Type-check Pandas code and require newer pyarrow.

[thetorpedodog]

• Pandas now has canonical type stubs, which mypy can find and install.
• We no longer support py3.7, so we don't need the pyarrow hotfix.
• Type annotation fix related to installing Pandas stubs.

[johnkerl]

We no longer support py3.7, so we don't need the pyarrow hotfix.

@thetorpedodog this is a longer story -- we don't need the hotfix as long as we've got pyarrow >= 14

But here is the current status on that, which is not done yet:

• [python] Try 3.12 again [WIP] TileDB-SOMA#2692
• [Python] AWS SDK 1.11 support in pyarrow wheels? apache/arrow#42154 (comment)

This is confusing, so to be extra-clear here:

• On MacOS, there is a fatal error unless pyarrow < 13
• We've lived that way for a while
• Trying to have TileDB-SOMA support Python 3.12 ([python] Try 3.12 again [WIP] TileDB-SOMA#2692) -- is blocked since pyarrow < 13 doesn't exist with Python 3.12
• This has also, separately, impacted the attempted TileDB-SOMA 1.12 release tiledbsoma 1.12.0 pre-check TileDB-Inc/tiledbsoma-feedstock#171 but in a way which has been worked around for now.

TL;DR -- we need pyarrow-hotfix for now. And I'll deal with this, once all the above issues are resolved, on single-cell-data/TileDB-SOMA#1926

[johnkerl]

Following on from my review comment: let's keep pyarrow-hotfix and update the reason-why-it-is-needed comment (which has gone stale)

[thetorpedodog]

pyarrow-hotfix has been restored.

[thetorpedodog]

To do this, I (after some trial and error):

1. Removed all the entries from the [[tool.mypy.overrides]] module = [...] setting, so that mypy would no longer ignore any modules
2. Ran update-requirements-txt to rebuild the requirements files.
3. Looked at the mypy output from update-requirements-txt and re-enabled ignoring modules that had no type stubs (and also fixed any issues that arose).