Cargo.toml

[workspace]
members = [
    "crates/*",
    "crates/stubs/*",
    "crates/experiments/reconcile-viewer",
]
default-members = ["crates/*", "crates/experiments/reconcile-viewer"]
# Excluded crates require special build toolchains or targets:
# - WASM crates: build with wasm-pack or --target wasm32-unknown-unknown
# - pampa/fuzz: requires nightly Rust + libfuzzer-sys (Linux/macOS only), run via `cargo fuzz`
# crates/experiments is a container directory, not a crate, so we exclude it from crates/* matching.
exclude = [
    "crates/wasm-quarto-hub-client",
    "crates/wasm-qmd-parser",
    "crates/experiments",
    "crates/pampa/fuzz",
    # WASM-only drop-in replacement for tree-sitter-language; used via
    # [patch.crates-io] in wasm-quarto-hub-client. Collides with the
    # real tree-sitter-language crate (same `links` key) if both appear
    # in the same workspace graph. See
    # claude-notes/plans/2026-04-20-wasm-shim-merge.md.
    "crates/tree-sitter-language-wasm-shim",
    # cpic — standalone pharmacogenomics crate (its own [workspace], serde +
    # serde_json only). cockpit-server path-depends on it for the /cpic panel;
    # excluding it here makes cargo treat it as a separate workspace root so the
    # cross-boundary path dep resolves (else: "multiple workspace roots found").
    "cpic",
]
resolver = "2"

[workspace.package]
version = "0.7.0"
authors = ["Posit Software, PBC"]
homepage = "https://github.com/posit-dev/quarto-markdown-syntax"
keywords = ["parser"]
categories = ["development-tools"]
license = "MIT"
repository = "https://github.com/posit-dev/quarto-markdown-syntax"
edition = "2024"

[workspace.dependencies]
anyhow = "1.0.101"
quick-xml = "0.39"
ariadne = "0.6"
clap = { version = "4.5", features = ["derive", "cargo", "env"] }
insta = "1.46.3"
memchr = "2.7.6"
once_cell = "1.21"
proc-macro2 = { version = "1.0.106", features = ["span-locations"] }
schemars = "1.2.1"
serde = { version = "1.0.228", features = ["derive"] }
serde_json = "1.0.149"
smallvec = { version = "1.13", features = ["serde"] }
serde_yaml = "0.9"
thiserror = "2.0"
toml = "0.9.11"
tracing-subscriber = { version = "0.3", features = ["env-filter"] }
yaml-rust2 = "0.11"
async-trait = "0.1"
tokio-util = "0.7"
pollster = "0.4"
regex = "1.12"
scraper = "0.26"
grass = "0.13.4"
include_dir = "0.7"
flate2 = "1.1"
uuid = { version = "1", features = ["v4"] }
base64 = "0.22"
walkdir = "2"
syn = { version = "2", features = ["full", "visit", "parsing"] }

tokio = { version = "1", features = ["rt-multi-thread", "macros"] }

# LSP server dependencies (native only)
tower-lsp = "0.20"
lsp-types = "0.97"

[workspace.dependencies.proc-macro-error2]
version = "2.0.1"
default-features = false

[workspace.dependencies.tests_macros]
path = "./crates/tests_macros"

[workspace.dependencies.tracing]
version = "0.1.44"
features = ["std"]
default-features = false

[workspace.dependencies.tree-sitter]
version = "0.26"

[workspace.dependencies.tree-sitter-highlight]
version = "0.26"

[workspace.dependencies.tree-sitter-qmd]
path = "./crates/tree-sitter-qmd"

[workspace.dependencies.tree-sitter-sexpr]
path = "./crates/tree-sitter-sexpr"

[workspace.dependencies.wasm-qmd-parser]
path = "./crates/wasm-qmd-parser"

[workspace.dependencies.pampa]
path = "./crates/pampa"
default-features = false

[workspace.dependencies.quarto-core]
path = "./crates/quarto-core"

[workspace.dependencies.quarto-util]
path = "./crates/quarto-util"

[workspace.dependencies.quarto-yaml]
path = "./crates/quarto-yaml"

[workspace.dependencies.quarto-yaml-validation]
path = "./crates/quarto-yaml-validation"

[workspace.dependencies.quarto-error-reporting]
version = "0.1.0"

[workspace.dependencies.quarto-error-catalog]
path = "./crates/quarto-error-catalog"

[workspace.dependencies.quarto-source-map]
version = "0.1.0"

