Update to chennapoda branch #413
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…ib from the test. (BhallaLab#310)
…hallaLab#308) * Fixes as suggested by PyLint. Added a target pylint in cmake file. * Do pylint testing on OSX. * Fixed import statement. * Fixed pylint errors, removed unneccessary file. * Test of available attributes in moose. * Install python-libsbml and pyneuroml on OSX before running pylint. * Removed temporary attributes from test. * plot_utils is not so important. It failes when python-tk not found. * Fixed boost segfault with dense solver. Also remove GSL specific attrib from the test. * Tweak to cmake on OSX. New clang-llvm compiler options added to ignore unused pragmas. Import hhfit only when required. * None of thest depends on matplotlib anymore. Added one more rdesineur tests from moose-examples scripts. * Fix travis: Install python-tk and python3-tk on travis.
Added NMDAR to rdesigneurProtos.
* Fixes as suggested by PyLint. Added a target pylint in cmake file. * Do pylint testing on OSX. * Fixed import statement. * Fixed pylint errors, removed unneccessary file. * Test of available attributes in moose. * Install python-libsbml and pyneuroml on OSX before running pylint. * Removed temporary attributes from test. * plot_utils is not so important. It failes when python-tk not found. * Fixed boost segfault with dense solver. Also remove GSL specific attrib from the test. * Tweak to cmake on OSX. New clang-llvm compiler options added to ignore unused pragmas. Import hhfit only when required. * None of thest depends on matplotlib anymore. Added one more rdesineur tests from moose-examples scripts. * Fix travis: Install python-tk and python3-tk on travis. * TIDY UP: basecode and benchmarks can be built independantly. [skip ci] * Compiles as standalone. [skip ci] * One more directory is standalone. * Diffusion dir is standalone as well [skip ci] * hsolve built in isolation as well [skip ci] * ksolve is now tidied up [skip ci] * needs local testing now. * This passes locally with python3. * include_guard is not in cmake2.8. * More more fixes identified by clang-check. * Added Cell.cpp to build system. This class is probably broken but good to keep it included.
Some fixes to Ca-dependent channel prototypes in rdesigneur.
```AttributeError: 'NML2Reader' object has no attribute 'rate_fn_map'``` This is causing failure of moose-examples: https://travis-ci.org/BhallaLab/moose-examples/jobs/436070992
Do not treat warning as errors. It causes headaches with new compiler versions and OSX updates.
…t is corrected as now saving the value of scene coOrdinates (BhallaLab#313)
* Update README.md Updated installation instructions. - Removed open build service repo. - Added nightly version. * Use system python on travis. Using full paths. * Use xcode 10.0
Update to rdesigneur for backward compatibility in passiveDistrib specification
Hotfix NML2. If self.network not found, sett the temperate to 25 deg C.
BhallaLab#318) * CylMesh are written to SBML with annotation field and only zeroth element/voxel is taken * originaly volex's volume and volex details are populated, but now cylMesh volume with volex details is populated
…written for both cubeMesh or CylMesh
Channel are written back to genesis and zeroth voxel moose object is …
This works, but only because of an implementation detail: short strings are interned as part of module code. But the rules are complicated and we should not rely on this. See http://guilload.com/python-string-interning/ for a nice writeup. Python3.8 now warns about this.
neuroml: do not use "is" with strings
…k made for integer in the expression,writeSBML:added autlayout which was required for writting cspace model while writting from command line, for cplxpool's x-y coordinates and motor/diff constant are added,fixXreac: check to see if object exist before _moose.connect, case where object is deleted but _xref_ annotation info field still hold the reference
* Fixed Ca channel proto, thanks to Harshavardan * Fix to vclamp in rdesigneur. Fix to ConcChan handling involving many files * Fix to HSolve so that assignment of passive properties Em, Cm and Rm reflects in the solver calculations without having to rebuild the entire solver. * Fix conversion for ConcChan in ReadKkit, corresponding fix to calculations in Dsolve * Fixed test_Xchan1.py to work with fixed ConcChan permeability units
