Skip unnecessary submodule updates during hook repo clone

[shaanmajid]

Summary

Skip git submodule update --init --recursive after cloning a hook repo when the checked-out repo has neither .gitmodules nor gitlink entries.

Most hook repositories do not use submodules. Before this change, prek still ran git submodule update for every cloned remote repo, which adds an avoidable Git subprocess on cold cache paths.

The new behavior keeps the existing submodule path when either:

• .gitmodules exists
• the checked-out index contains gitlinks (160000 entries)

That preserves behavior for normal submodule repos, broken .gitmodules cases, and gitlink-without-.gitmodules edge cases.

Benchmarks

Benchmarked cold prek list with fresh isolated PREK_HOME against local mirrors of real hook repositories to avoid network variance. Baseline was upstream/master; changed was this branch. Each scenario used 40 runs and 6 warmups.

Repo	Rev	Files	Baseline	Changed	Result
pre-commit/pre-commit-hooks	v6.0.0	106	132.3 ± 12.6 ms	84.5 ± 11.0 ms	1.57x faster
astral-sh/ruff-pre-commit	v0.9.9	10	113.4 ± 14.2 ms	76.8 ± 7.1 ms	1.48x faster
psf/black	25.1.0	424	274.7 ± 24.9 ms	231.6 ± 18.9 ms	1.19x faster

All benchmarked repos had no .gitmodules and no gitlinks. Trace logs confirmed the old path ran:

git submodule update --init --recursive --depth=1

The new path checked gitlinks with:

git ls-files -z -s

and skipped submodule update.

[codecov]

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 93.00%. Comparing base (eb02499) to head (db7cf71).
⚠️ Report is 1 commits behind head on master.

Additional details and impacted files

@@            Coverage Diff             @@
##           master    #2255      +/-   ##
==========================================
+ Coverage   92.90%   93.00%   +0.10%     
==========================================
  Files         127      127              
  Lines       27583    27674      +91     
==========================================
+ Hits        25625    25739     +114     
+ Misses       1958     1935      -23     

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[prek-ci-bot]

📦 Cargo Bloat Comparison

Binary size change: +0.00% (26.8 MiB → 26.8 MiB)

Expand for cargo-bloat output

Head Branch Results

 File  .text     Size             Crate Name
 1.2%   2.5% 332.0KiB        aws_lc_sys aws_lc_0_41_0_aes_gcm_encrypt_avx512
 1.2%   2.5% 332.0KiB        aws_lc_sys aws_lc_0_41_0_aes_gcm_decrypt_avx512
 0.3%   0.7%  95.6KiB              prek prek::languages::<impl prek::config::Language>::run::{{closure}}::{{closure}}
 0.3%   0.7%  92.0KiB              prek prek::languages::<impl prek::config::Language>::install::{{closure}}
 0.3%   0.7%  91.5KiB              prek prek::languages::<impl prek::config::Language>::run::{{closure}}::{{closure}}
 0.2%   0.5%  65.4KiB             prek? <prek::cli::Command as clap_builder::derive::Subcommand>::augment_subcommands
 0.2%   0.4%  49.4KiB annotate_snippets annotate_snippets::renderer::render::render
 0.2%   0.4%  49.0KiB              prek prek::run::{{closure}}
 0.2%   0.3%  43.6KiB              prek prek::cli::run::run::run::{{closure}}
 0.2%   0.3%  43.0KiB             prek? <prek::config::_::<impl serde_core::de::Deserialize for prek::config::Config>::deserialize::__Visitor as serde_core::de::Visitor>::visit_map
 0.1%   0.3%  34.2KiB               std core::ptr::drop_in_place<prek::languages::<impl prek::config::Language>::install::{{closure}}>
 0.1%   0.2%  33.4KiB              prek prek::archive::unpack::{{closure}}
 0.1%   0.2%  31.9KiB             prek? <prek::cli::RunOptions as clap_builder::derive::Args>::augment_args
 0.1%   0.2%  29.8KiB     granit_parser granit_parser::scanner::Scanner<T>::fetch_more_tokens
 0.1%   0.2%  28.0KiB        aws_lc_sys aws_lc_0_41_0_edwards25519_scalarmuldouble_alt
 0.1%   0.2%  27.8KiB             prek? <prek::config::_::<impl serde_core::de::Deserialize for prek::config::RemoteHook>::deserialize::__Visitor as serde_core::de::Visitor>::visit_map
 0.1%   0.2%  27.5KiB        aws_lc_sys aws_lc_0_41_0_edwards25519_scalarmuldouble
 0.1%   0.2%  26.8KiB              prek prek::cli::try_repo::try_repo::{{closure}}
 0.1%   0.2%  25.1KiB              prek prek::languages::ruby::installer::RubyInstaller::install::{{closure}}
 0.1%   0.2%  24.9KiB             prek? <prek::config::_::<impl serde_core::de::Deserialize for prek::config::LocalHook>::deserialize::__Visitor as serde_core::de::Visitor>::visit_map
42.0%  86.1%  11.2MiB                   And 24587 smaller methods. Use -n N to show more.
48.8% 100.0%  13.1MiB                   .text section size, the file size is 26.8MiB

