prek.toml

# Style enforcement, run by prek (https://github.com/j178/prek) locally via git
# hooks (`prek install`) and in CI, only touch new and changed files.
#
# See docs/coding.md for the rules these tools enforce.

# `prek install` installs only the pre-commit shim by default, which would leave
# the commit-msg hook below silently uninstalled. Naming both here means a plain
# `prek install` wires up everything this config declares.
default_install_hook_types = ["pre-commit", "commit-msg"]

# Never touch vendored submodules or the CuTeDSL kernel package (the DSL
# resolves names through its own tracing machinery, so ruff reports them as
# undefined). Generated CUBIN build inputs are not excluded because they are no
# longer written into the checkout; the materializer emits them into the build
# tree.
exclude = '''(?x)^(
    3rdparty/.*
  | .*\.(a|lib|so|dll|a3m)
  | examples/data/samples/templates/templates/.*\.cif
  | bionemo_ir/dsl_kernels/cute/.*
)$'''

[[repos]]
repo = "https://github.com/astral-sh/ruff-pre-commit"
rev = "v0.16.1"
hooks = [
  { id = "ruff-check", args = ["--fix"] },
  { id = "ruff-format" },
]

[[repos]]
# C/C++/CUDA formatting for cpp/ (handwritten kernels/bindings; see
# .clang-format). Pinned to one version so output doesn't ping-pong across
# machines.
repo = "https://github.com/pre-commit/mirrors-clang-format"
rev = "v22.1.8"
hooks = [
  # .h/.hpp/.cuh are already tagged c/c++/cuda by identify, so these three
  # types cover headers too (there is no "h" tag; the header tag is "header").
  { id = "clang-format", types_or = ["c", "c++", "cuda"] },
]

[[repos]]
repo = "https://github.com/rvben/rumdl-pre-commit"
rev = "v0.2.49"
hooks = [
  { id = "rumdl", args = ["--fix"] },
]

[[repos]]
repo = "https://github.com/shellcheck-py/shellcheck-py"
rev = "v0.11.0.1"
hooks = [
  { id = "shellcheck", args = ["-x"] },
]

[[repos]]
repo = "https://github.com/maxwinterstein/shfmt-py"
rev = "v4.0.0"
hooks = [
  # -i 2: 2-space indent; -ci: indent switch cases; -bn: binary ops at line start.
  { id = "shfmt", args = ["-w", "-i", "2", "-ci", "-bn"] },
]

[[repos]]
repo = "https://github.com/Lucas-C/pre-commit-hooks"
rev = "v1.5.6"
hooks = [
  # Full NVIDIA SPDX Apache header on all source (.license-header.txt).
  # --use-current-year matches any existing header regardless of its year/range
  # (so existing headers are left alone) and stamps new files with the current
  # year; only inserts where missing. Two entries: `#` comment style for
  # python/shell/cmake, C-block style for c/c++/cuda.
  { id = "insert-license", name = "insert license (python, shell, cmake)", types_or = [
    "python",
    "shell",
    "cmake",
  ], args = [
    "--license-filepath",
    ".license-header.txt",
    "--comment-style",
    "#",
    "--use-current-year",
  ] },
  { id = "insert-license", name = "insert license (c, c++, cuda)", types_or = [
    "c",
    "c++",
    "cuda",
  ], args = [
    "--license-filepath",
    ".license-header.txt",
    "--comment-style",
    "/*| *| */",
    "--use-current-year",
  ] },
]

[[repos]]
repo = "local"

# Markdown license comments belong inside YAML frontmatter. The GitHub PR and
# issue templates retain HTML comments because GitHub copies them into bodies.
[[repos.hooks]]
id = "insert-markdown-license"
name = "insert license (markdown, mdx)"
entry = "python3 scripts/insert_markdown_license.py"
language = "system"
files = '''(?i)\.mdx?$'''
exclude = '''^\.github/(PULL_REQUEST_TEMPLATE\.md|ISSUE_TEMPLATE/.*\.md)$'''

# Canonical docs checks: Fern nav coverage, link policy, public-API examples,
# and dual-target (GitHub + Fern) math style. CI's docs:check runs the same
# script and then `fern check` on the generated site; the Fern CLI step stays
# CI-only. Whole-docset, not per-file — coverage and anchor checks cannot be
# answered from the changed files alone.
[[repos.hooks]]
id = "docs-check"
name = "docs checks (fern coverage, links, math)"
entry = "python3 fern/src/check.py --no-sync"
language = "system"
pass_filenames = false
files = '''(?x)^(
    bionemo_ir/.*\.py$
  | docs/.*
  | fern/.*
  | \.agents/.*\.mdx?$
  | [^/]+\.mdx?$
  | \.rumdl\.toml$
)'''

[[repos]]
# Per-commit title linting (commit-msg stage): enforces the Conventional Commits
# subject via `cz check`. Config in pyproject.toml [tool.commitizen]; the same
# tool generates the changelog / bumps the version later. Local dev aid — under
# ff + squash-on the enforced gate is the MR/PR title. Runs from the commit-msg
# shim, which `default_install_hook_types` above installs.
repo = "https://github.com/commitizen-tools/commitizen"
rev = "v4.17.0"
hooks = [
  { id = "commitizen" },
]