…dMooseIdMap,writesbml: added annotation for cplxpool, autolayout for cspaccemodels (BhallaLab#374)
…nel is written as MMenz and Km in kinetics law updated based on no. substrate
while writting genesis file compartment is added as a group
* Don't run streamer multitab tests on OSX/Travis. * Disable all socket streamer tests. * - Make python3 default python. - cmake 3.12 is minimum required. - Fixes to Python API. strncpy can not write to `const char*`. Instead initialize with value. - Build system fixes. * Fixes for gcc5 series. It is not smart enough to figure out which field is being updated. These needs to be ported to branch chamcham as well. * Create cmake.yml * Updated commands. * removing github actions. * Create build.yml * Added sudo ... * Run sudo apt-update ... * Fixed the name of package... * Fixed make and test targets. * Added workflow file. * Update build.yml
…all platforms (BhallaLab#385) * Don't run streamer multitab tests on OSX/Travis. * Disable all socket streamer tests. * added moose.about(). Show essential information about moose project * Add .gitlab-ci.yml * Update .gitlab-ci.yml * - Make python3 default python. - cmake 3.12 is minimum required. - Fixes to Python API. strncpy can not write to `const char*`. Instead initialize with value. - Build system fixes. * Fixes for gcc5 series. It is not smart enough to figure out which field is being updated. These needs to be ported to branch chamcham as well. * Create cmake.yml * Updated commands. * removing github actions. * Create build.yml * Added sudo ... * Run sudo apt-update ... * Fixed the name of package... * Fixed make and test targets. * Added workflow file. * Update build.yml * Using python setup.py to build the module. * Not yet complete because we still don't have static linking to gsl . * Temp commit: Build locally. * Run in inside a docker image to tweak. * Some more tweaks. * Added centos build docker file. * Docker build was successful. Needs to improve test function... * Added centos build docker file. Docker build was successful. Needs to improve test function... setup.py is working just fine. CMake and python's setup.py can use each other. Time to remove pymoose/setup.cmake.py file. Removed the cmake helper script. It has been moved to topmost directory where it can be used on its own. Squashed commit of the following: commit 374bf50 Author: Dilawar Singh <[email protected]> Date: Tue Feb 4 14:22:29 2020 +0530 This seems to work just fine. commit 4746ec4 Author: Dilawar Singh <[email protected]> Date: Mon Feb 3 21:54:25 2020 +0530 testing is required. commit d2ddaf7 Author: Dilawar Singh <[email protected]> Date: Mon Feb 3 21:34:59 2020 +0530 Seems to be just fine now. commit 63dceb4 Merge: c743aed 5499353 Author: Dilawar <[email protected]> Date: Mon Feb 3 15:32:41 2020 +0000 Merge branch 'setup.py_and_cmake' of https://github.com/dilawar/moose-core into setup.py_and_cmake commit c743aed Author: Dilawar <[email protected]> Date: Mon Feb 3 15:32:05 2020 +0000 Some more changes. commit 5499353 Author: Dilawar Singh <[email protected]> Date: Mon Feb 3 20:52:43 2020 +0530 Use cmake2.8 commit c8b365a Author: Dilawar Singh <[email protected]> Date: Mon Feb 3 20:37:54 2020 +0530 Lets test it in fresh docker image. removed uninstall target, use pip to uninstall moose. Added path in target_link_directories macro for target moose.bin. MOOSE's python module. * Minor tweaks... * Some more tweaks. * Added command test to setup.py which calls ctest. * Temp commit. * Removed the target_link_directories command which is available only in very recent cmake. * Added docker-file for suse. * Updated cmake file; build directory is now part of directories to search. * Update build.yml Fixed the test command in github actions. * Use latest xcode. * Squashed commit of the following: commit ecdc1a8 Author: Dilawar Singh <[email protected]> Date: Wed Feb 5 14:15:46 2020 +0530 Use latest xcode. commit 2a81096 Merge: a4a2338 e7cd7c0 Author: Dilawar Singh <[email protected]> Date: Wed Feb 5 14:14:24 2020 +0530 Merge remote-tracking branch 'bhallalab/master' commit a4a2338 Author: Dilawar Singh <[email protected]> Date: Wed Feb 5 13:42:26 2020 +0530 Update build.yml Fixed the test command in github actions. commit cb0095f Merge: 4408bee 71c9756 Author: Dilawar Singh <[email protected]> Date: Wed Feb 5 14:10:24 2020 +0530 Merge branch 'devel' of https://github.com/dilawar/moose-core commit 71c9756 Author: