Upgrade software dependencies 2026-05-25 (#8051) by achave11-ucsc · Pull Request #8065 · DataBiosphere/azul

achave11-ucsc · 2026-05-30T05:09:11Z

Linked issue: #8051

Checklist

Author

PR is assigned to the author
Status of PR is In progress
Target branch is develop
Name of PR branch matches upgrades/yyyy-mm-dd
PR is linked to the upgrade issue it resolves
Status of linked issue is In progress
PR description links to linked issue
PR title matches Upgrade software dependencies yyyy-mm-dd
PR title references the linked issue

Author (upgrading deployments)

Ran make docker_images.json and committed the resulting changes _{or this PR does not modify azul_docker_images, or any other variables referenced in the definition of that variable}
Documented upgrading of deployments in UPGRADING.rst _{or this PR does not require upgrading deployments}
Added u tag to commit title _{or this PR does not require upgrading deployments}
This PR is labeled upgrade _{or does not require upgrading deployments}
This PR is labeled deploy:shared _{or does not modify docker_images.json, and does not require deploying the shared component for any other reason}
This PR is labeled deploy:gitlab _{or does not require deploying the gitlab component}
This PR is labeled backup:gitlab
This PR is labeled deploy:runner _{or does not require deploying the runner image}

Author (before every review)

System administrator (after approval)

Actually approved the PR
Labeled linked issue as no demo
A comment to this PR details the completed security design review
PR title is appropriate as title of merge commit
N reviews label is accurate
Status of PR is Approved
PR is assigned to only the operator and the author

Operator

Squashed PR branch and rebased onto develop
Sanity-checked history
Pushed PR branch to GitHub

Operator (deploy `.shared` and `.gitlab` components)

Ran _select dev.shared && CI_COMMIT_REF_NAME=develop make -C terraform/shared apply_keep_unused _{or this PR is not labeled deploy:shared}
Ran _select dev.gitlab && python scripts/create_gitlab_snapshot.py --no-restart (see operator manual for details) _{or this PR is not labeled backup:gitlab}
Ran _select dev.gitlab && CI_COMMIT_REF_NAME=develop make -C terraform/gitlab apply _{or this PR is not labeled deploy:gitlab}
Ran _select anvildev.shared && CI_COMMIT_REF_NAME=develop make -C terraform/shared apply_keep_unused _{or this PR is not labeled deploy:shared}
Ran _select anvildev.gitlab && python scripts/create_gitlab_snapshot.py --no-restart (see operator manual for details) _{or this PR is not labeled backup:gitlab}
Ran _select anvildev.gitlab && CI_COMMIT_REF_NAME=develop make -C terraform/gitlab apply _{or this PR is not labeled deploy:gitlab}
Checked the items in the next section _{or this PR is labeled deploy:gitlab}
PR is assigned to only the system administrator and the author _{or this PR is not labeled deploy:gitlab}

System administrator (post-deploy of `.gitlab` component)

Background migrations for dev.gitlab are complete _{or this PR is not labeled deploy:gitlab}
Background migrations for anvildev.gitlab are complete _{or this PR is not labeled deploy:gitlab}
PR is assigned to only the operator and the author

Operator (deploy runner image)

Ran _select dev.gitlab && make -C terraform/gitlab/runner _{or this PR is not labeled deploy:runner}
Ran _select anvildev.gitlab && make -C terraform/gitlab/runner _{or this PR is not labeled deploy:runner}

Operator (sandbox build)

Added sandbox label
Pushed PR branch to GitLab dev
Pushed PR branch to GitLab anvildev
Build passes in sandbox deployment
Build passes in anvilbox deployment
Reviewed build logs for anomalies in sandbox deployment
Reviewed build logs for anomalies in anvilbox deployment
Applied upgrade instructions from UPGRADING.rst to sandbox _{or this PR is not labeled upgrade, or upgrade instructions do not apply to sandbox}
Applied upgrade instructions from UPGRADING.rst to anvilbox _{or this PR is not labeled upgrade, or upgrade instructions do not apply to anvilbox}

Operator (merge the branch)

All status checks passed and the PR is mergeable
The title of the merge commit starts with the title of this PR
Added PR # reference to merge commit title
Collected commit title tags in merge commit title _{but excluded any p tags}
Closed related Dependabot PRs with a comment referencing the corresponding commit in this PR _{or this PR does not include any such commits}
Pushed merge commit to GitHub
Status of PR is Merged lower
Status of blocked issues is Triage _{or no issues are blocked on the linked issue}

Operator (main build)

Operator

At least 24 hours have passed since anvildev.shared was last deployed
Ran scripts/export_inspector_findings.py against anvildev, imported results to Google Sheet and posted screenshot of relevant¹ findings as a comment on the linked issue.
Propagated the upgrade and API labels to the next promotion PRs _{or this PR carries neither of these labels}
Propagated the deploy:shared, deploy:gitlab, deploy:runner and backup:gitlab labels to the next promotion PRs _{or this PR carries none of these labels}
Propagated any specific instructions related to the deploy:shared, deploy:gitlab, deploy:runner and backup:gitlab labels, from the description of this PR to that of the next promotion PRs _{or this PR carries none of these labels}
PR is assigned to only the system administrator

¹A relevant finding is a high or critical vulnerability in an image
that is used within the security boundary. Images not used within the boundary
are tracked in azul.docker_images under a key starting with _.

System administrator

No currently reported vulnerability requires immediate attention
PR is assigned to no one

Shorthand for review comments

L line is too long
W line wrapping is wrong
Q bad quotes
F other formatting problem

coveralls · 2026-06-01T17:38:51Z

coverage: 84.801%. remained the same — upgrades/2026-05-25 into develop

codecov · 2026-06-01T17:53:41Z

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 84.72%. Comparing base (be75124) to head (658c309).

