Skip to content

Fix/update packages to address security alert#89

Open
woodsh17 wants to merge 5 commits into
productionfrom
fix/update_package_security_alert
Open

Fix/update packages to address security alert#89
woodsh17 wants to merge 5 commits into
productionfrom
fix/update_package_security_alert

Conversation

@woodsh17

@woodsh17 woodsh17 commented Jun 8, 2026

Copy link
Copy Markdown
Member

📋 PR Checklist

  • This PR is tagged as a draft if it is still under development and not ready for review.

    This avoids auto-triggering the slower tests in the CI and needlessly wasting resources.

  • I have ensured that all my commits follow angular commit message conventions.

    Format: <type>[optional scope]: <subject>
    Example: fix(af3): add missing crop transform to the af3 pipeline

    This affects semantic versioning as follows:

    • fix: patch version increment (0.0.1 → 0.0.2)
    • feat: minor version increment (0.0.1 → 0.1.0)
    • BREAKING CHANGE: major version increment (0.0.1 → 1.0.0)
    • All other types do not affect versioning

    The format ensures readable changelogs through auto-generation from commit messages.

  • I have run make format on the codebase before submitting the PR (this autoformats the code and lints it).

  • I have named the PR in angular PR message format as well (c.f. above), with a sensible tag line that summarizes all the changes in the PR.

    This is useful as the name of the PR is the default name of the commit that will be used if you merge with a squash & merge.
    Format: <type>[optional scope]: <subject>
    Example: fix(af3): add missing crop transform to the af3 pipeline


ℹ️ PR Description

This PR updates packages in pyproject.toml to address security risks

What changes were made and why?

Updated packages are:
urlib3, pillow, idna, requests, filelock, cryptography, tornado, python-dotenv, pygments

How were the changes tested?

I ran the slow and not slow tests locally. I did not run the benchmark tests locally.

Additional Notes

@nscorley nscorley left a comment

Copy link
Copy Markdown
Collaborator

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

Thank you! One small question about torch requirements

Comment thread pyproject.toml Outdated
ml = [
# atomworks-ml dependencies
"torch>=2.2.0",
"torch>=2.8.0",

Copy link
Copy Markdown
Collaborator

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

What is the reason we need this torch bump? It's a pretty important dependency and I know of some projects that were using 2.7

Copy link
Copy Markdown
Member Author

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

This was based on this alert, but we can revert it back to 2.2.0 for now.

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment

Labels

None yet

Projects

None yet

Development

Successfully merging this pull request may close these issues.

2 participants