Dilawar Singh <[email protected]> Date: Tue Feb 4 23:20:11 2020 +0530 Updated cmake file; build directory is now part of directories to search. commit 2f0d93a Author: Dilawar Singh <[email protected]> Date: Tue Feb 4 23:00:55 2020 +0530 Added docker-file for suse. commit 82adc1c Author: Dilawar Singh <[email protected]> Date: Tue Feb 4 22:43:53 2020 +0530 Removed the target_link_directories command which is available only in very recent cmake. commit 3605566 Author: Dilawar Singh <[email protected]> Date: Tue Feb 4 17:46:22 2020 +0530 Temp commit. commit 6248e12 Author: Dilawar Singh <[email protected]> Date: Tue Feb 4 17:43:14 2020 +0530 Added command test to setup.py which calls ctest. commit a3d25aa Author: Dilawar Singh <[email protected]> Date: Tue Feb 4 16:49:40 2020 +0530 Some more tweaks. commit 9a14b5c Author: Dilawar Singh <[email protected]> Date: Tue Feb 4 15:35:58 2020 +0530 Minor tweaks... commit 9f475b3 Author: Dilawar Singh <[email protected]> Date: Mon Feb 3 14:01:12 2020 +0530 Added centos build docker file. Docker build was successful. Needs to improve test function... setup.py is working just fine. CMake and python's setup.py can use each other. Time to remove pymoose/setup.cmake.py file. Removed the cmake helper script. It has been moved to topmost directory where it can be used on its own. Squashed commit of the following: commit 374bf50 Author: Dilawar Singh <[email protected]> Date: Tue Feb 4 14:22:29 2020 +0530 This seems to work just fine. commit 4746ec4 Author: Dilawar Singh <[email protected]> Date: Mon Feb 3 21:54:25 2020 +0530 testing is required. commit d2ddaf7 Author: Dilawar Singh <[email protected]> Date: Mon Feb 3 21:34:59 2020 +0530 Seems to be just fine now. commit 63dceb4 Merge: c743aed 5499353 Author: Dilawar <[email protected]> Date: Mon Feb 3 15:32:41 2020 +0000 Merge branch 'setup.py_and_cmake' of https://github.com/dilawar/moose-core into setup.py_and_cmake commit c743aed Author: Dilawar <[email protected]> Date: Mon Feb 3 15:32:05 2020 +0000 Some more changes. commit 5499353 Author: Dilawar Singh <[email protected]> Date: Mon Feb 3 20:52:43 2020 +0530 Use cmake2.8 commit c8b365a Author: Dilawar Singh <[email protected]> Date: Mon Feb 3 20:37:54 2020 +0530 Lets test it in fresh docker image. removed uninstall target, use pip to uninstall moose. Added path in target_link_directories macro for target moose.bin. MOOSE's python module. commit 4408bee Author: Dilawar Singh <[email protected]> Date: Mon Feb 3 16:00:45 2020 +0530 Docker build was successful. Needs to improve test function... commit 892b9c3 Author: Dilawar Singh <[email protected]> Date: Mon Feb 3 14:01:12 2020 +0530 Added centos build docker file. commit 5777ede Author: Dilawar Singh <[email protected]> Date: Mon Feb 3 08:05:43 2020 +0000 Some more tweaks. commit ac30142 Author: Dilawar Singh <[email protected]> Date: Mon Feb 3 13:08:53 2020 +0530 Run in inside a docker image to tweak. commit 8bee4d0 Author: Dilawar Singh <[email protected]> Date: Sun Feb 2 04:03:40 2020 +0530 Temp commit: Build locally. commit 4d8342e Author: Dilawar Singh <[email protected]> Date: Sun Feb 2 03:54:14 2020 +0530 Not yet complete because we still don't have static linking to gsl . commit 18e65d5 Author: Dilawar Singh <[email protected]> Date: Sun Feb 2 03:47:38 2020 +0530 Using python setup.py to build the module. commit 7a8f52d Merge: 6a7de61 1bbbc2d Author: Dilawar Singh <[email protected]> Date: Sun Feb 2 03:12:45 2020 +0530 Merge branch 'devel' of https://github.com/dilawar/moose-core into devel commit 6a7de61 Merge: 27f62f5 749f1b8 Author: Dilawar Singh <[email protected]> Date: Sun Feb 2 02:30:13 2020 +0530 Merge branch 'master' of https://github.com/dilawar/moose-core commit 749f1b8 Author: Dilawar Singh <[email protected]> Date: Sun Feb 2 00:18:52 2020 +0530 Update build.yml commit f089c1c Author: Dilawar Singh <[email protected]> Date: Sat Feb 1 22:49:27 2020 +0530 Added workflow file. commit 3502f13 Author: Dilawar Singh <[email protected]> Date: Sat Feb 1 22:46:39 2020 +0530 Fixed make and test targets. commit 0768916 Author: Dilawar Singh <[email protected]> Date: Sat Feb 1 22:43:40 2020 +0530 Fixed the name of package... commit 1998950 Author: Dilawar Singh <[email protected]> Date: Sat Feb 1 22:42:04 2020 +0530 Run sudo apt-update ... commit 2cf3294 Author: Dilawar Singh <[email protected]> Date: Sat Feb 1 22:40:20 2020 +0530 Added sudo ... commit 06aa508 Author: Dilawar Singh <[email protected]> Date: Sat Feb 1 22:38:24 2020 +0530 Create build.yml commit 08950de Author: Dilawar Singh <[email protected]> Date: Sat Feb 1 22:03:15 2020 +0530 removing github actions. commit f471483 Author: Dilawar Singh <[email protected]> Date: Sat Feb 1 21:50:33 2020 +0530 Updated commands. commit 7453901 Author: Dilawar Singh <[email protected]> Date: Sat Feb 1 21:39:29 2020 +0530 Create cmake.yml commit 69a3aae Author: Dilawar Singh <[email protected]> Date: Fri Jan 31 09:28:14 2020 +0000 Fixes for gcc5 series. It is not smart enough to figure out which field is being updated. These needs to be ported to branch chamcham as well. commit 9e0b0d1 Author: Dilawar Singh <[email protected]> Date: Fri Jan 31 13:02:32 2020 +0530 - Make python3 default python. - cmake 3.12 is minimum required. - Fixes to Python API. strncpy can not write to `const char*`. Instead initialize with value. - Build system fixes. commit 27f62f5 Merge: 2062ab2 ebfb5dc Author: Dilawar Singh <[email protected]> Date: Mon Jun 3 12:06:58 2019 +0530 Merge branch 'master' of github.com:dilawar/moose-core commit ebfb5dc Merge: 45216b3 526c5b0 Author: Dilawar Singh <[email protected]> Date: Sun Jun 2 19:22:16 2019 +0530 Merge branch 'master' of https://github.com/dilawar/moose-core commit 1bbbc2d Author: Dilawar Singh <[email protected]> Date: Fri Apr 19 14:45:57 2019 +0530 added moose.about(). Show essential information about moose project commit c319cb4 Merge: 45216b3 1b38d64 Author: Dilawar Singh <[email protected]> Date: Fri Apr 19 14:36:14 2019 +0530 Merge branch 'master' of github.com:BhallaLab/moose-core into devel commit 45216b3 Merge: 740fb44 58292d6 Author: Dilawar Singh <[email protected]> Date: Fri Apr 19 14:35:14 2019 +0530 Merge branch 'master' of github.com:dilawar/moose-core commit 740fb44 Merge: 3520120 f227bb0 Author: Dilawar Singh <[email protected]> Date: Thu Mar 7 11:18:57 2019 +0530 Merge branch 'master' of github.com:BhallaLab/moose-core commit 3520120 Author: Dilawar Singh <[email protected]> Date: Wed Feb 13 14:12:53 2019 +0530 Disable all socket streamer tests. commit 2dd9688 Author: Dilawar Singh <[email protected]> Date: Wed Feb 13 13:11:50 2019 +0530 Don't run streamer multitab tests on OSX/Travis. * Setup.py works with both python2 and python3. * Using timer to timeout the test. This removes a very old bug.. * Removing old tests; move them to moose-examples. * matplotlib is always optional for tests. * setup.py seems to be building just fine. Needs tweaking in the tests. * Using setup.py file to build and install pymoose. * Fixes to github actions.. * Fixes to YAML file. * Create pymoose.yml Build with different version of python. * Some more fixes to github workflows. * Install dependencies... * Updated a bit more ... * make debian fronend non-interactive... * Added missing dependencies. * Use pip to install numpy/matplotlib before build. * Remove build tests here. [skip ci] * Update .gitlab-ci.yml * Squashed commit of the following: commit 287a26a Author: Dilawar Singh <[email protected]> Date: Wed Feb 5 21:51:22 2020 +0530 Remove build tests here. [skip ci] commit af3b1ec Author: Dilawar Singh <[email protected]> Date: Wed Feb 5 21:41:07 2020 +0530 Use pip to install numpy/matplotlib before build. commit ddebb11 Author: Dilawar Singh <[email protected]> Date: Wed Feb 5 21:39:05 2020 +0530 Added missing dependencies. commit 347353b Author: Dilawar Singh <[email protected]> Date: Wed Feb 5 21:37:18 2020 +0530 make debian fronend non-interactive... commit 3e69fe7 Author: Dilawar Singh <[email protected]> Date: Wed Feb 5 21:30:11 2020 +0530 Updated a bit more ... commit 7da6a98 Author: Dilawar Singh <[email protected]> Date: Wed Feb 5 21:27:21 2020 +0530 Install dependencies... commit 5d4c5ec Author: Dilawar Singh <[email protected]> Date: Wed Feb 5 21:22:54 2020 +0530 Some more fixes to github workflows. commit 6dd377c Author: Dilawar Singh <[email protected]> Date: Wed Feb 5 21:12:31 2020 +0530 Fixes to YAML file. commit 14529ca Author: Dilawar Singh <[email protected]> Date: Wed Feb 5 21:08:05 2020 +0530 Fixes to github actions.. commit 7be23ed Author: Dilawar Singh <[email protected]> Date: Wed Feb 5 21:06:58 2020 +0530 Using setup.py file to build and install pymoose. commit 0c3f743 Author: Dilawar Singh <[email protected]> Date: Wed Feb 5 18:44:20 2020 +0530 setup.py seems to be building just