Add hook group filters to prek run

[j178]

Adds hook group tags and --group/--no-group run selection.

Closes #1385

[chatgpt-codex-connector]

💡 Codex Review

Here are some automated review suggestions for this pull request.

Reviewed commit: d98ed8a99a

ℹ️ About Codex in GitHub

Your team has set up Codex to review pull requests in this repo. Reviews are triggered when you

• Open a pull request for review
• Mark a draft as ready
• Comment "@codex review".

If Codex has suggestions, it will comment; otherwise it will react with 👍.

Codex can also answer questions or update the PR. Try commenting "@codex address that feedback".

[codecov]

Codecov Report

❌ Patch coverage is 95.91078% with 11 lines in your changes missing coverage. Please review.
✅ Project coverage is 92.51%. Comparing base (9b0047f) to head (a75d22a).

Files with missing lines	Patch %	Lines
crates/prek/src/cli/run/selector.rs	92.04%	7 Missing ⚠️
crates/prek/src/config.rs	90.69%	4 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##           master    #2141      +/-   ##
==========================================
+ Coverage   92.49%   92.51%   +0.02%     
==========================================
  Files         122      122              
  Lines       25813    26016     +203     
==========================================
+ Hits        23877    24070     +193     
- Misses       1936     1946      +10     

☔ View full report in Codecov by Harness.
📢 Have feedback on the report? Share it here.

🚀 New features to boost your workflow:

• ❄️ Test Analytics: Detect flaky tests, report on failures, and find test suite problems.
• 📦 JS Bundle Analysis: Save yourself from yourself by tracking and limiting bundle sizes in JS merges.

[Copilot]

Pull request overview

Adds a new hook-level groups tag and CLI selection via --group/--no-group so users can run subsets of hooks (e.g., CI profiles) without overloading Git hook stages. This extends config parsing, hook construction, selection/filtering, docs, schema, and adds integration coverage to ensure excluded hooks are not installed.

Changes:

• Add groups to hook configuration types and runtime Hook, plus validation and schema/docs updates.
• Add --group / --no-group to prek run and prek try-repo, with group filtering applied before stage filtering and before install.
• Add integration tests and snapshot updates for group selection behavior, manifest-key ignoring, and install avoidance.

Reviewed changes

Copilot reviewed 31 out of 31 changed files in this pull request and generated 3 comments.

Show a summary per file

File	Description
prek.schema.json	Adds groups to hook schemas.
docs/reference/configuration.md	Documents the new groups hook field with examples.
docs/reference/cli.md	Documents --group/--no-group and clarifies stage behavior interaction.
docs/proposals/hook-groups.md	Design proposal/spec for group-based selection semantics.
docs/authoring-hooks.md	Notes groups as config-only (not a manifest field).
crates/prek/tests/validate.rs	Tests manifest warnings/ignoring for config-only keys (groups, priority).
crates/prek/tests/skipped_hooks.rs	Ensures group-excluded installable hooks don’t create environments.
crates/prek/tests/run.rs	Adds end-to-end tests for include/exclude, precedence, unknown groups, and stage intersection.
crates/prek/src/snapshots/prek__config__tests__read_yaml_config.snap	Snapshot updates for groups in parsed config.
crates/prek/src/snapshots/prek__config__tests__read_toml_config.snap	Snapshot updates for groups in parsed config.
crates/prek/src/snapshots/prek__config__tests__read_config_with_nested_merge_keys.snap	Snapshot updates for groups in parsed config.
crates/prek/src/snapshots/prek__config__tests__read_config_with_merge_keys.snap	Snapshot updates for groups in parsed config.
crates/prek/src/snapshots/prek__config__tests__parse_repos.snap	Snapshot updates for groups in parsed config.
crates/prek/src/snapshots/prek__config__tests__parse_repos-6.snap	Snapshot updates for groups in parsed config.
crates/prek/src/snapshots/prek__config__tests__parse_repos-4.snap	Snapshot updates for groups in parsed config.
crates/prek/src/snapshots/prek__config__tests__parse_repos-3.snap	Snapshot updates for groups in parsed config.
crates/prek/src/snapshots/prek__config__tests__parse_hooks-3.snap	Snapshot updates for groups in parsed config.
crates/prek/src/snapshots/prek__config__tests__numeric_rev_is_parsed_as_string.snap	Snapshot updates for groups in parsed config.
crates/prek/src/snapshots/prek__config__tests__meta_hooks-5.snap	Snapshot updates for groups in parsed config.
crates/prek/src/snapshots/prek__config__tests__language_version.snap	Snapshot updates for groups in parsed config.
crates/prek/src/main.rs	Wires CLI args through to the run implementation.
crates/prek/src/hooks/meta_hooks.rs	Initializes meta hooks with groups: None.
crates/prek/src/hooks/builtin_hooks/mod.rs	Initializes builtin hooks with groups: None.
crates/prek/src/hook.rs	Adds groups to hook spec/runtime hook and validates group names.
crates/prek/src/config.rs	Adds groups to hook config structs and override application.
crates/prek/src/cli/try_repo.rs	Passes group filters into the shared run path.
crates/prek/src/cli/run/selector.rs	Implements GroupFilters (include/exclude + unused reporting).
crates/prek/src/cli/run/run.rs	Applies group filtering in hook selection and adjusts stage behavior when group mode is active.
crates/prek/src/cli/run/mod.rs	Re-exports GroupFilters.
crates/prek/src/cli/mod.rs	Adds CLI flags --group/--no-group and documents stage interaction.
crates/prek/src/cli/hook_impl.rs	Ensures hook-impl calls run without any group filters.

