.DS_Store
.conda
.vscode

# Folders
dev
**/_dev
**/_dev

# Wildcard Folders
**/Autofiles/BifurcationData
**/__pycache__
**/tvbo.egg-info

backend_test.pkl
Icon?
tests/tvb_validation

# Documentation
docs/_build/
docs/_site/
docs/_site/
docs/api/
docs/auto_examples/
docs/**/*.ipynb
docs/**/*.py
!docs/Replication/**/*.py
docs/gen_modules/
docs/_api/
docs/apidocs/
docs/**/.gen_stamp
docs/**/.struct_stamp
docs/**/.gen_stamp
docs/**/.struct_stamp
build
.litellm_cache
output
test_export
tvbo/data/tvb-go/go-basic.obo
.pdm-python
.tvb_ext_ontology.log
**.mako.py
tvbo/.temp
simulation_cache.pkl
requirements.old.txt
_archive
gitlab_token.txt
tvbo-runtime.*

# Quarto builds
*.html
*.pdf
*.docx
*.log
*_cache/
*.knit.md
*.sty
*.aux
.manuscript/.quarto/
manuscript/manuscript_files
manuscript/_extensions
manuscript/_output

/.luarc.json
manuscript/elsarticle.cls
manuscript/manuscript.spl
manuscript/elsarticle-num.bst
manuscript/elsarticle-num-names.bst
manuscript/manuscript/_output
*_assignments.csv
tvbo/data/tvb-go/go.obo
manuscript/code/dev-fig-kg-interoperability.spl
manuscript/code/elsarticle.cls
manuscript/code/elsarticle-num.bst
manuscript/manuscript.tex
manuscript/manuscript.toc
manuscript/code/dev*

*.ipynb
docs/Use-Cases
manuscript/.quarto-logs
manuscript/_freeze
manuscript/_inspo
_extensions
docs/_site
docs/datamodel
docs/_site_libs
.quarto
docs/_freeze
tvbo/database/_extra
tvbo/database/_extra
manuscript/_notes

manuscript
docs/Usage/_output
presentation
docs/Interoperability/*.ivp
docs/Interoperability/*.so
docs/Interoperability/*.f90
temp
rwongwang_kernel.cu
docs/site_libs
docs/**/figure-html
docs/Interoperability/NetworkDynamics.jl/*.gif
docs/Interoperability/NetworkDynamics.jl/_output
Manifest.toml
Project.toml
_test_*
_check_*
docs/Interoperability/Pyrates/_*
uv.lock
pyrates_run.py
pyrates_run_*.py
tvbo/database/studies/**/*.md
tvbo/database/studies/**/*.png
c.ivp
qif.cpython-313-darwin.so
qif.f90
docs/Interoperability/BIDS/derivatives/
_*.py
!__init__.py
tvbo/data/tvbo_data/atlas/schaefer2018_original_mni
tvbo/data/tvbo_data/atlas/*.nii.gz
tvbo/data/tvbo_data/_archive_connectome
replication_studies

_archive/database

# Compiled Mako templates
tvbo/templates/modules/*.py.mako.py
docs/Interoperability/NeuroML/examples/_*.*
results/*.dat
