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* 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 <dilawars@ncbs.res.in> Date: Sun Apr 12 19:03:24 2020 +0530 moved __init__.py and moose.py to pybind folder. commit 77afafd49dc6e99b1c00c060b00181d1190e1c7b Author: Dilawar Singh <dilawars@ncbs.res.in> Date: Sun Apr 12 18:03:28 2020 +0530 Use not gui backend. commit 6ad911c73c5f9d01846c5869263c12ee82e1bdf8 Author: Dilawar Singh <dilawars@ncbs.res.in> Date: Sun Apr 12 13:23:33 2020 +0530 Variable and Cinfo need not be exposed. commit 5fec8497593a9d77b5ed5832336747c6cd8fb33c Author: Dilawar Singh <dilawars@ncbs.res.in> Date: Sun Apr 12 12:27:13 2020 +0530 Create moose element from vec and field. commit ab3d85dc0f023a4cda2a9cf7ecfae97d860567b2 Author: Dilawar Singh <dilawars@ncbs.res.in> Date: Sun Apr 12 11:21:21 2020 +0530 Added support for ["string", double] valueFinfoItem. commit 9c967c02abd565c90d452d200f778e1d2ed78349 Author: Anushree Narjala <anushree.narjala@gmail.com> Date: Sun Apr 12 10:03:17 2020 +0530 seed is an int and can't be empty. commit cc7ea95 Author: Dilawar Singh <dilawars@ncbs.res.in> Date: Sat Apr 11 15:46:11 2020 +0530 This is a really good commit. `.num` is supported now. commit 2185c65 Author: Dilawar Singh <dilawars@ncbs.res.in> Date: Sat Apr 11 12:28:39 2020 +0530 Added doxygen target. commit 32c3fc7 Author: Dilawar Singh <dilawars@ncbs.res.in> Date: Fri Apr 10 13:09:09 2020 +0530 Finfo is also vectorised. commit d716124 Author: Dilawar Singh <dilawars@ncbs.res.in> 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 <dilawars@ncbs.res.in> Date: Thu Apr 9 21:07:04 2020 +0530 Use old PyRun code. Pybind11 does not have subterpreter support. commit 2587c0d Author: Dilawar Singh <dilawars@ncbs.res.in> Date: Thu Apr 9 13:58:16 2020 +0530 Added a test for testing pyrun. commit f3a4925 Author: Dilawar Singh <dilawars@ncbs.res.in> 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 <dilawars@ncbs.res.in> Date: Thu Apr 9 11:15:01 2020 +0530 Fixes https://gitlab.com/dilawar/moose-core/-/issues/7 commit 31f2b8f Author: Dilawar Singh <dilawars@ncbs.res.in> Date: Wed Apr 8 23:16:37 2020 +0530 If Function is not valid_, return quietly. commit b91a0ef Author: Dilawar Singh <dilawars@ncbs.res.in> Date: Wed Apr 8 22:25:06 2020 +0530 All tests are passing now. commit 0ce71ac Author: Dilawar Singh <dilawars@ncbs.res.in> Date: Wed Apr 8 20:13:39 2020 +0530 genesis and kkit are reverted back to master. commit 6535c46 Author: Dilawar Singh <dilawars@ncbs.res.in> Date: Wed Apr 8 19:03:13 2020 +0530 isA is working just fine. commit bf118f4 Author: Dilawar Singh <dilawars@ncbs.res.in> 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 <dilawars@ncbs.res.in> 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 <dilawars@ncbs.res.in> 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 <dilawars@ncbs.res.in> Date: Tue Apr 7 21:45:13 2020 +0530 Vectorize function later. commit 4624651 Author: Dilawar Singh <dilawars@ncbs.res.in> Date: Tue Apr 7 20:48:47 2020 +0530 name, path, and parent of moose.vec are not vectorised. commit 6126a64 Author: Dilawar Singh <dilawars@ncbs.res.in> Date: Tue Apr 7 19:20:28 2020 +0530 snippets/savemodel.py is causing problem now. commit 15eae1d