functionality can be built in. * closes #401 * Fixed another bug: -DWTIH_BOOST=ON could not override GSL after WITH_GSL was cached by cmake. Ie, if once built with default options, there was no way to use BOOST without cleaning up the old build completely. * check is made if solver has space while reading/writing SBML files,small change to port the code to py3 * Squashed commit of the following: commit b313f8d72537b6d8218857d0f0ef81268bc05f81 Author: Dilawar Singh <[email protected]> Date: Sun Apr 12 19:03:24 2020 +0530 moved __init__.py and moose.py to pybind folder. commit 77afafd49dc6e99b1c00c060b00181d1190e1c7b Author: Dilawar Singh <[email protected]> Date: Sun Apr 12 18:03:28 2020 +0530 Use not gui backend. commit 6ad911c73c5f9d01846c5869263c12ee82e1bdf8 Author: Dilawar Singh <[email protected]> Date: Sun Apr 12 13:23:33 2020 +0530 Variable and Cinfo need not be exposed. commit 5fec8497593a9d77b5ed5832336747c6cd8fb33c Author: Dilawar Singh <[email protected]> Date: Sun Apr 12 12:27:13 2020 +0530 Create moose element from vec and field. commit ab3d85dc0f023a4cda2a9cf7ecfae97d860567b2 Author: Dilawar Singh <[email protected]> Date: Sun Apr 12 11:21:21 2020 +0530 Added support for ["string", double] valueFinfoItem. commit 9c967c02abd565c90d452d200f778e1d2ed78349 Author: Anushree Narjala <[email protected]> Date: Sun Apr 12 10:03:17 2020 +0530 seed is an int and can't be empty. commit cc7ea95 Author: Dilawar Singh <[email protected]> Date: Sat Apr 11 15:46:11 2020 +0530 This is a really good commit. `.num` is supported now. commit 2185c65 Author: Dilawar Singh <[email protected]> Date: Sat Apr 11 12:28:39 2020 +0530 Added doxygen target. commit 32c3fc7 Author: Dilawar Singh <[email protected]> Date: Fri Apr 10 13:09:09 2020 +0530 Finfo is also vectorised. commit d716124 Author: Dilawar Singh <[email protected]> Date: Fri Apr 10 12:03:53 2020 +0530 Negative indexing is allowed. Fixes one more moose-examples neuroml/LIF/twoLIFxml_firing.py commit a2d6a38 Author: Dilawar Singh <[email protected]> Date: Thu Apr 9 21:07:04 2020 +0530 Use old PyRun code. Pybind11 does not have subterpreter support. commit 2587c0d Author: Dilawar Singh <[email protected]> Date: Thu Apr 9 13:58:16 2020 +0530 Added a test for testing pyrun. commit f3a4925 Author: Dilawar Singh <[email protected]> Date: Thu Apr 9 11:25:11 2020 +0530 when `-DWITH_BOOST=ON` is passed to cmake, it now overrides `WITH_GSL` option. Also fixes build failure. commit 2127c3a Author: Dilawar Singh <[email protected]> Date: Thu Apr 9 11:15:01 2020 +0530 Fixes https://gitlab.com/dilawar/moose-core/-/issues/7 commit 31f2b8f Author: Dilawar Singh <[email protected]> Date: Wed Apr 8 23:16:37 2020 +0530 If Function is not valid_, return quietly. commit b91a0ef Author: Dilawar Singh <[email protected]> Date: Wed Apr 8 22:25:06 2020 +0530 All tests are passing now. commit 0ce71ac Author: Dilawar Singh <[email protected]> Date: Wed Apr 8 20:13:39 2020 +0530 genesis and kkit are reverted back to master. commit 6535c46 Author: Dilawar Singh <[email protected]> Date: Wed Apr 8 19:03:13 2020 +0530 isA is working just fine. commit bf118f4 Author: Dilawar Singh <[email protected]> Date: Wed Apr 8 14:18:23 2020 +0530 We can now assign moose.vec to a field which takes Id. refactoring. int -> double, bool -> (int, double) coercing is allowed. Fixed script /home1/dilawars/Work.HG/GITLAB/moose-examples/snippets/interpol2d.py in https://gitlab.com/dilawar/moose-examples/-/issues/1 commit fb57aaf Author: Dilawar Singh <[email protected]> Date: Wed Apr 8 13:21:19 2020 +0530 overloading template function is not so straight-forward when typecasting can happen by itslf e.g. int and unsigned int. commit 22aeb43 Author: Dilawar Singh <[email protected]> Date: Wed Apr 8 09:52:57 2020 +0530 moose.element return single ObjId and not vec as I mistakenly assumed. commit ea81f1c Author: Dilawar Singh <[email protected]> Date: Tue Apr 7 21:45:13 2020 +0530 Vectorize function later. commit 4624651 Author: Dilawar Singh <[email protected]> Date: Tue Apr 7 20:48:47 2020 +0530 name, path, and parent of moose.vec are not vectorised. commit 6126a64 Author: Dilawar Singh <[email protected]> Date: Tue Apr 7 19:20:28 2020 +0530 snippets/savemodel.py is causing problem now. commit 15eae1d Author: Dilawar Singh <[email protected]> Date: Tue Apr 7 18:08:37 2020 +0530 vec values are returned as numpy array. commit cc89202 Author: Dilawar Singh <[email protected]> Date: Tue Apr 7 16:55:00 2020 +0530 Default parameters in connect is now working. First argument is not needed if it is a class member function. commit 8092a8e Author: Dilawar Singh <[email protected]> Date: Tue Apr 7 16:19:16 2020 +0530 If a Shell function retuns Id, wrap it in a MooseVec. The current API has this behaviour. commit 8ca430c Author: Dilawar Singh <[email protected]> Date: Tue Apr 7 13:54:52 2020 +0530 TODO: Id should be wrapped as moose.vec commit d6552e6 Author: Dilawar Singh <[email protected]> Date: Tue Apr 7 12:05:31 2020 +0530 Passes snippets/synapse.py https://gitlab.com/dilawar/moose-examples/-/issues/1 commit 3ea0a66 Author: Dilawar Singh <[email protected]> Date: Tue Apr 7 11:23:27 2020 +0530 Support more return types. commit 0862930 Author: Dilawar Singh <[email protected]> Date: Tue Apr 7 10:44:35 2020 +0530 MooseVec can now handle fieldElement as well. commit 1d40e74 Author: Dilawar Singh <[email protected]> Date: Mon Apr 6 21:03:58 2020 +0530 Needs some major overhaul of API. commit 3116b05 Author: Dilawar Singh <[email protected]> Date: Mon Apr 6 15:04:32 2020 +0530 Removed melement. commit 8baffdc Author: Dilawar Singh <[email protected]> Date: Mon Apr 6 15:00:59 2020 +0530 Support more fieldType. Fixes one more failing script in moose examples. commit b3a3e84 Author: Dilawar Singh <[email protected]> Date: Mon Apr 6 14:01:28 2020 +0530 Time to run examples now. commit 731fc47 Author: Dilawar Singh <[email protected]> Date: Mon Apr 6 13:44:38 2020 +0530 type checking has been moved to C++ code. its bit tricky here and not as readable as it should be. May be I can leave this at the python level. commit 790efdf Author: Dilawar Singh <[email protected]> Date: Mon Apr 6 13:24:30 2020 +0530 Some more progress. Getting a bit more faster than the current API. commit 4e24621 Author: Dilawar Singh <[email protected]> Date: Mon Apr 6 13:17:18 2020 +0530 Overloaded funtions. commit bc95f4d Author: Dilawar Singh <[email protected]> Date: Mon Apr 6 12:25:23 2020 +0530 Enabled helper functions. commit aeecc41 Author: Dilawar Singh <[email protected]> Date: Mon Apr 6 00:17:06 2020 +0530 beat the old api in microbenchmarks as well. commit 6e88eff Author: Dilawar Singh <[email protected]> Date: Sun Apr 5 23:56:00 2020 +0530 minor tweaks. commit 1dd9390 Author: Dilawar Singh <[email protected]> Date: Sun Apr 5 23:46:37 2020 +0530 moose.create is fast but moose.delete is bit slow. commit 0eda1b7 Author: Dilawar Singh <[email protected]> Date: Sun Apr 5 22:39:37 2020 +0530 forward declaration and compile fixes. commit a3bdd69 Author: Dilawar Singh <[email protected]> Date: Sun Apr 5 20:05:43 2020 +0530 Added benchmark file. commit e294eea Author: Dilawar Singh <[email protected]> Date: Sun Apr 5 19:55:01 2020 +0530 added micro benchmarks. commit 5979dc4 Author: Dilawar Singh <[email protected]> Date: Sat Apr 4 23:25:28 2020 +0530 Added documentations. commit 56c12f4 Author: Dilawar Singh <[email protected]> Date: Sat Apr 4 22:21:40 2020 +0530 All tests are passing.. needs to add some tests.. commit f039fad Author: Dilawar Singh <[email protected]> Date: Sat Apr 4 21:58:28 2020 +0530 _cmoose to _moose. commit 9543258 Author: Dilawar Singh <[email protected]> Date: Sat Apr 4 19:57:21 2020 +0530 Needs to fix some more API issues. commit 4d6c147 Author: Dilawar Singh <[email protected]> Date: Sat Apr 4 17:49:15 2020 +0530 Added version 2.5 commit f0efd21 Author: Dilawar Singh <[email protected]> Date: Sat Apr 4 17:41:41 2020 +0530 Removed a broken test and renamed one. The namedvars tests is moved to fixme (not supported). commit cd3dc5a Author: Dilawar Singh <[email protected]> Date: Sat Apr 4 12:11:59 2020 +0530 Needs final touch. commit 5262dc4 Author: Dilawar Singh <[email protected]> Date: Sat Apr 4 12:03:56 2020 +0530 Added one more missing attribute. commit 7757643 Author: Dilawar Singh <[email protected]> Date: Sat Apr 4 11:25:53 2020 +0530 test commit [skip ci] commit cb8a970 Author: Dilawar Singh <[email protected]> Date: Sat Apr 4 10:28:06 2020 +0530 old test is back. commit 06e3357 Author: Dilawar Singh <[email protected]> Date: Sat Apr 4 10:24:53 2020 +0530 Fixed the issue with isinstance(x, moose.CubeMesh). Now it is working fine. commit 685ab75 Author: Dilawar Singh <[email protected]> Date: Sat Apr 4 07:26:24 2020 +0530 One more test is passing. commit 6188e09 Author: Dilawar Singh <[email protected]> Date: Sat Apr 4 07:25:25 2020 +0530 Restored old values in the test. commit 349f8ea Author: Dilawar Singh <[email protected]> Date: Sat Apr 4 05:55:15 2020 +0530 fixes to one more tests. commit c90986a Author: Dilawar Singh <[email protected]> Date: Sat Apr 4 05:42:22 2020 +0530 Now do a local testing. commit e6a6575 Author: Dilawar Singh <[email protected]> Date: Sat Apr 4 05:37:26 2020 +0530 numerical assertion of oscillatory tests are hard. commit 5af49e9 Author: Dilawar Singh <[email protected]> Date: Sat Apr 4 05:26:34 2020 +0530 Almost all tests are passing. commit d7f03bd Author: Dilawar Singh <[email protected]> Date: Sat Apr 4 04:54:44 2020 +0530 remove 'value' attribute from the ObjId, it was conflicting with MString 'value'. commit ce79591 Author: Dilawar Singh <[email protected]> Date: Sat Apr 4 04:43:36 2020 +0530 Needs to fix doc. commit 113dddc Author: Dilawar Singh <[email protected]> Date: Sat Apr 4 04:36:02 2020 +0530 more tests are passing. all test_Xreacs are passing now. commit 29ff41c Author: Dilawar Singh <[email protected]> Date: Sat Apr 4 04:31:33 2020 +0530 Use ObjId instread of Id in buildMeshJunction. commit 33e9591 Author: Dilawar Singh <[email protected]> Date: Sat Apr 4 04:27:38 2020 +0530 Passing ObjId as Id is creating trouble. commit 537779e Author: Dilawar Singh <[email protected]> Date: Sat Apr 4 03:59:30 2020 +0530 one more test passes. commit 650309a Author: Dilawar Singh <[email protected]> Date: Sat Apr 4 03:05:28 2020 +0530 delete works. commit b13e051 Author: Dilawar Singh <[email protected]> Date: Sat Apr 4 02:13:31 2020 +0530 Some more tests [skip ci] commit e518d35 Author: Dilawar Singh <[email protected]> Date: Sat Apr 4 01:42:15 2020 +0530 One more test is passed. commit c783578 Author: Dilawar Singh <[email protected]> Date: Sat Apr 4 01:37:24 2020 +0530 isinstance support is added. commit 2a28f9a Author: Dilawar Singh <[email protected]> Date: Fri Apr 3 22:15:46 2020 +0530 Added tests to normalizepath. commit 4c2086a Author: Dilawar Singh <[email protected]> Date: Fri Apr 3 22:08:30 2020 +0530 Global random number generator is moved from basecode to randnum. commit 6a2b7b7 Author: Dilawar Singh <[email protected]> Date: Fri Apr 3 20:09:21 2020 +0530 Couple of seg-faults to take care of. commit 8a90db2 Author: Dilawar Singh <[email protected]> Date: Fri Apr 3 18:27:52 2020 +0530 Fixed one more test. commit 1798a1e Author: Dilawar Singh <[email protected]> Date: Fri Apr 3 14:18:47 2020 +0530 Need to fix rdesignuer now. commit 0be10c0 Author: Dilawar Singh <[email protected]> Date: Fri Apr 3 12:59:16 2020 +0530 Finfo can also return .vec. commit 226d616 Author: Dilawar Singh <[email protected]> Date: Fri Apr 3 12:35:32 2020 +0530 Function is also fixed. commit b68a97b Author: Dilawar Singh <[email protected]> Date: Fri Apr 3 12:22:29 2020 +0530 SynapseTest is also passing. commit 8f2a039 Author: Dilawar Singh <[email protected]> Date: Fri Apr 3 11:38:20 2020 +0530 Fixes all the c++ tests commit 173b9d2 Author: Dilawar Singh <[email protected]> Date: Fri Apr 3 11:28:47 2020 +0530 ObjId.vec create a vec on the fly. commit e71fea0 Author: Dilawar Singh <[email protected]> Date: Thu Apr 2 22:39:02 2020 +0530 Same problem on OSX. One more test is failing. commit 47e25f9 Author: Dilawar Singh <[email protected]> Date: Thu Apr 2 22:08:41 2020 +0530 Some more fixes. moose.element is not honoring dataIndex. commit 9de507a Author: Dilawar Singh <[email protected]> Date: Thu Apr 2 20:17:29 2020 +0530 bebug vec and connection list. commit d7f0a26 Author: Dilawar Singh <[email protected]> Date: Thu Apr 2 19:22:00 2020 +0530 Refactoring. commit 2221410 Author: Dilawar Singh <[email protected]> Date: Thu Apr 2 16:17:48 2020 +0530 Added .clang-format file. commit 7a8437d Author: Dilawar Singh <[email protected]> Date: Thu Apr 2 12:44:32 2020 +0530 more progress. Lets have lunch first now. commit 0ed8933 Author: Dilawar Singh <[email protected]> Date: Thu Apr 2 12:25:44 2020 +0530 Fix Xreacs later. commit 04d4d2f Author: Dilawar Singh <[email protected]> Date: Thu Apr 2 11:52:19 2020 +0530 Refactoring. If Finfo* is passed, no need to pass rttitype and fname. We can get these values from Finfo. commit 77cc0b1 Author: Dilawar Singh <[email protected]> Date: Wed Apr 1 21:21:06 2020 +0530 refacorted codebase... commit 52cfdf7 Author: Dilawar Singh <[email protected]> Date: Wed Apr 1 21:06:13 2020 +0530 Added extra header for Finfo ... commit b16dd1c Author: Dilawar Singh <[email protected]> Date: Wed Apr 1 19:58:56 2020 +0530 Needs to implement LookupFinfo set. commit 8199fc0 Author: Dilawar Singh <[email protected]> Date: Wed Apr 1 18:48:25 2020 +0530 Disable pybind11. commit 5c25dad Author: Dilawar Singh <[email protected]> Date: Wed Apr 1 18:48:02 2020 +0530 One more tests seem to pass. commit 40a4559 Author: Dilawar Singh <[email protected]> Date: Wed Apr 1 18:22:52 2020 +0530 Some more fixes. commit dd9b50e Author: Dilawar Singh <[email protected]> Date: Wed Apr 1 17:59:50 2020 +0530 Perfect. One more test passes. commit fec019b Author: Dilawar Singh <[email protected]> Date: Wed Apr 1 15:41:22 2020 +0530 Refactoring and some more generic programming. commit 9eb2308 Author: Dilawar Singh <[email protected]> Date: Tue Mar 31 20:48:57 2020 +0530 small fixes. Changes in API requires .id . commit 7de3228 Author: Dilawar Singh <[email protected]> Date: Tue Mar 31 19:13:51 2020 +0530 Minor tweak to a test. commit c541b91 Author: Dilawar Singh <[email protected]> Date: Tue Mar 31 19:08:36 2020 +0530 One more test passed. commit 5cc3d3b Merge: ce579ac 1abb6f1 Author: Dilawar Singh <[email protected]> Date: Tue Mar 31 18:59:23 2020 +0530 Merge branch 'pybind11_shell' into temp commit ce579ac Author: Dilawar Singh <[email protected]> Date: Tue Mar 31 18:58:59 2020 +0530 renmaed. commit 16bbc3e Author: Dilawar Singh <[email protected]> Date: Tue Mar 31 18:20:55 2020 +0530 phew. I made a boo boo before. commit 1abb6f1 Merge: 24df86a fa06c38 Author: Dilawar Singh <[email protected]> Date: Tue Mar 31 02:24:30 2020 +0530 Merge branch 'pybind11_shell' of gitlab.com:dilawar/moose-core into pybind11_shell commit fa06c38 Author: Dilawar Singh <[email protected]> Date: Tue Mar 31 02:14:22 2020 +0530 Id and ObjId are not playing well together... commit 48832b1 Author: Dilawar Singh <[email protected]> Date: Tue Mar 31 01:30:34 2020 +0530 test_synchan is a good example; possible we should return moose.vec there. commit 8667c13 Author: Dilawar Singh <[email protected]> Date: Tue Mar 31 01:28:02 2020 +0530 temp commit. commit 24df86a Author: Dilawar Singh <[email protected]> Date: Mon Mar 30 23:39:46 2020 +0530 Temp commit. Exposing only Id. commit 448b8b5 Author: Dilawar Singh <[email protected]> Date: Mon Mar 30 23:14:51 2020 +0530 more tests are passing... commit d1b4990 Author: Dilawar Singh <[email protected]> Date: Mon Mar 30 20:35:39 2020 +0530 Need to find a solution.. commit 6b5082b Author: Dilawar Singh <[email protected]> Date: Mon Mar 30 19:05:44 2020 +0530 Refactoring and have a working moose.vec API. commit 98d8d34 Author: Dilawar Singh <[email protected]> Date: Mon Mar 30 18:05:07 2020 +0530 [skip ci] needs tweaking in the API. commit 0f7929c Author: Dilawar Singh <[email protected]> Date: Mon Mar 30 14:40:37 2020 +0530 Support vec. But first need a nap. commit 93d6e83 Author: Dilawar Singh <[email protected]> Date: Mon Mar 30 13:33:05 2020 +0530 refactoring. commit fd03015 Author: Dilawar Singh <[email protected]> Date: Mon Mar 30 13:17:31 2020 +0530 random works. commit fc34547 Author: Dilawar Singh <[email protected]> Date: Mon Mar 30 11:49:00 2020 +0530 Need to polish the API. commit 6af0f2c Author: Dilawar Singh <[email protected]> Date: Mon Mar 30 11:00:03 2020 +0530 Lets move to DestFinfo. commit 476d700 Author: Dilawar Singh <[email protected]> Date: Mon Mar 30 07:53:31 2020 +0530 Return type. commit 778208a Merge: dab5af4 dd65791 Author: Dilawar Singh <[email protected]> Date: Mon Mar 30 07:42:04 2020 +0530 Merge branch 'pybind11_shell' of gitlab.com:dilawar/moose-core into pybind11_shell commit dd65791 Author: Dilawar Singh <[email protected]> Date: Mon Mar 30 06:54:42 2020 +0530 Updated [skip ci] commit 76ec2a1 Author: Dilawar Singh <[email protected]> Date: Sun Mar 29 23:00:02 2020 +0530 [skip ci] some more changes. commit c4d7bc6 Author: Dilawar Singh <[email protected]> Date: Sun Mar 29 22:24:57 2020 +0530 We go both API integrated. commit f0ac785 Author: Dilawar Singh <[email protected]> Date: Sun Mar 29 21:48:18 2020 +0530 LookupField is a function. commit aee928e Author: Dilawar Singh <[email protected]> Date: Sun Mar 29 21:11:48 2020 +0530 Do the rest tomorrow. commit e118e12 Author: Dilawar Singh <[email protected]> Date: Sun Mar 29 20:45:21 2020 +0530 Retuning binding to std::function which return the Finfo value. commit dab5af4 Author: Dilawar Singh <[email protected]> Date: Sun Mar 29 18:01:12 2020 +0530 isA is method. Time to make it a subscriptable dictionary. commit c7a7b24 Author: Dilawar Singh <[email protected]> Date: Sun Mar 29 15:34:42 2020 +0530 Lets handle LookupField::set and get. commit a06e478 Author: Dilawar Singh <[email protected]> Date: Sun Mar 29 01:13:46 2020 +0530 Deal with it tomorrow. commit bb1cae5 Author: Dilawar Singh <[email protected]> Date: Sun Mar 29 00:28:22 2020 +0530 Getting there. [skip ci] commit 5cccf8b Author: Dilawar Singh <[email protected]> Date: Sat Mar 28 22:33:21 2020 +0530 Some refactoring. Back to same functionality [skip ci]. commit a979de6 Author: Dilawar Singh <[email protected]> Date: Sat Mar 28 20:46:01 2020 +0530 Updated a bit more .. commit b43c617 Author: Dilawar Singh <[email protected]> Date: Sat Mar 28 19:47:58 2020 +0530 New API works fantastic. commit 0deb291 Author: Dilawar Singh <[email protected]> Date: Sat Mar 28 19:40:19 2020 +0530 Incremental change. Dynamic attributes. commit 7f2539c Author: Dilawar Singh <[email protected]> Date: Sat Mar 28 19:31:31 2020 +0530 Subclassing _ObjId now. commit 0f64cd0 Author: Dilawar Singh <[email protected]> Date: Sat Mar 28 18:12:57 2020 +0530 Dynamic attributes are needed now. commit eff08b2 Author: Dilawar Singh <[email protected]> Date: Sat Mar 28 16:16:13 2020 +0530 All test passes. Needs to work on the API now. commit 8791df7 Author: Dilawar Singh <[email protected]> Date: Sat Mar 28 15:40:35 2020 +0530 Blazingly fast. commit 070f735 Author: Dilawar Singh <[email protected]> Date: Sat Mar 28 14:06:47 2020 +0530 Perfect. The base API works now. Not time to do a profiling. commit 07a1348 Author: Dilawar Singh <[email protected]> Date: Sat Mar 28 00:28:22 2020 +0530 This is for tomorow. commit 72f7b62 Author: Dilawar Singh <[email protected]> Date: Fri Mar 27 21:43:33 2020 +0530 Work from home. commit 4ea29e9 Author: Dilawar Singh <[email protected]> Date: Fri Mar 27 20:32:19 2020 +0530 May be later. commit eff6f90 Author: Dilawar Singh <[email protected]> Date: Fri Mar 27 17:57:40 2020 +0530 Not sure about the testKsolve.cpp tests. commit bef104c Author: Dilawar Singh <[email protected]> Date: Fri Mar 27 17:11:34 2020 +0530 Do testing with master branch. commit 0078af1 Author: Dilawar Singh <[email protected]> Date: Fri Mar 27 14:45:40 2020 +0530 get can not overloaded pretty well. Use different name for getting different value. It is verbose now but we can override later. commit 915e10f Merge: 911bd03 bf2d609 Author: Dilawar Singh <[email protected]> Date: Fri Mar 27 13:56:46 2020 +0530 Merge branch 'pybind11_shell' of gitlab.com:dilawar/moose-core into pybind11_shell commit bf2d609 Author: Dilawar Singh <[email protected]> Date: Fri Mar 27 14:11:18 2020 +0530 add test function. commit 911bd03 Author: Dilawar Singh <[email protected]> Date: Fri Mar 27 13:56:12 2020 +0530 local changes. commit cc7144f Author: Dilawar Singh <[email protected]> Date: Fri Mar 27 13:50:40 2020 +0530 Move to