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General ODE System Solver

Home Page: https://computationalphysiology.github.io/goss

License: GNU Lesser General Public License v3.0

CMake 1.72% C++ 62.49% C 1.75% Python 33.60% Makefile 0.42% Dockerfile 0.02%

cpp ode ode-solver odeint python

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goss's Issues

Make conda package

Since boost is a runtime dependency, we need a way to install boost easily (as part of the installation of goss). Probably the simplest way to achieve this is through conda.

Currently we need to run cmake - make - make install in order to install goss, but it would be good to make a setup.py with a CMakeExtesion similar to https://github.com/ComputationalPhysiology/cellmodel-inversion-gpu/blob/master/setup.py so that we can install goss with pip.

Add Readme file

We should add a readme file explaining how to install, how to get started,++

More python2 -> python3 updates

There are still a few python things in the swig wrapper code, see e.g

goss/goss/swig/post.i

Line 276 in b5c9404

def iteritems(self):

This should be updated but we need to be a bit careful when poking around in this file.

Clean up Make files

There are a lot of CMakefiles that has to be updated.

In particular we have a few old cmake policies
https://github.com/ComputationalPhysiology/goss/blob/master/CMakeLists.txt#L20-L22

and probably a few other departed statements.

Resolve discrepancy in state variable sorting

(Using base_model.ode example) There is a difference in the sorting of state variables between gotran.load() and goss.ParameterizedODE()

Add documentation

We should make documentation and make it available on GitHub pages

Running goss requires `boost`

When running any of the demo in a fresh environment without boost, gives the following error

python oscilator_v1.py 
Loaded ODE model 'oscilator' with:
     Num full states: 2
      Num parameters: 0
Traceback (most recent call last):
  File "oscilator_v1.py", line 36, in <module>
    oscilator = goss.ODE(load_ode("oscilator.ode"))
  File "/venv/lib/python3.7/site-packages/goss/ode.py", line 22, in __init__
    self._cpp_object = jit(args[0], **kwargs)
  File "/venv/lib/python3.7/site-packages/goss/compilemodule.py", line 113, in jit
    code_params=code_params,
  File "/venv/lib/python3.7/site-packages/goss/compilemodule.py", line 67, in cppyy_jit
    cppyy.cppdef(cpp_code)
  File "/venv/lib/python3.7/site-packages/cppyy/__init__.py", line 196, in cppdef
    raise SyntaxError('Failed to parse the given C++ code%s' % err.err)
SyntaxError: Failed to parse the given C++ code
In file included from input_line_21:18:
In file included from /venv/lib/python3.7/site-packages/goss/include/goss/Timer.h:30:
In file included from /venv/lib/python3.7/site-packages/goss/include/goss/LogManager.h:26:
/venv/lib/python3.7/site-packages/goss/include/goss/Logger.h:31:10: fatal error: 'boost/scoped_ptr.hpp' file not found
#include <boost/scoped_ptr.hpp>
         ^~~~~~~~~~~~~~~~~~~~~~

Fails to build wheels for MacOS - ARM64

There are currently some problems with linking to libomp on MacOS and ARM64, see e.g Homebrew/homebrew-core#112107 (comment)

One way to potentially deal with this is to use the approach taken here: https://github.com/dmlc/xgboost/blob/master/tests/ci_build/build_python_wheels.sh

computationalphysiology / goss Goto Github PK

goss's People

Stargazers

Watchers

goss's Issues

Make conda package

Make goss pip installable

Add Readme file

More python2 -> python3 updates

Clean up Make files

Resolve discrepancy in state variable sorting

Add documentation

Running goss requires `boost`

Fails to build wheels for MacOS - ARM64

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