fine. Needs tweaking in the tests. commit 3667a00 Author: Dilawar Singh <[email protected]> Date: Wed Feb 5 17:41:12 2020 +0530 matplotlib is always optional for tests. commit f26d0cc Author: Dilawar Singh <[email protected]> Date: Wed Feb 5 17:35:17 2020 +0530 Removing old tests; move them to moose-examples. commit 8058ede Author: Dilawar Singh <[email protected]> Date: Wed Feb 5 17:23:47 2020 +0530 Using timer to timeout the test. This removes a very old bug.. commit 6b87396 Author: Dilawar Singh <[email protected]> Date: Wed Feb 5 16:01:16 2020 +0530 Setup.py works with both python2 and python3. commit ecdc1a8 Author: Dilawar Singh <[email protected]> Date: Wed Feb 5 14:15:46 2020 +0530 Use latest xcode. commit 2a81096 Merge: a4a2338 e7cd7c0 Author: Dilawar Singh <[email protected]> Date: Wed Feb 5 14:14:24 2020 +0530 Merge remote-tracking branch 'bhallalab/master' commit a4a2338 Author: Dilawar Singh <[email protected]> Date: Wed Feb 5 13:42:26 2020 +0530 Update build.yml Fixed the test command in github actions. commit cb0095f Merge: 4408bee 71c9756 Author: Dilawar Singh <[email protected]> Date: Wed Feb 5 14:10:24 2020 +0530 Merge branch 'devel' of https://github.com/dilawar/moose-core commit 71c9756 Author: Dilawar Singh <[email protected]> Date: Tue Feb 4 23:20:11 2020 +0530 Updated cmake file; build directory is now part of directories to search. commit 2f0d93a Author: Dilawar Singh <[email protected]> Date: Tue Feb 4 23:00:55 2020 +0530 Added docker-file for suse. commit e7cd7c0 Author: Dilawar Singh <[email protected]> Date: Tue Feb 4 22:47:27 2020 +0530 Hotfix | Packaging issues on OSX (BhallaLab#383) * Don't run streamer multitab tests on OSX/Travis. * Disable all socket streamer tests. * - Make python3 default python. - cmake 3.12 is minimum required. - Fixes to Python API. strncpy can not write to `const char*`. Instead initialize with value. - Build system fixes. * Fixes for gcc5 series. It is not smart enough to figure out which field is being updated. These needs to be ported to branch chamcham as well. * Create cmake.yml * Updated commands. * removing github actions. * Create build.yml * Added sudo ... * Run sudo apt-update ... * Fixed the name of package... * Fixed make and test targets. * Added workflow file. * Update build.yml commit 82adc1c Author: Dilawar Singh <[email protected]> Date: Tue Feb 4 22:43:53 2020 +0530 Removed the target_link_directories command which is available only in very recent cmake. commit 3605566 Author: Dilawar Singh <[email protected]> Date: Tue Feb 4 17:46:22 2020 +0530 Temp commit. commit 6248e12 Author: Dilawar Singh <[email protected]> Date: Tue Feb 4 17:43:14 2020 +0530 Added command test to setup.py which calls ctest. commit a3d25aa Author: Dilawar Singh <[email protected]> Date: Tue Feb 4 16:49:40 2020 +0530 Some more tweaks. commit 9a14b5c Author: Dilawar Singh <[email protected]> Date: Tue Feb 4 15:35:58 2020 +0530 Minor tweaks... commit 9f475b3 Author: Dilawar Singh <[email protected]> Date: Mon Feb 3 14:01:12 2020 +0530 Added centos build docker file. Docker build was successful. Needs to improve test function... setup.py is working just fine. CMake and python's setup.py can use each other. Time to remove pymoose/setup.cmake.py file. Removed the cmake helper script. It has been moved to topmost directory where it can be used on its own. Squashed commit of the following: commit 374bf50 Author: Dilawar Singh <[email protected]> Date: Tue Feb 4 14:22:29 2020 +0530 This seems to work just fine. commit 4746ec4 Author: Dilawar Singh <[email protected]> Date: Mon Feb 3 21:54:25 2020 +0530 testing is required. commit d2ddaf7 Author: Dilawar Singh <[email protected]> Date: Mon Feb 3 21:34:59 2020 +0530 Seems to be just fine now. commit 63dceb4 Merge: c743aed 5499353 Author: Dilawar <[email protected]> Date: Mon Feb 3 15:32:41 2020 +0000 Merge branch 'setup.py_and_cmake' of https://github.com/dilawar/moose-core into setup.py_and_cmake commit c743aed Author: Dilawar <[email protected]> Date: Mon Feb 3 15:32:05 2020 +0000 Some more changes. commit 5499353 Author: Dilawar Singh <[email protected]> Date: Mon Feb 3 20:52:43 2020 +0530 Use cmake2.8 commit c8b365a Author: Dilawar Singh <[email protected]> Date: Mon Feb 3 20:37:54 2020 +0530 Lets test it in fresh docker image. removed uninstall target, use pip to uninstall moose. Added path in target_link_directories macro for target moose.bin. MOOSE's