Author: Dilawar Singh <dilawars@ncbs.res.in> Date: Tue Apr 7 18:08:37 2020 +0530 vec values are returned as numpy array. commit cc89202 Author: Dilawar Singh <dilawars@ncbs.res.in> 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 <dilawars@ncbs.res.in> 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 <dilawars@ncbs.res.in> Date: Tue Apr 7 13:54:52 2020 +0530 TODO: Id should be wrapped as moose.vec commit d6552e6 Author: Dilawar Singh <dilawars@ncbs.res.in> 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 <dilawars@ncbs.res.in> Date: Tue Apr 7 11:23:27 2020 +0530 Support more return types. commit 0862930 Author: Dilawar Singh <dilawars@ncbs.res.in> Date: Tue Apr 7 10:44:35 2020 +0530 MooseVec can now handle fieldElement as well. commit 1d40e74 Author: Dilawar Singh <dilawars@ncbs.res.in> Date: Mon Apr 6 21:03:58 2020 +0530 Needs some major overhaul of API. commit 3116b05 Author: Dilawar Singh <dilawars@ncbs.res.in> Date: Mon Apr 6 15:04:32 2020 +0530 Removed melement. commit 8baffdc Author: Dilawar Singh <dilawars@ncbs.res.in> 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 <dilawars@ncbs.res.in> Date: Mon Apr 6 14:01:28 2020 +0530 Time to run examples now. commit 731fc47 Author: Dilawar Singh <dilawars@ncbs.res.in> 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 <dilawars@ncbs.res.in> 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 <dilawars@ncbs.res.in> Date: Mon Apr 6 13:17:18 2020 +0530 Overloaded funtions. commit bc95f4d Author: Dilawar Singh <dilawars@ncbs.res.in> Date: Mon Apr 6 12:25:23 2020 +0530 Enabled helper functions. commit aeecc41 Author: Dilawar Singh <dilawars@ncbs.res.in> Date: Mon Apr 6 00:17:06 2020 +0530 beat the old api in microbenchmarks as well. commit 6e88eff Author: Dilawar Singh <dilawars@ncbs.res.in> Date: Sun Apr 5 23:56:00 2020 +0530 minor tweaks. commit 1dd9390 Author: Dilawar Singh <dilawars@ncbs.res.in> Date: Sun Apr 5 23:46:37 2020 +0530 moose.create is fast but moose.delete is bit slow. commit 0eda1b7 Author: Dilawar Singh <dilawars@ncbs.res.in> Date: Sun Apr 5 22:39:37 2020 +0530 forward declaration and compile fixes. commit a3bdd69 Author: Dilawar Singh <dilawars@ncbs.res.in> Date: Sun Apr 5 20:05:43 2020 +0530 Added benchmark file. commit e294eea Author: Dilawar Singh <dilawars@ncbs.res.in> Date: Sun Apr 5 19:55:01 2020 +0530 added micro benchmarks. commit 5979dc4 Author: Dilawar Singh <dilawars@ncbs.res.in> Date: Sat Apr 4 23:25:28 2020 +0530 Added documentations. commit 56c12f4 Author: Dilawar Singh <dilawars@ncbs.res.in> Date: Sat Apr 4 22:21:40 2020 +0530 All tests are passing.. needs to add some tests.. commit f039fad Author: Dilawar Singh <dilawars@ncbs.res.in> Date: Sat Apr 4 21:58:28 2020 +0530 _cmoose to _moose. commit 9543258 Author: Dilawar Singh <dilawars@ncbs.res.in> Date: Sat Apr 4 19:57:21 2020 +0530 Needs to fix some more API issues. commit 4d6c147 Author: Dilawar Singh <dilawars@ncbs.res.in> Date: Sat Apr 4 17:49:15 2020 +0530 Added version 2.5 commit f0efd21 Author: Dilawar Singh <dilawars@ncbs.res.in> 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 <dilawars@ncbs.res.in> Date: Sat Apr 4 12:11:59 2020 +0530 Needs final touch. commit 5262dc4 Author: Dilawar Singh <dilawars@ncbs.res.in> Date: Sat Apr 4 12:03:56 2020 +0530 Added one more missing attribute. commit 7757643 Author: Dilawar Singh <dilawars@ncbs.res.in> Date: Sat Apr 4 11:25:53 2020 +0530 test commit [skip ci] commit cb8a970 Author: Dilawar Singh <dilawars@ncbs.res.in> Date: Sat Apr 4 10:28:06 2020 +0530 old test is back. commit 06e3357 Author: Dilawar Singh <dilawars@ncbs.res.in> 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 <dilawars@ncbs.res.in> Date: Sat Apr 4 07:26:24 2020 +0530 One more test is passing. commit 6188e09 Author: Dilawar Singh <dilawars@ncbs.res.in> Date: Sat Apr 4 07:25:25 2020 +0530 Restored old values in the test. commit 349f8ea Author: Dilawar Singh <dilawars@ncbs.res.in> Date: Sat Apr 4 05:55:15 2020 +0530 fixes to one more tests. commit c90986a Author: Dilawar Singh <dilawars@ncbs.res.in> Date: Sat Apr 4 05:42:22 2020 +0530 Now do a local testing. commit e6a6575 Author: Dilawar Singh <dilawars@ncbs.res.in> Date: Sat Apr 4 05:37:26 2020 +0530 numerical assertion of oscillatory tests are hard. commit 5af49e9 Author: Dilawar Singh <dilawars@ncbs.res.in> Date: Sat Apr 4 05:26:34 2020 +0530 Almost all tests are passing. commit d7f03bd Author: Dilawar Singh <dilawars@ncbs.res.in> 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 <dilawars@ncbs.res.in> Date: Sat Apr 4 04:43:36 2020 +0530 Needs to fix doc. commit 113dddc Author: Dilawar Singh <dilawars@ncbs.res.in> Date: Sat Apr 4 04:36:02 2020 +0530 more tests are passing. all test_Xreacs are passing now. commit 29ff41c Author: Dilawar Singh <dilawars@ncbs.res.in> Date: Sat Apr 4 04:31:33 2020 +0530 Use ObjId instread of Id in buildMeshJunction. commit 33e9591 Author: Dilawar Singh <dilawars@ncbs.res.in> Date: Sat Apr 4 04:27:38 2020 +0530 Passing ObjId as Id is creating trouble. commit 537779e Author: Dilawar Singh <dilawars@ncbs.res.in> Date: Sat Apr 4 03:59:30 2020 +0530 one more test passes. commit 650309a Author: Dilawar Singh <dilawars@ncbs.res.in> Date: Sat Apr 4 03:05:28 2020 +0530 delete works. commit b13e051 Author: Dilawar Singh <dilawars@ncbs.res.in> Date: Sat Apr 4 02:13:31 2020 +0530 Some more tests [skip ci] commit e518d35 Author: Dilawar Singh <dilawars@ncbs.res.in> Date: Sat Apr 4 01:42:15 2020 +0530 One more test is passed. commit c783578 Author: Dilawar Singh <dilawars@ncbs.res.in> Date: Sat Apr 4 01:37:24 2020 +0530 isinstance support is added. commit 2a28f9a Author: Dilawar Singh <dilawars@ncbs.res.in> Date: Fri Apr 3 22:15:46 2020 +0530 Added tests to normalizepath. commit 4c2086a Author: Dilawar Singh <dilawars@ncbs.res.in> Date: Fri Apr 3 22:08:30 2020 +0530 Global random number generator is moved from basecode to randnum. commit 6a2b7b7 Author: Dilawar Singh <dilawars@ncbs.res.in> Date: Fri Apr 3 20:09:21 2020 +0530 Couple of seg-faults to take care of. commit 8a90db2 Author: Dilawar Singh <dilawars@ncbs.res.in> Date: Fri Apr 3 18:27:52 2020 +0530 Fixed one more test. commit 1798a1e Author: Dilawar Singh <dilawars@ncbs.res.in> Date: Fri Apr 3 14:18:47 2020 +0530 Need to fix rdesignuer now. commit 0be10c0 Author: Dilawar Singh <dilawars@ncbs.res.in> Date: Fri Apr 3 12:59:16 2020 +0530 Finfo can also return .vec. commit 226d616 Author: Dilawar Singh <dilawars@ncbs.res.in> Date: Fri Apr 3 12:35:32 2020 +0530 Function is also fixed. commit b68a97b Author: Dilawar Singh <dilawars@ncbs.res.in> Date: Fri Apr 3 12:22:29 2020 +0530 SynapseTest is also passing. commit 8f2a039 Author: Dilawar Singh <dilawars@ncbs.res.in> Date: Fri Apr 3 11:38:20 2020 +0530 Fixes all the c++ tests commit 173b9d2 Author: Dilawar Singh <dilawars@ncbs.res.in> Date: Fri Apr 3 11:28:47 2020 +0530 ObjId.vec create a vec on the fly. commit e71fea0 Author: Dilawar Singh <dilawars@ncbs.res.in> Date: Thu Apr 2 22:39:02 2020 +0530 Same problem on OSX. One more test is failing. commit 47e25f9 Author: Dilawar Singh <dilawars@ncbs.res.in> Date: Thu Apr 2 22:08:41 2020 +0530 Some more fixes. moose.element is not honoring dataIndex. commit 9de507a Author: Dilawar Singh <dilawars@ncbs.res.in> Date: Thu Apr 2 20:17:29 2020 +0530 bebug vec and connection list. commit d7f0a26 Author: Dilawar Singh <dilawars@ncbs.res.in> Date: Thu Apr 2 19:22:00 2020 +0530 Refactoring. commit 2221410 Author: Dilawar Singh <dilawars@ncbs.res.in> Date: Thu Apr 2 16:17:48 2020 +0530 Added .clang-format file. commit 7a8437d Author: Dilawar Singh <dilawars@ncbs.res.in> Date: Thu Apr 2 12:44:32 2020 +0530 more progress. Lets have lunch first now. commit 0ed8933 Author: Dilawar Singh <dilawars@ncbs.res.in> Date: Thu Apr 2 12:25:44 2020 +0530 Fix Xreacs later. commit 04d4d2f Author: Dilawar Singh <dilawars@ncbs.res.in> 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 <dilawars@ncbs.res.in> Date: Wed Apr 1 21:21:06 2020 +0530 refacorted codebase... commit 52cfdf7 Author: Dilawar Singh <dilawars@ncbs.res.in> Date: Wed Apr 1 21:06:13 2020 +0530 Added extra header for Finfo ... commit b16dd1c Author: Dilawar Singh <dilawars@ncbs.res.in> Date: Wed Apr 1 19:58:56 2020 +0530 Needs to implement LookupFinfo set. commit 8199fc0 Author: Dilawar Singh <dilawars@ncbs.res.in> Date: Wed Apr 1 18:48:25 2020 +0530 Disable pybind11. commit 5c25dad Author: Dilawar Singh <dilawars@ncbs.res.in> Date: Wed Apr 1 18:48:02 2020 +0530 One more tests seem to pass. commit 40a4559 Author: Dilawar Singh <dilawars@ncbs.res.in> Date: Wed Apr 1 18:22:52 2020 +0530 Some more fixes. commit dd9b50e Author: Dilawar Singh <dilawars@ncbs.res.in> Date: Wed Apr 1 17:59:50 2020 +0530 Perfect. One more test passes. commit fec019b Author: Dilawar Singh <dilawars@ncbs.res.in> Date: Wed Apr 1 15:41:22 2020 +0530 Refactoring and some more generic programming. commit 9eb2308 Author: Dilawar Singh <dilawars@ncbs.res.in> Date: Tue Mar 31 20:48:57 2020 +0530 small fixes. Changes in API requires .id . commit 7de3228 Author: Dilawar Singh <dilawars@ncbs.res.in> Date: Tue Mar 31 19:13:51 2020 +0530 Minor tweak to a test. commit c541b91 Author: Dilawar Singh <dilawars@ncbs.res.in> Date: Tue Mar 31 19:08:36 2020 +0530 One more test passed. commit 5cc3d3b Merge: ce579ac 1abb6f1 Author: Dilawar Singh <dilawars@ncbs.res.in> Date: Tue Mar 31 18:59:23 2020 +0530 Merge branch 'pybind11_shell' into temp commit ce579ac Author: Dilawar Singh <dilawars@ncbs.res.in> Date: Tue Mar 31 18:58:59 2020 +0530 renmaed. commit 16bbc3e Author: Dilawar Singh <dilawars@ncbs.res.in> Date: Tue Mar 31 18:20:55 2020 +0530 phew. I made a boo boo before. commit 1abb6f1 Merge: 24df86a fa06c38 Author: Dilawar Singh <dilawars@ncbs.res.in> 