Add the --repo CLI Flag to prek run for repository-level hook selection

[pygarap]

Important

This PR resolves #2513

Adds a repeatable --repo <REPO> option to prek run for selecting hooks by their configured repository.

Supported usage:

prek run --repo local
prek run --repo meta
prek run --repo builtin
prek run --repo OWNER/REPOSITORY
prek run --repo https://github.com/OWNER/REPOSITORY
prek run --repo local --repo meta --repo builtin --repo OWNER/REPOSITORY

[chatgpt-codex-connector]

Codex Review Summary

This comment shows the latest Codex review activity on this pull request.

Review	Status	Commit	Review trigger
📝 Code Review	✅ Completed 2026-08-30T20:08:56.883310Z	fc30f3f	New commits

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[Copilot]

Pull request overview

Note

Copilot was unable to run its full agentic suite in this review.

Adds a --repo CLI option to filter selected hooks by their configured repository, including GitHub URL/shorthand normalization, and ensures non-matching remotes are not fetched/initialized.

Changes:

• Introduce --repo to select hooks by configured repository (supports local/meta/builtin, full URLs, GitHub shorthand).
• Apply repository filters during workspace hook initialization and warn on unmatched --repo selectors.
• Add documentation and tests validating selection behavior and avoiding cloning unreachable remotes.

Reviewed changes

Copilot reviewed 12 out of 12 changed files in this pull request and generated 4 comments.

Show a summary per file

File	Description
docs/workspace.md	Documents repository selection semantics in workspace mode and examples.
docs/usage.md	Adds user-facing --repo usage and explains interactions with other filters.
docs/reference/cli.md	Adds --repo to CLI reference output.
docs/internals.md	Notes that --repo filtering happens before remote dedupe/initialization.
docs/diff.md	Mentions --repo in prek vs pre-commit differences.
crates/prek/tests/workspace.rs	Adds workspace-mode tests covering repo filtering across nested projects.
crates/prek/tests/run.rs	Adds run-mode tests for special repos, filter composition, and unmatched warnings; updates completion snapshot.
crates/prek/src/workspace.rs	Plumbs repo filters into workspace hook init planning and filters repos early.
crates/prek/src/cli/run/selector.rs	Implements RepoFilter with GitHub URL/shorthand canonicalization + unit tests.
crates/prek/src/cli/run/run.rs	Parses --repo, passes filters into init, and reports unused repo selectors.
crates/prek/src/cli/run/mod.rs	Re-exports RepoFilter.
crates/prek/src/cli/mod.rs	Defines the --repo argument and help text.

---

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[prek-ci-bot]

📦 Cargo Bloat Comparison

.text size change: +0.00% (12.6 MiB → 12.6 MiB)

Expand for cargo-bloat output

Head Branch Results

File  .text     Size             Crate Name
0.1%   2.6% 332.0KiB        aws_lc_sys aws_lc_0_44_0_aes_gcm_encrypt_avx512
0.1%   2.6% 332.0KiB        aws_lc_sys aws_lc_0_44_0_aes_gcm_decrypt_avx512
0.0%   0.7%  96.5KiB              prek <prek::cli::Command as clap_builder::derive::Subcommand>::augment_subcommands
0.0%   0.4%  52.1KiB              prek prek::run::{closure#0}
0.0%   0.4%  50.1KiB              prek <<prek::config::hook::HookWire as serde_core::de::Deserialize>::deserialize::__Visitor as serde_core::de::Visitor>::visit_map::<&mut <serde_saphyr::de::deserializer::YamlDeserializer as serde_core::de::Deserializer>::deserialize_map::MA>
0.0%   0.4%  48.7KiB annotate_snippets annotate_snippets::renderer::render::render
0.0%   0.3%  43.9KiB              prek <<prek::config::Config as serde_core::de::Deserialize>::deserialize::__Visitor as serde_core::de::Visitor>::visit_map::<&mut <serde_saphyr::de::deserializer::YamlDeserializer as serde_core::de::Deserializer>::deserialize_map::MA>
0.0%   0.3%  40.2KiB              prek <prek::cli::RunOptions as clap_builder::derive::Args>::augment_args
0.0%   0.3%  38.7KiB              prek prek::cli::run::run::run::{closure#0}
0.0%   0.2%  31.0KiB              prek <prek::languages::rust::rust::Rust as prek::languages::LanguageBackend>::install::{closure#0}
0.0%   0.2%  28.8KiB              prek prek::archive::unpack::<fs_err::tokio::file::File, &std::path::PathBuf>::{closure#0}
0.0%   0.2%  28.7KiB      serde_saphyr <granit_parser::scanner::Scanner<granit_parser::input::str::StrInput>>::fetch_more_tokens
0.0%   0.2%  28.2KiB      serde_saphyr <granit_parser::scanner::Scanner<granit_parser::input::str::StrInput>>::fetch_more_tokens
0.0%   0.2%  28.0KiB        aws_lc_sys aws_lc_0_44_0_edwards25519_scalarmuldouble_alt
0.0%   0.2%  27.5KiB        aws_lc_sys aws_lc_0_44_0_edwards25519_scalarmuldouble
0.0%   0.2%  27.3KiB              toml <toml::de::deserializer::value::ValueDeserializer as serde_core::de::Deserializer>::deserialize_any::<<prek::config::hook::HookWire as serde_core::de::Deserialize>::deserialize::__Visitor>
0.0%   0.2%  27.0KiB              prek prek::archive::unpack::<fs_err::tokio::file::File, &std::path::PathBuf>::{closure#0}
0.0%   0.2%  27.0KiB              prek prek::archive::unpack::<fs_err::tokio::file::File, &std::path::PathBuf>::{closure#0}
0.0%   0.2%  27.0KiB              prek prek::archive::unpack::<fs_err::tokio::file::File, &std::path::PathBuf>::{closure#0}
0.0%   0.2%  27.0KiB              prek prek::archive::unpack::<fs_err::tokio::file::File, &std::path::PathBuf>::{closure#0}
4.2%  86.8%  11.0MiB                   And 20339 smaller methods. Use -n N to show more.
4.9% 100.0%  12.6MiB                   .text section size, the file size is 258.4MiB

