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More flexible processing of ODEs #19

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May 14, 2020
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ba38aae
add integration test
Apr 9, 2019
9cf7d48
Merge remote-tracking branch 'upstream/master' into integration_test
Apr 15, 2019
53e0620
add integration test
Apr 17, 2019
74b5ae0
fix examples to correspond to paper notation of high-to-low different…
Apr 17, 2019
a8aebc3
refactor shape_from_function() and shape_from_ode() into Shape classm…
Apr 18, 2019
4d6fcd9
refactor integration test to work with new JSON output format
Apr 18, 2019
fa65ee4
change list to dictionary in output JSON
Apr 19, 2019
793e107
minor cleanup and reformatting
Apr 19, 2019
ade3551
change initial values list to dictionary
Apr 21, 2019
7ca9c80
change initial values list to dictionary
Apr 21, 2019
bf59cd2
change list to dictionary in output JSON
Apr 21, 2019
cb11255
minor code cleanup
Apr 21, 2019
a32f6f2
remove superfluous code (result gets overwritten on subsequent lines)
Apr 23, 2019
5a7e4ec
clean up spike train generator and spike arrival handling code
Apr 23, 2019
e204901
add unit testing for specifying equations with initial values
Apr 23, 2019
eeb0423
minor cleanup of integration test
Apr 23, 2019
48c2b74
reflect changes to I/O formats in README
Apr 23, 2019
fa6926c
specifying parameters should not be required if stiffness test is ski…
Apr 23, 2019
683b4c8
make debug plot optional (default disabled) on integration test
Apr 23, 2019
9496f4a
fix following changes in I/O formats
Apr 23, 2019
181c6d3
add scipy to module requirements; needed in integration test
Apr 23, 2019
cdddde0
fix test prediction following new I/O formats
Apr 23, 2019
708f79f
fix integration test name; try to avoid underflow error by setting er…
Apr 23, 2019
ba6dc8a
change underflow exception handling to troubleshoot underflow issue
Apr 24, 2019
c2c2292
use explicit namespace dictionary for exec() and eval() calls
Apr 24, 2019
6d7892e
merge shape and ode concepts
May 2, 2019
e2e14dc
assemble global system matrix
May 7, 2019
bd68747
dependency analysis based on global system matrix
May 7, 2019
6668c45
propagate not-linear-constant-coefficient shape property along depend…
May 8, 2019
c05e96f
propagate not-linear-constant-coefficient shape property along depend…
May 8, 2019
1907faa
propagate not-linear-constant-coefficient shape property along depend…
May 8, 2019
6f48921
propagator calculation and JSON output
May 9, 2019
4493738
Merge remote-tracking branch 'upstream/master' into merge_shape_ode_c…
May 9, 2019
a3fabd1
update integration test to match new JSON I/O format
May 13, 2019
966794d
update integration test to match new JSON I/O format
May 14, 2019
d803eb2
bug fix in separating linear/nonlinear parts of expression
May 15, 2019
480a61d
bug fix in separating linear/nonlinear parts of expression
May 15, 2019
c96e5d5
mixed analytic/numeric integration
May 22, 2019
2d57f82
mixed analytic/numeric integration
May 22, 2019
7a1d7fb
mixed analytic/numeric integration
May 22, 2019
05fc016
spike stimulus delivery for mixed analytic/numeric stiffness tester
May 23, 2019
083383e
fix integration test
May 23, 2019
836762f
separate linear and constant coefficient unit test into separate file
Jun 4, 2019
efc6f06
caching option for analytic integrator
Jun 11, 2019
2857c1e
stiffness detector recommends implicit for canonical stiff problem
Jun 13, 2019
b96648a
add tests for proper construction of system matrix
Jun 17, 2019
761d667
fix and test for splitting into linear/nonlinear part
Jun 18, 2019
b8410e7
cleanup and bugfixes after refactoring
Jun 18, 2019
bf833b8
before removal of real=True assumption