gulgula. commit d41e7eb Author: Dilawar Singh <[email protected]> Date: Fri Mar 27 04:18:44 2020 +0530 Allmost there. commit d913ceb Author: Dilawar Singh <[email protected]> Date: Fri Mar 27 01:50:18 2020 +0530 addMsg -> connect . commit 8793d33 Author: Dilawar Singh <[email protected]> Date: Fri Mar 27 01:10:24 2020 +0530 get/set are on ObjId . commit d99115c Author: Dilawar Singh <[email protected]> Date: Fri Mar 27 00:47:20 2020 +0530 Ok. Vector and numpy are working. commit 2f3bc04 Author: Dilawar Singh <[email protected]> Date: Thu Mar 26 23:02:03 2020 +0530 move to bebinca for fast compilation. commit a94fec9 Author: Dilawar Singh <[email protected]> Date: Thu Mar 26 18:29:50 2020 +0530 children and parent is not working. commit 756ec3a Author: Dilawar Singh <[email protected]> Date: Wed Mar 25 14:53:17 2020 +0530 Some more fixes. It will be too much debugging to get it right. commit 77451f1 Author: Dilawar Singh <[email protected]> Date: Tue Mar 24 15:07:09 2020 +0530 All the learning experience is over. Pybind11 is great. commit 6edda7a Author: Dilawar Singh <[email protected]> Date: Tue Mar 24 00:55:13 2020 +0530 Add a bit more fields. commit e32c468 Author: Dilawar Singh <[email protected]> Date: Mon Mar 23 23:30:19 2020 +0530 I can complete this API tomorrow. commit 7aaddf7 Author: Dilawar Singh <[email protected]> Date: Mon Mar 23 22:54:35 2020 +0530 added more functions [skip ci] commit 7f1b709 Author: Dilawar Singh <[email protected]> Date: Mon Mar 23 16:38:34 2020 +0530 disable build for now on gitlab ci commit ae2739d Author: Dilawar Singh <[email protected]> Date: Mon Mar 23 15:05:22 2020 +0530 pybind11 module is named _cmoose and it different from _moose. commit 0c33684 Author: Dilawar Singh <[email protected]> Date: Mon Mar 23 14:45:32 2020 +0530 I got wildcardFind to function. commit 65b307c Author: Dilawar Singh <[email protected]> Date: Mon Mar 23 13:33:22 2020 +0530 Fixed the bug I caused by using smart pointer. I am so silly... commit fe596e3 Merge: d5d29bb f4070da Author: Dilawar Singh <[email protected]> Date: Mon Mar 23 12:45:01 2020 +0530 Merge branch 'issue_397' of gitlab.com:dilawar/moose-core into pybind11 commit d5d29bb Author: Dilawar Singh <[email protected]> Date: Sun Mar 22 23:12:58 2020 +0530 Time to support / in path. commit 270ea8c Author: Dilawar Singh <[email protected]> Date: Sun Mar 22 22:50:21 2020 +0530 empty element() commit a1eed3a Author: Dilawar Singh <[email protected]> Date: Sun Mar 22 22:39:55 2020 +0530 temp commit. commit a70b5fe Author: Dilawar Singh <[email protected]> Date: Sun Mar 22 15:44:56 2020 +0530 Great. Lets try cython as well. commit 038490f Author: Dilawar Singh <[email protected]> Date: Sun Mar 22 15:44:27 2020 +0530 Try cython now. commit 8bbf900 Author: Dilawar Singh <[email protected]> Date: Sun Mar 22 13:43:02 2020 +0530 _moose goes to python/moose directory. commit 014bde2 Merge: 8f60899 ad58dc5 Author: Dilawar Singh <[email protected]> Date: Sun Mar 22 13:18:20 2020 +0530 Merge branch 'issue_397' into pybind11 commit f4070da Merge: ad58dc5 5e660e9 Author: Dilawar Singh <[email protected]> Date: Sat Mar 21 22:21:16 2020 +0530 Merge branch 'refactoring' into issue_397 commit 5e660e9 Author: dilawars <[email protected]> Date: Sat Mar 21 21:24:21 2020 +0530 include cmath in Pool.cpp as well. Failed compilation with gcc5.3 commit ad58dc5 Author: dilawars <[email protected]> Date: Sat Mar 21 21:24:21 2020 +0530 include cmath in Pool.cpp as well. Failed compilation with gcc5.3 commit c4d55aa Author: Dilawar Singh <[email protected]> Date: Sat Mar 21 15:45:16 2020 +0530 Minor cleanup in macros and loggers. numCores now use thread library to determine number of available threads. commit f8dcb12 Author: Dilawar Singh <[email protected]> Date: Sat Mar 21 15:32:02 2020 +0530 NUMPY is essential dependency; therefore numpy code is no longer included conditionally. USE_NUMPY is implied and have been removed from cmake. commit 9ef658e Author: Dilawar Singh <[email protected]> Date: Sat Mar 21 15:15:43 2020 +0530 Fix to #397 commit 8f60899 Author: Dilawar Singh <[email protected]> Date: Tue Mar 17 18:27:54 2020 +0530 Perfecto. Create works. commit aa95a0c Author: Dilawar Singh <[email protected]> Date: Sun Mar 15 22:10:07 2020 +0530 pybind11 bindings. commit da9d1d9 Merge: 0e85a57 36c0026 Author: Dilawar Singh <[email protected]> Date: Sun Mar 15 15:40:06 2020 +0530 Merge commit '36c0026886c70e39c505f8715e65a7c3cf1e6ade' as 'external/pybind11' commit 36c0026 Author: Dilawar Singh <[email protected]> Date: Sun Mar 15 15:40:06 2020 +0530 Squashed 'external/pybind11/' content from commit 4f72ef846 git-subtree-dir: external/pybind11 git-subtree-split: 4f72ef846fe8453596230ac285eeaa0ce3278bb4 * Minor fixes to pybind11. * Fix #409 When `moose.Function('abc')` is created, set expression to "0". Expression is not empty by default. This is to mimic the old behaviour. Note that at this point, derivative is not defined and is `nan` (old behaviour: derivative is 0.0). * Ready for a draft PR and initial disucssion. * Return numpy array instead of vector. Probably not the most memory efficient way for returning vector<double> but since most pyMOOSE scripts assume that returned data is numpy array, we return the numpy array. TODO: benchmarking. * Fixed: moose.le can caused segfault when used on moose.vec This also fixes script mgblock.py BhallaLab/moose-examples#71 * Fixed: moose.le can caused segfault when used on moose.vec This also fixes script mgblock.py BhallaLab/moose-examples#71 * removed mkdoc.py from pybind11. * Fixed a pylint error as well python2/python3 compatibility * wildcard -> reacSystemPath Stoic::path is depreacted bcause it collides with Neutral::path. * Fixed another set. * Travis fix: Install pytest on OSX as well. * fix gitlab pipeline install pytest * isinstance is replace to isA added to this, validation.py: error msg is sent back, writeKkit.py: while writting genesis file if any object is not written then errorlog is send/printed which is usefull durning command line * fix test py_run. Relax the matching to 90% using difflib (from 95%). * grenerate documentation on the fly. * Work in progress: __doc__ string from cWork in progress: __doc__ string from cWork in progress: __doc__ string from cWork in progress: __doc__ string from c++ * Keeping the C++ type and Python's type name same. * Cleanup * pydoc support moved moose.py content to __init__.py. This way pydoc works great also fixed travis build. * moose.doc is working now. _moose.generateDoc is the underlying function. Needs to cleanup documentation a bit now. Fixed regression. * update to docs Disabled C++ signature in Python documentations. Added docstring to __init__.py * more docstring are added [skip ci] * Added datetime and other string to version_info. * All functions have docstring. * loadmodel docstring is added. * temp commit. * showmsg is ported