[workspace.dependencies.quarto-xml]
path = "./crates/quarto-xml"

[workspace.dependencies.quarto-doctemplate]
path = "./crates/quarto-doctemplate"

[workspace.dependencies.quarto-treesitter-ast]
path = "./crates/quarto-treesitter-ast"

[workspace.dependencies.quarto-pandoc-types]
path = "./crates/quarto-pandoc-types"

[workspace.dependencies.quarto-analysis]
path = "./crates/quarto-analysis"

[workspace.dependencies.quarto-ast-reconcile]
path = "./crates/quarto-ast-reconcile"

[workspace.dependencies.quarto-config]
path = "./crates/quarto-config"

[workspace.dependencies.quarto-system-runtime]
path = "./crates/quarto-system-runtime"

[workspace.dependencies.quarto-project-create]
path = "./crates/quarto-project-create"

[workspace.dependencies.quarto-lsp-core]
path = "./crates/quarto-lsp-core"

[workspace.dependencies.quarto-lsp]
path = "./crates/quarto-lsp"

[workspace.dependencies.quarto-brand]
path = "./crates/quarto-brand"

[workspace.dependencies.quarto-sass]
path = "./crates/quarto-sass"

[workspace.dependencies.quarto-highlight]
path = "./crates/quarto-highlight"

[workspace.dependencies.quarto-highlight-encoding]
path = "./crates/quarto-highlight-encoding"

[workspace.dependencies.quarto-hub]
path = "./crates/quarto-hub"

[workspace.dependencies.quarto-navigation]
path = "./crates/quarto-navigation"

[workspace.dependencies.quarto-publish]
path = "./crates/quarto-publish"

[workspace.dependencies.quarto-test]
path = "./crates/quarto-test"

[workspace.dependencies.quarto-trace]
path = "./crates/quarto-trace"

[workspace.dependencies.quarto-trace-server]
path = "./crates/quarto-trace-server"

# ── AdaWorldAPI q2 fork additions: graph-notebook + Gotham GUI ──
# Re-applied onto fresh upstream after the no-shared-history resync
# (claude/q2-upstream-replant). Consumed by our additive crates
# (cockpit-server, stubs/*, aiwar-ingest, neural-debug). Per
# .claude/rules/architectural-compliance.md the lance-graph deps are the
# REAL ../lance-graph/crates/* (sibling repo), never substitutes.
[workspace.dependencies.notebook-query]
path = "./crates/stubs/notebook-query"

[workspace.dependencies.lance-graph]
path = "../lance-graph/crates/lance-graph"
default-features = false
# ndarray-hpc required: lance-graph's vector_ops/fingerprint/hydrate call
# ndarray::hpc::* unconditionally, so the feature must be on even with
# default-features off.
features = ["ndarray-hpc"]

[workspace.dependencies.lance-graph-planner]
path = "../lance-graph/crates/lance-graph-planner"

[workspace.dependencies.bgz17]
path = "../lance-graph/crates/bgz17"

[workspace.dependencies.thinking-engine]
path = "../lance-graph/crates/thinking-engine"

[workspace.dependencies.cognitive-shader-driver]
path = "../lance-graph/crates/cognitive-shader-driver"

[workspace.dependencies.lance-graph-contract]
path = "../lance-graph/crates/lance-graph-contract"
# guid-v2-tail: the OSINT/Gotham rows use the v2 tail (leaf·family·identity, all
# u16). family(u16) is the deterministic basin (round→anchor), NOT a category and
# NOT a Louvain cluster — location is permanent via the HHTL, the basin is an
# interface the node adapts to.
# NOTE: guid-v3-tail is NOT enabled workspace-wide. Only `osint-bake` mints on the
# V3 cascade tail (the FMA bake), so it requests `guid-v3-tail` on its OWN dep
# (crates/osint-bake/Cargo.toml). Enabling it here forced EVERY member — including
# cockpit-server — to require a lance-graph-contract carrying the feature, which
# broke the Railway cockpit build against the deliberately-pinned LANCE_GRAPH_REF
# (Dockerfile COUNT_FUSE lockstep). cockpit-server uses no V3 minting; it needs
# only guid-v2-tail (the OSINT/Gotham v2 leaf·family·identity tail).
features = ["guid-v2-tail"]

# OGAR Active-Record activation crate — the real `impl lance_graph_contract::
# ClassView` (OgarClassView) used for DISPLAY only. default-features = light: the
# emit() DDL formatter, NO surrealdb tree (the surrealql-parser feature is opt-in
# and deliberately NOT enabled here).
[workspace.dependencies.lance-graph-ogar]
path = "../lance-graph/crates/lance-graph-ogar"