Base Branch Results

File  .text     Size             Crate Name
0.1%   2.6% 332.0KiB        aws_lc_sys aws_lc_0_44_0_aes_gcm_encrypt_avx512
0.1%   2.6% 332.0KiB        aws_lc_sys aws_lc_0_44_0_aes_gcm_decrypt_avx512
0.0%   0.7%  96.5KiB              prek <prek::cli::Command as clap_builder::derive::Subcommand>::augment_subcommands
0.0%   0.4%  52.0KiB              prek prek::run::{closure#0}
0.0%   0.4%  50.1KiB              prek <<prek::config::hook::HookWire as serde_core::de::Deserialize>::deserialize::__Visitor as serde_core::de::Visitor>::visit_map::<&mut <serde_saphyr::de::deserializer::YamlDeserializer as serde_core::de::Deserializer>::deserialize_map::MA>
0.0%   0.4%  48.7KiB annotate_snippets annotate_snippets::renderer::render::render
0.0%   0.3%  43.9KiB              prek <<prek::config::Config as serde_core::de::Deserialize>::deserialize::__Visitor as serde_core::de::Visitor>::visit_map::<&mut <serde_saphyr::de::deserializer::YamlDeserializer as serde_core::de::Deserializer>::deserialize_map::MA>
0.0%   0.3%  40.2KiB              prek <prek::cli::RunOptions as clap_builder::derive::Args>::augment_args
0.0%   0.3%  37.6KiB              prek prek::cli::run::run::run::{closure#0}
0.0%   0.2%  31.1KiB              prek <prek::languages::rust::rust::Rust as prek::languages::LanguageBackend>::install::{closure#0}
0.0%   0.2%  28.7KiB      serde_saphyr <granit_parser::scanner::Scanner<granit_parser::input::str::StrInput>>::fetch_more_tokens
0.0%   0.2%  28.6KiB              prek prek::archive::unpack::<fs_err::tokio::file::File, &std::path::PathBuf>::{closure#0}
0.0%   0.2%  28.2KiB      serde_saphyr <granit_parser::scanner::Scanner<granit_parser::input::str::StrInput>>::fetch_more_tokens
0.0%   0.2%  28.0KiB        aws_lc_sys aws_lc_0_44_0_edwards25519_scalarmuldouble_alt
0.0%   0.2%  27.5KiB        aws_lc_sys aws_lc_0_44_0_edwards25519_scalarmuldouble
0.0%   0.2%  27.3KiB              toml <toml::de::deserializer::value::ValueDeserializer as serde_core::de::Deserializer>::deserialize_any::<<prek::config::hook::HookWire as serde_core::de::Deserialize>::deserialize::__Visitor>
0.0%   0.2%  27.1KiB              prek prek::archive::unpack::<fs_err::tokio::file::File, &std::path::PathBuf>::{closure#0}
0.0%   0.2%  27.0KiB              prek prek::archive::unpack::<fs_err::tokio::file::File, &std::path::PathBuf>::{closure#0}
0.0%   0.2%  27.0KiB              prek prek::archive::unpack::<fs_err::tokio::file::File, &std::path::PathBuf>::{closure#0}
0.0%   0.2%  26.9KiB              prek prek::archive::unpack::<fs_err::tokio::file::File, &std::path::PathBuf>::{closure#0}
4.2%  86.8%  11.0MiB                   And 20401 smaller methods. Use -n N to show more.
4.9% 100.0%  12.6MiB                   .text section size, the file size is 258.7MiB

[prek-ci-bot]

⚡️ Hyperfine Benchmarks

Summary: 7 regressions, 4 improvements above the 10% threshold.

