feat(install): warn about hooks that won't run with the installed shims

[BitWeaverDev]

Closes #2056

What

prek install only installs shims for the hook types you ask for — --hook-type, or default_install_hook_types, falling back to pre-commit. If the config has hooks pinned to a different stage (the classic case being a slower stages: [pre-push] hook), those hooks just silently never run after a plain prek install, and it's easy not to notice.

This adds a warning at install time that names the hooks whose stages aren't covered and points at the fix:

warning: The following hooks won't run automatically because their stages aren't being installed:
  - `push-only` (pre-push)
hint: install the missing hook type(s) with `prek install --hook-type <type>`, or set `default_install_hook_types` in your config.

Notes on the approach

• Config only, no hook init. Each hook's stages are resolved straight from config (stages → default_stages → all), so install stays offline and fast. The trade-off is that a remote hook narrowed only by its manifest (not by the project config) won't be flagged — that's the conservative choice: no false positives, no new network I/O, and it covers the case from the issue.
• manual is skipped, since manual-only hooks have no Git shim and aren't meant to run automatically.
• Pulled the hook-stage resolution into Stages::resolve so install and HookSpec::apply_project_defaults share one implementation instead of duplicating the fallback rules.
• No behaviour change to anything that runs — it's purely an extra warning.

Tests

Added integration coverage in tests/install.rs: an unmatched hook warns (while an all-stages sibling does not), installing the matching --hook-type silences it, manual-only never warns, and default_stages inheritance is taken into account.

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[codecov]

Codecov Report

❌ Patch coverage is 94.39252% with 6 lines in your changes missing coverage. Please review.
✅ Project coverage is 93.14%. Comparing base (cccc61b) to head (8a8de51).

Files with missing lines	Patch %	Lines
crates/prek/src/cli/install.rs	94.18%	5 Missing ⚠️
crates/prek/src/config.rs	94.73%	1 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##           master    #2205      +/-   ##
==========================================
- Coverage   93.16%   93.14%   -0.03%     
==========================================
  Files         127      127              
  Lines       28182    28280      +98     
==========================================
+ Hits        26257    26342      +85     
- Misses       1925     1938      +13     

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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
 0.4%   0.7%  97.8KiB              prek prek::languages::<impl prek::config::Language>::run::{{closure}}::{{closure}}
 0.3%   0.7%  93.7KiB              prek prek::languages::<impl prek::config::Language>::run::{{closure}}::{{closure}}
 0.3%   0.7%  92.1KiB              prek prek::languages::<impl prek::config::Language>::install::{{closure}}
 0.2%   0.5%  66.7KiB             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%  49.2KiB             prek? <prek::config::_::<impl serde_core::de::Deserialize for prek::config::Config>::deserialize::__Visitor as serde_core::de::Visitor>::visit_map
 0.2%   0.4%  49.0KiB              prek prek::run::{{closure}}
 0.2%   0.3%  42.5KiB              prek prek::cli::run::run::run::{{closure}}
 0.1%   0.3%  34.4KiB               std core::ptr::drop_in_place<prek::languages::<impl prek::config::Language>::install::{{closure}}>
 0.1%   0.2%  32.9KiB              prek prek::archive::unpack::{{closure}}
 0.1%   0.2%  32.1KiB             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%  27.2KiB             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%  24.7KiB              prek prek::cli::try_repo::try_repo::{{closure}}
 0.1%   0.2%  24.7KiB              prek prek::languages::ruby::installer::RubyInstaller::install::{{closure}}
 0.1%   0.2%  24.0KiB             prek? <prek::config::_::<impl serde_core::de::Deserialize for prek::config::LocalHook>::deserialize::__Visitor as serde_core::de::Visitor>::visit_map
42.1%  86.2%  11.3MiB                   And 24573 smaller methods. Use -n N to show more.
48.9% 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
 0.4%   0.7%  97.8KiB              prek prek::languages::<impl prek::config::Language>::run::{{closure}}::{{closure}}
 0.3%   0.7%  93.7KiB              prek prek::languages::<impl prek::config::Language>::run::{{closure}}::{{closure}}
 0.3%   0.7%  92.1KiB              prek prek::languages::<impl prek::config::Language>::install::{{closure}}
 0.2%   0.5%  66.4KiB             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::config::_::<impl serde_core::de::Deserialize for prek::config::Config>::deserialize::__Visitor as serde_core::de::Visitor>::visit_map
 0.2%   0.4%  47.7KiB              prek prek::run::{{closure}}
 0.2%   0.3%  43.0KiB              prek prek::cli::run::run::run::{{closure}}
 0.1%   0.3%  34.4KiB               std core::ptr::drop_in_place<prek::languages::<impl prek::config::Language>::install::{{closure}}>
 0.1%   0.2%  32.8KiB              prek prek::archive::unpack::{{closure}}
 0.1%   0.2%  32.1KiB             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%  27.7KiB             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%  24.7KiB              prek prek::cli::try_repo::try_repo::{{closure}}
 0.1%   0.2%  24.7KiB              prek prek::languages::ruby::installer::RubyInstaller::install::{{closure}}
 0.1%   0.2%  24.1KiB             prek? <prek::config::_::<impl serde_core::de::Deserialize for prek::config::LocalHook>::deserialize::__Visitor as serde_core::de::Visitor>::visit_map
42.1%  86.1%  11.3MiB                   And 24573 smaller methods. Use -n N to show more.
48.9% 100.0%  13.1MiB                   .text section size, the file size is 26.8MiB