to c++. * added more docstring and moved some functions to public api. * Merged hrani changes and mine from new bindings. removed 'basestring' * # This is a combination of 2 commits. # This is the 1st commit message: python2 support. Added python2 support as well. It will be easy to remove later. _moose.element is a good way to convert string/objid/id to melement. # This is the commit message #2: writeKkit * python2 support. Added python2 support as well. It will be easy to remove later. _moose.element is a good way to convert string/objid/id to melement. writeKkit python2 support. Added python2 support as well. It will be easy to remove later. python2 support. Added python2 support as well. It will be easy to remove later. _moose.element is a good way to convert string/objid/id to melement. writeKkit python2 support. Added python2 support as well. It will be easy to remove later. * basestring -> str * fixes to `pip install` Added missing folders. * Fixed pylint error. * moose.getField accepts two argument instead of 3. Updated rmogul.py file. * fix: compiles with clang++ typeid(X) when X is an incomplete type is not supported by C++ standard. Suprisingly this was compiling fine with gcc but not with clang++. version is set to 3.2.0.dev$(today) * travis fixes: OSX PyRun tests compares last 50 lines rather than whole text. This way we can ignore lines with different timestamp. * builds on osx locally. * tests passes with 3.8 as well. * On OSX, stream does not flush properly? Using difflib to test the ratio between got and expected string. * flush the streams before calling tests... * Don't run the trvais/osx Not sure why but only on travis+OSX, pyrun test does not pass. It fails because whole buffer is not dumped to the tty. * Fixes to pyrun tests. * Time to post the API. * listmsg has been moved to C++. * docstring to writeNML2 * Fixed typo in docstring. Ready to be reviewed. * showfield and showfields are both supported. `moose.showfield` is an alias for `moose.showfields`. * Added back moose.ce Co-authored-by: Dilawar Singh <[email protected]> Co-authored-by: HarshaRani <[email protected]> Co-authored-by: Anushree Narjala <[email protected]> * loadModel does not return a tuple anymore. Not sure when this changes were made but someplace loadModel assumes a tuple is returned and other place it does not. * Fixes to issue #414 - Tweaks to rdesigneur - Added missing function overloads in the python API. * Added missing __version__, version() still works. Co-authored-by: Dilawar Singh <[email protected]> Co-authored-by: Dilawar Singh <[email protected]> Co-authored-by: HarshaRani <[email protected]> Co-authored-by: Anushree Narjala <[email protected]>
* Fixed typo #426 * getFieldNames is available for element also Both are equivalent >>> a = moose.Stoich('a') >>> v1 = moose.getFieldNames(a, 'value') >>> v2 = a.getFieldNames('value') >>> assert v1 == v2 If not argument is passed to `getFieldNames`, it returns are field types. Co-authored-by: HarshaRani <[email protected]>
* Update readSBML.py Complex Pool now copied under Enzyme which in-turn copies the set concentration * Update readSBML.py Complex Pool now copied under Enzyme which in-turn copies the concentration
…nko oscillator model.
…partment reactions.
…ent of conc or concInit on BufPool is now equivalent
…proper path for ConcChans
…Dsolve,Reac,Stoich.cpp,helper.h keeping as its
* duplicate stray test. Included in core/test_doctests * fixes to build, >25 tests are failing.
…Toggle views on and off.
* minimum gcc version is 5.X and hdf5 included in cmake as default * CMake correction
* minimum gcc version is 5.X and hdf5 included in cmake as default * CMake correction * Added basepath if exist to compartment Annotation * function input connection done after enzyme, func.expr fixed, corrected stoichiometry for edge case * edgecase if extra path exist it is taken care while writting/reading into/from SBML * correction in basepath to basePath in readSBML
changed the version number from 3.2 to 3.3 and vpython was added
* Updated README file for jalebi release * Version updated in setup script * Py3.10update (#451) * Update setup.py changed the version number from 3.2 to 3.3 and vpython was added * removed parse and symbol modules * Update pymoose.yml added 3.9 and 3.10 * Update pymoose.yml Co-authored-by: Anal Kumar <[email protected]> * Neuro ml2 (#453) * Updated and tested NeuroML2 import * Use moose.neuroml2.reader * Harsha's changes * copy issue solved by deleting library * Harsha's changes for test_reader.py * Solved filename issue * test_createCellPrototype asserting the name of the cell issue * Update githubaction.yml * Update githubaction.yml * Fix for input list * Update githubaction.yml * Update setup.py * Remove my copy actions file * test_connectivity unittest for Neuroml2 * resolved seg fault in test_connectivity in test_reader.py * Corrected eqn to calculate Ra * passiveCell.nml tested * tests single compartment firing neuroml2 cell Co-authored-by: Padraig Gleeson <[email protected]> Co-authored-by: analkumar2 <[email protected]> * Update setup.py * Update setup.py dev is removed from setup file Co-authored-by: Anal Kumar <[email protected]> Co-authored-by: Padraig Gleeson <[email protected]>
* Fixes to get the LSODA ODE engine to work with chem solvers. * Fixes to VoxelPools to handle LSODA a bit better * LSODA bug-fixes. SeqSynHandler bug-fixes. Co-authored-by: HarshaRani <[email protected]>
* Added readout of per-voxel rate terms for reactions using Ksolve::rateVec * Reverting to old getConcKf and getNumKf code for Reac, but the hooks for individual voxel access remain. Co-authored-by: HarshaRani <[email protected]>
* Added readout of per-voxel rate terms for reactions using Ksolve::rateVec * Reverting to old getConcKf and getNumKf code for Reac, but the hooks for individual voxel access remain. * Fixes for LSODA to work with diffusion. Co-authored-by: HarshaRani <[email protected]>
kkit: dangling reaction and enzyme are not saved, lsoda is added to solver
small clean up moose.element added
* Special character specific to libsbml and moose * Update pymoose.yml clean and update
removal of python-tk
* Fixed showmsg() bug in pybind11 based version. The newer implementation of showmsg() shows the outgoing messages with misdirected arrows. Fixed now. * Added newer version of pybind11 * Swapped clocks for channel and compartment to fix #467 * This actually fixes scheduling for channels and compartments #467 The previous commit only updated the docs. This one modifies the actual tick assignments. Now electrical compartments are scheduled on ticks 2 and 3 and channels (all derived from ChanBase) on 4. * Minor fix for compiler warning on loop var creating copy from const * Removed CMake generated compile command. the compile command file is generated by cmake in each build environment and should not be part of the repo.