[prek-ci-bot]

📦 Cargo Bloat Comparison

Binary size change: +0.38% (26.2 MiB → 26.3 MiB)

Expand for cargo-bloat output

Head Branch Results

 File  .text     Size             Crate Name
 1.2%   2.6% 332.0KiB        aws_lc_sys aws_lc_0_41_0_aes_gcm_encrypt_avx512
 1.2%   2.6% 332.0KiB        aws_lc_sys aws_lc_0_41_0_aes_gcm_decrypt_avx512
 0.3%   0.7%  89.9KiB              prek prek::languages::<impl prek::config::Language>::run::{{closure}}::{{closure}}
 0.3%   0.6%  80.4KiB              prek prek::languages::<impl prek::config::Language>::run::{{closure}}::{{closure}}
 0.3%   0.5%  69.8KiB              prek prek::languages::<impl prek::config::Language>::install::{{closure}}
 0.2%   0.5%  62.1KiB             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%  48.1KiB              prek prek::run::{{closure}}
 0.2%   0.3%  44.1KiB              prek prek::cli::run::run::run::{{closure}}
 0.1%   0.2%  31.9KiB             prek? <prek::cli::RunOptions as clap_builder::derive::Args>::augment_args
 0.1%   0.2%  30.6KiB             prek? <prek::config::_::<impl serde_core::de::Deserialize for prek::config::Config>::deserialize::__Visitor as serde_core::de::Visitor>::visit_map
 0.1%   0.2%  29.6KiB               std core::ptr::drop_in_place<prek::languages::<impl prek::config::Language>::install::{{closure}}>
 0.1%   0.2%  28.1KiB      serde_saphyr 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%  26.9KiB              prek prek::cli::try_repo::try_repo::{{closure}}
 0.1%   0.2%  24.3KiB              prek prek::hooks::meta_hooks::MetaHooks::run::{{closure}}
 0.1%   0.2%  23.0KiB      serde_saphyr granit_parser::scanner::Scanner<T>::fetch_more_tokens
 0.1%   0.2%  22.3KiB         [Unknown] Lp384_montjscalarmul_alt_p384_montjadd
 0.1%   0.2%  21.8KiB     serde_saphyr? <serde_saphyr::de::YamlDeserializer as serde_core::de::Deserializer>::deserialize_map
41.7%  86.4%  11.0MiB                   And 24096 smaller methods. Use -n N to show more.
48.3% 100.0%  12.7MiB                   .text section size, the file size is 26.3MiB