[prek-ci-bot]

⚡️ Hyperfine Benchmarks

Summary: 3 regressions, 2 improvements above the 10% threshold.

Environment

• OS: Linux 6.17.0-1018-azure
• CPU: 4 cores
• prek version: prek 0.4.8+6 (7054e74 2026-07-05)
• Rust version: rustc 1.96.1 (31fca3adb 2026-06-26)
• 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	2.0 ± 0.1	1.8	2.3	1.03 ± 0.05
prek-head --version	1.9 ± 0.1	1.8	2.1	1.00

prek list

Command	Mean [ms]	Min [ms]	Max [ms]	Relative
prek-base list	9.5 ± 8.3	7.7	83.2	1.15 ± 1.02
prek-head list	8.3 ± 0.7	7.8	14.5	1.00

✅ Performance improvement for prek list: 13.3900% faster

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

Command	Mean [ms]	Min [ms]	Max [ms]	Relative
prek-base validate-config .pre-commit-config.yaml	2.9 ± 0.1	2.8	3.0	1.00
prek-head validate-config .pre-commit-config.yaml	3.2 ± 1.3	2.7	11.3	1.11 ± 0.44

⚠️ Warning: Performance regression for prek validate-config .pre-commit-config.yaml: 11.0500% slower

prek sample-config

Command	Mean [ms]	Min [ms]	Max [ms]	Relative
prek-base sample-config	2.2 ± 0.1	2.1	3.1	1.00 ± 0.07
prek-head sample-config	2.2 ± 0.1	2.1	2.7	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	61.1 ± 2.4	56.5	64.5	1.01 ± 0.05
prek-head run --all-files	60.5 ± 1.5	58.1	62.6	1.00

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

Command	Mean [ms]	Min [ms]	Max [ms]	Relative
prek-base run --all-files	62.9 ± 4.9	58.1	76.6	1.04 ± 0.09
prek-head run --all-files	60.3 ± 2.3	56.9	64.4	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	60.7 ± 2.3	56.9	65.7	1.00
prek-head run --all-files	61.1 ± 2.2	56.5	66.2	1.01 ± 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	17.5 ± 2.0	16.4	27.9	1.04 ± 0.12
prek-head run trailing-whitespace --all-files	16.8 ± 0.4	16.0	17.5	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	22.3 ± 1.5	20.1	24.9	1.00
prek-head run end-of-file-fixer --all-files	22.8 ± 1.9	20.4	27.0	1.02 ± 0.11

prek run check-json --all-files

Command	Mean [ms]	Min [ms]	Max [ms]	Relative
prek-base run check-json --all-files	7.2 ± 0.3	6.7	8.0	1.04 ± 0.05
prek-head run check-json --all-files	6.9 ± 0.2	6.4	7.4	1.00

