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[MRG] TraceFitter.refine with calculated gradient #29

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merged 24 commits into from
Mar 13, 2020
Merged

[MRG] TraceFitter.refine with calculated gradient #29

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3816d0a
WIP: Optionally use gradients in TraceFitter.refine
mstimberg Feb 27, 2020
59ed8fa
Work around an issue with older sympy versions
mstimberg Mar 5, 2020
5110c68
Allow specifying iter_cb for refine (instead of normal callback)
mstimberg Mar 5, 2020
62e0fcb
Turn the normalization factor back into divisive
mstimberg Mar 5, 2020
ca54de7
Fix tests that still used multiplicative normalization
mstimberg Mar 5, 2020
3ed0b56
Fix bug in sensitivity calculations
mstimberg Mar 6, 2020
75df433
Initialize sensitivity parameter based on param_init
mstimberg Mar 6, 2020
4b8c446
Remove unnecessary sensitivity equations
mstimberg Mar 6, 2020
561019b
Remove left-over print statement
mstimberg Mar 9, 2020
73f2aab
refactor simulation, make refine+generate work with standalone
mstimberg Mar 10, 2020
e16a50a
Only send on report to coveralls
mstimberg Mar 10, 2020
42e3109
Fix travis.yml
mstimberg Mar 10, 2020
ded5dee
Use bash conditional in travis.yml
mstimberg Mar 10, 2020
1d9cfbc
...and fix that conditional
mstimberg Mar 10, 2020
d62a007
More fixes for travis.yml
mstimberg Mar 10, 2020
a112362
Final fix for travis
mstimberg Mar 10, 2020
cc5d04d
Minor fixes in Fitter
mstimberg Mar 10, 2020
761176f
Add basic test for refine(calc_gradient=True)
mstimberg Mar 10, 2020
2c082d1
Add init for sensitivity equations
mstimberg Mar 10, 2020
c756c9c
Make refine's callback function consistent with fit's callback
mstimberg Mar 13, 2020
8be93e3
Minor docstring fixes
mstimberg Mar 13, 2020
92ffe0c
Make `generate` return a `Quantity` instead of `VariableView` for traces
mstimberg Mar 13, 2020
e0c6449
Test refines callback behaviour
mstimberg Mar 13, 2020
db10a53
Add a number of tests
mstimberg Mar 13, 2020
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7 changes: 6 additions & 1 deletion .travis.yml
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Original file line number Diff line number Diff line change
@@ -1,4 +1,5 @@
dist: xenial
os: linux
language: python
python:
- "3.6"
Expand All @@ -13,4 +14,8 @@ install:
# command to run tests
script:
- pytest --cov=brian2modelfitting
- coveralls

after_success:
- if [ "$TRAVIS_PYTHON_VERSION" == "3.6" ]; then
travis_retry coveralls;
fi
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