Base Branch Results

 File  .text     Size             Crate Name
 1.2%   2.5% 332.0KiB        aws_lc_sys aws_lc_0_41_0_aes_gcm_encrypt_avx512
 1.2%   2.5% 332.0KiB        aws_lc_sys aws_lc_0_41_0_aes_gcm_decrypt_avx512
 0.3%   0.7%  95.6KiB              prek prek::languages::<impl prek::config::Language>::run::{{closure}}::{{closure}}
 0.3%   0.7%  92.0KiB              prek prek::languages::<impl prek::config::Language>::install::{{closure}}
 0.3%   0.7%  91.4KiB              prek prek::languages::<impl prek::config::Language>::run::{{closure}}::{{closure}}
 0.2%   0.5%  65.2KiB             prek? <prek::cli::Command as clap_builder::derive::Subcommand>::augment_subcommands
 0.2%   0.4%  49.4KiB annotate_snippets annotate_snippets::renderer::render::render
 0.2%   0.4%  48.9KiB              prek prek::run::{{closure}}
 0.2%   0.3%  43.6KiB              prek prek::cli::run::run::run::{{closure}}
 0.2%   0.3%  42.6KiB             prek? <prek::config::_::<impl serde_core::de::Deserialize for prek::config::Config>::deserialize::__Visitor as serde_core::de::Visitor>::visit_map
 0.1%   0.3%  34.2KiB               std core::ptr::drop_in_place<prek::languages::<impl prek::config::Language>::install::{{closure}}>
 0.1%   0.3%  33.4KiB              prek prek::archive::unpack::{{closure}}
 0.1%   0.2%  31.9KiB             prek? <prek::cli::RunOptions as clap_builder::derive::Args>::augment_args
 0.1%   0.2%  29.8KiB     granit_parser granit_parser::scanner::Scanner<T>::fetch_more_tokens
 0.1%   0.2%  28.0KiB        aws_lc_sys aws_lc_0_41_0_edwards25519_scalarmuldouble_alt
 0.1%   0.2%  27.5KiB        aws_lc_sys aws_lc_0_41_0_edwards25519_scalarmuldouble
 0.1%   0.2%  27.3KiB             prek? <prek::config::_::<impl serde_core::de::Deserialize for prek::config::RemoteHook>::deserialize::__Visitor as serde_core::de::Visitor>::visit_map
 0.1%   0.2%  25.9KiB              prek prek::cli::try_repo::try_repo::{{closure}}
 0.1%   0.2%  25.0KiB              prek prek::languages::ruby::installer::RubyInstaller::install::{{closure}}
 0.1%   0.2%  24.7KiB             prek? <prek::config::_::<impl serde_core::de::Deserialize for prek::config::LocalHook>::deserialize::__Visitor as serde_core::de::Visitor>::visit_map
42.0%  86.1%  11.2MiB                   And 24558 smaller methods. Use -n N to show more.
48.8% 100.0%  13.0MiB                   .text section size, the file size is 26.8MiB

[prek-ci-bot]

⚡️ Hyperfine Benchmarks

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

Environment

• OS: Linux 6.17.0-1018-azure
• CPU: 4 cores
• prek version: prek 0.4.5+28 (0290c52 2026-06-27)
• Rust version: rustc 1.96.0 (ac68faa20 2026-05-25)
• 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	2.0	2.6	1.00
prek-head --version	2.2 ± 0.2	2.0	3.1	1.01 ± 0.08

prek list

Command	Mean [ms]	Min [ms]	Max [ms]	Relative
prek-base list	9.0 ± 0.1	8.8	9.5	1.00
prek-head list	9.3 ± 0.4	8.9	12.8	1.03 ± 0.05

