Align stage defaulting behavior with pre-commit by j178 · Pull Request #1788 · j178/prek

j178 · 2026-03-13T12:57:24Z

I noticed this difference in behavior while looking into #1785.

This change fixes stage defaulting to match pre-commit, especially around explicit empty stage lists.

The key edge case is default_stages: []:

in pre-commit, omitted default_stages means all stages
explicit default_stages: [] means no stages.

Before:

explicit empty stage configuration could be treated like the default-all case
omitted and explicitly empty values were not distinguished correctly in effective behavior

After:

omitted default_stages still behaves as all stages
explicit default_stages: [] now stays empty

This change fixes stage defaulting to match pre-commit, especially around explicit empty stage lists. The key edge case is `default_stages: []`: in pre-commit, omitted `default_stages` means all stages explicit `default_stages: []` means no stages. Before: explicit empty stage configuration could be treated like the default-all case omitted and explicitly empty values were not distinguished correctly in effective behavior After: omitted `default_stages` still behaves as all stages explicit `default_stages: []` now stays empty

codecov · 2026-03-13T12:59:49Z

Codecov Report

❌ Patch coverage is 96.35036% with 5 lines in your changes missing coverage. Please review.
✅ Project coverage is 91.69%. Comparing base (91a82cb) to head (b2c8960).
⚠️ Report is 1 commits behind head on master.

Files with missing lines	Patch %	Lines
crates/prek/src/hook.rs	96.55%	4 Missing ⚠️
crates/prek/src/config.rs	95.23%	1 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##           master    #1788      +/-   ##
==========================================
+ Coverage   91.66%   91.69%   +0.02%     
==========================================
  Files          98       98              
  Lines       19878    20005     +127     
==========================================
+ Hits        18222    18344     +122     
- Misses       1656     1661       +5

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Copilot

Pull request overview

This PR adjusts how stages / default_stages are defaulted so prek can distinguish between an omitted default_stages (treat as “all stages”) vs an explicitly empty default_stages: [] (treat as “no stages”), matching upstream pre-commit semantics.

Changes:

Change stage defaulting logic to preserve default_stages: [] as an explicit empty stage set.
Update Stages parsing and formatting so stages: [] deserializes to an empty set (instead of “all”).
Add tests covering omitted vs explicitly empty stage lists.

Reviewed changes

Copilot reviewed 2 out of 2 changed files in this pull request and generated 1 comment.

File	Description
`crates/prek/src/hook.rs`	Updates hook-stage defaulting during hook build and adds regression tests for default stage behavior.
`crates/prek/src/config.rs`	Changes `Stages` semantics so empty stage lists deserialize as empty and updates related tests/output formatting.

crates/prek/src/hook.rs

prek-ci-bot · 2026-03-13T13:04:19Z

📦 Cargo Bloat Comparison

Binary size change: +0.00% (24.7 MiB → 24.7 MiB)

Expand for cargo-bloat output

Head Branch Results

 File  .text     Size             Crate Name
 1.3%   2.7% 332.0KiB        aws_lc_sys aws_lc_0_38_0_aes_gcm_encrypt_avx512
 1.3%   2.7% 332.0KiB        aws_lc_sys aws_lc_0_38_0_aes_gcm_decrypt_avx512
 0.3%   0.6%  77.0KiB              prek prek::languages::<impl prek::config::Language>::run::{{closure}}::{{closure}}
 0.3%   0.6%  69.8KiB              prek prek::languages::<impl prek::config::Language>::run::{{closure}}::{{closure}}
 0.3%   0.6%  68.3KiB             prek? <prek::cli::Command as clap_builder::derive::Subcommand>::augment_subcommands
 0.2%   0.4%  51.0KiB annotate_snippets annotate_snippets::renderer::render::render
 0.2%   0.4%  50.6KiB              prek prek::languages::<impl prek::config::Language>::install::{{closure}}
 0.2%   0.4%  46.8KiB              prek prek::run::{{closure}}
 0.2%   0.3%  41.9KiB              prek prek::cli::run::run::run::{{closure}}
 0.1%   0.3%  32.0KiB             prek? <prek::cli::RunArgs as clap_builder::derive::Args>::augment_args
 0.1%   0.2%  28.0KiB        aws_lc_sys aws_lc_0_38_0_edwards25519_scalarmuldouble_alt
 0.1%   0.2%  27.8KiB      serde_saphyr saphyr_parser_bw::scanner::Scanner<T>::fetch_more_tokens
 0.1%   0.2%  27.5KiB        aws_lc_sys aws_lc_0_38_0_edwards25519_scalarmuldouble
 0.1%   0.2%  25.8KiB              prek prek::cli::try_repo::try_repo::{{closure}}
 0.1%   0.2%  24.9KiB             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%  23.0KiB              prek prek::hooks::meta_hooks::MetaHooks::run::{{closure}}
 0.1%   0.2%  22.4KiB      serde_saphyr saphyr_parser_bw::scanner::Scanner<T>::fetch_more_tokens
 0.1%   0.2%  22.3KiB         [Unknown] Lp384_montjscalarmul_alt_p384_montjadd
 0.1%   0.2%  22.0KiB               std core::ptr::drop_in_place<prek::languages::<impl prek::config::Language>::install::{{closure}}>
 0.1%   0.2%  21.6KiB              prek prek::workspace::Project::init_hooks::{{closure}}
41.1%  85.9%  10.2MiB                   And 23277 smaller methods. Use -n N to show more.
47.8% 100.0%  11.8MiB                   .text section size, the file size is 24.7MiB

