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jordanereis

epigrass's Issues

optimize parallel run of models

Currently, sites run their models using a process pool created in their parent graph.
Is there a more efficient way to do this than of forking a new process for every site at every timestep?

Error - The 'panel' distribution was not found and is required by epigrass

We have a bug report for epigrass in Debian.

Here are the set of commands used to run the test :

# Run simulations with demo models
epirunner script.epg
epirunner rio.epg
epirunner flu.epg
epirunner sars.epg
epirunner star.epg
epirunner script.epg
epirunner mesh.epg

Running the tests against these commands gives the following error in debian:

Traceback (most recent call last):
  File "/usr/bin/epirunner", line 33, in <module>
    sys.exit(load_entry_point('epigrass==3.0.3', 'console_scripts',
'epirunner')())
  File "/usr/bin/epirunner", line 25, in importlib_load_entry_point
    return next(matches).load()
  File "/usr/lib/python3.9/importlib/metadata.py", line 77, in load
    module = import_module(match.group('module'))
  File "/usr/lib/python3.9/importlib/__init__.py", line 127, in
import_module
    return _bootstrap._gcd_import(name[level:], package, level)
  File "<frozen importlib._bootstrap>", line 1030, in _gcd_import
  File "<frozen importlib._bootstrap>", line 1007, in _find_and_load
  File "<frozen importlib._bootstrap>", line 986, in _find_and_load_unlocked
  File "<frozen importlib._bootstrap>", line 680, in _load_unlocked
  File "<frozen importlib._bootstrap_external>", line 850, in exec_module
  File "<frozen importlib._bootstrap>", line 228, in
_call_with_frames_removed
  File "/usr/lib/python3/dist-packages/Epigrass/manager.py", line 20, in
<module>
    from Epigrass.simobj import graph, edge, siteobj
  File "/usr/lib/python3/dist-packages/Epigrass/simobj.py", line 19, in
<module>
    from Epigrass import models
  File "/usr/lib/python3/dist-packages/Epigrass/models.py", line 14, in
<module>
    from epimodels.continuous.models import SIR, SEIR
  File "/usr/lib/python3/dist-packages/epimodels/continuous/models.py",
line 12, in <module>
    import numba
  File "/usr/lib/python3/dist-packages/numba/__init__.py", line 19, in
<module>
    from numba.core import config
  File "/usr/lib/python3/dist-packages/numba/core/config.py", line 16,
in <module>
    import llvmlite.binding as ll
  File "/usr/lib/python3/dist-packages/llvmlite/binding/__init__.py",
line 4, in <module>
    from .dylib import *
  File "/usr/lib/python3/dist-packages/llvmlite/binding/dylib.py", line
3, in <module>
    from llvmlite.binding import ffi
  File "/usr/lib/python3/dist-packages/llvmlite/binding/ffi.py", line
137, in <module>
    from pkg_resources import resource_filename
  File "/usr/lib/python3/dist-packages/pkg_resources/__init__.py", line
3243, in <module>
    def _initialize_master_working_set():
  File "/usr/lib/python3/dist-packages/pkg_resources/__init__.py", line
3226, in _call_aside
    f(*args, **kwargs)
  File "/usr/lib/python3/dist-packages/pkg_resources/__init__.py", line
3255, in _initialize_master_working_set
    working_set = WorkingSet._build_master()
  File "/usr/lib/python3/dist-packages/pkg_resources/__init__.py", line
568, in _build_master
    ws.require(__requires__)
  File "/usr/lib/python3/dist-packages/pkg_resources/__init__.py", line
886, in require
    needed = self.resolve(parse_requirements(requirements))
  File "/usr/lib/python3/dist-packages/pkg_resources/__init__.py", line
772, in resolve
    raise DistributionNotFound(req, requirers)
pkg_resources.DistributionNotFound: The 'panel' distribution was not
found and is required by epigrass

Can you take a look give a pointer as to what is causing this ?

Thanks

documentation (README.md/ Wiki) for users/ contributors

Hi, I, like many, have a lot of time at home. I am interested in contributing to projects that can help in the crisis we all face. I would like to help with documentation, but need pointers on where to start, to help your github page become more robust! Thanks!

must manually install cython via pip

Here is the error when installing epigrass

pip3 install epigrass
Collecting epigrass
  Downloading https://files.pythonhosted.org/packages/4e/b1/b1ea10683666fa5036f237a0b83537009e873fc7294818800b62cbc0eaf5/epigrass-2.6.1.tar.gz (4.9MB)
    100% |████████████████████████████████| 4.9MB 236kB/s 
    Complete output from command python setup.py egg_info:
    Traceback (most recent call last):
      File "<string>", line 1, in <module>
      File "/tmp/pip-build-bdcxn_8w/epigrass/setup.py", line 2, in <module>
        from Cython.Build import cythonize
    ModuleNotFoundError: No module named 'Cython'
    
    ----------------------------------------
Command "python setup.py egg_info" failed with error code 1 in /tmp/pip-build-bdcxn_8w/epigrass/

Of course the manual solution is extremely easy
pip3 install cython

However, you successfully pull in things like numpy, so this should be easy to remedy

Build a web dashboard

Buid a dashboard which can be used localy or used to deploy the results of a simulation

We will initially prototype it in panel.

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