Build and reuse a run-scoped file index

[j178]

Build a run-scoped file index once and reuse per-project file views during hook installation and execution, avoiding repeated project × file scans.

Benchmark

profiling profile, 1,000 projects / 101,001 tracked files, prek run --all-files --dry-run, 2 warmups and 10 runs:

	Mean
Baseline	2.228 s
This PR	158.7 ms

14.04 ± 0.24× faster (92.88% less time). Average maximum RSS increased from 36.58 MiB to 38.91 MiB (+2.33 MiB).

The baseline ProjectFiles::for_project hotspot (38.56% of samples) disappears from the optimized flamegraph.

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[codecov]

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 93.33%. Comparing base (79cf621) to head (e7f9ab6).

Additional details and impacted files

@@            Coverage Diff             @@
##           master    #2361      +/-   ##
==========================================
- Coverage   93.36%   93.33%   -0.03%     
==========================================
  Files         129      129              
  Lines       27408    27427      +19     
==========================================
+ Hits        25589    25600      +11     
- Misses       1819     1827       +8     

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[prek-ci-bot]

📦 Cargo Bloat Comparison

Binary size change: +0.00% (29.1 MiB → 29.1 MiB)

Expand for cargo-bloat output

Head Branch Results

 File  .text     Size             Crate Name
 1.1%   2.3% 332.0KiB        aws_lc_sys aws_lc_0_42_0_aes_gcm_encrypt_avx512
 1.1%   2.3% 332.0KiB        aws_lc_sys aws_lc_0_42_0_aes_gcm_decrypt_avx512
 0.3%   0.6%  79.3KiB              prek <prek::cli::Command as clap_builder::derive::Subcommand>::augment_subcommands
 0.2%   0.4%  52.0KiB              prek <<prek::config::Config as serde_core::de::Deserialize>::deserialize::__Visitor as serde_core::de::Visitor>::visit_map::<<serde_saphyr::de::deserializer::YamlDeserializer as serde_core::de::Deserializer>::deserialize_map::MA>
 0.2%   0.3%  49.4KiB annotate_snippets annotate_snippets::renderer::render::render
 0.1%   0.3%  41.1KiB              prek prek::cli::run::run::run::{closure#0}
 0.1%   0.3%  39.5KiB              prek prek::run::{closure#0}
 0.1%   0.2%  32.1KiB              prek <prek::cli::RunOptions as clap_builder::derive::Args>::augment_args
 0.1%   0.2%  30.1KiB     granit_parser <granit_parser::scanner::Scanner<granit_parser::input::str::StrInput>>::fetch_more_tokens
 0.1%   0.2%  28.6KiB    cargo_metadata <&mut serde_json::de::Deserializer<serde_json::read::StrRead> as serde_core::de::Deserializer>::deserialize_struct::<<cargo_metadata::Package as serde_core::de::Deserialize>::deserialize::__Visitor>
 0.1%   0.2%  28.0KiB        aws_lc_sys aws_lc_0_42_0_edwards25519_scalarmuldouble_alt
 0.1%   0.2%  27.9KiB              prek <<prek::config::RemoteHook as serde_core::de::Deserialize>::deserialize::__Visitor as serde_core::de::Visitor>::visit_map::<<serde_saphyr::de::deserializer::YamlDeserializer as serde_core::de::Deserializer>::deserialize_map::MA>
 0.1%   0.2%  27.5KiB        aws_lc_sys aws_lc_0_42_0_edwards25519_scalarmuldouble
 0.1%   0.2%  26.1KiB              prek prek::cli::try_repo::try_repo::{closure#0}
 0.1%   0.2%  25.6KiB              prek <<prek::config::LocalHook as serde_core::de::Deserialize>::deserialize::__Visitor as serde_core::de::Visitor>::visit_map::<<serde_saphyr::de::deserializer::YamlDeserializer as serde_core::de::Deserializer>::deserialize_map::MA>
 0.1%   0.2%  25.2KiB              prek <<prek::config::UpdateOptions as serde_core::de::Deserialize>::deserialize::__Visitor as serde_core::de::Visitor>::visit_map::<<serde_saphyr::de::deserializer::YamlDeserializer as serde_core::de::Deserializer>::deserialize_map::MA>
 0.1%   0.2%  24.9KiB               xml <xml::reader::parser::PullParser>::dispatch_token
 0.1%   0.2%  24.4KiB              prek <prek::languages::node::installer::NodeInstaller>::install::{closure#0}
 0.1%   0.2%  24.0KiB     granit_parser <granit_parser::scanner::Scanner<serde_saphyr::de::buffered_input::ReaderInput>>::fetch_more_tokens
 0.1%   0.2%  22.3KiB         [Unknown] Lp384_montjscalarmul_alt_p384_montjadd
42.0%  88.2%  12.2MiB                   And 25805 smaller methods. Use -n N to show more.
47.7% 100.0%  13.9MiB                   .text section size, the file size is 29.1MiB

