Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Double the SeqXML parser block size for libexpat 2.6.0 #4683

Merged
merged 2 commits into from
Mar 29, 2024

Conversation

peterjc
Copy link
Member

@peterjc peterjc commented Mar 28, 2024

If this works, it closes #4640 and confirms my hunch that the root cause of the failure under libexpat 2.6.x was CPython issue 115133 due to a CVE security fix.

  • I hereby agree to dual licence this and any previous contributions under both
    the Biopython License Agreement AND the BSD 3-Clause License.

  • I have read the CONTRIBUTING.rst file, have run pre-commit
    locally, and understand that continuous integration checks will be used to
    confirm the Biopython unit tests and style checks pass with these changes.

  • I have added my name to the alphabetical contributors listings in the files
    NEWS.rst and CONTRIB.rst as part of this pull request, am listed
    already, or do not wish to be listed. (This acknowledgement is optional.)

Hopefully this will fix biopython#4640.

If it does, this is due to CPython issue 115133
and is a side effect of a CVE security fix.
@peterjc peterjc merged commit 7e0befc into biopython:master Mar 29, 2024
35 checks passed
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.

two test failures affecting Bio.SeqIO.SeqXmlIO in Debian sid
1 participant