.gitignore

__pycache__/
.vscode
.DS_Store

*.engine
*.engine.config
*.cache
*.nsys-rep
*.npy
!tests/common/test_utils/*.npy
.VSCodeCounter
cpp/build*
build
!bionemo_ir/bench/build
!builders/
*.egg-info/
.coverage
*.onnx
tmp/
venv/
.venv/
.local/
.hypothesis/
.idea/
dump*/
*.dot
*.prof
*.log
*.pkl
*.hdf5
*.lock
!uv.lock
config.json
/*.svg
cpp/cmake-build-*
# Where `make -C docker wheel` and `pip wheel` drop build output.
/dist/
# examples/folding/run_demo.py writes predictions here by default.
/output/
# Per-developer opt-out of the CuTeDSL extension build; committing it would turn
# the extension off for every checkout.
build.env
# Keep only the authoritative public indexes and Git-LFS packs from CuTeDSL
# artifacts. Compiler caches and legacy/generated payloads remain local.
cpp/kernels/cutedsl_*/cubins/*
!cpp/kernels/cutedsl_*/cubins/index.json
!cpp/kernels/cutedsl_*/cubins/records/
!cpp/kernels/cutedsl_*/cubins/records/*.json
!cpp/kernels/cutedsl_*/cubins/packs/
!cpp/kernels/cutedsl_*/cubins/packs/*.tar.xz
# Default output-root name used by setup.py and materializer diagnostics.
bioir_cubins/
bionemo_ir/bin
bionemo_ir/libs/*
!bionemo_ir/libs/__init__.py
bionemo_ir/bindings.*.so
bionemo_ir/bindings.pyi
bionemo_ir/bindings/**/*.pyi
*docs/cpp_docs*
*docs/source/_cpp_gen*
*.swp

# Testing
.coverage.*

# build/debug
*.safetensors
*.patch
!.agents/skills/bench-perf-oss/models/misc/*.patch

# User config files
CMakeUserPresets.json
compile_commands.json
*.bin
.dir-locals.el
.pip_cache/
*.pt
!tests/**/data/*_golden.pt
/boltz/

# Local agent/editor state that can hold tokens. Anything more specific to your
# own tooling belongs in .git/info/exclude, not here.
.env
.mcp.json
.claude/

# Personal, machine-specific agent instructions (see CLAUDE.md)
CLAUDE.local.md

# Fern CLI local state.
fern/.fern/
fern/.build/
node_modules/

# Verified outbound tool downloads and executables.
/sync/.tools/