Fix Secdeps

Audit and fix security vulnerabilities reported by GitHub Dependabot for this repository.

Steps

Fetch all open Dependabot alerts using gh api repos/rhesis-ai/rhesis/dependabot/alerts and group them by package name, showing: package, ecosystem, severity, affected manifests, patched version, and summary.
Classify each vulnerability into one of these categories:
- Direct dependency bump: The vulnerable package is declared in pyproject.toml or package.json and can be upgraded.
- Transitive override: The vulnerable package is a transitive dependency — fix via npm overrides or uv constraint-dependencies.
- Unused dependency: The vulnerable package (or its parent) is no longer used and can be removed. Ask the user to confirm before removing.
- No patch available: No fixed version exists upstream. Flag for monitoring only.
- Major version upgrade: A fix exists but requires a major version bump that may break things. Flag for separate evaluation.
Present a summary table to the user grouped by category, showing the fix approach and risk level for each. Ask the user which groups to proceed with.
Apply fixes in this order:
- Python direct deps: Use uv lock --upgrade-package <pkg> in the affected project directories. If a version pin in pyproject.toml blocks the upgrade, relax the pin (e.g. ==X.Y.Z to >=X.Y.Z) and explain why.
- Remove unused deps: Remove from package.json/pyproject.toml and regenerate lockfiles.
- npm transitive deps: Add or update entries in the overrides section of package.json, then run npm install --package-lock-only to regenerate the lockfile.
- Python transitive deps: Add or update entries in [tool.uv] constraint-dependencies in pyproject.toml, then run uv lock.
Verify each fix:
- For npm: confirm npm install --package-lock-only reports 0 new vulnerabilities (pre-existing unrelated ones are acceptable).
- For Python: confirm the lockfile shows the patched version using grep -A1 'name = "<pkg>"' uv.lock.
Show a final summary of: alerts resolved, alerts remaining (with reason), and all files changed (git diff --stat).

Important rules

Never modify lockfiles by hand — always regenerate them with npm install --package-lock-only or uv lock.
When relaxing a version pin, use >=current_version rather than removing the constraint entirely.
For npm overrides, set the minimum to the exact patched version from the advisory (e.g. >=3.1.3).
Run Python lock commands from the project directory containing the pyproject.toml, not the repo root.
Do not auto-commit. Present the changes and let the user decide.

Steps

Fetch all open Dependabot alerts using gh api repos/rhesis-ai/rhesis/dependabot/alerts and group them by package name, showing: package, ecosystem, severity, affected manifests, patched version, and summary.

Classify each vulnerability into one of these categories:

Direct dependency bump: The vulnerable package is declared in pyproject.toml or package.json and can be upgraded.
Transitive override: The vulnerable package is a transitive dependency — fix via npm overrides or uv constraint-dependencies.
Unused dependency: The vulnerable package (or its parent) is no longer used and can be removed. Ask the user to confirm before removing.
No patch available: No fixed version exists upstream. Flag for monitoring only.
Major version upgrade: A fix exists but requires a major version bump that may break things. Flag for separate evaluation.

Present a summary table to the user grouped by category, showing the fix approach and risk level for each. Ask the user which groups to proceed with.

Apply fixes in this order:

Python direct deps: Use uv lock --upgrade-package <pkg> in the affected project directories. If a version pin in pyproject.toml blocks the upgrade, relax the pin (e.g. ==X.Y.Z to >=X.Y.Z) and explain why.
Remove unused deps: Remove from package.json/pyproject.toml and regenerate lockfiles.
npm transitive deps: Add or update entries in the overrides section of package.json, then run npm install --package-lock-only to regenerate the lockfile.
Python transitive deps: Add or update entries in [tool.uv] constraint-dependencies in pyproject.toml, then run uv lock.

Verify each fix:

For npm: confirm npm install --package-lock-only reports 0 new vulnerabilities (pre-existing unrelated ones are acceptable).
For Python: confirm the lockfile shows the patched version using grep -A1 'name = "<pkg>"' uv.lock.

Show a final summary of: alerts resolved, alerts remaining (with reason), and all files changed (git diff --stat).

Important rules

Never modify lockfiles by hand — always regenerate them with npm install --package-lock-only or uv lock.

When relaxing a version pin, use >=current_version rather than removing the constraint entirely.

For npm overrides, set the minimum to the exact patched version from the advisory (e.g. >=3.1.3).

Run Python lock commands from the project directory containing the pyproject.toml, not the repo root.

Do not auto-commit. Present the changes and let the user decide.

Fix Secdeps

Additional Files (3)

Steps

Important rules

Related Skills

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2. Apply Deepthink Protocol (reason about dependencies

Additional Files (3)

Steps

Important rules