Jun 20, 2019
40778ca
remove inconsistently applied real assumption
Jun 20, 2019
a69a092
fix caching numerical roundoff issue in analytic integrator
Jun 21, 2019
a5f1c37
autowrap to speed up analytic integrator
Jun 22, 2019
7fc5f1e
auto-detect presence of matplotlib
Jun 22, 2019
1df11ef
auto-detect presence of graphviz
Jun 22, 2019
ed03a0f
add cython to requirements.txt (for sympy autowrap())
Jun 22, 2019
0c4245e
auto-detect presence of matplotlib
Jun 22, 2019
4858fd5
use one with-gsl and one without-gsl job in Travis-CI
Jun 22, 2019
2a0ba6e
use one with-gsl and one without-gsl job in Travis-CI
Jun 22, 2019
0cab32a
use one with-gsl and one without-gsl job in Travis-CI
Jun 22, 2019
1c7814e
use one with-gsl and one without-gsl job in Travis-CI
Jun 22, 2019
cad284f
use one with-gsl and one without-gsl job in Travis-CI
Jun 22, 2019
3009e83
use one with-gsl and one without-gsl job in Travis-CI
Jun 22, 2019
86066e2
use one with-gsl and one without-gsl job in Travis-CI
Jun 22, 2019
f7592f4
use one with-gsl and one without-gsl job in Travis-CI
Jun 22, 2019
d8a5cac
add feature in stiffness tester to alias spikes to fixed time grid
Jun 28, 2019
558d954
split MixedIntegrator into separate class
Jul 1, 2019
dfb6740
numerical test for MixedIntegrator
Jul 1, 2019
53d139c
test for spike aliasing in numeric integrator
Jul 2, 2019
c76693e
fix tests
Jul 3, 2019
745f6b1
update README intro blurb
Jul 3, 2019
b5918f1
update README intro blurb
Jul 3, 2019
5b87986
update README intro blurb
Jul 3, 2019
b545a77
update README intro blurb
Jul 3, 2019
9eb9126
custom sympy expression printer
Jul 25, 2019
cd03191
cleanup input sanity checking
Aug 30, 2019
24acbc4
update setup.py version info
Aug 30, 2019
91d3fc2
add friendly error message when imaginary number was found in propaga…
Oct 25, 2019
3749356
better sanity checks on the input
Oct 30, 2019
cd1f03f
add homogeneity check for odes
Nov 3, 2019
d6fccfc
use Python logging module; eliminate print() calls
Nov 6, 2019
3ae536b
add heuristic for when not to call sympy.simplify() due to excessive …
Nov 6, 2019
ab5b8f1
clean up pygsl importing
Nov 7, 2019
5ab506e
clean up pygsl importing
Nov 7, 2019
34ff3cd
add code coverage report to Travis CI testing
Nov 7, 2019
cae4949
update README
Nov 7, 2019
7e9f9cd
update README; add missing import
Nov 7, 2019
33fdc20
update README
Nov 7, 2019
a887033
code linting; fix issue with default function parameters
Nov 12, 2019
a4e0bd2
remove debug statement
Nov 12, 2019
d2ae159
fix refactoring of get_all_variable_symbols()
Nov 12, 2019
35da21b
clean up unit tests
Nov 12, 2019
da99b49
fix bug due to state variable order
Nov 12, 2019
43aecc5
suppress warnings from potentially ineffective mpl.use('backend')
Nov 13, 2019
7632775
remove stray file
Nov 13, 2019
de1af46
add dependency analysis section to README
Nov 18, 2019
9c11d80
add dependency analysis section to README
Nov 18, 2019
f3badd8
add solver selection section to README
Nov 18, 2019
d1ce914
fix markdown syntax in README
Nov 18, 2019
707751f
add flow diagram
Nov 21, 2019
ae0c744
add flow diagram
Nov 21, 2019
b783747
add flow diagram
Nov 21, 2019
75ad385
add flow diagram
Nov 21, 2019
983dab1
add flow diagram
Nov 21, 2019
578943d
add flow diagram
Nov 21, 2019
d6d4204
add flow diagram
Nov 21, 2019
f068fd1
update README
Dec 3, 2019
26d7be6
update dependency analysis figures
Dec 3, 2019
897e17e
update README
Dec 3, 2019
c4ea825
update README
Dec 3, 2019
74737b5
update README
Dec 3, 2019
a47bb95
update README
Dec 4, 2019
90c16a0
code cleanup; introduce abs and rel integration tolerances
Dec 4, 2019
ae612ba
update requirements.txt file
Dec 4, 2019
d87fbd0
code cleanup
Dec 4, 2019
6f5c8c0
clean up argument parsing and error handling in command-line invocati…