[workspace.dependencies.causal-edge]
path = "../lance-graph/crates/causal-edge"

[workspace.dependencies.graph-flow]
path = "./crates/stubs/graph-flow"

# The REAL AdaWorldAPI/ndarray fork, consumed DIRECTLY — the SAME local checkout
# lance-graph compiles (`../ndarray`), so the whole binary unifies on one fork.
# No wrapper crate: when everything compiles into a single binary from local
# source, wrapping ndarray behind another crate buys nothing — it only hides
# `ndarray::simd` / `ndarray::hpc` (the AVX-512→AVX2→scalar polyfill, compile-time
# `target-cpu=x86-64-v4` + runtime `simd_caps()`) behind a pointless indirection.
[workspace.dependencies.ndarray]
path = "../ndarray"
default-features = false
features = ["std", "hpc-extras"]

[workspace.dependencies.q2-ndarray]
path = "./crates/stubs/q2-ndarray"

[workspace.dependencies.axum]
version = "0.7"
features = ["ws"]

[workspace.dependencies.tower-http]
version = "0.5"
features = ["fs", "cors"]

[workspace.dependencies.async-stream]
version = "0.3"

[workspace.dependencies.futures-core]
version = "0.3"

# deno JS runtime — cockpit-server executes .qmd JS/TS cells via deno_core (the
# deliberate "better than neo4j" live-cell engine; q2 upstream carries no deno).
# crates.io deno_core 0.376 is ARCHIVED and its stale temporal_rs won't build
# against current icu_calendar. Repoint to the AdaWorldAPI/deno fork (deno_core
# 0.404 at libs/core, current V8). Per .claude/rules/architectural-compliance.md
# + the workspace fork rule: the fork, NEVER crates.io.
[workspace.dependencies.deno_core]
git = "https://github.com/AdaWorldAPI/deno"
branch = "main"

[workspace.dependencies.serde_v8]
git = "https://github.com/AdaWorldAPI/deno"
branch = "main"

[workspace.lints.rust]
# coverage_nightly is used by pampa for code coverage instrumentation on nightly Rust
unexpected_cfgs = { level = "warn", check-cfg = ['cfg(coverage_nightly)'] }
# Enforce the SourceInfo provenance contract — callers must use SourceInfo::for_test() or
# an explicit Generated{by: <kind>}; SourceInfo::default() is forbidden.
deprecated = "deny"

[workspace.lints.clippy]
# Architectural issues - fixing these requires significant refactoring
large_enum_variant = "allow"  # Would require boxing large enum variants
result_large_err = "allow"    # Would require boxing all error types
too_many_arguments = "allow"  # Some functions legitimately need many parameters
fn_params_excessive_bools = "allow"  # Related to too_many_arguments
wrong_self_convention = "allow"  # as_inline(self) intentionally consumes self
type_complexity = "allow"  # Complex types are sometimes clearer inline
inherent_to_string = "allow"  # OutputBuilder::to_string is intentional naming
ptr_arg = "allow"  # &Vec vs &[_] requires API changes
only_used_in_recursion = "allow"  # Not a problem
arc_with_non_send_sync = "allow"  # May be intentional for single-threaded use
large_stack_arrays = "allow"  # May be intentional for performance
enum_variant_names = "allow"  # Stylistic preference
items_after_test_module = "allow"  # Module organization preference
result_unit_err = "allow"  # API design choice
assertions_on_constants = "allow"  # Used for test documentation
doc_lazy_continuation = "allow"  # Doc formatting preference
doc_overindented_list_items = "allow"  # Doc formatting preference
match_like_matches_macro = "allow"  # Sometimes match is clearer
suspicious_doc_comments = "allow"  # False positives
needless_else = "allow"  # Sometimes improves readability
if_same_then_else = "allow"  # May be intentional for clarity
assigning_clones = "allow"  # Requires many changes for marginal benefit
cloned_ref_to_slice_refs = "allow"  # Minor optimization
manual_strip = "allow"  # Sometimes clearer than strip_prefix
needless_range_loop = "allow"  # Sometimes index access is intentional
const_is_empty = "allow"  # False positive in tests
needless_for_each = "allow"  # Style preference

