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Miscellaneous #327

Merged
merged 31 commits into from
Jun 9, 2018
Merged

Miscellaneous #327

merged 31 commits into from
Jun 9, 2018

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dweindl
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@dweindl dweindl commented May 31, 2018 •
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More robust packaging, various smaller extensions fixes and cleanup of Python API.

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dweindl commented May 31, 2018 •
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@FFroehlich I think there is something wrong with the sensitivities. Can you please have a look at the sensitivities at the bottom of: https://github.com/ICB-DCM/AMICI/blob/dw_misc/python/examples/example_steadystate/ExampleSteadystate.ipynb

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coveralls commented May 31, 2018 •
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Coverage Status

Coverage remained the same at 69.896% when pulling 4947faa on dw_misc into 331ad23 on master.

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codecov bot commented May 31, 2018 •
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Codecov Report

Merging #327 into master will not change coverage.
The diff coverage is n/a.

Impacted file tree graph

@@          Coverage Diff           @@
##           master    #327   +/-   ##
======================================
  Coverage    70.1%   70.1%           
======================================
  Files          31      31           
  Lines        3596    3596           
======================================
  Hits         2521    2521           
  Misses       1075    1075
Flag Coverage Δ
#cpp 70.1% <ø> (ø) ⬆️
#python ?
Impacted Files Coverage Δ
include/amici/rdata.h 0% <ø> (ø) ⬆️

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dweindl added 14 commits June 1, 2018 10:25
@dweindl
feature(python) Allow blas selection for amici base package installat…
10468df 
…ion via environment variables
@dweindl
doc(python) Add model info to example
a8a4852
@dweindl
Fix(python) Fix negative log likelihood
647c3a7
@dweindl
Feature(python) Expose std::vector<amici::AMICI_parameter_scaling> as…
cafae2e 
… ParameterScalingVector
@dweindl
doc(core) Fix dimension order
11aa721
@dweindl
ci(python) Run gradient check for example models (don't fail test yet)
82bb8f1
@dweindl
ci(travis) Install scipy
b4271a6
@dweindl
build(cmake) CMake cleanup
dbed13c
@dweindl
ci(travis) Test creating and installing sdist on ci server
4eb8c8c
@dweindl
fix(python) Increase chances of finding swig on OSX
a346845
@dweindl
ci(python) Don't use pyenv pip which is broken by recent update
270895e 
  File '/opt/pyenv/versions/3.6/bin/pip3', line 7, in <module>
    from pip import main
ImportError: cannot import name 'main'
@dweindl
fix(python) Catch hdf5.cpp not found problem
b335b89
@dweindl
doc(doxygen) Ignore autogenerated file
97649bf
@dweindl
fix(python) Set sensitivity flag for dydp (thx FFroehlich)
9be5680
@dweindl dweindl requested a review from FFroehlich June 8, 2018 19:22
@dweindl dweindl merged commit 32ff587 into master Jun 9, 2018
@dweindl dweindl deleted the dw_misc branch June 9, 2018 10:10
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@FFroehlich FFroehlich FFroehlich approved these changes

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@dweindl @coveralls @FFroehlich