Base Branch Results

 File  .text     Size             Crate Name
 1.2%   2.6% 332.0KiB        aws_lc_sys aws_lc_0_41_0_aes_gcm_encrypt_avx512
 1.2%   2.6% 332.0KiB        aws_lc_sys aws_lc_0_41_0_aes_gcm_decrypt_avx512
 0.3%   0.7%  89.9KiB              prek prek::languages::<impl prek::config::Language>::run::{{closure}}::{{closure}}
 0.3%   0.6%  81.9KiB              prek prek::languages::<impl prek::config::Language>::run::{{closure}}::{{closure}}
 0.3%   0.5%  69.8KiB              prek prek::languages::<impl prek::config::Language>::install::{{closure}}
 0.2%   0.5%  60.7KiB             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%  48.2KiB              prek prek::run::{{closure}}
 0.2%   0.3%  42.0KiB              prek prek::cli::run::run::run::{{closure}}
 0.1%   0.3%  33.3KiB             prek? <prek::cli::RunArgs as clap_builder::derive::Args>::augment_args
 0.1%   0.2%  30.6KiB             prek? <prek::config::_::<impl serde_core::de::Deserialize for prek::config::Config>::deserialize::__Visitor as serde_core::de::Visitor>::visit_map
 0.1%   0.2%  29.6KiB               std core::ptr::drop_in_place<prek::languages::<impl prek::config::Language>::install::{{closure}}>
 0.1%   0.2%  28.1KiB      serde_saphyr 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%  26.2KiB              prek prek::cli::try_repo::try_repo::{{closure}}
 0.1%   0.2%  23.9KiB              prek prek::hooks::meta_hooks::MetaHooks::run::{{closure}}
 0.1%   0.2%  23.0KiB      serde_saphyr granit_parser::scanner::Scanner<T>::fetch_more_tokens
 0.1%   0.2%  22.3KiB         [Unknown] Lp384_montjscalarmul_alt_p384_montjadd
 0.1%   0.2%  21.5KiB      clap_builder clap_builder::parser::parser::Parser::get_matches_with
41.7%  86.3%  10.9MiB                   And 24041 smaller methods. Use -n N to show more.
48.2% 100.0%  12.6MiB                   .text section size, the file size is 26.2MiB

[prek-ci-bot]

⚡️ Hyperfine Benchmarks

Summary: 0 regressions, 3 improvements above the 10% threshold.

Environment

• OS: Linux 6.17.0-1015-azure
• CPU: 4 cores
• prek version: prek 0.4.3+16 (facf9fe 2026-06-04)
• 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	2.1	2.7	1.04 ± 0.08
prek-head --version	2.2 ± 0.1	2.0	3.0	1.00

prek list

Command	Mean [ms]	Min [ms]	Max [ms]	Relative
prek-base list	9.2 ± 0.6	8.8	13.5	1.00
prek-head list	9.7 ± 6.4	8.6	72.4	1.06 ± 0.70

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	3.3	1.07 ± 0.04
prek-head validate-config .pre-commit-config.yaml	2.9 ± 0.1	2.8	3.2	1.00

prek sample-config

Command	Mean [ms]	Min [ms]	Max [ms]	Relative
prek-base sample-config	2.6 ± 0.2	2.4	4.0	1.06 ± 0.11
prek-head sample-config	2.4 ± 0.1	2.3	3.3	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	79.0 ± 3.8	73.4	86.4	1.00
prek-head run --all-files	80.2 ± 4.5	73.5	91.1	1.02 ± 0.08

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

Command	Mean [ms]	Min [ms]	Max [ms]	Relative
prek-base run --all-files	76.8 ± 3.1	72.3	83.1	1.00
prek-head run --all-files	77.3 ± 3.5	73.0	88.3	1.01 ± 0.06

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	78.3 ± 5.9	72.5	113.8	1.00
prek-head run --all-files	78.4 ± 3.1	73.3	84.5	1.00 ± 0.08

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	20.8 ± 0.8	19.9	23.6	1.02 ± 0.05
prek-head run trailing-whitespace --all-files	20.5 ± 0.5	19.8	21.7	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	26.7 ± 2.2	23.7	31.7	1.02 ± 0.12
prek-head run end-of-file-fixer --all-files	26.3 ± 2.3	22.9	31.3	1.00

prek run check-json --all-files

Command	Mean [ms]	Min [ms]	Max [ms]	Relative
prek-base run check-json --all-files	7.8 ± 0.3	7.3	8.8	1.03 ± 0.06
prek-head run check-json --all-files	7.6 ± 0.3	7.1	8.6	1.00

prek run check-yaml --all-files

Command	Mean [ms]	Min [ms]	Max [ms]	Relative
prek-base run check-yaml --all-files	7.4 ± 0.1	7.3	7.8	1.01 ± 0.03
prek-head run check-yaml --all-files	7.4 ± 0.2	7.1	7.7	1.00

prek run check-toml --all-files

Command	Mean [ms]	Min [ms]	Max [ms]	Relative
prek-base run check-toml --all-files	7.7 ± 0.3	7.3	8.5	1.02 ± 0.06
prek-head run check-toml --all-files	7.5 ± 0.3	7.0	8.4	1.00

prek run check-xml --all-files

Command	Mean [ms]	Min [ms]	Max [ms]	Relative
prek-base run check-xml --all-files	7.9 ± 0.6	7.3	10.7	1.02 ± 0.09
prek-head run check-xml --all-files	7.8 ± 0.3	7.3	8.6	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	14.0 ± 1.2	11.9	16.5	1.03 ± 0.12
prek-head run detect-private-key --all-files	13.6 ± 1.1	11.8	15.9	1.00