# Keep these as warnings
cfg_not_test = "warn"
checked_conversions = "warn"
cloned_instead_of_copied = "warn"
copy_iterator = "warn"
dbg_macro = "warn"
empty_drop = "warn"
empty_enums = "warn"
empty_enum_variants_with_brackets = "warn"
expl_impl_clone_on_copy = "warn"
explicit_into_iter_loop = "warn"
filter_map_next = "warn"
flat_map_option = "warn"
float_cmp_const = "warn"
from_iter_instead_of_collect = "warn"
get_unwrap = "warn"
implicit_clone = "warn"
implicit_hasher = "warn"
index_refutable_slice = "warn"
inefficient_to_string = "warn"
invalid_upcast_comparisons = "warn"
iter_filter_is_ok = "warn"
iter_not_returning_iterator = "warn"
large_types_passed_by_value = "warn"
lossy_float_literal = "warn"
macro_use_imports = "warn"
manual_is_variant_and = "warn"
manual_ok_or = "warn"
manual_string_new = "warn"
map_flatten = "warn"
map_unwrap_or = "warn"
mismatching_type_param_order = "warn"
mut_mut = "warn"
naive_bytecount = "warn"
needless_bitwise_bool = "warn"
needless_continue = "allow"  # Sometimes continue is clearer for control flow
no_effect_underscore_binding = "warn"
option_as_ref_cloned = "warn"
rc_buffer = "warn"
rc_mutex = "warn"
ref_binding_to_reference = "warn"
ref_option_ref = "warn"
rest_pat_in_fully_bound_structs = "warn"
single_char_pattern = "warn"
stable_sort_primitive = "warn"
str_split_at_newline = "warn"
string_lit_chars_any = "warn"
unnecessary_box_returns = "warn"
unnecessary_join = "warn"
unnested_or_patterns = "warn"
unreadable_literal = "warn"
verbose_bit_mask = "warn"
verbose_file_reads = "warn"

[patch.crates-io]
lua-src = { path = "crates/lua-src-wasm" }
# Fork of runtimelib that adds venv-aware kernelspec discovery
# (`data_dirs_with_jupyter_paths`, `find_kernelspec_with_jupyter_paths`)
# and threads `searched_paths` through `RuntimeError::KernelNotFound`.
# Pinned to a SHA on cscheid/runtimed; will be removed once the
# upstream PR (bd-875x) lands and a release ships.
runtimelib = { git = "https://github.com/cscheid/runtimed", rev = "fc58eb48139a30cc559ac5973cb6debb00375b88" }
# `runtimelib` depends on `jupyter-protocol` via the runtimed workspace,
# so we must patch jupyter-protocol from the same SHA to avoid pulling
# in two distinct `jupyter_protocol::JupyterMessage` types.
jupyter-protocol = { git = "https://github.com/cscheid/runtimed", rev = "fc58eb48139a30cc559ac5973cb6debb00375b88" }

# Fold ogar-class-view's transitive `lance-graph-contract` (git
# AdaWorldAPI/lance-graph#main, pulled via lance-graph-ogar) onto q2's path copy
# = exactly ONE contract crate, so `OgarClassView`'s `impl ClassView` is for the
# SAME trait q2 names in `&dyn lance_graph_contract::ClassView`. Consumer
# requirement repeated from lance-graph-ogar's own Cargo header (codex P2, #564):
# the patch only takes effect in the workspace ROOT, so q2 must declare it here.
[patch."https://github.com/AdaWorldAPI/lance-graph"]
lance-graph-contract = { path = "../lance-graph/crates/lance-graph-contract" }

# Profiles must be set at the workspace level
[profile.dev]
# Tell `rustc` to optimize for small code size to
# work around "too many locals" error from wasm-pack
# https://github.com/wasm-bindgen/wasm-bindgen/issues/3451#issuecomment-1562982835
opt-level = "s"

# CI-only profile (used by `.github/workflows/test-suite.yml`). Strips
# debuginfo to fit GHA disk. Locally, omit `--cargo-profile ci` to get
# full debuginfo via the default `dev` profile.
# See claude-notes/2026-04-28-ci-disk-space-and-profile-ci.md.
[profile.ci]
inherits = "dev"
debug = "line-tables-only"

[profile.ci.package."*"]
debug = false

# Release-like profile with debug info preserved for profilers (samply, etc.).
# Used by perf-harness drivers; see claude-notes/instructions/performance-profiling.md.
[profile.release-perf]
inherits = "release"
debug = true
# samply / perf need unstripped symbols. Also keep inlining info for meaningful
# stacks — release's default `codegen-units` still lets LLVM inline aggressively,
# which is what we want to profile.
strip = false