Base Branch Results

 File  .text     Size             Crate Name
 1.1%   2.3% 332.0KiB        aws_lc_sys aws_lc_0_42_0_aes_gcm_encrypt_avx512
 1.1%   2.3% 332.0KiB        aws_lc_sys aws_lc_0_42_0_aes_gcm_decrypt_avx512
 0.3%   0.6%  79.3KiB              prek <prek::cli::Command as clap_builder::derive::Subcommand>::augment_subcommands
 0.2%   0.4%  52.4KiB              prek <<prek::config::Config as serde_core::de::Deserialize>::deserialize::__Visitor as serde_core::de::Visitor>::visit_map::<<serde_saphyr::de::deserializer::YamlDeserializer as serde_core::de::Deserializer>::deserialize_map::MA>
 0.2%   0.3%  49.4KiB annotate_snippets annotate_snippets::renderer::render::render
 0.1%   0.3%  41.3KiB              prek prek::cli::run::run::run::{closure#0}
 0.1%   0.3%  39.5KiB              prek prek::run::{closure#0}
 0.1%   0.2%  33.2KiB              prek prek::archive::unpack::<fs_err::tokio::file::File, &std::path::PathBuf>::{closure#0}
 0.1%   0.2%  32.1KiB              prek <prek::cli::RunOptions as clap_builder::derive::Args>::augment_args
 0.1%   0.2%  30.1KiB     granit_parser <granit_parser::scanner::Scanner<granit_parser::input::str::StrInput>>::fetch_more_tokens
 0.1%   0.2%  28.6KiB    cargo_metadata <&mut serde_json::de::Deserializer<serde_json::read::StrRead> as serde_core::de::Deserializer>::deserialize_struct::<<cargo_metadata::Package as serde_core::de::Deserialize>::deserialize::__Visitor>
 0.1%   0.2%  28.3KiB              prek <<prek::config::RemoteHook as serde_core::de::Deserialize>::deserialize::__Visitor as serde_core::de::Visitor>::visit_map::<<serde_saphyr::de::deserializer::YamlDeserializer as serde_core::de::Deserializer>::deserialize_map::MA>
 0.1%   0.2%  28.0KiB        aws_lc_sys aws_lc_0_42_0_edwards25519_scalarmuldouble_alt
 0.1%   0.2%  27.5KiB        aws_lc_sys aws_lc_0_42_0_edwards25519_scalarmuldouble
 0.1%   0.2%  26.2KiB              prek prek::cli::try_repo::try_repo::{closure#0}
 0.1%   0.2%  25.6KiB              prek <<prek::config::LocalHook as serde_core::de::Deserialize>::deserialize::__Visitor as serde_core::de::Visitor>::visit_map::<<serde_saphyr::de::deserializer::YamlDeserializer as serde_core::de::Deserializer>::deserialize_map::MA>
 0.1%   0.2%  25.2KiB              prek <<prek::config::UpdateOptions as serde_core::de::Deserialize>::deserialize::__Visitor as serde_core::de::Visitor>::visit_map::<<serde_saphyr::de::deserializer::YamlDeserializer as serde_core::de::Deserializer>::deserialize_map::MA>
 0.1%   0.2%  24.9KiB               xml <xml::reader::parser::PullParser>::dispatch_token
 0.1%   0.2%  24.4KiB              prek <prek::languages::node::installer::NodeInstaller>::install::{closure#0}
 0.1%   0.2%  24.0KiB     granit_parser <granit_parser::scanner::Scanner<serde_saphyr::de::buffered_input::ReaderInput>>::fetch_more_tokens
42.0%  88.1%  12.2MiB                   And 25792 smaller methods. Use -n N to show more.
47.7% 100.0%  13.9MiB                   .text section size, the file size is 29.1MiB

[prek-ci-bot]

⚡️ Hyperfine Benchmarks

Summary: 0 regressions, 1 improvements above the 10% threshold.

