Upgrading packages and removing pip-audit ignores

[lotif]

PR Type

Fix

Short Description

Clickup Ticket(s): NA

Upgrading packages to solve pip-audit issues. Also removing ignores that are no longer relevant and adding an ignore for the torch issue.

https://github.com/VectorInstitute/midst-toolkit/actions/runs/26310000289/job/77456124923?pr=139

Pacakges upgraded:

Updated idna v3.11 -> v3.16
Updated mako v1.3.10 -> v1.3.12
Updated pip v26.0.1 -> v26.1.1
Updated pygments v2.19.2 -> v2.
Updated pymdown-extensions v10.20 -> v10.21.3
Updated urllib3 v2.6.3 -> v2.7.0

Tests Added

NA

[coderabbitai]

📝 Walkthrough

Walkthrough

This PR removes hardcoded CVE exemptions from the pip-audit step in the GitHub Actions code checks workflow. The change eliminates the ignore-vulns configuration that was suppressing CVE-2026-4539 and CVE-2026-3219, allowing these vulnerabilities to be detected in subsequent dependency audits.

Estimated code review effort

🎯 1 (Trivial) | ⏱️ ~3 minutes

🚥 Pre-merge checks | ✅ 5

✅ Passed checks (5 passed)

Check name	Status	Explanation
Title check	✅ Passed	The title clearly and specifically summarizes the main changes: upgrading packages and removing pip-audit ignore directives that are no longer needed.
Docstring Coverage	✅ Passed	No functions found in the changed files to evaluate docstring coverage. Skipping docstring coverage check.
Linked Issues check	✅ Passed	Check skipped because no linked issues were found for this pull request.
Out of Scope Changes check	✅ Passed	Check skipped because no linked issues were found for this pull request.
Description check	✅ Passed	The PR description follows the required template with PR Type, Short Description, and Tests Added sections, though the Short Description contains a typo ('poackages') and the Clickup ticket link is marked as NA.

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✨ Finishing Touches

📝 Generate docstrings

• Create stacked PR
• Commit on current branch

🧪 Generate unit tests (beta)

• Create PR with unit tests
• Commit unit tests in branch marcelo/pip-audit

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