Upgrade Python runtime to 3.8.12 (#3439)

[amarjandu]

#3439

Python 3.8.3 patch is no longer needed after python/cpython#21154 was backported to 3.8.4 and above.

Announcement: "Heads up, you'll need to update to python 3.8.12 when you rebase."

Author

• PR title references issue
• PR title matches issue title (preceded by Fix: for bugs) _{or there is a good reason why they're different}
• Title of main commit references issue
• PR is connected to Zenhub issue and description links to issue

Author (reindex)

• 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}

Author (freebies & chains)

• Freebies are blocked on this PR _{or there are no freebies in this PR}
• Freebies are referenced in commit titles _{or there are no freebies in this PR}
• This PR is blocked by previous PR in the chain _{or this PR is not chained to another PR}
• Added chain label to the blocking 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}
• Added announcement to PR description _{or this PR does not require announcement}

Author (requirements, before every review)

• Ran make requirements_update _{or this PR leaves requirements*.txt, common.mk and Makefile untouched}
• Added R tag to commit title _{or this PR leaves requirements*.txt untouched}
• Added reqs label to PR _{or this PR leaves requirements*.txt untouched}

Author (before every review)

• make integration_test passes in personal deployment _{or this PR does not touch functionality that could break the IT}
• Rebased branch on develop, squashed old fixups

Primary reviewer (after approval)

• Commented in issue about demo expectations _{or labelled issue as no demo}
• Decided if PR can be labeled no sandbox
• PR title is appropriate as title of merge commit
• Moved ticket to Approved column
• Assigned PR to an operator

Operator (before pushing merge the commit)

• Checked reindex label and r commit title tag
• Checked that demo expectations are clear _{or issue is labeled as no demo}
• Rebased and squashed branch
• Sanity-checked history
• Pushed PR branch to Github
• Branch pushed to Gitlab and added sandbox label _{or PR is labeled no sandbox}
• Build passed in sandbox _{or PR is labeled no sandbox}
• Started reindex in sandbox _{or this PR does not require reindexing sandbox}
• Checked for failures in sandbox _{or this PR does not require reindexing sandbox}
• Added PR reference to merge commit title
• Collected commit title tags in merge commit title
• Moved linked issue to Merged column
• Pushed merge commit to Github

Operator (after pushing the merge commit)

• Made announcement requested by author _{or PR description does not contain an announcement}
• Moved freebies to Merged column _{or there are no freebies in this PR}
• Shortened the PR chain _{or this PR is not the base of another PR}
• Verified that N reviews labelling is accurate
• Pushed merge commit to Gitlab _{or this changes can be pushed later, together with another PR}
• Deleted PR branch from Github and Gitlab

Operator (reindex)

• Started reindex in dev _{or this PR does not require reindexing or does not target dev}
• Checked for failures in dev _{or this PR does not require reindexing or does not target dev}
• Started reindex in prod _{or this PR does not require reindexing or does not target prod}
• Checked for failures in prod _{or this PR does not require reindexing or does not target prod}

Operator

• Unassigned PR

[coveralls]

Coverage remained the same at 82.161% when pulling ab910cf on issues/amar/3439-update-python into 6ac7a60 on develop.

[codecov]

Codecov Report

Merging #3478 (ab910cf) into develop (6ac7a60) will not change coverage.
The diff coverage is n/a.

@@           Coverage Diff            @@
##           develop    #3478   +/-   ##
========================================
  Coverage    81.91%   81.91%           
========================================
  Files          123      123           
  Lines        14281    14281           
========================================
  Hits         11698    11698           
  Misses        2583     2583           

---

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[amarjandu]

Self note: 33e6ff798f5afc8f21c042ed4e8cd47b3ec44e06 passes IT, installed 3.8.12 + make req + deploy

[dsotirho-ucsc]

Approved.

[hannes-ucsc]

A few more mentions of 3.8.3 were just introduced:

https://github.com/DataBiosphere/azul/pull/3311/files#diff-b335630551682c19a781afebcf4d07bf978fb1f8ac04c6bf87428ed5106870f5R963

[hannes-ucsc]

Note the commit I just pushed. Since this touches the Dockerfile, it needs to be tagged R and labeled reqs and so on.

[amarjandu]

Self Note: added announcement, Updated commit tags, PR tags, ran make ru, reindex + IT pass

[achave11-ucsc]

Failed sandbox during test job. https://gitlab.dev.singlecell.gi.ucsc.edu/ucsc/azul/-/jobs/31704 It might have been caused by a3af5e6.

[amarjandu]

@hannes-ucsc I pinned tzlocal==4.0.1b1 and added a FIXME to remove the pinned beta when there is a new version released. Here is the related issue regebro/tzlocal#121

[hannes-ucsc]

This should refer to an Azul ticket that reference the tzlocal ticket.

[amarjandu]

4.0.1 was released, no need for a FIXME.

[hannes-ucsc]

Operator (@achave11), don't merge this before the promotion tomorrow. I want to let this stew in dev for a week.

[hannes-ucsc]

I remember that I was on the hook to fix something here but I don't remember what it was. But it looks like you've got this under control, @achave11.