python module. commit 4408bee Author: Dilawar Singh <[email protected]> Date: Mon Feb 3 16:00:45 2020 +0530 Docker build was successful. Needs to improve test function... commit 892b9c3 Author: Dilawar Singh <[email protected]> Date: Mon Feb 3 14:01:12 2020 +0530 Added centos build docker file. commit 5777ede Author: Dilawar Singh <[email protected]> Date: Mon Feb 3 08:05:43 2020 +0000 Some more tweaks. commit ac30142 Author: Dilawar Singh <[email protected]> Date: Mon Feb 3 13:08:53 2020 +0530 Run in inside a docker image to tweak. commit 8bee4d0 Author: Dilawar Singh <[email protected]> Date: Sun Feb 2 04:03:40 2020 +0530 Temp commit: Build locally. commit 4d8342e Author: Dilawar Singh <[email protected]> Date: Sun Feb 2 03:54:14 2020 +0530 Not yet complete because we still don't have static linking to gsl . commit 18e65d5 Author: Dilawar Singh <[email protected]> Date: Sun Feb 2 03:47:38 2020 +0530 Using python setup.py to build the module. commit 7a8f52d Merge: 6a7de61 1bbbc2d Author: Dilawar Singh <[email protected]> Date: Sun Feb 2 03:12:45 2020 +0530 Merge branch 'devel' of https://github.com/dilawar/moose-core into devel commit 1bbbc2d Author: Dilawar Singh <[email protected]> Date: Fri Apr 19 14:45:57 2019 +0530 added moose.about(). Show essential information about moose project commit c319cb4 Merge: 45216b3 1b38d64 Author: Dilawar Singh <[email protected]> Date: Fri Apr 19 14:36:14 2019 +0530 Merge branch 'master' of github.com:BhallaLab/moose-core into devel * Added pipeline. * Added missing setuptools. Update setuptools before building. * Install python-dev in dependencies... * Non-zero cpu count... * Updated gitlab CI. * Added scripts to build wheels. * Create dockerimage.yml Added action for building wheels. * Fixes the build failure on CentOS6. * Squashed commit of the following: commit f191857 Merge: 0401d10 27f3f6e Author: Dilawar Singh <[email protected]> Date: Fri Feb 7 13:49:21 2020 +0530 Merge branch 'devel' of https://github.com/dilawar/moose-core into devel commit 0401d10 Author: Dilawar Singh <[email protected]> Date: Fri Feb 7 13:48:15 2020 +0530 added travis+pypi token commit bce6dfe Author: Dilawar Singh <[email protected]> Date: Fri Feb 7 13:37:45 2020 +0530 build wheels on all platform. commit 27f3f6e Author: Dilawar Singh <[email protected]> Date: Fri Feb 7 06:54:37 2020 +0000 Let go back to manylinux1 image commit 9f93811 Author: Dilawar Singh <[email protected]> Date: Fri Feb 7 05:47:51 2020 +0000 Added a dummy target. commit 6fa716c Merge: 4dc5c3e 2b4bd1d Author: Dilawar Singh <[email protected]> Date: Thu Feb 6 13:41:31 2020 +0000 Merge branch 'master' of https://github.com/dilawar/moose-core into devel commit 4dc5c3e Author: Dilawar Singh <[email protected]> Date: Thu Feb 6 19:07:22 2020 +0530 Changes to buidl script [skip ci] commit 15532cb Author: Dilawar Singh <[email protected]> Date: Thu Feb 6 12:58:24 2020 +0000 Make the dummy extension optional. commit 725282a Author: Dilawar Singh <[email protected]> Date: Thu Feb 6 17:55:44 2020 +0530 Install required tools as well. commit 22fde7d Author: Dilawar Singh <[email protected]> Date: Thu Feb 6 16:13:01 2020 +0530 Dockerfile is added to build wheels in this repo itself. commit c08fb72 Author: Dilawar Singh <[email protected]> Date: Thu Feb 6 15:56:32 2020 +0530 renamed build script and fixes to some paths. * Removed dockerimage workflow for now [skip ci] * Minor tweaks to test on travis. Fixes FindGSL.cmake script. if(expr1 `OR` expr2) is fixed to if((expr1) OR (expr2)). Fixes to travis build script. sudo is not required to run this script. Fixes to the travis build. NSDF support is disabled. CLeanup in OSX build as well. Don't deploy to pypi. OSX build is passed locally. * Use a temp build directory. * Need a better way to create sdist. Added three targets. - make sdist create a source distribution for PyPi. - make upload_test upload the source distribution to TestPyPi. The command reads environment variable for user and password. export PYMOOSE_PYPI_USER=bhallalab export PYMOOSE_PYPI_PASSWORD=mypassword make upload_test - make upload Upload the source distribution to PyPI. export PYMOOSE_PYPI_USER=bhallalab export PYMOOSE_PYPI_PASSWORD=mypassword make upload Using date and rc tag to create a version for nightly release. Use twine to upload to test.pypi.org * Create stale.yml
Point release 3.2.1. The version bump is due to using new manylinux2010 images.