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

Command	Mean [ms]	Min [ms]	Max [ms]	Relative
prek-base validate-config .pre-commit-config.yaml	3.0 ± 0.1	2.9	3.1	1.00
prek-head validate-config .pre-commit-config.yaml	3.0 ± 0.1	2.9	3.9	1.01 ± 0.05

prek sample-config

Command	Mean [ms]	Min [ms]	Max [ms]	Relative
prek-base sample-config	2.4 ± 0.1	2.3	2.5	1.00
prek-head sample-config	2.4 ± 0.1	2.3	2.8	1.00 ± 0.04

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	75.5 ± 2.9	71.8	79.5	1.00
prek-head run --all-files	78.7 ± 3.2	73.6	84.9	1.04 ± 0.06

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

Command	Mean [ms]	Min [ms]	Max [ms]	Relative
prek-base run --all-files	74.9 ± 2.4	71.0	80.0	1.00
prek-head run --all-files	75.4 ± 2.7	71.8	79.8	1.01 ± 0.05

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	75.4 ± 2.4	70.5	80.5	1.01 ± 0.06
prek-head run --all-files	75.0 ± 3.6	69.9	91.7	1.00

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	20.4 ± 0.3	19.8	20.9	1.03 ± 0.02
prek-head run trailing-whitespace --all-files	19.9 ± 0.3	19.3	20.5	1.00

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	26.3 ± 1.8	24.1	31.9	1.00
prek-head run end-of-file-fixer --all-files	26.3 ± 1.9	23.7	30.6	1.00 ± 0.10

prek run check-json --all-files

Command	Mean [ms]	Min [ms]	Max [ms]	Relative
prek-base run check-json --all-files	7.6 ± 0.4	7.1	8.6	1.01 ± 0.06
prek-head run check-json --all-files	7.5 ± 0.3	7.2	8.0	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	7.7	1.00
prek-head run check-yaml --all-files	7.3 ± 0.1	7.1	7.6	1.00 ± 0.02

prek run check-toml --all-files

Command	Mean [ms]	Min [ms]	Max [ms]	Relative
prek-base run check-toml --all-files	7.4 ± 0.2	6.9	7.8	1.00 ± 0.04
prek-head run check-toml --all-files	7.3 ± 0.2	6.9	7.8	1.00

prek run check-xml --all-files

Command	Mean [ms]	Min [ms]	Max [ms]	Relative
prek-base run check-xml --all-files	7.5 ± 0.3	7.1	8.1	1.01 ± 0.06
prek-head run check-xml --all-files	7.4 ± 0.4	7.0	8.8	1.00

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 ± 1.2	11.7	15.6	1.00
prek-head run detect-private-key --all-files	13.7 ± 1.2	11.9	16.8	1.01 ± 0.13

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	17.8 ± 0.9	16.5	20.0	1.00
prek-head run fix-byte-order-marker --all-files	17.8 ± 0.8	16.7	20.0	1.00 ± 0.06

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	4.4 ± 0.1	4.3	4.4	1.00 ± 0.02

prek install-hooks (warm - with cache)

Command	Mean [ms]	Min [ms]	Max [ms]	Relative
prek-base install-hooks	4.4 ± 0.1	4.3	4.6	1.00
prek-head install-hooks	4.4 ± 0.0	4.4	4.5	1.01 ± 0.03

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	37.8 ± 1.1	36.2	40.4	1.01 ± 0.04
prek-head run	37.6 ± 0.8	36.2	39.1	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	7.6	8.0	1.00 ± 0.01
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	1.00
prek-head run --dry-run --all-files	6.7 ± 0.1	6.5	6.9	1.01 ± 0.03

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	11.7 ± 0.1	11.5	12.0	1.00
prek-head run check-hooks-apply --all-files	11.7 ± 0.1	11.6	11.9	1.00 ± 0.02

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

Command	Mean [ms]	Min [ms]	Max [ms]	Relative
prek-base run check-useless-excludes --all-files	11.9 ± 0.5	11.6	13.5	1.09 ± 0.13
prek-head run check-useless-excludes --all-files	10.9 ± 1.3	10.3	15.2	1.00

prek run identity --all-files

Command	Mean [ms]	Min [ms]	Max [ms]	Relative
prek-base run identity --all-files	9.6 ± 0.1	9.5	9.9	1.00
prek-head run identity --all-files	9.7 ± 0.1	9.5	9.9	1.00 ± 0.02

[j178]

Thank you, a very good improvement!