Fix: IT subtests manifest and repository_files fail due to lack of files (#5168)

[nadove-ucsc]

Connected issues: #5168

Checklist

Author

• PR is a draft
• Target branch is develop
• Name of PR branch matches issues/<GitHub handle of author>/<issue#>-<slug>
• PR title references all connected issues
• PR title matches¹ that of a connected issue _{or comment in PR explains why they're different}
• For each connected issue, there is at least one commit whose title references that issue
• PR is connected to all connected issues via ZenHub
• PR description links to connected issues
• Added partial label to PR _{or this PR completely resolves all connected issues}

¹ when the issue title describes a problem, the corresponding PR
title is Fix: followed by the issue title

Author (reindex, API changes)

• Added r tag to commit title _{or this PR does not require reindexing}
• Added reindex label to PR _{or this PR does not require reindexing}
• Added a (compatible changes) or A (incompatible ones) tag to commit title _{or this PR does not modify the Azul service API}
• Added API label to connected issues _{or this PR does not modify the Azul service API}

Author (chains)

• This PR is blocked by previous PR in the chain _{or this PR is not chained to another PR}
• Added base label to the blocking PR _{or this PR is not chained to another PR}
• Added chained label to this PR _{or this PR is not chained to another PR}

Author (upgrading)

• Documented upgrading of deployments in UPGRADING.rst _{or this PR does not require upgrading}
• Added u tag to commit title _{or this PR does not require upgrading}
• Added upgrade label to PR _{or this PR does not require upgrading}

Author (operator tasks)

• Added checklist items for additional operator tasks _{or this PR does not require additional tasks}

Author (hotfixes)

• Added F tag to main commit title _{or this PR does not include permanent fix for a temporary hotfix}
• Reverted the temporary hotfixes for any connected issues _{or the prod branch has no temporary hotfixes for any connected issues}

Author (before every review)

• Rebased PR branch on develop, squashed old fixups
• Ran make requirements_update _{or this PR does not touch requirements*.txt, common.mk, Makefile and Dockerfile}
• Added R tag to commit title _{or this PR does not touch requirements*.txt}
• Added reqs label to PR _{or this PR does not touch requirements*.txt}
• make integration_test passes in personal deployment _{or this PR does not touch functionality that could break the IT}

Peer reviewer (after requesting changes)

Uncheck the Author (before every review) checklists.

Peer reviewer (after approval)

• PR is not a draft
• Ticket is in Review requested column
• Requested review from primary reviewer
• Assigned PR to primary reviewer

Primary reviewer (after requesting changes)

Uncheck the before every review checklists. Update the N reviews label.

Primary reviewer (after approval)

• Actually approved the PR
• Labeled connected issues as demo or no demo
• Commented on connected issues about demo expectations _{or all connected issues are labeled no demo}
• Decided if PR can be labeled no sandbox
• PR title is appropriate as title of merge commit
• N reviews label is accurate
• Moved ticket to Approved column
• Assigned PR to current operator

Operator (before pushing merge the commit)

• Checked reindex label and r commit title tag
• Checked that demo expectations are clear _{or all connected issues are labeled no demo}
• PR has checklist items for upgrading instructions _{or PR is not labeled upgrade}
• Squashed PR branch and rebased onto develop
• Sanity-checked history
• Pushed PR branch to GitHub
• Pushed PR branch to GitLab dev and added sandbox label _{or PR is labeled no sandbox}
• Pushed PR branch to GitLab anvildev _{or PR is labeled no sandbox}
• Build passes in sandbox deployment _{or PR is labeled no sandbox}
• Build passes in anvilbox deployment _{or PR is labeled no sandbox}
• Reviewed build logs for anomalies in sandbox deployment _{or PR is labeled no sandbox}
• Reviewed build logs for anomalies in anvilbox deployment _{or PR is labeled no sandbox}
• Deleted unreferenced indices in sandbox _{or this PR does not remove catalogs or otherwise causes unreferenced indices}
• Deleted unreferenced indices in anvilbox _{or this PR does not remove catalogs or otherwise causes unreferenced indices}
• Started reindex in sandbox _{or this PR does not require reindexing sandbox}
• Started reindex in anvilbox _{or this PR does not require reindexing sandbox}
• Checked for failures in sandbox _{or this PR does not require reindexing sandbox}
• Checked for failures in anvilbox _{or this PR does not require reindexing sandbox}
• Title of merge commit starts with title from this PR
• Added PR reference to merge commit title
• Added commit title tags to merge commit title
• Moved connected issues to Merged column in ZenHub
• Pushed merge commit to GitHub