Base Branch Results

 File  .text     Size             Crate Name
 1.3%   2.7% 332.0KiB        aws_lc_sys aws_lc_0_38_0_aes_gcm_encrypt_avx512
 1.3%   2.7% 332.0KiB        aws_lc_sys aws_lc_0_38_0_aes_gcm_decrypt_avx512
 0.3%   0.6%  77.0KiB              prek prek::languages::<impl prek::config::Language>::run::{{closure}}::{{closure}}
 0.3%   0.6%  69.8KiB              prek prek::languages::<impl prek::config::Language>::run::{{closure}}::{{closure}}
 0.3%   0.6%  68.0KiB             prek? <prek::cli::Command as clap_builder::derive::Subcommand>::augment_subcommands
 0.2%   0.4%  51.0KiB annotate_snippets annotate_snippets::renderer::render::render
 0.2%   0.4%  50.6KiB              prek prek::languages::<impl prek::config::Language>::install::{{closure}}
 0.2%   0.4%  46.8KiB              prek prek::run::{{closure}}
 0.2%   0.3%  41.8KiB              prek prek::cli::run::run::run::{{closure}}
 0.1%   0.3%  32.0KiB             prek? <prek::cli::RunArgs as clap_builder::derive::Args>::augment_args
 0.1%   0.2%  28.0KiB        aws_lc_sys aws_lc_0_38_0_edwards25519_scalarmuldouble_alt
 0.1%   0.2%  27.8KiB      serde_saphyr saphyr_parser_bw::scanner::Scanner<T>::fetch_more_tokens
 0.1%   0.2%  27.5KiB        aws_lc_sys aws_lc_0_38_0_edwards25519_scalarmuldouble
 0.1%   0.2%  25.8KiB              prek prek::cli::try_repo::try_repo::{{closure}}
 0.1%   0.2%  24.9KiB             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%  23.0KiB              prek prek::hooks::meta_hooks::MetaHooks::run::{{closure}}
 0.1%   0.2%  22.4KiB      serde_saphyr saphyr_parser_bw::scanner::Scanner<T>::fetch_more_tokens
 0.1%   0.2%  22.3KiB         [Unknown] Lp384_montjscalarmul_alt_p384_montjadd
 0.1%   0.2%  22.0KiB               std core::ptr::drop_in_place<prek::languages::<impl prek::config::Language>::install::{{closure}}>
 0.1%   0.2%  21.6KiB              prek prek::workspace::Project::init_hooks::{{closure}}
41.1%  86.0%  10.2MiB                   And 23261 smaller methods. Use -n N to show more.
47.8% 100.0%  11.8MiB                   .text section size, the file size is 24.7MiB

prek-ci-bot · 2026-03-13T13:04:20Z

⚡️ Hyperfine Benchmarks

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

Environment

OS: Linux 6.14.0-1017-azure
CPU: 4 cores
prek version: prek 0.3.5+15 (6790580 2026-03-13)
Rust version: rustc 1.94.0 (4a4ef493e 2026-03-02)
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`	2.4 ± 0.1	2.2	2.7	1.01 ± 0.05
`prek-head --version`	2.3 ± 0.0	2.3	2.5	1.00

`prek list`

Command	Mean [ms]	Min [ms]	Max [ms]	Relative
`prek-base list`	8.9 ± 0.1	8.6	9.4	1.00 ± 0.02
`prek-head list`	8.8 ± 0.1	8.6	9.2	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	3.2	1.01 ± 0.02
`prek-head validate-config .pre-commit-config.yaml`	3.1 ± 0.0	3.0	3.2	1.00

`prek sample-config`

Command	Mean [ms]	Min [ms]	Max [ms]	Relative
`prek-base sample-config`	2.6 ± 0.0	2.5	2.7	1.00
`prek-head sample-config`	2.6 ± 0.0	2.5	2.7	1.00 ± 0.02

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`	150.7 ± 2.2	146.7	153.9	1.00
`prek-head run --all-files`	151.0 ± 2.4	148.0	156.4	1.00 ± 0.02

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

Command	Mean [ms]	Min [ms]	Max [ms]	Relative
`prek-base run --all-files`	150.7 ± 2.1	148.1	155.1	1.00 ± 0.02
`prek-head run --all-files`	150.3 ± 2.4	146.6	155.0	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`	149.6 ± 1.9	144.3	155.2	1.00
`prek-head run --all-files`	153.2 ± 20.1	145.7	291.8	1.02 ± 0.14

