Add system library dependencies to Fromager SBOM via auditwheel

[ronnll]

Wheels built by Calunga can link against system-provided shared libraries, but this information was missing from the SBOM shipped inside each wheel. This adds a new add-system-deps-to-sbom script that runs auditwheel show on each manylinux wheel after repair, parses the system library references and their versioned symbols, and injects them as SPDX Package entries with DEPENDS_ON relationships in the Fromager SBOM.

Assisted-by: Claude Opus 4.6 noreply@anthropic.com

Summary by Sourcery

Augment Fromager-generated SBOMs for manylinux wheels with system library dependency information derived from auditwheel output.

New Features:

• Add a script to extract system shared library dependencies via auditwheel and inject them as SPDX packages with DEPENDS_ON relationships into the Fromager SBOM for each repaired manylinux wheel.

Tests:

• Add a test script to validate that system dependency information is correctly added to the SBOM for built wheels.

[sourcery-ai]

Reviewer's guide (collapsed on small PRs)

Reviewer's Guide

Adds a post-repair step that inspects manylinux wheels with auditwheel to discover system-provided shared library dependencies and injects them into the Fromager SBOM as SPDX Packages with DEPENDS_ON relationships.

File-Level Changes

Change	Details	Files
Introduce a script to scan manylinux wheels with auditwheel and augment the Fromager SBOM with system library dependencies and their versioned symbols.	Add add-system-deps-to-sbom script that runs auditwheel show on each repaired manylinux wheel. Parse auditwheel output to extract linked system libraries and their versioned symbols. Emit corresponding SPDX Package entries and DEPENDS_ON relationships into the existing Fromager SBOM embedded in the wheel.	builder/scripts/add-system-deps-to-sbom
Wire the new SBOM augmentation step into the wheel build pipeline so it executes after auditwheel repair.	Update build-wheels script to invoke add-system-deps-to-sbom after repairing manylinux wheels. Ensure the step only runs for relevant wheel types and integrates with existing Fromager SBOM generation.	builder/scripts/build-wheels
Add tests for the system dependency SBOM enrichment logic.	Introduce test-add-system-deps script to cover parsing of auditwheel show output. Verify that expected SPDX Package entries and DEPENDS_ON relationships are produced for representative system library dependencies.	builder/scripts/test-add-system-deps

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[sourcery-ai]

Hey - I've found 1 security issue, and left some high level feedback:

Security issues:

• Detected subprocess function 'run' without a static string. If this data can be controlled by a malicious actor, it may be an instance of command injection. Audit the use of this call to ensure it is not controllable by an external resource. You may consider using 'shlex.escape()'. (link)

General comments:

• Consider hardening the auditwheel output parsing logic (e.g., handling unexpected formats, missing sections, or future auditwheel changes) so that failures degrade gracefully without breaking the wheel build or corrupting the SBOM.
• It may be worth ensuring the new add-system-deps-to-sbom step is idempotent (e.g., not duplicating SPDX Package/DEPENDS_ON entries when re-run) to avoid subtle SBOM growth or inconsistencies in incremental or retried builds.
• Since this script relies on auditwheel and manylinux-specific behavior, consider isolating any platform- or tool-specific assumptions behind small helper functions so future changes (e.g., non-manylinux targets or different tools) are easier to support.

Prompt for AI Agents

Please address the comments from this code review:

## Overall Comments
- Consider hardening the auditwheel output parsing logic (e.g., handling unexpected formats, missing sections, or future auditwheel changes) so that failures degrade gracefully without breaking the wheel build or corrupting the SBOM.
- It may be worth ensuring the new add-system-deps-to-sbom step is idempotent (e.g., not duplicating SPDX Package/DEPENDS_ON entries when re-run) to avoid subtle SBOM growth or inconsistencies in incremental or retried builds.
- Since this script relies on auditwheel and manylinux-specific behavior, consider isolating any platform- or tool-specific assumptions behind small helper functions so future changes (e.g., non-manylinux targets or different tools) are easier to support.

## Individual Comments

### Comment 1
<location path="builder/scripts/test-add-system-deps" line_range="276-277" />
<code_context>
        r = subprocess.run([sys.executable, str(SCRIPT_DIR / "add-system-deps-to-sbom"), str(whl)],
                           capture_output=True, text=True)
</code_context>
<issue_to_address>
**security (python.lang.security.audit.dangerous-subprocess-use-audit):** Detected subprocess function 'run' without a static string. If this data can be controlled by a malicious actor, it may be an instance of command injection. Audit the use of this call to ensure it is not controllable by an external resource. You may consider using 'shlex.escape()'.

*Source: opengrep*
</issue_to_address>

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[ronnll]

@jvulgan PTAL. The script has helper functions which are intentionally kept this way instead of being added to the main function for a more fail safe approach. Also, this was tested locally with the test-add-system-deps, but ill double check by by inspecting a package when merged. Lastly,, this was mostly generated by Claude but I've checked each line to ensure it's accurate. Sorry it's a bit long, but please feel free to ask any questions you have.

[ronnll]

@jvulgan updated, ptal!

[ronnll]

@jvulgan changes made. PTAL!

[jvulgan]

/lgtm