Operator (chain shortening)

• Changed the target branch of the blocked PR to develop _{or this PR is not labeled base}
• Removed the chained label from the blocked PR _{or this PR is not labeled base}
• Removed the blocking relationship from the blocked PR _{or this PR is not labeled base}
• Removed the base label from this PR _{or this PR is not labeled base}

Operator (after pushing the merge commit)

• Pushed merge commit to GitLab dev _{or PR is labeled no sandbox}
• Pushed merge commit to GitLab anvildev _{or PR is labeled no sandbox}
• Pushed merge commit to GitLab anvilprod _{or PR is labeled no sandbox}
• Build passes on GitLab dev¹
• Reviewed build logs for anomalies on GitLab dev¹
• Build passes on GitLab anvildev¹
• Reviewed build logs for anomalies on GitLab anvildev¹
• Build passes on GitLab anvilprod¹
• Reviewed build logs for anomalies on GitLab anvilprod¹
• Deleted PR branch from GitHub
• Deleted PR branch from GitLab dev
• Deleted PR branch from GitLab anvildev
• Deleted PR branch from GitLab anvilprod

¹ When pushing the merge commit is skipped due to the PR being
labelled no sandbox, the next build triggered by a PR whose merge commit is
pushed determines this checklist item.

Operator (reindex)

• Deleted unreferenced indices in dev _{or this PR does not remove catalogs or otherwise causes unreferenced indices}
• Deleted unreferenced indices in anvildev _{or this PR does not remove catalogs or otherwise causes unreferenced indices}
• Deleted unreferenced indices in anvilprod _{or this PR does not remove catalogs or otherwise causes unreferenced indices}
• Started reindex in dev _{or this PR does not require reindexing}
• Started reindex in anvildev _{or this PR does not require reindexing}
• Started reindex in anvilprod _{or this PR does not require reindexing}
• Checked for and triaged indexing failures in dev _{or this PR does not require reindexing}
• Checked for and triaged indexing failures in anvildev _{or this PR does not require reindexing}
• Checked for and triaged indexing failures in anvilprod _{or this PR does not require reindexing}
• Emptied fail queues in dev deployment _{or this PR does not require reindexing}
• Emptied fail queues in anvildev deployment _{or this PR does not require reindexing}
• Emptied fail queues in anvilprod deployment _{or this PR does not require reindexing}

Operator

• Unassigned PR

Shorthand for review comments

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

[codecov]

Codecov Report

Merging #5331 (3291ac8) into develop (1da02a1) will increase coverage by 0.01%.
The diff coverage is 0.00%.

❗ Current head 3291ac8 differs from pull request most recent head 9f9ad61. Consider uploading reports for the commit 9f9ad61 to get more accurate results

@@             Coverage Diff             @@
##           develop    #5331      +/-   ##
===========================================
+ Coverage    83.85%   83.86%   +0.01%     
===========================================
  Files          152      152              
  Lines        18533    18536       +3     
===========================================
+ Hits         15541    15546       +5     
+ Misses        2992     2990       -2     

Impacted Files	Coverage Δ
src/azul/terra.py	60.00% <ø> (ø)
test/integration_test.py	0.00% <0.00%> (ø)

... and 20 files with indirect coverage changes

[coveralls]

coverage: 83.877%. remained the same when pulling 9f9ad61 on issues/nadove-ucsc/5168-it-subtests-fail-lack-files into 1da02a1 on develop.

[dsotirho-ucsc]

Approved.

[dsotirho-ucsc]

Ready for approval once merge conflicts have been resolved.

[dsotirho-ucsc]

Approved.