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`	21.9 ± 0.8	20.7	23.7	1.01 ± 0.04
`prek-head run trailing-whitespace --all-files`	21.7 ± 0.4	20.8	22.5	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`	28.0 ± 1.5	25.4	30.8	1.00
`prek-head run end-of-file-fixer --all-files`	28.2 ± 1.7	25.2	31.9	1.01 ± 0.08

`prek run check-json --all-files`

Command	Mean [ms]	Min [ms]	Max [ms]	Relative
`prek-base run check-json --all-files`	12.8 ± 0.5	11.9	13.7	1.03 ± 0.05
`prek-head run check-json --all-files`	12.4 ± 0.4	11.8	13.7	1.00

`prek run check-yaml --all-files`

Command	Mean [ms]	Min [ms]	Max [ms]	Relative
`prek-base run check-yaml --all-files`	12.0 ± 0.2	11.6	12.4	1.00 ± 0.03
`prek-head run check-yaml --all-files`	11.9 ± 0.2	11.6	12.9	1.00

`prek run check-toml --all-files`

Command	Mean [ms]	Min [ms]	Max [ms]	Relative
`prek-base run check-toml --all-files`	12.2 ± 0.3	11.7	13.2	1.00
`prek-head run check-toml --all-files`	12.2 ± 0.4	11.5	13.3	1.00 ± 0.05

`prek run check-xml --all-files`

Command	Mean [ms]	Min [ms]	Max [ms]	Relative
`prek-base run check-xml --all-files`	12.0 ± 0.4	11.6	13.0	1.01 ± 0.04
`prek-head run check-xml --all-files`	12.0 ± 0.3	11.3	12.6	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`	4.9 ± 0.0	4.9	4.9	1.00 ± 0.02
`prek-head install-hooks`	4.9 ± 0.1	4.8	5.1	1.00

`prek install-hooks (warm - with cache)`

Command	Mean [ms]	Min [ms]	Max [ms]	Relative
`prek-base install-hooks`	4.8 ± 0.1	4.8	4.9	1.00 ± 0.02
`prek-head install-hooks`	4.8 ± 0.1	4.7	5.0	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`	18.7 ± 0.2	18.4	19.1	1.00
`prek-head run`	18.8 ± 0.3	18.5	19.7	1.01 ± 0.02

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

Command	Mean [ms]	Min [ms]	Max [ms]	Relative
`prek-base run --files '*.json'`	7.5 ± 0.1	7.3	7.6	1.00 ± 0.02
`prek-head run --files '*.json'`	7.4 ± 0.1	7.3	7.6	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`	12.4 ± 0.2	12.3	13.1	1.00
`prek-head run --dry-run --all-files`	12.5 ± 0.5	12.0	14.3	1.00 ± 0.04

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`	13.8 ± 1.0	12.6	15.3	1.10 ± 0.08
`prek-head run check-hooks-apply --all-files`	12.6 ± 0.1	12.4	12.8	1.00

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

Command	Mean [ms]	Min [ms]	Max [ms]	Relative
`prek-base run check-useless-excludes --all-files`	12.8 ± 0.3	12.4	13.7	1.01 ± 0.03
`prek-head run check-useless-excludes --all-files`	12.6 ± 0.1	12.4	12.8	1.00

`prek run identity --all-files`

Command	Mean [ms]	Min [ms]	Max [ms]	Relative
`prek-base run identity --all-files`	11.3 ± 0.2	11.0	11.6	1.01 ± 0.02
`prek-head run identity --all-files`	11.1 ± 0.1	11.0	11.3	1.00

j178 added the bug Something isn't working label Mar 13, 2026

Copilot AI review requested due to automatic review settings March 13, 2026 12:57

Copilot started reviewing on behalf of j178 March 13, 2026 12:58 View session

Copilot AI reviewed Mar 13, 2026

View reviewed changes

crates/prek/src/hook.rs Show resolved Hide resolved

j178 merged commit 6e90f64 into master Mar 13, 2026
55 checks passed

j178 deleted the empty-stages branch March 13, 2026 13:08

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Pull request overview

Reviewed changes

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prek-ci-bot bot commented Mar 13, 2026

📦 Cargo Bloat Comparison

Head Branch Results

Base Branch Results

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prek-ci-bot bot commented Mar 13, 2026

⚡️ Hyperfine Benchmarks

prek --version

prek list

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

prek sample-config

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

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

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

prek run trailing-whitespace --all-files

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

prek run check-json --all-files

prek run check-yaml --all-files

prek run check-toml --all-files

prek run check-xml --all-files

prek install-hooks (cold - no cache)

prek install-hooks (warm - with cache)

prek run (staged files only)

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

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

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

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

prek run identity --all-files

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j178 commented Mar 13, 2026 •

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`prek --version`

`prek list`

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

`prek sample-config`

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

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

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

`prek run trailing-whitespace --all-files`

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

`prek run check-json --all-files`

`prek run check-yaml --all-files`

`prek run check-toml --all-files`

`prek run check-xml --all-files`

`prek install-hooks (cold - no cache)`

`prek install-hooks (warm - with cache)`

`prek run (staged files only)`

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

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

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

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

`prek run identity --all-files`