__pycache__/
.idea/

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


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

## Lotka Volterra Python
./doc/examples/Lotka_Volterra/Lotka_Volterra_python/amici_models
./doc/examples/Lotka_Volterra/Lotka_Volterra_python/amici_models/*

./doc/examples/Lotka_Volterra/Lotka_Volterra_python/Lotka_Volterra_AMICI
./doc/examples/Lotka_Volterra/Lotka_Volterra_python/Lotka_Volterra_AMICI/*

./doc/examples/Lotka_Volterra/Lotka_Volterra_python/Lotka_Volterra_basic.xml

./doc/examples/Lotka_Volterra/Lotka_Volterra_python/Lotka_Volterra_PEtab/*
!./doc/examples/Lotka_Volterra/Lotka_Volterra_python/Lotka_Volterra_PEtab/measurement_table.tsv


## Lotka Volterra CLI
./doc/examples/Lotka_Volterra/Lotka_Volterra_CLI/Lotka_Volterra_PEtab/*
./doc/examples/Lotka_Volterra/Lotka_Volterra_CLI/Lotka_Volterra_PEtab.yml
./doc/examples/Lotka_Volterra/Lotka_Volterra_CLI/Lotka_Volterra_PEtab/*.xml


## Lotka Volterra Model Editor
./doc/examples/Lotka_Volterra/Lotka_Volterra_Model_Editor/*.yaml
./doc/examples/Lotka_Volterra/Lotka_Volterra_Model_Editor/*.xml
./doc/examples/Lotka_Volterra/Lotka_Volterra_Model_Editor/Lotka_Volterra_PEtab


## Sorensen example
./doc/examples/Sorensen/*.xml
./doc/examples/Sorensen/amici_models


## FSP examples
./doc/examples/Finite_State_Projection/amici_models
./doc/examples/Finite_State_Projection/*.xml

## Format Features

./doc/examples/Format_Features/__pycache__
./doc/examples/Format_Features/AMICI_models

./doc/examples/Format_Features/*.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

### PyCharm ###
# Covers JetBrains IDEs: IntelliJ, RubyMine, PhpStorm, AppCode, PyCharm, CLion, Android Studio, WebStorm and Rider
# Reference: https://intellij-support.jetbrains.com/hc/en-us/articles/206544839

# User-specific stuff
.idea/**/workspace.xml
.idea/**/tasks.xml
.idea/**/usage.statistics.xml
.idea/**/dictionaries
.idea/**/shelf

# Generated files
.idea/**/contentModel.xml

# Sensitive or high-churn files
.idea/**/dataSources/
.idea/**/dataSources.ids
.idea/**/dataSources.local.xml
.idea/**/sqlDataSources.xml
.idea/**/dynamic.xml
.idea/**/uiDesigner.xml
.idea/**/dbnavigator.xml

# Gradle
.idea/**/gradle.xml
.idea/**/libraries

# Gradle and Maven with auto-import
# When using Gradle or Maven with auto-import, you should exclude module files,
# since they will be recreated, and may cause churn.  Uncomment if using
# auto-import.
# .idea/artifacts
# .idea/compiler.xml
# .idea/jarRepositories.xml
# .idea/modules.xml
# .idea/*.iml
# .idea/modules
# *.iml
# *.ipr

# CMake
cmake-build-*/

# Mongo Explorer plugin
.idea/**/mongoSettings.xml

# File-based project format
*.iws

# IntelliJ
out/

# mpeltonen/sbt-idea plugin
.idea_modules/

# JIRA plugin
atlassian-ide-plugin.xml

# Cursive Clojure plugin
.idea/replstate.xml

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

# Editor-based Rest Client
.idea/httpRequests

# Android studio 3.1+ serialized cache file
.idea/caches/build_file_checksums.ser

### PyCharm Patch ###
# Comment Reason: https://github.com/joeblau/gitignore.io/issues/186#issuecomment-215987721

# *.iml
# modules.xml
# .idea/misc.xml
# *.ipr

# Sonarlint plugin
# https://plugins.jetbrains.com/plugin/7973-sonarlint
.idea/**/sonarlint/

# SonarQube Plugin
# https://plugins.jetbrains.com/plugin/7238-sonarqube-community-plugin
.idea/**/sonarIssues.xml

# Markdown Navigator plugin
# https://plugins.jetbrains.com/plugin/7896-markdown-navigator-enhanced
.idea/**/markdown-navigator.xml
.idea/**/markdown-navigator-enh.xml
.idea/**/markdown-navigator/

# Cache file creation bug
# See https://youtrack.jetbrains.com/issue/JBR-2257
.idea/$CACHE_FILE$

# CodeStream plugin
# https://plugins.jetbrains.com/plugin/12206-codestream
.idea/codestream.xml