* Update to install instructions... Point release 3.2.1. The version bump is due to using new manylinux2010 images. * - Added ExprTK based parser and removed muParser. EXPRTK is faster than muParser (see labnotes). - All tests have been passing. - Tweaks are made to exprtk operators/functions to make sure old expressions used scripts remains valid. * Added function ln(double v) to EXPRTK. Compatibility with muParser. All tests are passing. * It is working fine now with Vinu model. Needs to fix the sbmlParserReader which uses numVars_. * Some more cleanup. Testing on travis. Removed moose.Func(); user should use `moose.Function`. moose.Func was disabled long back. * GSolve also honors MOOSE_NUM_THREADS ... * Local tests are passing. Fixed memory leak issue. A little refactoring and memory segv at the end of the test is now clean. Removed unneeded/outdated tests and other scripts. Added new tests based on Vinu model. It is very comprehensive which tests multithreaded Ksolve/Gsolve, SBML, and moose.Function Update to install instructions... (BhallaLab#386) Point release 3.2.1. The version bump is due to using new manylinux2010 images. * Thanks to clang++; caught another memory related bug. If this passes, do a memory profiling. * Minor cleanup. Removed memory allocation and copying at couple of places. Still memory leaks in exprtk. I think I can't get rid of them. Parser is a member object rather than member pointer; still some leak but better version than before. * Renamed test folder for regular tests. Added custom test which uses 4 threads to run Ksolve. Modified atol and rtol in assertion in one of the tests. Using parallel version of Ksolve/Gsolve everywhere by setting MOOSE_NUM_THREADS=$(nproc) Increased `rtol` value to make sure tests passes with BOOST solver as well. When the boost's ode solvers are used, the number generated are slightly different. * - Added a docker file to run travis pipeline locally. - Fixed python2 seg-fault in new tests. The segv was because / means int division in python2. * Converting some rdesigneur scripts to tests; since we need to be able to plot in nonblocking mode, I've added `block` option in `rdes.display` function. Multiple tests using pydoc. They are based on rdesigneur tutorials. install requires matplotlib for rdesigneur. * - The seg-fault in rdesigneur tests are due to BhallaLab#388. * In the ksolve, we partition the interval beforehand now. The single-threaded and multi-threaded numbers are not the same. Fixed tests to accomodate slightly different values resulted n multi-threaded mode. * Categorised tests. Also turned all doctest to normal assertion tests. Moved alpha tests to fixme tests. * All tests passing locally with both GSL and BOOST. * Compilation fixes for the OSX build. One test marked as python3 only. The pyrun expression uses python3 specific division and print function. Causes segfault with python2 (wontfix)
* The default values changed in the commit (ba1065c) breaks example such as https://github.com/BhallaLab/moose-examples/blob/09ca09e68f163a0920653a9400214aff10b6ba16/snippets/rxdFuncDiffusion.py . The sparse matrix has upper limit of number of rows and columns to 20,000. In the example linked, new values makes it impossible to run the example as is. To overcome this, we notify the user whenever this limit is reached and ask them to set `diffLength` before setting up the `x1`. On top of this, we can also revert default values to original larger values. Not sure why these values were changed to the scale of 1e-6? Unless the reason is known, I am not going to change current values. The above linked example now works with this commit. * Script which switches solver is now working fine. Forgot to uncomment `unzombifyModel` in `~Stoich` in previous PR BhallaLab#387. * switch solver script is working fine now. Added to the test suite. * During zombiefication, deepcopy of parser is expected. Added more tests and fixed the deepcopy of parser issue. In Zombiefication, the parser was not deep copied resulting in erronous values in couple of tests. There is some memory leak now. * Prepare a PR now. Test on travis. Some tests might fail with BOOST. Memory leak is still there. * 1. Removed copy constructor from moose::Function. It was not used anywhere. Increased rtol value for a test. Multithreaded solvers gives different results. 2. Fixed all memory leaks. Probably I don't understand how EXPRTK really works. using smart pointers with EXPRTK caused memory leak. 3. Log memory leak on travis using valgrind. Install valgrind in docker images as well. * During zombiefication, deepcopy of parser is expected. Added fix and a test case. * Added more tests and fixed the deepcopy of parser issue. In Zombiefication, the parser was not deep coped resulting in erronous values in couple of tets. There is some memory leak now (not very large, 8 bytes per variable per expression). * Prepare a PR now. Test on travis. Some tests might fail with BOOST. Memory leak is still there. * removed copy constructor; it was not used anywhere. [skip ci] Increased rtol value for a test. Multithreaded solvers gives different results. * Fixed all memory leaks. Probably I don't understand how EXPRTK really works. using smart pointers with EXPRTK caused memory leak. Log memory leak on travis using valgrind. Fixed tests. Let the EXPRK object manage its memory. * BOOST/GSL are only needed in ksolve directory: tweaked cmake to change compilation flags on ksolve directory only. Build will be faster for various configurations. Moved one test to fixme (Vinu's model). * Updated gitlab pipeline. On a single threaded virtual machine, numThreads was set to 0 in couple of tests. Fixed that. Install pyneuroml to the pipeline. Small leeway in a test. * std can be close to zero. np.allclose may not handle it properly all the time. * boost solver with GSSA may have large variation. * boost solver with GSSA may have large variation. Test for the sum of all errors. * Increased the tolerance a bit more.
* - Tests are passing locally.
- MooseParser is a pointer in Function. Simplifies header include.
- Added wrapper.py which generates a derived class moose.A for each
_moose.A. `moose.A` provides `connect` function. Instead of,
moose.connect(a, 'f1', b, 'f2')
One can do,
a.connect('f1', b, 'f2')
* Developers emails are back in travis config file.
* If a symbol already exists, do not add it again. Fixed typo.
* If sympy not found, allow failure. Added sympy on travis but not on OSX. Don't install sympy with python2.
* removed custom OrderedDict. Python2.6 is not needed to be supported.
Centos6 is EOL.