Environment

• OS: Linux 6.17.0-1022-azure
• CPU: 4 cores
• prek version: prek 0.5.0+31 (cea03dc 2026-08-30)
• Rust version: rustc 1.98.0 (88d9e12ae 2026-08-18)
• 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	1.6 ± 0.1	1.4	2.0	1.00
prek-head --version	1.6 ± 0.0	1.5	1.7	1.01 ± 0.06

prek list

Command	Mean [ms]	Min [ms]	Max [ms]	Relative
prek-base list	10.7 ± 39.4	5.9	397.3	1.77 ± 6.51
prek-head list	6.1 ± 0.1	5.8	6.6	1.00

✅ Performance improvement for prek list: 43.5400% faster

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

⏭️ Skipped: .pre-commit-config.yaml not found

prek sample-config

Command	Mean [ms]	Min [ms]	Max [ms]	Relative
prek-base sample-config	4.0 ± 10.0	1.8	60.1	1.17 ± 3.69
prek-head sample-config	3.4 ± 6.3	1.7	39.5	1.00

✅ Performance improvement for prek sample-config: 14.6000% faster

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	23.8 ± 1.4	21.1	25.9	1.00
prek-head run --all-files	24.4 ± 1.5	20.9	26.0	1.03 ± 0.09

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

Command	Mean [ms]	Min [ms]	Max [ms]	Relative
prek-base run --all-files	24.2 ± 1.4	21.5	26.8	1.04 ± 0.08
prek-head run --all-files	23.4 ± 1.3	21.3	25.9	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	25.0 ± 15.2	20.7	129.9	1.00
prek-head run --all-files	29.1 ± 38.7	21.3	296.8	1.16 ± 1.70

⚠️ Warning: Performance regression for prek run --all-files (full builtin hook suite): 16.1400% slower

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	7.8 ± 0.4	7.0	8.7	1.02 ± 0.07
prek-head run trailing-whitespace --all-files	7.6 ± 0.3	7.0	8.2	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	6.8 ± 0.3	6.3	7.5	1.00
prek-head run end-of-file-fixer --all-files	15.8 ± 34.8	6.4	174.6	2.32 ± 5.12

⚠️ Warning: Performance regression for prek run end-of-file-fixer --all-files: 132.2400% slower

prek run check-json --all-files

Command	Mean [ms]	Min [ms]	Max [ms]	Relative
prek-base run check-json --all-files	6.2 ± 6.5	4.7	40.7	1.05 ± 1.46
prek-head run check-json --all-files	5.9 ± 5.4	4.7	34.6	1.00

prek run check-yaml --all-files

Command	Mean [ms]	Min [ms]	Max [ms]	Relative
prek-base run check-yaml --all-files	5.1 ± 0.3	4.7	6.3	1.00
prek-head run check-yaml --all-files	5.2 ± 0.7	4.7	7.1	1.02 ± 0.15

prek run check-toml --all-files

Command	Mean [ms]	Min [ms]	Max [ms]	Relative
prek-base run check-toml --all-files	5.0 ± 0.3	4.6	6.0	1.02 ± 0.07
prek-head run check-toml --all-files	4.9 ± 0.2	4.5	5.5	1.00

prek run check-xml --all-files

Command	Mean [ms]	Min [ms]	Max [ms]	Relative
prek-base run check-xml --all-files	4.9 ± 0.5	4.5	7.1	1.00
prek-head run check-xml --all-files	5.3 ± 2.7	4.6	19.5	1.10 ± 0.56

⚠️ Warning: Performance regression for prek run check-xml --all-files: 10.0500% slower

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

Command	Mean [ms]	Min [ms]	Max [ms]	Relative
prek-base run detect-private-key --all-files	9.6 ± 7.7	6.3	38.2	1.37 ± 1.11
prek-head run detect-private-key --all-files	7.0 ± 0.7	6.4	10.0	1.00

✅ Performance improvement for prek run detect-private-key --all-files: 26.9800% faster

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	11.2 ± 8.7	8.1	53.2	1.10 ± 0.95
prek-head run fix-byte-order-marker --all-files	10.1 ± 3.6	8.7	29.3	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	3.1 ± 0.1	3.0	3.2	1.00
prek-head install-hooks	3.1 ± 0.1	3.0	3.2	1.00 ± 0.04

prek install-hooks (warm - with cache)