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	29.0 ± 37.2	19.3	225.5	1.30 ± 1.66
prek-head run fix-byte-order-marker --all-files	22.4 ± 1.7	19.4	25.1	1.00

✅ Performance improvement for prek run fix-byte-order-marker --all-files: 22.8100% faster

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	4.5 ± 0.1	4.4	4.6	1.04 ± 0.03
prek-head install-hooks	4.4 ± 0.1	4.3	4.5	1.00

prek install-hooks (warm - with cache)

Command	Mean [ms]	Min [ms]	Max [ms]	Relative
prek-base install-hooks	4.9 ± 0.7	4.5	6.1	1.12 ± 0.16
prek-head install-hooks	4.4 ± 0.1	4.3	4.5	1.00

✅ Performance improvement for prek install-hooks (warm - with cache): 10.3900% faster

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	37.5 ± 0.9	36.2	38.7	1.00
prek-head run	39.6 ± 7.9	36.4	72.9	1.06 ± 0.21

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

Command	Mean [ms]	Min [ms]	Max [ms]	Relative
prek-base run --files '*.json'	22.0 ± 63.0	7.8	289.6	2.85 ± 8.14
prek-head run --files '*.json'	7.7 ± 0.1	7.6	7.9	1.00

✅ Performance improvement for prek run --files '*.json' (specific file type): 64.9000% 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	6.8 ± 0.0	6.7	6.9	1.03 ± 0.03
prek-head run --dry-run --all-files	6.6 ± 0.2	6.4	7.4	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	11.9 ± 0.1	11.8	12.1	1.00
prek-head run check-hooks-apply --all-files	12.9 ± 3.4	10.3	20.8	1.08 ± 0.28

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

Command	Mean [ms]	Min [ms]	Max [ms]	Relative
prek-base run check-useless-excludes --all-files	10.6 ± 0.1	10.5	10.8	1.02 ± 0.01
prek-head run check-useless-excludes --all-files	10.4 ± 0.1	10.3	10.6	1.00

prek run identity --all-files

Command	Mean [ms]	Min [ms]	Max [ms]	Relative
prek-base run identity --all-files	9.9 ± 0.1	9.7	10.2	1.02 ± 0.02
prek-head run identity --all-files	9.7 ± 0.1	9.5	9.9	1.00

[Copilot]

Pull request overview

Copilot reviewed 31 out of 31 changed files in this pull request and generated 2 comments.

[Copilot]

Pull request overview

Copilot reviewed 31 out of 31 changed files in this pull request and generated 6 comments.

[Copilot]

Pull request overview

Copilot reviewed 31 out of 31 changed files in this pull request and generated 5 comments.

[chatgpt-codex-connector]

💡 Codex Review

Here are some automated review suggestions for this pull request.

Reviewed commit: d71d0c3037

ℹ️ About Codex in GitHub

Your team has set up Codex to review pull requests in this repo. Reviews are triggered when you

• Open a pull request for review
• Mark a draft as ready
• Comment "@codex review".

If Codex has suggestions, it will comment; otherwise it will react with 👍.

Codex can also answer questions or update the PR. Try commenting "@codex address that feedback".

[chatgpt-codex-connector]

💡 Codex Review

Here are some automated review suggestions for this pull request.

Reviewed commit: 825be0824d

ℹ️ About Codex in GitHub

Your team has set up Codex to review pull requests in this repo. Reviews are triggered when you

• Open a pull request for review
• Mark a draft as ready
• Comment "@codex review".

If Codex has suggestions, it will comment; otherwise it will react with 👍.

Codex can also answer questions or update the PR. Try commenting "@codex address that feedback".

[Copilot]

Pull request overview

Copilot reviewed 34 out of 34 changed files in this pull request and generated 3 comments.

[Copilot]

Pull request overview

Copilot reviewed 33 out of 33 changed files in this pull request and generated 2 comments.