Dec 4, 2019
af3c65b
clean up argument parsing and error handling in command-line invocati…
Dec 4, 2019
89356c2
update funding acknowledgements in README
Dec 4, 2019
bc091ba
update spike stimulus description in README
Dec 4, 2019
3931f46
clean up docstrings, imports; update function-to-shape algorithm desc…
Dec 5, 2019
9b6f701
add 'From ode-toolbox results dictionary to simulation' to README
Jan 8, 2020
7c5d014
minor cleanup and missing imports
Jan 8, 2020
d1b9003
add stiffness testing example to README
Jan 8, 2020
665e725
address performance issues and list examples in README
Jan 8, 2020
70163ea
minor README cleanup
Jan 8, 2020
7305d04
minor cleanup
Jan 8, 2020
f5625ed
reinstate cython dependency, needed for autowrap
Jan 8, 2020
9bfb630
reinstate cython dependency, needed for autowrap
Jan 8, 2020
b9f2c25
minor cleanup
Jan 8, 2020
b530b1e
add decimally expanded possibility to unit test
Jan 8, 2020
b3e107c
add debugging statement to unit test
Jan 8, 2020
52223eb
add debugging statement to unit test
Jan 8, 2020
01c9d55
change fraction from Python division to sympy division
Jan 8, 2020
ef4962a
minor cleanup
Jan 8, 2020
508a292
clean up old example JSON files
Jan 8, 2020
cc46e68
clean up old example JSON files
Jan 8, 2020
b95d898
add hyperlinks to README
Jan 9, 2020
820e738
update workflow diagram
Jan 9, 2020
dbc1b9b
update workflow diagram
Jan 9, 2020
10dd2ae
update workflow diagram
Jan 9, 2020
9aaf00b
minor cleanup
Jan 9, 2020
7238f1e
refactor enable_stiffness to disable_stiffness
Jan 9, 2020
5d2d39b
add hyperlink to README
Jan 9, 2020
84cc113
minor cleanup
Jan 9, 2020
8879351
add hyperlinks to README
Jan 9, 2020
e208d5b
add hyperlinks to README
Jan 9, 2020
6cc6f69
update workflow diagram
Jan 9, 2020
e99503b
refactor documentation for readthedocs
Mar 11, 2020
7fb3b4b
refactor documentation for readthedocs
Mar 11, 2020
b962295
refactor documentation for readthedocs
Mar 11, 2020
36a719c
refactor documentation for readthedocs
Mar 11, 2020
d0324e4
refactor documentation for readthedocs
Mar 11, 2020
eec0c9f
refactor documentation for readthedocs
Mar 11, 2020
4f5916c
refactor documentation for readthedocs
Mar 11, 2020
b14d2b0
refactor documentation for readthedocs
Mar 11, 2020
d9e906e
refactor documentation for readthedocs
Mar 12, 2020
75131c8
refactor documentation for readthedocs
Mar 12, 2020
4610d18
refactor documentation for readthedocs
Mar 12, 2020
c89c740
refactor documentation for readthedocs
Mar 12, 2020
6750090
refactor documentation for readthedocs
Mar 12, 2020
305a03a
fix link in documentation
Mar 12, 2020
396a6e5
refactor documentation for readthedocs
Mar 12, 2020
84d3e81
refactor documentation for readthedocs
Mar 12, 2020
e18fac1
refactor documentation for readthedocs
Mar 12, 2020
e57bf04
refactor documentation for readthedocs
Mar 12, 2020
407cc81
refactor documentation for readthedocs
Mar 12, 2020
8014f38
refactor documentation for readthedocs
Mar 12, 2020
692975a
refactor documentation for readthedocs
Mar 12, 2020
7141adb
add link to ode-toolbox API documentation
clinssen Mar 12, 2020
1b43290
fix documentation formatting
clinssen Mar 17, 2020
19aa2d7
add sphinx API documentation links
clinssen Mar 17, 2020
0afa600
add sphinx API documentation links
clinssen Mar 17, 2020
a378377
add sphinx API documentation links
clinssen Mar 17, 2020
a46f33f
add sphinx API documentation links
clinssen Mar 17, 2020
92a6293
add sphinx API documentation links
clinssen Mar 17, 2020
27eef15
add sphinx API documentation links
clinssen Mar 17, 2020
244875a
add sphinx API documentation links
clinssen Mar 17, 2020
c49f151
fix docstring syntax
clinssen Mar 17, 2020
29734d9
fix docstring syntax
clinssen Mar 17, 2020
a1d73b2
add sphinx API documentation links