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 <dilawars@ncbs.res.in> Date: Tue Mar 31 02:14:22 2020 +0530 Id and ObjId are not playing well together... commit 48832b1 Author: Dilawar Singh <dilawars@ncbs.res.in> 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 <dilawars@ncbs.res.in> Date: Tue Mar 31 01:28:02 2020 +0530 temp commit. commit 24df86a Author: Dilawar Singh <dilawars@ncbs.res.in> Date: Mon Mar 30 23:39:46 2020 +0530 Temp commit. Exposing only Id. commit 448b8b5 Author: Dilawar Singh <dilawars@ncbs.res.in> Date: Mon Mar 30 23:14:51 2020 +0530 more tests are passing... commit d1b4990 Author: Dilawar Singh <dilawars@ncbs.res.in> Date: Mon Mar 30 20:35:39 2020 +0530 Need to find a solution.. commit 6b5082b Author: Dilawar Singh <dilawars@ncbs.res.in> Date: Mon Mar 30 19:05:44 2020 +0530 Refactoring and have a working moose.vec API. commit 98d8d34 Author: Dilawar Singh <dilawars@ncbs.res.in> Date: Mon Mar 30 18:05:07 2020 +0530 [skip ci] needs tweaking in the API. commit 0f7929c Author: Dilawar Singh <dilawars@ncbs.res.in> Date: Mon Mar 30 14:40:37 2020 +0530 Support vec. But first need a nap. commit 93d6e83 Author: Dilawar Singh <dilawars@ncbs.res.in> Date: Mon Mar 30 13:33:05 2020 +0530 refactoring. commit fd03015 Author: Dilawar Singh <dilawars@ncbs.res.in> Date: Mon Mar 30 13:17:31 2020 +0530 random works. commit fc34547 Author: Dilawar Singh <dilawars@ncbs.res.in> Date: Mon Mar 30 11:49:00 2020 +0530 Need to polish the API. commit 6af0f2c Author: Dilawar Singh <dilawars@ncbs.res.in> Date: Mon Mar 30 11:00:03 2020 +0530 Lets move to DestFinfo. commit 476d700 Author: Dilawar Singh <dilawars@ncbs.res.in> Date: Mon Mar 30 07:53:31 2020 +0530 Return type. commit 778208a Merge: dab5af4 dd65791 Author: Dilawar Singh <dilawars@ncbs.res.in> 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 <dilawars@ncbs.res.in> Date: Mon Mar 30 06:54:42 2020 +0530 Updated [skip ci] commit 76ec2a1 Author: Dilawar Singh <dilawars@ncbs.res.in> Date: Sun Mar 29 23:00:02 2020 +0530 [skip ci] some more changes. commit c4d7bc6 Author: Dilawar Singh <dilawars@ncbs.res.in> Date: Sun Mar 29 22:24:57 2020 +0530 We go both API integrated. commit f0ac785 Author: Dilawar Singh <dilawars@ncbs.res.in> Date: Sun Mar 29 21:48:18 2020 +0530 LookupField is a function. commit aee928e Author: Dilawar Singh <dilawars@ncbs.res.in> Date: Sun Mar 29 21:11:48 2020 +0530 Do the rest tomorrow. commit e118e12 Author: Dilawar Singh <dilawars@ncbs.res.in> Date: Sun Mar 29 20:45:21 2020 +0530 Retuning binding to std::function which return the Finfo value. commit dab5af4 Author: Dilawar Singh <dilawars@ncbs.res.in> Date: Sun Mar 29 18:01:12 2020 +0530 isA is method. Time to make it a subscriptable dictionary. commit c7a7b24 Author: Dilawar Singh <dilawars@ncbs.res.in> Date: Sun Mar 29 15:34:42 2020 +0530 Lets handle LookupField::set and get. commit a06e478 Author: Dilawar Singh <dilawars@ncbs.res.in> Date: Sun Mar 29 01:13:46 2020 +0530 Deal with it tomorrow. commit bb1cae5 Author: Dilawar Singh <dilawars@ncbs.res.in> Date: Sun Mar 29 00:28:22 2020 +0530 Getting there. [skip ci] commit 5cccf8b Author: Dilawar Singh <dilawars@ncbs.res.in> Date: Sat Mar 28 22:33:21 2020 +0530 Some refactoring. Back to same