Additional details and impacted files

@@           Coverage Diff            @@
##           develop    #8065   +/-   ##
========================================
  Coverage    84.72%   84.72%           
========================================
  Files          165      165           
  Lines        24245    24245           
========================================
  Hits         20541    20541           
  Misses        3704     3704

☔ View full report in Codecov by Harness.
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hannes-ucsc · 2026-06-04T16:01:09Z

                result = self._http_client.request(url=request.url,
                                                   method=request.method,
-                                                   headers=request.headers,
+                                                   headers=cast(Mapping[str, str], request.headers),


cast is almost always problematic. The only legitimate use is working around a bug in the type checker. Remove this commit and the dependency upgrade that requires it. File a follow-up issue.

hannes-ucsc · 2026-06-04T16:01:54Z

+            assert request.url is not None
+            assert request.method is not None
+            assert isinstance(request.body, (bytes, type(None)))


Note that we have not_none

achave11-ucsc requested a review from hannes-ucsc as a code owner May 30, 2026 05:09

achave11-ucsc self-assigned this May 30, 2026

achave11-ucsc linked an issue May 30, 2026 that may be closed by this pull request

Upgrade software dependencies 2026-05-25 #8051

Open

52 tasks

achave11-ucsc force-pushed the upgrades/2026-05-25 branch 2 times, most recently from 950f61e to ca064ee Compare June 1, 2026 17:26

achave11-ucsc force-pushed the upgrades/2026-05-25 branch from 01616f1 to eb92be3 Compare June 1, 2026 17:41

achave11-ucsc force-pushed the upgrades/2026-05-25 branch 6 times, most recently from ff514c0 to e5e4afa Compare June 2, 2026 05:07

achave11-ucsc assigned hannes-ucsc and unassigned hannes-ucsc Jun 2, 2026

achave11-ucsc force-pushed the upgrades/2026-05-25 branch from c7e35db to a140adc Compare June 2, 2026 15:53

achave11-ucsc assigned hannes-ucsc Jun 2, 2026

hannes-ucsc requested changes Jun 4, 2026

View reviewed changes

hannes-ucsc removed their assignment Jun 4, 2026

hannes-ucsc added the 1 review [process] Lead requested changes once label Jun 4, 2026

achave11-ucsc force-pushed the upgrades/2026-05-25 branch 3 times, most recently from ce68fba to dbfe779 Compare June 5, 2026 03:26

achave11-ucsc requested a review from hannes-ucsc June 5, 2026 03:41

nadove-ucsc removed their assignment Jun 9, 2026

nadove-ucsc and others added 16 commits June 9, 2026 13:43

Add nadove@ucsc.edu to operators

df2a126

[R] Update direct Python dependencies (#8051)

048a218

Add FIXME (#8083)

079f0b4

[R] Update Terraform to 1.15.5 (#8051)

229fbc7

Update AWS Terraform provider to 6.47.0 (#8051)

2d964de

Update External Terraform provider to 6.47.0 (#8051)

04683fe

Update Google Terraform provider to 7.34.0 (#8051)

f6ca13e

Update Null Terraform provider to 3.3.0 (#8051)

1642618

Update PyCharm to 2025.2.6.1-81 (#8051)

46ccf6a

Update BigQuery Emulator to 0.4.4-64 (#8051)

9a9a903

Update Docker to 29.5.2 (#8051)

9b311eb

Update GitLab to 19.0.1-ce.0 and runner to 19.0.1 (#8051)

f3e16e2

Update AL2023_release to 2023.11.20260526 (#8051)

245f5e0

Update AWS CLI to 2.34.62 (#8051)

ff1c99d

Ran make docker_images.json

67ce263

Fix invalid TF config (#8051)

023f15e

dsotirho-ucsc assigned hannes-ucsc and unassigned dsotirho-ucsc Jun 9, 2026

dsotirho-ucsc added the sandbox [process] Resolution is being verified in sandbox deployment label Jun 10, 2026

[R] Ran make requirements_update

658c309

dsotirho-ucsc force-pushed the upgrades/2026-05-25 branch from 539f900 to 658c309 Compare June 10, 2026 00:15

hannes-ucsc approved these changes Jun 10, 2026

View reviewed changes

dsotirho-ucsc merged commit d896a33 into develop Jun 10, 2026
10 checks passed

dsotirho-ucsc assigned dsotirho-ucsc and unassigned hannes-ucsc Jun 10, 2026

dsotirho-ucsc deleted the upgrades/2026-05-25 branch June 10, 2026 01:52

dsotirho-ucsc assigned hannes-ucsc and unassigned achave11-ucsc and dsotirho-ucsc Jun 10, 2026

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Upgrade software dependencies 2026-05-25 (#8051)#8065

Upgrade software dependencies 2026-05-25 (#8051)#8065
dsotirho-ucsc merged 17 commits into
developfrom
upgrades/2026-05-25

achave11-ucsc commented May 30, 2026 •

edited by dsotirho-ucsc

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Checklist

Author

Author (upgrading deployments)

Author (before every review)

System administrator (after approval)

Operator

Operator (deploy .shared and .gitlab components)

System administrator (post-deploy of .gitlab component)

Operator (deploy runner image)

Operator (sandbox build)

Operator (merge the branch)

Operator (main build)

Operator

System administrator

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achave11-ucsc commented May 30, 2026 •

edited by dsotirho-ucsc

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Operator (deploy `.shared` and `.gitlab` components)

System administrator (post-deploy of `.gitlab` component)

coveralls commented Jun 1, 2026 •

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codecov Bot commented Jun 1, 2026 •

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