Environment

• OS: Linux 6.17.0-1020-azure
• CPU: 4 cores
• prek version: prek 0.4.10+4 (ce80307 2026-07-19)
• Rust version: rustc 1.97.1 (8bab26f4f 2026-07-14)
• Hyperfine version: hyperfine 1.20.0

CLI Commands

Benchmarking basic commands in the main repo:

prek --version

Command	Mean [ms]	Min [ms]	Max [ms]	Relative
prek-base --version	2.2 ± 0.1	2.1	2.5	1.05 ± 0.05
prek-head --version	2.1 ± 0.1	2.0	2.4	1.00

prek list

Command	Mean [ms]	Min [ms]	Max [ms]	Relative
prek-base list	9.2 ± 0.9	8.9	17.5	1.02 ± 0.10
prek-head list	9.1 ± 0.1	8.9	9.5	1.00

prek validate-config .pre-commit-config.yaml

Command	Mean [ms]	Min [ms]	Max [ms]	Relative
prek-base validate-config .pre-commit-config.yaml	3.1 ± 0.1	3.0	3.4	1.02 ± 0.04
prek-head validate-config .pre-commit-config.yaml	3.1 ± 0.1	3.0	3.2	1.00

prek sample-config

Command	Mean [ms]	Min [ms]	Max [ms]	Relative
prek-base sample-config	2.4 ± 0.0	2.3	2.5	1.01 ± 0.03
prek-head sample-config	2.4 ± 0.1	2.3	2.5	1.00

Cold vs Warm Runs

Comparing first run (cold) vs subsequent runs (warm cache):

prek run --all-files (cold - no cache)

Command	Mean [ms]	Min [ms]	Max [ms]	Relative
prek-base run --all-files	75.3 ± 2.4	72.1	79.0	1.00
prek-head run --all-files	75.9 ± 2.6	70.5	79.0	1.01 ± 0.05

prek run --all-files (warm - with cache)

Command	Mean [ms]	Min [ms]	Max [ms]	Relative
prek-base run --all-files	76.1 ± 7.6	70.8	107.1	1.03 ± 0.11
prek-head run --all-files	74.2 ± 2.3	69.5	77.1	1.00

Full Hook Suite

Running the builtin hook suite on the benchmark workspace:

prek run --all-files (full builtin hook suite)

Command	Mean [ms]	Min [ms]	Max [ms]	Relative
prek-base run --all-files	74.4 ± 2.6	70.2	81.6	1.00
prek-head run --all-files	75.6 ± 2.6	70.4	80.8	1.02 ± 0.05

Individual Hook Performance

Benchmarking each hook individually on the test repo:

prek run trailing-whitespace --all-files

Command	Mean [ms]	Min [ms]	Max [ms]	Relative
prek-base run trailing-whitespace --all-files	19.6 ± 0.3	19.0	20.4	1.00
prek-head run trailing-whitespace --all-files	19.7 ± 0.3	19.2	20.3	1.00 ± 0.02

prek run end-of-file-fixer --all-files

Command	Mean [ms]	Min [ms]	Max [ms]	Relative
prek-base run end-of-file-fixer --all-files	25.8 ± 2.3	23.1	31.7	1.01 ± 0.12
prek-head run end-of-file-fixer --all-files	25.4 ± 2.0	23.0	29.6	1.00

prek run check-json --all-files

Command	Mean [ms]	Min [ms]	Max [ms]	Relative
prek-base run check-json --all-files	7.5 ± 0.2	7.0	7.9	1.01 ± 0.04
prek-head run check-json --all-files	7.4 ± 0.2	7.1	7.9	1.00

prek run check-yaml --all-files

Command	Mean [ms]	Min [ms]	Max [ms]	Relative
prek-base run check-yaml --all-files	7.3 ± 0.1	7.1	7.5	1.00 ± 0.02
prek-head run check-yaml --all-files	7.3 ± 0.1	7.1	7.6	1.00