Added 3.11 and 3.12
Not packing so pip install . should be fine
Co-authored-by: Arash Partow <[email protected]>
Typo
Python 3.7 reached end of life will be removing from github action
* Fixed showmsg() bug in pybind11 based version. The newer implementation of showmsg() shows the outgoing messages with misdirected arrows. Fixed now. * Added newer version of pybind11 * Swapped clocks for channel and compartment to fix #467 * This actually fixes scheduling for channels and compartments #467 The previous commit only updated the docs. This one modifies the actual tick assignments. Now electrical compartments are scheduled on ticks 2 and 3 and channels (all derived from ChanBase) on 4. * Minor fix for compiler warning on loop var creating copy from const * Removed CMake generated compile command. the compile command file is generated by cmake in each build environment and should not be part of the repo. * Added error message at neuroml import error, corrected imports. * Updated neuroml2 reader. Yet to debug Granule_98 model. * Updated neuroml2 reader to handle spherical compartment for CaPool Also created separate test script for Granule98 model. * Fixed deprecated imp module use in rdesigneur. - rdesigneur used imp module, now replaced by importlib. - commented out debug logs from neuroml2 reader - TODO: tests/support has files which conflict with tests/core. These seem to be old test code which may better be removed. * Updated test script for Granule98 model --------- Co-authored-by: HarshaRani <[email protected]>
commit b38b6af Author: Subhasis Ray <[email protected]> Date: Tue Apr 23 12:29:49 2024 +0530 Reverted windows build attempts. commit 4c60035 Author: Subhasis Ray <[email protected]> Date: Tue Apr 23 11:52:46 2024 +0530 Updated workflow commit 95febb9 Author: Subhasis Ray <[email protected]> Date: Tue Apr 23 11:51:56 2024 +0530 Updated wortkflow commit 5042502 Author: Subhasis Ray <[email protected]> Date: Tue Apr 23 11:34:03 2024 +0530 Updated workflow file. commit ac6ba27 Author: Subhasis Ray <[email protected]> Date: Tue Apr 23 11:27:33 2024 +0530 Update workflow commit 5ae39a9 Author: Subhasis Ray <[email protected]> Date: Tue Apr 23 11:25:11 2024 +0530 Updated workflow commit b62cf5d Author: Subhasis Ray <[email protected]> Date: Tue Apr 23 11:15:22 2024 +0530 Update workflow commit be7132e Author: Subhasis Ray <[email protected]> Date: Tue Apr 23 11:13:35 2024 +0530 Updated build commit e7e2925 Author: subhacom <[email protected]> Date: Tue Apr 23 11:08:39 2024 +0530 Update pymoose.yml commit cc6bce8 Author: subhacom <[email protected]> Date: Tue Apr 23 11:07:10 2024 +0530 Update pymoose.yml commit 28eadbf Author: subhacom <[email protected]> Date: Tue Apr 23 11:05:46 2024 +0530 Update pymoose.yml commit e9ae785 Author: Subhasis Ray <[email protected]> Date: Tue Apr 23 11:00:15 2024 +0530 github workflow msvc/gsl commit 6aba825 Author: Subhasis Ray <[email protected]> Date: Tue Apr 23 10:58:51 2024 +0530 github workflow: msvc/gsl build commit 31617f5 Author: Subhasis Ray <[email protected]> Date: Tue Apr 23 10:52:46 2024 +0530 github workflow: windows GSL build test commit 8ac5de1 Author: Subhasis Ray <[email protected]> Date: Tue Apr 23 10:48:32 2024 +0530 github workflow: windows build of GSL commit 96b9583 Author: Subhasis Ray <[email protected]> Date: Tue Apr 23 10:46:55 2024 +0530 github workflow: Testing GSL build for windows commit 60363ec Author: Subhasis Ray <[email protected]> Date: Tue Apr 23 00:17:23 2024 +0530 Bumped up cmake version to 3.20 - Also trying to install GSL via vcpkg for WIN32 commit e475389 Author: Subhasis Ray <[email protected]> Date: Tue Apr 23 00:00:53 2024 +0530 Fixed github workflow file commit 7169d23 Author: Subhasis Ray <[email protected]> Date: Mon Apr 22 23:59:36 2024 +0530 Trying to fix win build commit a80fd8e Author: Subhasis Ray <[email protected]> Date: Mon Apr 22 23:56:49 2024 +0530 Fixing github workflow for WIN/MSVC build commit a9909bf Author: Subhasis Ray <[email protected]> Date: Mon Apr 22 23:41:53 2024 +0530 Switched from C++11 to C++14 - MSVC 2015 and later do not support c++11 - causing build to fail commit ae43694 Author: Subhasis Ray <[email protected]> Date: Mon Apr 22 23:25:34 2024 +0530 Github workflow update for windows build - C++11 support check does not work for MSVC cl. Trying a fix. commit a3fe008 Author: Subhasis Ray <[email protected]> Date: Mon Apr 22 23:08:16 2024 +0530 Github workflow for windows build: fixing micromamba options commit b22e200 Author: Subhasis Ray <[email protected]> Date: Mon Apr 22 23:04:26 2024 +0530 Fixing windows build workflow: micromamba path commit f68e4b0 Author: Subhasis Ray <[email protected]> Date: Mon Apr 22 23:01:09 2024 +0530 Attempt fixing micromamba for windows build commit fd99794 Author: Subhasis Ray <[email protected]> Date: Mon Apr 22 22:58:19 2024 +0530 Added windows build action to guthub workflow commit 5b458d8 Author: Subhasis Ray <[email protected]> Date: Mon Apr 22 22:43:01 2024 +0530 Fix to github workflow for build commit 401bd27 Author: Subhasis Ray <[email protected]> Date: Mon Apr 22 22:40:32 2024 +0530 Further fix to build commit 0d7d2aa Author: Subhasis Ray <[email protected]> Date: Mon Apr 22 22:25:34 2024 +0530 Further fix to micromamba commit b88d231 Author: Subhasis Ray <[email protected]> Date: Mon Apr 22 22:23:14 2024 +0530 Further fix to micromamba command commit 1401e35 Author: Subhasis Ray <[email protected]> Date: Mon Apr 22 22:21:03 2024 +0530 Fixed micromamba commands commit 7cc0289 Author: Subhasis Ray <[email protected]> Date: Mon Apr 22 22:16:23 2024 +0530 Fix for github action commit 2c4c4ed Author: Subhasis Ray <[email protected]> Date: Mon Apr 22 22:07:29 2024 +0530 Attempting github action to build for both Ubuntu and MacOSX M1 commit d91ca02 Author: Subhasis Ray <[email protected]> Date: Mon Apr 22 21:20:26 2024 +0530 Build updated - Removed deprecated CMake version setting - Removed python2: out of life. Only supporting Python>=3.8 - Removed pybind11: should be installed directly with pip - Added MacOSX build workflow: to be tested * Modified test script for Granule98 to take model dir arg * Fixed github workflow to build on Ubuntu and MacOSX Squashed commit of the following: commit b38b6af Author: Subhasis Ray <[email protected]> Date: Tue Apr 23 12:29:49 2024 +0530 Reverted windows build attempts. commit 4c60035 Author: Subhasis Ray <[email protected]> Date: Tue Apr 23 11:52:46 2024 +0530 Updated workflow commit 95febb9 Author: Subhasis Ray <[email protected]> Date: Tue Apr 23 11:51:56 2024 +0530 Updated wortkflow commit 5042502 Author: Subhasis Ray <[email protected]> Date: Tue Apr 23 11:34:03 2024 +0530 Updated workflow file. commit ac6ba27 Author: Subhasis Ray <[email protected]> Date: Tue Apr 23 11:27:33 2024 +0530 Update workflow commit 5ae39a9 Author: Subhasis Ray <[email protected]> Date: Tue Apr 23 11:25:11 2024 +0530 Updated workflow commit b62cf5d Author: Subhasis Ray <[email protected]> Date: Tue Apr 23 11:15:22 2024 +0530 Update workflow commit be7132e Author: Subhasis Ray <[email protected]> Date: Tue Apr 23 11:13:35 2024 +0530 Updated build commit e7e2925 Author: subhacom <[email protected]> Date: Tue Apr 23 11:08:39 2024 +0530 Update pymoose.yml commit cc6bce8 Author: subhacom <[email protected]> Date: Tue Apr 23 11:07:10 2024 +0530 Update pymoose.yml commit 28eadbf Author: subhacom <[email protected]> Date: Tue Apr 23 11:05:46 2024 +0530 Update pymoose.yml commit e9ae785 Author: Subhasis Ray <[email protected]> Date: Tue Apr 23 11:00:15 2024 +0530 github workflow msvc/gsl commit 6aba825 Author: Subhasis Ray <[email protected]> Date: Tue Apr 23 10:58:51 2024 +0530 github workflow: msvc/gsl build commit 31617f5 Author: Subhasis Ray <[email protected]> Date: Tue Apr 23 10:52:46 2024 +0530 github workflow: windows GSL build test commit 8ac5de1 Author: Subhasis Ray <[email protected]> Date: Tue Apr 23 10:48:32 2024 +0530 github workflow: windows build of GSL commit 96b9583 Author: Subhasis Ray <[email protected]> Date: Tue Apr 23 10:46:55 2024 +0530 github workflow: Testing GSL build for windows commit 60363ec Author: Subhasis Ray <[email protected]> Date: Tue Apr 23 00:17:23 2024 +0530 