functionality [skip ci]. commit a979de6 Author: Dilawar Singh <dilawars@ncbs.res.in> Date: Sat Mar 28 20:46:01 2020 +0530 Updated a bit more .. commit b43c617 Author: Dilawar Singh <dilawars@ncbs.res.in> Date: Sat Mar 28 19:47:58 2020 +0530 New API works fantastic. commit 0deb291 Author: Dilawar Singh <dilawars@ncbs.res.in> Date: Sat Mar 28 19:40:19 2020 +0530 Incremental change. Dynamic attributes. commit 7f2539c Author: Dilawar Singh <dilawars@ncbs.res.in> Date: Sat Mar 28 19:31:31 2020 +0530 Subclassing _ObjId now. commit 0f64cd0 Author: Dilawar Singh <dilawars@ncbs.res.in> Date: Sat Mar 28 18:12:57 2020 +0530 Dynamic attributes are needed now. commit eff08b2 Author: Dilawar Singh <dilawars@ncbs.res.in> Date: Sat Mar 28 16:16:13 2020 +0530 All test passes. Needs to work on the API now. commit 8791df7 Author: Dilawar Singh <dilawars@ncbs.res.in> Date: Sat Mar 28 15:40:35 2020 +0530 Blazingly fast. commit 070f735 Author: Dilawar Singh <dilawars@ncbs.res.in> 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 <dilawars@ncbs.res.in> Date: Sat Mar 28 00:28:22 2020 +0530 This is for tomorow. commit 72f7b62 Author: Dilawar Singh <dilawars@ncbs.res.in> Date: Fri Mar 27 21:43:33 2020 +0530 Work from home. commit 4ea29e9 Author: Dilawar Singh <dilawars@ncbs.res.in> Date: Fri Mar 27 20:32:19 2020 +0530 May be later. commit eff6f90 Author: Dilawar Singh <dilawars@ncbs.res.in> Date: Fri Mar 27 17:57:40 2020 +0530 Not sure about the testKsolve.cpp tests. commit bef104c Author: Dilawar Singh <dilawars@ncbs.res.in> Date: Fri Mar 27 17:11:34 2020 +0530 Do testing with master branch. commit 0078af1 Author: Dilawar Singh <dilawars@ncbs.res.in> 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 <dilawars@ncbs.res.in> 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 <dilawars@ncbs.res.in> Date: Fri Mar 27 14:11:18 2020 +0530 add test function. commit 911bd03 Author: Dilawar Singh <dilawars@ncbs.res.in> Date: Fri Mar 27 13:56:12 2020 +0530 local changes. commit cc7144f Author: Dilawar Singh <dilawars@ncbs.res.in> Date: Fri Mar 27 13:50:40 2020 +0530 Move to gulgula. commit d41e7eb Author: Dilawar Singh <dilawars@ncbs.res.in> Date: Fri Mar 27 04:18:44 2020 +0530 Allmost there. commit d913ceb Author: Dilawar Singh <dilawars@ncbs.res.in> Date: Fri Mar 27 01:50:18 2020 +0530 addMsg -> connect . commit 8793d33 Author: Dilawar Singh <dilawars@ncbs.res.in> Date: Fri Mar 27 01:10:24 2020 +0530 get/set are on ObjId . commit d99115c Author: Dilawar Singh <dilawars@ncbs.res.in> Date: Fri Mar 27 00:47:20 2020 +0530 Ok. Vector and numpy are working. commit 2f3bc04 Author: Dilawar Singh <dilawars@ncbs.res.in> Date: Thu Mar 26 23:02:03 2020 +0530 move to bebinca for fast compilation. commit a94fec9 Author: Dilawar Singh <dilawars@ncbs.res.in> Date: Thu Mar 26 18:29:50 2020 +0530 children and parent is not working. commit 756ec3a Author: Dilawar Singh <dilawars@ncbs.res.in> 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 <dilawars@ncbs.res.in> Date: Tue Mar 24 15:07:09 2020 +0530 All the learning experience is over. Pybind11 is great. commit 6edda7a Author: Dilawar Singh <dilawars@ncbs.res.in> Date: Tue Mar 24 00:55:13 2020 +0530 Add a bit more fields. commit e32c468 Author: Dilawar Singh <dilawars@ncbs.res.in> Date: Mon Mar 23 23:30:19 2020 +0530 I can complete this API tomorrow. commit 7aaddf7 Author: Dilawar Singh <dilawars@ncbs.res.in> Date: Mon Mar 23 22:54:35 2020 +0530 added more functions [skip ci] commit 7f1b709 Author: Dilawar Singh <dilawars@ncbs.res.in> Date: Mon Mar 23 16:38:34 2020 +0530 disable build for now on gitlab ci commit ae2739d Author: Dilawar Singh <dilawars@ncbs.res.in> Date: Mon Mar 23 15:05:22 2020 +0530 pybind11 module is named _cmoose and it different from _moose. commit 0c33684 Author: Dilawar Singh <dilawars@ncbs.res.in> Date: Mon Mar 23 14:45:32 2020 +0530 I got wildcardFind to function. commit 65b307c Author: Dilawar Singh <dilawars@ncbs.res.in> 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 <dilawars@ncbs.res.in> 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 <dilawars@ncbs.res.in> Date: Sun Mar 22 23:12:58 2020 +0530 Time to support / in path. commit 270ea8c Author: Dilawar Singh <dilawars@ncbs.res.in> Date: Sun Mar 22 22:50:21 2020 +0530 empty element() commit a1eed3a Author: Dilawar Singh <dilawars@ncbs.res.in> Date: Sun Mar 22 22:39:55 2020 +0530 temp commit. commit a70b5fe Author: Dilawar Singh <dilawars@ncbs.res.in> Date: Sun Mar 22 15:44:56 2020 +0530 Great. Lets try cython as well. commit 038490f Author: Dilawar Singh <dilawars@ncbs.res.in> Date: Sun Mar 22 15:44:27 2020 +0530 Try cython now. commit 8bbf900 Author: Dilawar Singh <dilawars@ncbs.res.in> Date: Sun Mar 22 13:43:02 2020 +0530 _moose goes to python/moose directory. commit 014bde2 Merge: 8f60899 ad58dc5 Author: Dilawar Singh <dilawars@ncbs.res.in> Date: Sun Mar 22 13:18:20 2020 +0530 Merge branch 'issue_397' into pybind11 commit f4070da Merge: ad58dc5 5e660e9 Author: Dilawar Singh <dilawars@ncbs.res.in> Date: Sat Mar 21 22:21:16 2020 +0530 Merge branch 'refactoring' into issue_397 commit 5e660e9 Author: dilawars <dilawars@nargis.ncbs.res.in> 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 <dilawars@nargis.ncbs.res.in> 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 <dilawars@ncbs.res.in> 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 <dilawars@ncbs.res.in> 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 <dilawars@ncbs.res.in> Date: Sat Mar 21 15:15:43 2020 +0530 Fix to #397 commit 8f60899 Author: Dilawar Singh <dilawars@ncbs.res.in> Date: Tue Mar 17 18:27:54 2020 +0530 Perfecto. Create works. commit aa95a0c Author: Dilawar Singh <dilawars@ncbs.res.in> Date: Sun Mar 15 22:10:07 2020 +0530 pybind11 bindings. commit da9d1d9 Merge: 0e85a57 36c0026 Author: Dilawar Singh <dilawars@ncbs.res.in> Date: Sun Mar 15 15:40:06 2020 +0530 Merge commit '36c0026886c70e39c505f8715e65a7c3cf1e6ade' as 'external/pybind11' commit 36c0026 Author: Dilawar Singh <dilawars@ncbs.res.in> 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 <dilawars@ncbs.res.in> Co-authored-by: HarshaRani <hrani@ncbs.res.in> Co-authored-by: Anushree Narjala <anushree.narjala@gmail.com> * 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 <dilawars@ncbs.res.in> Co-authored-by: Dilawar Singh <dilawar@users.noreply.github.com> Co-authored-by: HarshaRani <hrani@ncbs.res.in> Co-authored-by: Anushree Narjala <anushree.narjala@gmail.com>
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