prek run check-toml --all-files

Command	Mean [ms]	Min [ms]	Max [ms]	Relative
prek-base run check-toml --all-files	7.4 ± 0.3	7.0	8.1	1.01 ± 0.05
prek-head run check-toml --all-files	7.4 ± 0.3	7.0	8.0	1.00

prek run check-xml --all-files

Command	Mean [ms]	Min [ms]	Max [ms]	Relative
prek-base run check-xml --all-files	7.3 ± 0.4	6.9	8.3	1.00
prek-head run check-xml --all-files	7.4 ± 0.4	7.0	8.5	1.01 ± 0.08

prek run detect-private-key --all-files

Command	Mean [ms]	Min [ms]	Max [ms]	Relative
prek-base run detect-private-key --all-files	13.6 ± 1.3	11.9	16.8	1.00
prek-head run detect-private-key --all-files	13.7 ± 1.6	11.9	18.7	1.01 ± 0.15

prek run fix-byte-order-marker --all-files

Command	Mean [ms]	Min [ms]	Max [ms]	Relative
prek-base run fix-byte-order-marker --all-files	18.5 ± 2.6	16.8	28.4	1.02 ± 0.15
prek-head run fix-byte-order-marker --all-files	18.2 ± 0.7	17.2	19.6	1.00

Installation Performance

Benchmarking hook installation (fast path hooks skip Python setup):

prek install-hooks (cold - no cache)

Command	Mean [ms]	Min [ms]	Max [ms]	Relative
prek-base install-hooks	4.4 ± 0.1	4.3	4.5	1.00
prek-head install-hooks	4.5 ± 0.0	4.4	4.5	1.02 ± 0.02

prek install-hooks (warm - with cache)

Command	Mean [ms]	Min [ms]	Max [ms]	Relative
prek-base install-hooks	4.5 ± 0.1	4.5	4.6	1.02 ± 0.03
prek-head install-hooks	4.4 ± 0.1	4.3	4.6	1.00

File Filtering/Scoping Performance

Testing different file selection modes:

prek run (staged files only)

Command	Mean [ms]	Min [ms]	Max [ms]	Relative
prek-base run	37.3 ± 1.0	36.1	40.7	1.00 ± 0.04
prek-head run	37.2 ± 0.9	36.3	39.4	1.00

prek run --files '*.json' (specific file type)

Command	Mean [ms]	Min [ms]	Max [ms]	Relative
prek-base run --files '*.json'	7.8 ± 0.1	7.7	8.1	1.01 ± 0.02
prek-head run --files '*.json'	7.7 ± 0.1	7.6	7.9	1.00

Workspace Discovery & Initialization

Benchmarking hook discovery and initialization overhead:

prek run --dry-run --all-files (measures init overhead)

Command	Mean [ms]	Min [ms]	Max [ms]	Relative
prek-base run --dry-run --all-files	6.6 ± 0.1	6.5	7.0	1.01 ± 0.02
prek-head run --dry-run --all-files	6.6 ± 0.1	6.4	6.7	1.00

Meta Hooks Performance

Benchmarking meta hooks separately:

prek run check-hooks-apply --all-files

Command	Mean [ms]	Min [ms]	Max [ms]	Relative
prek-base run check-hooks-apply --all-files	11.5 ± 0.2	11.4	12.2	1.12 ± 0.02
prek-head run check-hooks-apply --all-files	10.3 ± 0.1	10.2	10.6	1.00

✅ Performance improvement for prek run check-hooks-apply --all-files: 10.5500% faster

prek run check-useless-excludes --all-files

Command	Mean [ms]	Min [ms]	Max [ms]	Relative
prek-base run check-useless-excludes --all-files	10.4 ± 0.1	10.3	10.6	1.00
prek-head run check-useless-excludes --all-files	10.5 ± 0.7	10.2	13.0	1.01 ± 0.07

prek run identity --all-files

Command	Mean [ms]	Min [ms]	Max [ms]	Relative
prek-base run identity --all-files	9.9 ± 0.8	9.5	12.3	1.03 ± 0.08
prek-head run identity --all-files	9.5 ± 0.1	9.4	9.7	1.00