.gitignore

CMakeFiles/*

build/*
build-debug/*
build_xcode/*
swig/python/build/*
tests/cpp/build/*
tests/cpp/build_xcode/*
tests/cpp/Testing/*

doc-venv/*
doc/*
fonts/*
images/*
stylesheets/*
documentation/_build/*
documentation/_exhale_cpp_api/*
documentation/_exhale_matlab_api/*
documentation/_doxyoutput_amici_cpp/*
documentation/_doxyoutput_amici_matlab/*
sed-ml/*

models/*
!models/model_dirac
models/model_dirac/build/*
!models/model_steadystate
models/model_steadystate/build/*
!models/model_jakstat_adjoint
models/model_jakstat_adjoint/build/*
!models/model_jakstat_adjoint_o2
models/model_jakstat_adjoint_o2/build/*
!models/model_neuron
models/model_neuron/build/*
!models/model_neuron_o2
models/model_neuron_o2/build/*
!models/model_events
models/model_events/build/*
!models/model_nested_events
models/model_nested_events/build/*
!models/model_robertson
models/model_robertson/build/*
!models/model_calvetti
models/model_calvetti/build/*

amici_models/

simulate_model_*_hdf.m
simulate_model_*.m

index.html

AMICI.mlappinstall

Makefile
cmake_install.cmake
CMakeCache.txt
CMakeLists.txt.user

.coveralls.yml
.directory
.project
.pydevproject
.settings/
.idea/*
.DS_Store
.ipynb_checkpoints/
python/.idea/*

*.a
*.info
*.o
*.obj
*.eps
*.mexmaci64
*.mexa64
*.mexw64
*.mexmaci32
*.mexa32
*.mexw32
*.eps
*.md5
*.json
*.mat
*.m~
*.plist
*.make
*.bin
*.csv
*.log
*.pyc
*.so
*.bak
*.sav

matlab/mtoc/config/latexextras.sty-e
matlab/mtoc/config/latexextras.sty
matlab/mtoc/config/Doxyfile-e
matlab/mtoc/Doxyfile
matlab/mtoc/config/mtocpp_filter.sh

cppcheck.txt
coverage_py.xml
testSuite.txt

__pycache__

/misc.xml

python/testSpeedy.py
python/test.txt

tests/test/*
*/tests/test_model_steadystate_scaled/*
*/tests/test_model_presimulation/*
*/tests/test_model_presimulation_pysb/*
*/tests/test_model_presimulation_sbml/*
*/tests/test_model_units/*
*/tests/model_constant_species_cl/*
*/tests/model_constant_species/*
*/tests/test_likelihoods/*
*/tests/bax_pore_sequential_amici/*
*/tests/bax_pore_amici/*
*/tests/bngwiki_egfr_simple_amici/*
*/tests/bngwiki_egfr_simple_deletemolecules_amici/*
*/tests/earm_1_3_amici/*
*/tests/earm_1_0_amici/*
*/tests/expression_observables_amici/*
*/tests/robertson_amici/*
*/tests/tyson_oscillator_amici/*
*/tests/bngwiki_simple_amici/*
*/tests/bngwiki_enzymatic_cycle_mm_amici/*
*/tests/move_connected_amici/*
*/tests/michment_amici/*
*/tests/kinase_cascade_amici/*
*/tests/hello_pysb_amici/*
*/tests/fricker_2010_apoptosis_amici/*
*/tests/explicit_amici/*
*/tests/fixed_initial_amici/*
*/tests/localfunc_amici/*
tests/cpp/writeResults.h5
tests/cpp/writeResults.h5.bak
tests/sbml-test-suite/*
tests/sbml-test-suite/
tests/sedml-test-suite/
*/sbml-semantic-test-cases/*
tests/SBMLTestModels/
tests/benchmark-models/test_bmc
tests/petab_test_suite
petab_test_suite
*/tests/BIOMD0000000529/*

python/examples/example_steadystate/model_steadystate_scaled/*
python/examples/example_presimulation/model_presimulation/*
python/examples/example_presimulation/model_presimulation_re/*
python/examples/example_constant_species/model_constant_species_reduced/*
python/examples/example_constant_species/model_constant_species/*
python/examples/example_jax/amici_models/*
python/tests/sbml_test_models/*
python/tests/piecewise_test/*

python/sdist/amici.egg-info/*
python/sdist/amici/version.txt
python/sdist/amici/amici.py
python/sdist/amici/amici_wrap.cxx
python/sdist/amici/amici_without_hdf5.py
python/sdist/amici/amici_wrap_without_hdf5.cxx
python/sdist/amici/include/
python/sdist/amici/lib/
python/sdist/amici/share/
python/sdist/build/*
python/sdist/amici/git_version.txt

python/sdist/dist

AMICI_guide.pdf

ThirdParty/bionetgen.tar.gz
ThirdParty/BioNetGen-*
ThirdParty/doxygen/*
ThirdParty/mtocpp-master*
ThirdParty/sundials/build/*
ThirdParty/SuiteSparse/lib/*
ThirdParty/SuiteSparse/include/
ThirdParty/SuiteSparse/share/*
ThirdParty/SuiteSparse/install/*
ThirdParty/SuperLU_MT_3.1/
ThirdParty/superlu_mt_3.1.tar.gz
ThirdParty/swig-*
ThirdParty/ragel-*.tar.gz
_untracked/

documentation/generated/*

# vim
*.swp
tests/performance/CS_Signalling_ERBB_RAS_AKT/
tests/performance/CS_Signalling_ERBB_RAS_AKT_petab/*
coverage_SBMLSuite.xml
Benchmark-Models-PEtab/
/test_bmc/

CS_Signalling_ERBB_RAS_AKT/
cache_fiddy/*
debug/*
tests/benchmark-models/cache_fiddy/*
venv/*
.coverage