.gitignore

default-*
.vscode
*.o
cython_debug
mesh.c
poisson.c
stokes.c
analytic_sol.c
maths.c
swarm.c
*_debug.txt
compile.log
*.log
.env
**/__pycache__
*.so
examples/.ipynb_checkpoints/*
examples/PoissonEq/poisson
*.h5
*.xmf
python/underworld3
examples/c_examples/PoissonEq/poisson
examples/c_examples/CartesianStokes/stokes
build
keep
old
**/underworld3.egg-info/*
keep/*
*.swp
nohup.out
src/underworld3/_uwid.py
# Auto-generated version file (derived from git tags by setuptools_scm)
src/underworld3/_version.py

# TeX/LaTeX/PDF build artifacts (comprehensive)
*.aux
*.lof
*.log
*.lot
*.fls
*.out
*.toc
*.fmt
*.fot
*.cb
*.cb2
.*.lb
*.bbl
*.bcf
*.blg
*-blx.aux
*-blx.bib
*.run.xml
*.fdb_latexmk
*.synctex
*.synctex(busy)
*.synctex.gz
*.synctex.gz(busy)
*.pdfsync
*.nav
*.snm
*.vrb
*.xdv
*.idx
*.ilg
*.ind
*.glg
*.glo
*.gls
*.ist
*.acn
*.acr
*.alg
*.glsdefs
*.lzo
*.lzs
*.slg
*.slo
*.sls

# Quarto build artifacts (comprehensive coverage for all docs subdirectories)
docs/_build/
docs/.quarto/
docs/_freeze/
docs/*/_build/
docs/*/.quarto/
docs/*/_freeze/
docs/*/*/_build/
docs/*/*/.quarto/
docs/*/*/_freeze/
docs/**/*.pdf
docs/**/*.tex
docs/**/*.aux
docs/**/*.log
docs/**/*.toc
docs/**/*.out
docs/**/*.fls
docs/**/*.fdb_latexmk
docs/**/*.synctex.gz
docs/**/*.nav
docs/**/*.snm
docs/**/*.vrb

# Additional documentation build artifacts
docs/**/.ipynb_checkpoints/
docs/**/site_libs/
docs/**/libs/
docs/**/_site/
docs/**/dist/
docs/**/node_modules/
docs/**/.sass-cache/
docs/**/.jekyll-cache/
docs/**/.jekyll-metadata
docs/**/*.rdb
docs/**/*.rdx

documentation/index.aux
documentation/index.pdf
documentation/index.tex
documentation/index.log
documentation/index.toc

# Jupyter Book build relics

Jupyterbook/_build
Jupyterbook/static_slides
/Lectures/static_slides/slideshows
*slideshows*
Jupyterbook/node_modules/.yarn-integrity
Jupyterbook/Notebooks_old*
package-lock.json

# Myst build relics

Documentation/_build
Documentation/_build/templates

# joss-build-bot relics

joss-paper/paper.crossref
joss-paper/paper.pdf

.ash_history


# Example output files (comprehensive exclusion)

# Mesh files
uw_*.msh
*.msh
*.h5
*.xdmf
*.vtk
*.pbin

# Visualization outputs (exclude generated, allow curated assets)
docs/examples/**/output/**
docs/examples/**/*.png
docs/examples/**/*.jpg
docs/examples/**/*.gif
docs/examples/**/*.mp4
docs/examples/**/*.html
# But allow curated documentation images
!docs/examples/assets/**

# Additional example artifacts
docs/examples/**/*.txt
docs/examples/**/*.dat
docs/examples/**/*.csv
docs/examples/**/*.log
docs/examples/**/checkpoint_*
docs/examples/**/restart_*
docs/examples/**/.meshes/

# Any checkpoints from notebooks (since .md files can be run in setups with 
# jupytext and will produce spurious/unexpected checkpoints.

.ipynb_checkpoints

# Autobuilt documentation

uw3_api_docs
uw3_api_docs/*

# pytest

.pytest_cache/*


# Visualisation artefacts
ignore*vtk
ignore*msh
tmp*vtk
tmp*msh

# Docker build artefacts

docker/underworld3_components

# Other
*DS_Store
Jupyterbook/.DS_Store
Jupyterbook/Notebooks/.DS_Store
Jupyterbook/Notebooks/Examples-NavierStokes/order_1/NS_test_Re_250_0.06_step_0.png
Documentation/index.aux

# Claude Code files (track commands, ignore settings)
CLAUDE.md
.claude/*
!.claude/commands/
.claude/commands/*
!.claude/commands/*.md

# Prevent future markdown clutter in root (allow essential docs only)
/*_ANALYSIS.md
/*_REPORT.md
/*_SUMMARY.md
/*_STATUS.md
/*_PROGRESS.md
/*_REVIEW.md
/*_PLAN.md
/*_FIXES.md
/SESSION_SUMMARY*.md
/PHASE_*.md
# Exceptions for essential docs
!TODO.md
!README.md
!CLAUDE.md
!CONTRIBUTING.md
!CHANGES.md
!SPELLING_CONVENTION.md
!LICENSE.md

# Temporary test files (can be deleted)
temp_tests_deletable/
debug_*.py
/test_*.py
# Allow legitimate test files in tests/ directory
!tests/**/test_*.py

# IDE and editor artifacts
.ropeproject/
.vscode/

# Mesh cache directory
.meshes/

# Additional cache directories
.pytest_cache/

# Visualization output files (generated during notebook execution)
docs/beginner/tutorials/html5/*.html
# Pixi environment (directory in main repo, symlink in worktrees)
.pixi
.pixi-env
# PETSc build (directory in main repo, symlink in worktrees)
petsc-custom/petsc
petsc-custom/.petsc-version
Untitled*.ipynb