* Hotfix | some old scripts in moose-examples failed because of regression caused by BhallaLab#390. * Added graph utility. Renamed to network_utils. Imported by default when moose.utils is imported. Renamed functions. * Added Boost ODE based solvers of MarkovChannel. Now GSL is optional. Renamed MarkovGslSolver class to MarkovOdeSolver. It compiles with both boost and gsl. * This is squashed version of BhallaLab#281 - Added new solver based on 'LSODA' method. This is a CPP version of the LSODA library for integration into MOOSE simulator. These source code are released under MIT license which is compatible with MOOSE. See Credit below. Adds three tests (1 python). Results are equivalent to scipy's lsoda solver. Following changes are made to this version: Used <array> and <vector> instead of raw array where-ever possible. Craeted a class LSODA and added a function to integrate it smoothly with moose. Various tweaks in various functions especially initialization. Core computing functions starts with index 1 rather than 0; this is hidden away from MOOSE api. The performance of this solver is really good. In debug mode, on a small model, I got 6.7x speedup without any multi-threading. The solver is not recommended for stiff systems. Once it is integrated we do more profiling vis-a-vis standard RK5 solver. - Licensing Work by Heng Li was released under MIT Incense which is less restrictive than GNU-GPLv3. See here. The LSODA class is released under the same license. - Logs https://docs.google.com/document/d/e/2PACX-1vQ3wU9xiMSMVcluDrNSzuSGHsttOqAqc8xN4a9qo7wFfYjwl-0KhKyY1LlM5XkQ_5CqJd3eFnUCYiAb/pub - Credit The original was aquired from http://www.ccl.net/cca/software/SOURCES/C/kinetics2/index.shtml and modified by Heng Li [email protected]. Heng merged several C files into one and added a simpler interface. His version can be found http://lh3lh3.users.sourceforge.net/download/lsoda.c .
* Don't run streamer multitab tests on OSX/Travis. * Disable all socket streamer tests. * no way to setup proxy yet. * Temp commit. * Some more changes but not complete. * local tests. * build was successful. * Added pytest compatible tests. Generates test report at the end. * Fixed hhfit tests. * test commit [seg fault] skip ci * Removed benchamark code. * Added dependencies to requirements.txt file. Set verbosity to 0. Minor cleanup. local tests are passing... Added test: rdesineur loads chan proto from a given file. * Fixed hhfit test. Added scipy to run hhfit test. * Fixed one more test. * test it on xcode10.3 * Some fixes to test_hhfit. The module selects a best function 'fuzzingly'. * - Removed getopt in pymoose code. It was causing segfault on OSX. Not sure why. `getopt` is no longer needed there. - Use scipy in tests as well. hhfit requires scipy. - Added target coverage for make. - Enabled coverage on travis. - Fixes to unicode/str issues b/w python2 and 3. * - Fixes to issue BhallaLab#393 - Don't let user use buggy gcc 4.8.x which does not proper regex support. See https://stackoverflow.com/questions/12530406/is-gcc-4-8-or-earlier-buggy-about-regular-expressions * updated docker file for centos:7 . Install devtoolset-8. * Some more tweak to test_hhfit.py file. THe hhfit function does not always return the demanded function but could also return a function which is a better fit (it is designed this way). Without this fix, the test could fail on a separte run or on a separte platform. * Update writeKkit.py Fixed email id. Co-authored-by: Dilawar Singh <[email protected]>
) * saving data to npy format in streamer is now bug free. Added three tests: 2 python and 1 at cpp level. * boost::filesystem is no longer used even when boost is used. * Default tick for Streamer is 10s. * Able to run nml2 example with python3 (BhallaLab/moose#253). Co-authored-by: Dilawar Singh <[email protected]>
* Fix to BhallaLab#397 * NUMPY is essential dependency; therefore numpy code is no longer included conditionally. USE_NUMPY is implied and have been removed from cmake. * Minor cleanup in macros and loggers. numCores now use thread library to determine number of available threads. * include cmath in Pool.cpp as well. Failed compilation with gcc5.3 * include cmath in Pool.cpp as well. Failed compilation with gcc5.3 Co-authored-by: Dilawar Singh <[email protected]> Co-authored-by: dilawars <[email protected]>
…en in MMenz form,readSBML:Enzyme-cplx connection of reactant/product's are done based on stoichiometry number and reading back channel from MMenz, connected input pool with msg as 'in' and output pool msg as 'out' (BhallaLab#400) Co-authored-by: HarshaRani <[email protected]>
* writeSBML: channel's annotation is cleaned up and channel's are written in MMenz form,readSBML:Enzyme-cplx connection of reactant/product's are done based on stoichiometry number and reading back channel from MMenz, connected input pool with msg as 'in' and output pool msg as 'out' * rgba color converted to hex color Co-authored-by: HarshaRani <[email protected]>
removed 'basestring'
removed 'basestring' Co-authored-by: Dilawar Singh <[email protected]>
upibhalla
reviewed
May 1, 2020
|
No. Chennalpoda is the next release (3.2.0). The tests in the master branch
run on this branch as well.
…On Fri, May 1, 2020 at 3:44 PM Upinder S Bhalla ***@***.***> wrote:
***@***.**** commented on this pull request.
410 is approved. Will this require some additional tests in chennapoda in
order to merge?
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Merge today's master branch to Chennapoda branch. In case #410 is merged, we'll have a quick way to go back to current bindings.