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Inference bug fixes #50

Merged
merged 30 commits into from
Jun 16, 2020
Merged

Inference bug fixes #50

merged 30 commits into from
Jun 16, 2020

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ayush9pandey
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Lots of minor bug fixes in the inference package.

Working pull-request, not yet ready to merge.

@ayush9pandey
fixed multiple sbml bugs
d08c64c
@ayush9pandey
removed duplicate function getAllIds
ee799b2
@ayush9pandey
minor bug fixed
93200ad
@ayush9pandey
inference development branch
bdf21bc
@ayush9pandey
minor change: changed SBML version from L3V1 to L3V2
22c6a52
@ayush9pandey
comments added for todos
fa59cb5
@ayush9pandey
Merge branch 'master' of https://github.com/biocircuits/bioscrape int…
5149f2e 
…o inference
@ayush9pandey
Merge branch 'master' into inference
51fe75d
@ayush9pandey
added cost_progress attribute to emcee_interface to monitor cost prog…
142f63b 
…ress.
@ayush9pandey
fixed param id interface - simple linear example works perfectly (mat…
5eb533f 
…h checks out as well)
@ayush9pandey
merging with master
4f6ea7e
@ayush9pandey
working pid inference, need to fix example and finish todos
a604064
@ayush9pandey
all inference examples working perfectly. advanced tools need fixing
d57743b
@ayush9pandey
gaussian priors speedup by 2x and priors all parameter requirement fixed
dddbeb9
@ayush9pandey
multiple trajectories data working, priors working
f87e5da
@ayush9pandey
multiple initial conditions, multiple trajectories, multiple paramete…
3b00696 
…rs - all working
@ayush9pandey
renamed files, working version
8826a8a
@ayush9pandey
merged with master
09dbcb9
@ayush9pandey
basic examples notebook renamed
6abaef5
@ayush9pandey
fixed gaussian prior
d81b1c5
@ayush9pandey
added 'positive' element check in prior dictionary for each parameter…
6ce910d 
… prior
@ayush9pandey
fixed positive flag for parameter priors
71a43d1
@ayush9pandey
added sbml_warnings keyword argument to import_sbml
a735154
@ayush9pandey ayush9pandey self-assigned this Jun 15, 2020
@ayush9pandey
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This PR is ready now as well.

@ayush9pandey
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I think Travis CI is not properly setup causing the build to fail. @sclamons ?

All checks in the previous build also failed. So, I guess, for now we can merge this @WilliamIX and worry about fixing Travis CI later?

@WilliamIX WilliamIX merged commit 1a365ec into master Jun 16, 2020
@WilliamIX WilliamIX deleted the inference branch June 16, 2020 04:56
@WilliamIX
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My understanding from Sam is that testing doesn't work yet, so we can ignore these issues for now.

This was referenced Jun 16, 2020
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@ayush9pandey @WilliamIX