.gitignore

**/__pycache__/
*.egg-info/

# PyCharm
.idea/

# files generated by tests
yaml2sbml/tests/test_yaml2sbml/sbml_test.xml

# Documentation build
/doc/build

### Files generated when running the notebooks (AMICI + PEtab files)

**/amici_models/
**/AMICI_models/

## FSP examples

/doc/examples/Finite_State_Projection/gene_expression.xml

## Format Features

/doc/examples/Format_Features/functions_in_rhs.xml
/doc/examples/Format_Features/step_function.xml
/doc/examples/Format_Features/time_dependent_rhs.xml

## Lotka Volterra

/doc/examples/Lotka_Volterra/Lotka_Volterra_CLI/Lotka_Volterra_PEtab.yml
/doc/examples/Lotka_Volterra/Lotka_Volterra_CLI/Lotka_Volterra_PEtab/
/doc/examples/Lotka_Volterra/Lotka_Volterra_CLI/Lotka_Volterra_basic.xml

/doc/examples/Lotka_Volterra/Lotka_Volterra_Model_Editor/Lotka_Volterra_PEtab.yaml
/doc/examples/Lotka_Volterra/Lotka_Volterra_Model_Editor/Lotka_Volterra_PEtab/
/doc/examples/Lotka_Volterra/Lotka_Volterra_Model_Editor/Lotka_Volterra_basic.xml
/doc/examples/Lotka_Volterra/Lotka_Volterra_Model_Editor/Lotka_Volterra_basic.yaml

/doc/examples/Lotka_Volterra/Lotka_Volterra_python/Lotka_Volterra_AMICI/
/doc/examples/Lotka_Volterra/Lotka_Volterra_python/Lotka_Volterra_PEtab/Lotka_Volterra_with_observables.xml
/doc/examples/Lotka_Volterra/Lotka_Volterra_python/Lotka_Volterra_PEtab/experimental_conditions_Lotka_Volterra_with_observables.tsv
/doc/examples/Lotka_Volterra/Lotka_Volterra_python/Lotka_Volterra_PEtab/observables_Lotka_Volterra_with_observables.tsv
/doc/examples/Lotka_Volterra/Lotka_Volterra_python/Lotka_Volterra_PEtab/parameters_Lotka_Volterra_with_observables.tsv
/doc/examples/Lotka_Volterra/Lotka_Volterra_python/Lotka_Volterra_PEtab/problem.yml
/doc/examples/Lotka_Volterra/Lotka_Volterra_python/Lotka_Volterra_basic.xml

## Sorensen

/doc/examples/Sorensen/Fig71_Sorensen1985.xml

### JupyterNotebooks ###

# gitignore template for Jupyter Notebooks
# website: http://jupyter.org/

.ipynb_checkpoints
*/.ipynb_checkpoints/*

# IPython
profile_default/
ipython_config.py

# Remove previous ipynb_checkpoints
#   git rm -r .ipynb_checkpoints/

### macOS ###
# General
.DS_Store
.AppleDouble
.LSOverride

# Icon must end with two \r
Icon

# Thumbnails
._*

# Files that might appear in the root of a volume
.DocumentRevisions-V100
.fseventsd
.Spotlight-V100
.TemporaryItems
.Trashes
.VolumeIcon.icns
.com.apple.timemachine.donotpresent

# Directories potentially created on remote AFP share
.AppleDB
.AppleDesktop
Network Trash Folder
Temporary Items
.apdisk

# Build
/build/
/dist/

# File-based project format
*.iws

# IntelliJ
out/

# mpeltonen/sbt-idea plugin
.idea_modules/

# JIRA plugin
atlassian-ide-plugin.xml

# Crashlytics plugin (for Android Studio and IntelliJ)
com_crashlytics_export_strings.xml
crashlytics.properties
crashlytics-build.properties
fabric.properties

# vim
*.swp

# tox
/.tox

# coverage
/.coverage
/htmlcov
/coverage.xml