refactor(tooling): complete shared maintenance adoption - #265
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- Route setup, managed execution, dependency updates, release metadata, and documentation and fixture checks through pinned research-repo-tools. - Declare managed Cargo and security tools centrally and reuse shared setup in hosted CI while preserving uncached release benchmark jobs. - Remove duplicate maintenance helpers and their dedicated tests, retaining scientific scripts, benchmark evidence, and consumer policy adapters. - Add shared OSV and Gitleaks recipes, upgrade PyJWT with crypto support, and narrowly allow a historical compatibility identifier false positive. - Document the current shared setup contract and deliberate update policies. Closes #254
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Included review availability: This review used your included allowance. 2 included reviews remain after this review. Your included PR review attempts over the past 7 days set your current allowance at 3 reviews per hour. 📝 WalkthroughWalkthroughThe repository adopts shared tooling for development setup and maintenance commands. GitHub workflows and Just recipes use shared tooling, local maintenance scripts are removed, and security scan commands, integration tests, and documentation are updated. ChangesShared tooling and workflow setup
Maintenance and security
Documentation
Priority: ➖ Normal Estimated code review effort: 4 (Complex) | ~60 minutes Change: Refactor Sequence Diagram(s)sequenceDiagram
participant Workflow
participant SetupTools
participant ResearchRepoTools
participant ManagedPaths
Workflow->>SetupTools: Invoke declared-tool setup
SetupTools->>ResearchRepoTools: Run locked setup with managed tools home
ResearchRepoTools->>ManagedPaths: Install declared tools
SetupTools->>ResearchRepoTools: Export and verify managed paths
ResearchRepoTools->>ManagedPaths: Provide verified paths
Merge Risk: ⚪ Minimal · up to The workflow preserves scan failures while preventing empty or malformed reports from being uploaded. No actionable merge-blocking risk was found in the selected change; required hosted checks should still pass before merging. 🚥 Pre-merge checks | ✅ 4✅ Passed checks (4 passed)
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Review comments at @.github/workflows/zizmor.yml:
- Around line 38-43: Update the “Run declared zizmor with SARIF output” step to
preserve zizmor’s exit status while preventing an empty or truncated SARIF file
from being uploaded. Check the output after the scan, remove it if it is empty,
then exit with the captured scan status so findings still fail the step.
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tests/semgrep/.github/workflows/release-cache-policy.ymlis excluded by!tests/semgrep/**tests/semgrep/.github/workflows/zizmor_policy.ymlis excluded by!tests/semgrep/**uv.lockis excluded by!**/*.lock
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.github/actions/prepare-release-benchmarks/action.yml.github/actions/setup-just/action.yml.github/actions/setup-tools/action.yml.github/workflows/benchmarks.yml.github/workflows/ci.yml.github/workflows/codecov.yml.github/workflows/rust-clippy.yml.github/workflows/semgrep-sarif.yml.github/workflows/zizmor.yml.gitleaks.tomlCONTRIBUTING.mdREADME.mdSECURITY.mddocs/BENCHMARKING.mddocs/RELEASING.mddocs/code_organization.mdjustfilepyproject.tomlrust-toolchain.tomlscripts/README.mdscripts/check_docs_version_sync.pyscripts/check_markdown_lines.pyscripts/check_semgrep_fixtures.pyscripts/tests/test_cargo_update_integration.pyscripts/tests/test_changelog_integration.pyscripts/tests/test_check_docs_version_sync.pyscripts/tests/test_check_markdown_lines.pyscripts/tests/test_check_semgrep_fixtures.pyscripts/tests/test_justfile_discoverability.pyscripts/tests/test_maintenance_integration.pyscripts/tests/test_release_baseline.pyscripts/tests/test_review_integration.pyscripts/tests/test_security_integration.pyscripts/tests/test_toolchain_integration.pyscripts/tests/test_update_cargo_tool_pins.pyscripts/tests/test_update_python_dev_pins.pyscripts/tests/test_update_release_version.pyscripts/update_cargo_tool_pins.pyscripts/update_python_dev_pins.pyscripts/update_release_version.pysemgrep.yaml
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- scripts/tests/test_check_semgrep_fixtures.py
- scripts/tests/test_check_docs_version_sync.py
- scripts/tests/test_check_markdown_lines.py
- scripts/tests/test_update_cargo_tool_pins.py
- scripts/check_semgrep_fixtures.py
- scripts/check_markdown_lines.py
- .github/actions/setup-just/action.yml
- scripts/tests/test_update_release_version.py
- scripts/update_release_version.py
- scripts/update_cargo_tool_pins.py
- scripts/tests/test_update_python_dev_pins.py
- scripts/update_python_dev_pins.py
- scripts/check_docs_version_sync.py
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Codecov Report✅ All modified and coverable lines are covered by tests. Additional details and impacted files@@ Coverage Diff @@
## main #265 +/- ##
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Coverage 98.00% 98.00%
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Files 13 13
Lines 6726 6726
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Hits 6592 6592
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- Preserve the scanner exit status while checking its report before upload. - Remove empty or malformed SARIF output so failed scans cannot publish an unusable report; retain valid reports containing findings. Refs #254
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Complete the remaining maintenance migration to the locked PyPI release
research-repo-tools==0.1.7. The repository now owns declarations, configuration, thin recipes, and consumer integration checks; the shared package owns common maintenance implementation.Changes
pyproject.toml; keep the couplednum-bigint/num-rationalrequirement exclusions and the exact shared-package constraint.pyjwt[crypto]>=2.15.1,<3and locking 2.15.1. Limit the Gitleaks exception to the exact historical identifier assignment in its owning file.Issue #254 acceptance
This completes the remaining adoption after the merged changelog and review integrations. Consumer checks exercise the published package, actual Just recipes, managed tool inventory, native Cargo updates against a disposable local registry, and native uv resolution/synchronization against offline wheels. They cover direct commands, aliases, aggregate ordering, failures, tool/dependency isolation, included groups, and compatibility exclusions.
The issue's generated
bootstrap.sh/bootstrap.ps1andtoolchain bootstrapwording is superseded by the published 0.1.7 contract: setup starts with an existing uv and usesresearch-repo-tools setup.CONTRIBUTING.mddocuments that contract explicitly. Normal setup and CI resolve the shared package from PyPI without a sibling checkout or editable shared-package install.Local macOS validation is complete. The required Ubuntu, macOS, and Windows hosted matrix must pass before merging.
Validation
just checkand finaljust cipassed, including 552 Python tests, 893 runnable Rust tests, default/exact doctests, benchmark compilation, and repository static checks.just coverage-ci, Markdown/TOML formatting and checks, and spelling checks passed.just security-secretspassed. After the PyJWT update, OSV reports no Python findings;just securitystill exits 1 for the existingRUSTSEC-2024-0436unmaintainedpastedependency inCargo.lock. That documented advisory remains visible and unsuppressed.Closes #254
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