clinssen Mar 17, 2020
e5e01f0
add sphinx API documentation links
clinssen Mar 17, 2020
4eb9aa1
add sphinx API documentation links
clinssen Mar 17, 2020
8f89516
remove stray file
clinssen Mar 17, 2020
66b142a
documentation updates: add flow diagram
clinssen Mar 17, 2020
86b5415
fix PNG export of figures
clinssen Mar 17, 2020
991d6b0
fix PNG export of figures
clinssen Mar 17, 2020
7ba658d
fix PNG export of figures
clinssen Mar 17, 2020
0738893
fix PNG export of figures
clinssen Mar 17, 2020
767a709
fix PNG export of figures
clinssen Mar 17, 2020
a671c27
add toctree to documentation
clinssen Mar 17, 2020
3ca2ef7
update logo background
clinssen Mar 17, 2020
837a69c
add toctree to documentation
clinssen Mar 17, 2020
29f94bc
update logo background
clinssen Mar 17, 2020
471db83
add toctree to documentation
clinssen Mar 17, 2020
33e9c11
add toctree to documentation
clinssen Mar 17, 2020
8945f78
fix section title
clinssen Mar 17, 2020
eff0f5b
update section headers in documentation
clinssen Mar 17, 2020
f760e00
minor documentation cleanup
clinssen Mar 18, 2020
7912e67
fix section link
clinssen Mar 20, 2020
de6553d
update links to github in documentation
clinssen Mar 25, 2020
0e74ed9
update CSS style sheet to improve text contrast in readthedocs advert…
clinssen Mar 28, 2020
48cf677
do not collapse navigation on readthedocs
clinssen Mar 29, 2020
fd8e9fb
do not collapse navigation on readthedocs
clinssen Mar 29, 2020
2074435
process @sarakonradi's documentation feedback
clinssen Mar 30, 2020
6f9f6b1
process @sarakonradi's documentation feedback
clinssen Mar 30, 2020
6c5087f
lower case letter for vector
clinssen Mar 30, 2020
d2a473e
improve API documentation and code formatting
clinssen May 5, 2020
1814185
improve API documentation and code formatting
clinssen May 5, 2020
fa1a847
improve API documentation and code formatting
clinssen May 5, 2020
391d811
improve API documentation and code formatting
clinssen May 5, 2020
9c5cd5b
improve API documentation and code formatting
clinssen May 5, 2020
efa44ee
improve API documentation and code formatting
clinssen May 5, 2020
a31260b
improve API documentation and code formatting
clinssen May 5, 2020
81ad4e3
improve API documentation and code formatting
clinssen May 5, 2020
27ce453
improve API documentation and code formatting
clinssen May 5, 2020
349e0f5
reduce default verbosity from DEBUG to INFO
clinssen May 7, 2020
6faca62
replace print() with logging
clinssen May 13, 2020
da4c9ae
clean up iaf_cond_alpha example
clinssen May 13, 2020
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31 changes: 24 additions & 7 deletions .travis.yml
Original file line number Diff line number Diff line change
Expand Up @@ -2,22 +2,39 @@ language: python

sudo: required

git:
depth: 1

env:
- export WITH_GSL=0
- export WITH_GSL=1

python:
- "2.7"
- "3.5"
- "3.6"

before_install:
- wget http://ftp.wrz.de/pub/gnu/gsl/gsl-2.5.tar.gz
- tar -xvzf gsl-2.5.tar.gz
- cd gsl-2.5
- ./configure && make && sudo make install
- cd ..
- if [ $WITH_GSL == 1 ]; then
wget http://ftp.wrz.de/pub/gnu/gsl/gsl-2.5.tar.gz ;
tar -xvzf gsl-2.5.tar.gz ;
cd gsl-2.5 ;
./configure && make && sudo make install ;
cd .. ;
fi
- export LD_LIBRARY_PATH=/usr/local/lib

install:
- if [ $WITH_GSL == 1 ]; then
pip install pygsl ;
fi
- pip install -r requirements.txt
- pip install cython
- pip install codecov pytest-cov

script:
- python setup.py install
- python setup.py test
#- coverage run -m pytest -s --pdb tests
- python -m pytest -s --pdb -o log_cli=true -o log_cli_level="DEBUG" --cov=./ tests

after_success:
- codecov
314 changes: 0 additions & 314 deletions README.md

This file was deleted.

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