prek run check-yaml --all-files

Command	Mean [ms]	Min [ms]	Max [ms]	Relative
prek-base run check-yaml --all-files	6.8 ± 0.4	6.5	8.5	1.00
prek-head run check-yaml --all-files	6.8 ± 0.2	6.6	7.5	1.00 ± 0.06

prek run check-toml --all-files

Command	Mean [ms]	Min [ms]	Max [ms]	Relative
prek-base run check-toml --all-files	7.1 ± 0.3	6.6	7.9	1.00
prek-head run check-toml --all-files	7.1 ± 0.4	6.6	7.8	1.00 ± 0.07

prek run check-xml --all-files

Command	Mean [ms]	Min [ms]	Max [ms]	Relative
prek-base run check-xml --all-files	7.6 ± 1.1	6.8	11.6	1.07 ± 0.17
prek-head run check-xml --all-files	7.1 ± 0.6	6.5	9.0	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	12.1 ± 0.9	10.2	13.8	1.00
prek-head run detect-private-key --all-files	12.2 ± 1.2	10.4	15.8	1.01 ± 0.12

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	15.0 ± 0.5	14.2	16.2	1.00
prek-head run fix-byte-order-marker --all-files	16.2 ± 1.9	15.0	26.0	1.08 ± 0.13

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	4.6	1.03 ± 0.04
prek-head install-hooks	4.3 ± 0.1	4.2	4.4	1.00

prek install-hooks (warm - with cache)

Command	Mean [ms]	Min [ms]	Max [ms]	Relative
prek-base install-hooks	4.3 ± 0.2	4.1	4.6	1.00
prek-head install-hooks	4.3 ± 0.0	4.3	4.4	1.01 ± 0.05

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	37.7 ± 14.9	31.8	88.7	1.01 ± 0.62
prek-head run	37.4 ± 17.5	32.1	111.8	1.00

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

Command	Mean [ms]	Min [ms]	Max [ms]	Relative
prek-base run --files '*.json'	13.4 ± 17.0	6.9	66.5	1.40 ± 2.28
prek-head run --files '*.json'	9.6 ± 9.7	7.1	50.9	1.00

✅ Performance improvement for prek run --files '*.json' (specific file type): 28.5700% faster

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 ± 0.2	6.2	7.1	1.00
prek-head run --dry-run --all-files	9.4 ± 9.9	6.2	48.1	1.41 ± 1.49

⚠️ Warning: Performance regression for prek run --dry-run --all-files (measures init overhead): 41.0400% slower

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	14.6 ± 11.5	10.0	56.0	1.00
prek-head run check-hooks-apply --all-files	15.1 ± 20.1	9.3	87.8	1.03 ± 1.60

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

Command	Mean [ms]	Min [ms]	Max [ms]	Relative
prek-base run check-useless-excludes --all-files	9.4 ± 0.1	9.2	9.7	1.00 ± 0.02
prek-head run check-useless-excludes --all-files	9.4 ± 0.1	9.2	9.6	1.00

prek run identity --all-files

Command	Mean [ms]	Min [ms]	Max [ms]	Relative
prek-base run identity --all-files	9.3 ± 0.3	8.9	9.8	1.00
prek-head run identity --all-files	11.9 ± 9.3	8.8	45.5	1.28 ± 1.00

⚠️ Warning: Performance regression for prek run identity --all-files: 27.7200% slower

[j178]

Thanks! This is a common source of confusion and has come up a few times before, so I'm open to improving the situation.

That said, I don't think this should be a warning. A warning implies something is wrong and should be fixed, but it is perfectly valid to not install a Git hook and only run a hook manually by its id when that is intended. I think this should be framed more as a tip/reminder instead.

[BitWeaverDev]

That's a fair point, and yeah, framing it as a warning does imply something needs fixing when really it's often on purpose. I went ahead and reworked it: dropped the warning: prefix entirely and now it prints as an informational note on stdout instead of stderr. The wording now reads along the lines of "these hooks are configured for stages that aren't installed, so they'll only run when invoked manually or from CI, not automatically" and explicitly says no action is needed if that's intentional, with the hook type / default_install_hook_types hint still there for anyone who does want it installed. Tests are updated to match. Will push shortly once I rebase onto master.