Bumped up cmake version to 3.20 - Also trying to install GSL via vcpkg for WIN32 commit e475389 Author: Subhasis Ray <[email protected]> Date: Tue Apr 23 00:00:53 2024 +0530 Fixed github workflow file commit 7169d23 Author: Subhasis Ray <[email protected]> Date: Mon Apr 22 23:59:36 2024 +0530 Trying to fix win build commit a80fd8e Author: Subhasis Ray <[email protected]> Date: Mon Apr 22 23:56:49 2024 +0530 Fixing github workflow for WIN/MSVC build commit a9909bf Author: Subhasis Ray <[email protected]> Date: Mon Apr 22 23:41:53 2024 +0530 Switched from C++11 to C++14 - MSVC 2015 and later do not support c++11 - causing build to fail commit ae43694 Author: Subhasis Ray <[email protected]> Date: Mon Apr 22 23:25:34 2024 +0530 Github workflow update for windows build - C++11 support check does not work for MSVC cl. Trying a fix. commit a3fe008 Author: Subhasis Ray <[email protected]> Date: Mon Apr 22 23:08:16 2024 +0530 Github workflow for windows build: fixing micromamba options commit b22e200 Author: Subhasis Ray <[email protected]> Date: Mon Apr 22 23:04:26 2024 +0530 Fixing windows build workflow: micromamba path commit f68e4b0 Author: Subhasis Ray <[email protected]> Date: Mon Apr 22 23:01:09 2024 +0530 Attempt fixing micromamba for windows build commit fd99794 Author: Subhasis Ray <[email protected]> Date: Mon Apr 22 22:58:19 2024 +0530 Added windows build action to guthub workflow commit 5b458d8 Author: Subhasis Ray <[email protected]> Date: Mon Apr 22 22:43:01 2024 +0530 Fix to github workflow for build commit 401bd27 Author: Subhasis Ray <[email protected]> Date: Mon Apr 22 22:40:32 2024 +0530 Further fix to build commit 0d7d2aa Author: Subhasis Ray <[email protected]> Date: Mon Apr 22 22:25:34 2024 +0530 Further fix to micromamba commit b88d231 Author: Subhasis Ray <[email protected]> Date: Mon Apr 22 22:23:14 2024 +0530 Further fix to micromamba command commit 1401e35 Author: Subhasis Ray <[email protected]> Date: Mon Apr 22 22:21:03 2024 +0530 Fixed micromamba commands commit 7cc0289 Author: Subhasis Ray <[email protected]> Date: Mon Apr 22 22:16:23 2024 +0530 Fix for github action commit 2c4c4ed Author: Subhasis Ray <[email protected]> Date: Mon Apr 22 22:07:29 2024 +0530 Attempting github action to build for both Ubuntu and MacOSX M1 commit d91ca02 Author: Subhasis Ray <[email protected]> Date: Mon Apr 22 21:20:26 2024 +0530 Build updated - Removed deprecated CMake version setting - Removed python2: out of life. Only supporting Python>=3.8 - Removed pybind11: should be installed directly with pip - Added MacOSX build workflow: to be tested --------- Co-authored-by: HarshaRani <[email protected]>
* parent 94fe3d6 author Subhasis Ray <[email protected]> 1715590080 +0530 committer Subhasis Ray <[email protected]> 1715619586 +0530 parent 94fe3d6 author Subhasis Ray <[email protected]> 1715590080 +0530 committer Subhasis Ray <[email protected]> 1715618717 +0530 - Updated includes in sourcecode for pybind11 - Fixed cmake file for finding system pybind11 - Updated github workflow to use micromamba setup from github marketplace * Added simple test of importing moose
…hub workflow to build on Windows, Linux and MacOS (#491) * Fixed typo in macro check for BOOST * Updates for Windows MSVC build In setup.py and CMakeLists.txt for build - Added switches for compiler flags for Windows/MSVC - Removed possible override of version in CMakeLists.txt: setup.py should be the only source of version info - Archive format set to zip for windows - Using module name moose instead of _moose, the underscore is added as PREFIX - Platform dependent shared lib file name extension - Removed platform name CMAKE from cmake file - Updated setup.py to allow release build on windows In C++ code - Switched all new style logical opeartors (and, or, not)to C style (&&, ||, !) - these are not recognized by MSVC compiler - Added windows port of getopt in external - Removed SocketStreamer conditionally for Win32 build. Win32 does not have socket library. TODO: look at ports. - CylBase uses a constant PI which does not exist in win32 standard library. Replaced it with cmath's M_PI. Hope they are the same. - Corrected cnpy function for checking numpy file header - Minor correction on printf formatting to avoid warning for size_t build updates for windows - Undefine _DEBUG macro for release builds Added build instructions for windows * Squashed commit of the following: commit fc5f053 Merge: 45f4341 71598d1 Author: Subhasis Ray <[email protected]> Date: Sun Nov 10 15:14:44 2024 +0530 Merge branch 'master' of https://github.com/BhallaLab/moose-core into windows_build commit 45f4341 Author: Subhasis Ray <[email protected]> Date: Sun Nov 10 15:02:51 2024 +0530 github actions: try to fix gsl availability commit 17f91bb Author: Subhasis Ray <[email protected]> Date: Sun Nov 10 14:01:39 2024 +0530 github action fixes commit 9159696 Author: Subhasis Ray <[email protected]> Date: Sun Nov 10 13:59:08 2024 +0530 github actions: Avoid pip upgared commit 9537a5c Author: Subhasis Ray <[email protected]> Date: Sun Nov 10 13:57:52 2024 +0530 Further fix to github action: activateing mamba env commit 7e67573 Author: Subhasis Ray <[email protected]> Date: Sun Nov 10 13:54:11 2024 +0530 Fix github action commit ab7d52a Author: Subhasis Ray <[email protected]> Date: Sun Nov 10 13:53:05 2024 +0530 Fixing automatic build commit 6c4b99a Author: Subhasis Ray <[email protected]> Date: Sun Nov 10 01:49:39 2024 +0530 github actions: further fix for ubuntu commit 1c143e6 Author: Subhasis Ray <[email protected]> Date: Sun Nov 10 01:41:58 2024 +0530 github actions: fix ninja installation on ubuntu latest commit cbba8a5 Author: Subhasis Ray <[email protected]> Date: Sun Nov 10 01:39:30 2024 +0530 github actions: fix for meson installation on ubuntu-lates commit 863d7f7 Author: Subhasis Ray <[email protected]> Date: Sun Nov 10 01:23:57 2024 +0530 Fixing github actions to build commit f1d9981 Merge: 65b8ea6 fa3b764 Author: Subhasis Ray <[email protected]> Date: Sun Nov 10 01:12:55 2024 +0530 Merge branch 'windows_build' of https://github.com/subhacom/moose-core into windows_build commit 65b8ea6 Author: Subhasis Ray <[email protected]> Date: Sun Nov 10 01:12:07 2024 +0530 Another attempt at fixing github workflow commit fa3b764 Author: subhacom <[email protected]> Date: Sun Nov 10 01:04:46 2024 +0530 Update pymoose.yml: tab and space mixup in github editor commit 3cd5d0e Author: subhacom <[email protected]> Date: Sun Nov 10 01:03:41 2024 +0530 Update pymoose.yml commit ecfa505 Author: Subhasis Ray <[email protected]> Date: Sun Nov 10 00:58:37 2024 +0530 Fixed tab issues in workflow commit 15c8b44 Author: Subhasis Ray <[email protected]> Date: Sun Nov 10 00:56:49 2024 +0530 attempt to fix workflow commit bf294b8 Author: Subhasis Ray <[email protected]> Date: Sun Nov 10 00:24:06 2024 +0530 Updated exprtk and fixed some deprecation warnings from meson commit 71598d1 Author: Anal Kumar <[email protected]> Date: Fri Nov 8 13:30:32 2024 +0530 Execute the module to access the funtion in its namespace (#480) commit 38fc00f Author: Subhasis Ray <[email protected]> Date: Fri Nov 8 11:29:28 2024 +0530 Added moose class/object check in moose.isinstance_ function commit 7c82f69 Author: Subhasis Ray <[email protected]> Date: Sun Oct 27 16:51:16 2024 +0530 Minor update of build instructions. commit 5c325c1 Author: Subhasis Ray <[email protected]> Date: Sun Oct 27 12:26:55 2024 +0530 Added instructions on build options commit 575760e Author: Subhasis Ray <[email protected]> Date: Fri Oct 18 15:39:07 2024 +0530 neuroml2 reader: Added option to use interpolation by default commit 3cc2291 Author: Subhasis Ray <[email protected]> Date: Thu Oct 3 12:20:43 2024 +0530 Minor fix for non-conda build commit 584394f Author: Subhasis Ray <[email protected]> Date: Tue Sep 3 22:02:57 2024 +0530 HHChannel2D cleanup Addrsses issue #482 commit a20c95b Author: Subhasis Ray <[email protected]> Date: Tue Sep 3 19:09:38 2024 +0530 Windows build working, HHChannel fixed, pymoose cleaned up This commit puts together several bug fixes and cleanups. Meson-based build functional now. - Windows MSVC Build works. - Tested on WSL-Ubuntu as well - Removed cmake build