Command	Mean [ms]	Min [ms]	Max [ms]	Relative
prek-base install-hooks	3.0 ± 0.1	2.9	3.1	1.00
prek-head install-hooks	6.4 ± 7.3	3.1	19.5	2.15 ± 2.46

⚠️ Warning: Performance regression for prek install-hooks (warm - with cache): 114.5000% slower

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	14.8 ± 2.1	14.0	23.6	1.05 ± 0.15
prek-head run	14.2 ± 0.3	13.7	14.7	1.00

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

Command	Mean [ms]	Min [ms]	Max [ms]	Relative
prek-base run --files '*.json'	4.9 ± 6.1	3.4	30.9	1.00
prek-head run --files '*.json'	5.6 ± 9.3	3.3	45.1	1.15 ± 2.40

⚠️ Warning: Performance regression for prek run --files '*.json' (specific file type): 15.0300% slower

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	6.3 ± 6.5	4.3	32.4	1.00
prek-head run --dry-run --all-files	6.8 ± 10.6	4.3	51.7	1.09 ± 2.04

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	5.2 ± 0.1	5.0	5.4	1.00
prek-head run check-hooks-apply --all-files	17.1 ± 42.4	5.3	170.1	3.27 ± 8.08

⚠️ Warning: Performance regression for prek run check-hooks-apply --all-files: 226.5700% slower

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

Command	Mean [ms]	Min [ms]	Max [ms]	Relative
prek-base run check-useless-excludes --all-files	7.0 ± 6.4	5.1	30.2	1.00
prek-head run check-useless-excludes --all-files	21.9 ± 44.0	5.2	146.1	3.11 ± 6.86

⚠️ Warning: Performance regression for prek run check-useless-excludes --all-files: 210.5300% slower

prek run identity --all-files

Command	Mean [ms]	Min [ms]	Max [ms]	Relative
prek-base run identity --all-files	15.9 ± 39.7	4.4	158.5	1.39 ± 4.75
prek-head run identity --all-files	11.4 ± 26.6	4.5	107.6	1.00

✅ Performance improvement for prek run identity --all-files: 28.0700% faster

[Copilot]

🟢 Approval recommended

The implementation is scoped, composes cleanly with existing selection filters, and is backed by targeted unit and snapshot tests plus thorough docs.

Review details

• Files reviewed: 12/12 changed files
• Comments generated: 0 new
• Review effort level: Lite

[pygarap]

@codex review

[codecov]

Codecov Report

❌ Patch coverage is 99.40828% with 1 line in your changes missing coverage. Please review.
✅ Project coverage is 94.09%. Comparing base (d74b1d3) to head (fc30f3f).

Files with missing lines	Patch %	Lines
crates/prek/src/cli/run/selector.rs	99.27%	1 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##           master    #2659      +/-   ##
==========================================
+ Coverage   94.06%   94.09%   +0.02%     
==========================================
  Files         141      141              
  Lines       29831    29994     +163     
==========================================
+ Hits        28060    28222     +162     
- Misses       1771     1772       +1     

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

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[chatgpt-codex-connector]

Codex Review: Didn't find any major issues. Another round soon, please!

Reviewed commit: 0387e8fb80

ℹ️ About Codex in GitHub

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• Comment "@codex review".

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[Copilot]

🟢 Approval recommended

The implementation matches the documented semantics, filters remotes before initialization as intended, and includes targeted test coverage for matching, composition, and warning behavior.

Review details

• Files reviewed: 12/12 changed files
• Comments generated: 0 new
• Review effort level: Lite

[Copilot]

Copilot was unable to review this pull request because the user who requested the review has reached their quota limit.

[chatgpt-codex-connector]

💡 Codex Review

Here are some automated review suggestions for this pull request.

Reviewed commit: 633b5aa0d5

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]

🟢 Approval recommended

The implementation matches the documented behavior, applies filtering early to avoid unnecessary cloning, and includes targeted unit/snapshot test coverage for key cases.

Review details

• Files reviewed: 12/12 changed files
• Comments generated: 0 new
• Review effort level: Lite

[pygarap]

@j178 When you have a chance to review this PR, please let me know if there is anything you would like me to change to help move it forward. Thanks 🙏

[j178]

Thanks. I’d prefer to wait until we get a bit more feedback or support in #2513 before moving forward with the implementation.

[pygarap]

@j178 Of course, that makes sense, thank you for clarifying.

Would you consider adding a label for feature requests, either in Issues or Discussions, that are ready for contributors to pick up and implement in a PR? Thanks 🙏

[j178]

See #2542:

Once a proposal is sufficiently clear, fits prek's direction, and has a realistic implementation path, a linked issue can be created to track the work.