Skip to content

SECURITY-36 3.10.10#477

Merged
bio-boris merged 36 commits into
developfrom
SECURITY-36-2
Aug 6, 2024
Merged

SECURITY-36 3.10.10#477
bio-boris merged 36 commits into
developfrom
SECURITY-36-2

Conversation

@bio-boris

@bio-boris bio-boris commented Jul 25, 2024

Copy link
Copy Markdown
Collaborator

Description of PR purpose/changes

  • Update clients to work with mongo7 by updating pymongo and mongoengine
  • Fix linting issues from flake8 and black
  • Update outdated libraries that can no longer be pip installed
  • The latest Dockerfile build contains conda which installs python 3.12.4 so these changes will pin python to 3.10 and save us headache in the future
  • Speed up tests by moving docker build step out
  • Create matrix of tests to run against mongo3.6 and mongo7

@bio-boris bio-boris changed the base branch from SECURITY-36 to develop July 25, 2024 22:03
@bio-boris bio-boris changed the title 3.10.10 SECURITY-36 3.10.10 Jul 26, 2024
@bio-boris bio-boris marked this pull request as ready for review August 2, 2024 20:35
Comment thread docker-compose.yml Outdated

mongodb:
image: mongo:3.2
image: mongo:7.0

Copy link
Copy Markdown
Contributor

Choose a reason for hiding this comment

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

We only test against mongo3 in this PR.

Copy link
Copy Markdown
Collaborator Author

Choose a reason for hiding this comment

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

I thought we agreed to add tests against both in the next PR?

Copy link
Copy Markdown
Contributor

Choose a reason for hiding this comment

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

👍

Comment thread requirements.txt
mongoengine==0.28.2
psutil==5.8.0
pymongo==3.12.0
pymongo==4.8.0

Copy link
Copy Markdown
Contributor

Choose a reason for hiding this comment

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

revert back pymongo version

Copy link
Copy Markdown
Contributor

Choose a reason for hiding this comment

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

👍

* Update ee2-tests.yml to matrix

---------

Co-authored-by: Boris <bio-boris@github.com>
@codecov

codecov Bot commented Aug 6, 2024

Copy link
Copy Markdown

Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 88.68%. Comparing base (1307bce) to head (db1acc5).
Report is 303 commits behind head on develop.

Additional details and impacted files
@@             Coverage Diff             @@
##           develop     #477      +/-   ##
===========================================
+ Coverage    83.84%   88.68%   +4.84%     
===========================================
  Files           22       29       +7     
  Lines         1993     2740     +747     
===========================================
+ Hits          1671     2430     +759     
+ Misses         322      310      -12     

☔ View full report in Codecov by Sentry.
📢 Have feedback on the report? Share it here.

@bio-boris bio-boris requested a review from Xiangs18 August 6, 2024 16:23
@Xiangs18

Xiangs18 commented Aug 6, 2024

Copy link
Copy Markdown
Contributor

@bio-boris Both Kafka and ZooKeeper containers exit after starting them with Docker Compose. Is this expected?

@bio-boris

Copy link
Copy Markdown
Collaborator Author

@Xiangs18 Kafka seems to stay up when I try it, but zookeeper crashes. It looks like the tests still pass (But throw warnings in the logs when they are removed the docker-compose file as per #485 )

@Xiangs18

Xiangs18 commented Aug 6, 2024

Copy link
Copy Markdown
Contributor
Screenshot 2024-08-06 at 1 02 47 PM

@bio-boris

Copy link
Copy Markdown
Collaborator Author

We discussed this oob

  • We deployed this to CI
  • Ran a job
  • Checked job logs
  • Checked the job browser

And things are working

@Xiangs18 Xiangs18 left a comment

Copy link
Copy Markdown
Contributor

Choose a reason for hiding this comment

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

LGTM

@bio-boris bio-boris merged commit d5d79b0 into develop Aug 6, 2024
@bio-boris bio-boris deleted the SECURITY-36-2 branch August 6, 2024 21:15
bio-boris added a commit that referenced this pull request Aug 7, 2024
* Update RELEASE_NOTES.md

* add dependabot.yml && fix .pre-commit-config.yaml file (#478)

* add dependabot
* fix pre-comit config
* black format fix
* flake8 fix

* SECURITY-36 3.10.10 (#477)

* Testing upgrades
* Update mongo version
* Update python to  3.10.10
* Update ee2-tests.yml
* SECURITY-36 Mongo3.6/Mongo7 Matrix (#484)
* Linting
* Bump version and release notes



---------

Co-authored-by: Boris <bio-boris@github.com>

* Bump actions/setup-python from 4 to 5 in /.github/workflows (#481)

Bumps [actions/setup-python](https://github.com/actions/setup-python) from 4 to 5.
- [Release notes](https://github.com/actions/setup-python/releases)
- [Commits](actions/setup-python@v4...v5)

---
updated-dependencies:
- dependency-name: actions/setup-python
  dependency-type: direct:production
  update-type: version-update:semver-major
...

Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>

---------

Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: Sijie Xiang <xiangs18@bu.edu>
Co-authored-by: Boris <bio-boris@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
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