files (CMakeLists.txt) HHChannel class hierarchy - Original version of HHChannel was using the diamond of death multiple inheritance. While linux/gcc was forgiving of this, on Windows MSVC this was producing strange errors issue#483. - Turns out this design was not essential and single inheritance along the line ChanBase->ChanCommon->HHChannelBase->HHChannel sufficed. pybind11 based pymoose This code was quite dirty with static member functions under __Finfo__ which had no relations with the class. Reorganized the code here. commit 4c0b13c Author: Subhasis Ray <[email protected]> Date: Sun Sep 1 02:58:37 2024 +0530 Cleanup of build process. - cleanups to avoid multiple definitions: no more forcing linker to allow multiple definition - redifinition of doubleEq removed - some type-conversions made explicit to avoid warnings - set compiler to use c/c++-17 - separate settings for MSVC and MS Windows: llvm-clang can also work commit 9f85fe9 Author: Subhasis Ray <[email protected]> Date: Wed Aug 28 16:53:30 2024 +0530 Fixed small bug in neuroml2 reader commit 5d58ac0 Author: Subhasis Ray <[email protected]> Date: Tue Aug 27 13:08:58 2024 +0530 Minor fix in neuroml2 reader commit 8b9f01c Author: Subhasis Ray <[email protected]> Date: Mon Aug 26 17:42:10 2024 +0530 Further cleanup of neuroml2 reader The results can be sensitive to ranges and resolution used in gate tables. Made these parameters of the NML2Reader's read() method. Set defaults to create good fit for Granule 98 model. commit f7dec7b Author: Subhasis Ray <[email protected]> Date: Mon Aug 26 12:16:28 2024 +0530 Got 2D channel to work when reading in NeuroML2 commit 717e0a9 Merge: 8cdacb7 da455e2 Author: Subhasis Ray <[email protected]> Date: Fri Aug 23 11:46:29 2024 +0530 Merge branch 'windows_build' commit 8cdacb7 Author: Subhasis Ray <[email protected]> Date: Tue Jul 30 15:26:51 2024 +0530 Support for voltage and Ca dependent channel in NeuroML2 reader - array_eval_component() reimplements neuroml expression evaluation using numpy vectorization. This adds dependency on pint for unit handling. - Numerous other fixes and cleanups. commit da455e2 Author: Subhasis Ray <[email protected]> Date: Tue Jul 30 15:26:51 2024 +0530 Removed optimization in favor of simplicity - The switch between Ca dependent and voltage dependent gates put inside for loop instead of having one loop under each condition. commit 8c4db05 Author: Subhasis Ray <[email protected]> Date: Tue Jul 30 15:18:13 2024 +0530 Fixes to NeuroML2 reader - Fixed the calculation of gate parameters for HH-type channels with non-standard formula - String formatting switched to f-strings - Refactored functions for updating gates/creating HHChannels - Added some function docstrings commit c3534b5 Author: Subhasis Ray <[email protected]> Date: Fri Jul 19 18:54:25 2024 +0530 Code cleanup of morphology reading commit ce9cb73 Author: Subhasis Ray <[email protected]> Date: Wed Jul 17 10:14:17 2024 +0530 Windows portability fix - Removed function filepath_exists to check existence of a file: now this is done portably with the `access` (unix) or `_access` (win) function call. commit 629d00d Author: Subhasis Ray <[email protected]> Date: Tue Jul 16 14:46:13 2024 +0530 meson build updated for Ubuntu (tested on WSL) - Updated meson.build files to build on Ubuntu with gcc - Added instructions for Ubuntu build - Updated instructions for Windows build - Fixed minor issue with loading kkit file commit 2aac80f Author: Subhasis Ray <[email protected]> Date: Mon Jul 15 10:39:38 2024 +0530 Some more cleanup in meson build commit 6c1016f Author: Subhasis Ray <[email protected]> Date: Mon Jul 15 10:38:03 2024 +0530 Fixed typo. commit 258424a Author: Subhasis Ray <[email protected]> Date: Mon Jul 15 10:33:57 2024 +0530 Minor fixes to meson build and pyproject commit 52bf161 Author: Subhasis Ray <[email protected]> Date: Wed Jul 10 11:24:17 2024 +0530 Windows MSVC build working with meson. - Updated guide to windows build commit e4b7655 Author: Subhasis Ray <[email protected]> Date: Tue Jul 9 23:12:24 2024 +0530 Finally, working windows build with meson commit 0ca6b94 Author: Subhasis Ray <[email protected]> Date: Mon Jul 8 03:53:57 2024 +0530 Added meson build files commit c0e0229 Author: Subhasis Ray <[email protected]> Date: Wed Jul 3 08:54:05 2024 +0530 Updated mac build/installation guide commit 7e8427c Author: Subhasis Ray <[email protected]> Date: Wed Jul 3 07:14:53 2024 +0530 Added guide for mac build commit f02bc6f Author: Subhasis Ray <[email protected]> Date: Tue Jul 2 17:39:49 2024 +0530 Added troubleshooting advice for WSL. commit 130b674 Author: Subhasis Ray <[email protected]> Date: Tue Jul 2 12:35:56 2024 +0530 Correction in wsl guide commit caeeab5 Author: Subhasis Ray <[email protected]> Date: Tue Jul 2 12:30:25 2024 +0530 Added a guide for setting up moose on WSL2 commit b8eb0ba Author: Subhasis Ray <[email protected]> Date: Thu Jun 20 12:39:51 2024 +0530 Try fixing apple build commit e3d6607 Author: Subhasis Ray <[email protected]> Date: Thu Jun 20 12:20:29 2024 +0530 Fixed cmake file to not include extern/getopt on non-win32 commit 7906424 Author: Subhasis Ray <[email protected]> Date: Thu Jun 20 10:20:37 2024 +0530 Trying to fix syntax error from newer C++ standard commit 0cd5950 Author: Subhasis Ray <[email protected]> Date: Thu Jun 20 09:23:20 2024 +0530 Build updates for WIN32/MSVC commit 5756e38 Author: Subhasis Ray <[email protected]> Date: Wed Jun 12 16:56:03 2024 +0530 Fixed lib name for moose used in linking moose.bin commit e71ce2f Author: Subhasis Ray <[email protected]> Date: Wed Jun 12 16:49:13 2024 +0530 Fixes to build configs - setup.py for two passes of cmake - first to create config, second to run build tool - pybind11/CMakeLists.txt - going back to no prefix, directly put `_moose` for target. Reverted pyd suffix to dll on windows commit 965d1a1 Author: Subhasis Ray <[email protected]> Date: Wed Jun 12 16:16:00 2024 +0530 Attempt to fix build - setup.py: use `cmake --build` for all systems - switch filename suffix pyd back to dll for windows commit 035ee0e Author: Subhasis Ray <[email protected]> Date: Wed Jun 12 15:09:48 2024 +0530 Trying c++11 for mac build to fix syntax issue commit 1d8de04 Author: Subhasis Ray <[email protected]> Date: Wed Jun 12 15:02:51 2024 +0530 Fixup for getopt on Windows commit d6bc7ff Author: Subhasis Ray <[email protected]> Date: Wed Jun 12 14:47:32 2024 +0530 Minor fixup for platform check with WIN32 macro
* Modifications for automatic packaging on github * Added changelog * Fixes for NeuroML2 reader - Exponential operator '^' in neurml2 expressions replaced by '**' - Corrected voltage and ca dependency checks - Added scalar check for result of expression evaluation - in some cases it can be actually a constant expression evaluating to a scalar * Fixed an error with SBML reading. * github hosted runner for MacOS - fix for pkgconfig Looks like github fixed the issue with pkg-config, so earlier workaround now causing error * Updated AUTHORS
* Fixes in docs and HDF5 support - Fixed issue #495 - Enabled HDF5 supported build and fixed HDF5 linking issue - Updated installation instructions, README. - Updated packaging to upload wheels only on master branch * Fix for mesonbuild/meson#13985 Fixes build issue on Ubuntu * Raise exception in `connect` and `element` when failed - The shell only generates an error message when an attempt to connect two objects via message fails. This caused hard to debug errors. Now the wrapper function raises RuntimeError in such case. - `element(path)` returned the roor element when `path` does not exist, again causing hard to find bugs. This now raises RuntimeError. * Minor fix in installation instructions * Updated moose.element() to raise error for nonexistent path * Implemented HHChannelF and HHGateF for formula based evaluation - Refactored HHChannelBase and created a class hierarchy for HHGate - Added test scripts for HHChannelF (`test_hhchannelf.py`) and updated test for HHChannel (`test_hhchannel.py`) - Moved voltage clamp code for test fixture into `tests/core/ephys.py` - Removed old `Func` class from default scheduling
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