Modernize all Python 3.8 annotations

[ml-evs]

This PR is complementary to #1745. I will first investigate how easy it is to merge the two...

• Add pyupgrade --py39-plus as a pre-commit hook and run it
• Use 3.9 as base version of CI/pre-commit to avoid any compatibility issues between tools

[ml-evs]

I have to dash, @CasperWA once the tests pass here I will merge and then force update the big migration PR... I have kept a backup at ml-evs/backup-pydantic-v2-orig that we can always go back to, but otherwise I will review the rebased version next week. Thanks again for your help!

[codecov]

Codecov Report

Merging #1815 (ef611f8) into master (cf45488) will decrease coverage by 0.10%.
The diff coverage is 99.07%.

@@            Coverage Diff             @@
##           master    #1815      +/-   ##
==========================================
- Coverage   90.77%   90.68%   -0.10%     
==========================================
  Files          74       74              
  Lines        4629     4616      -13     
==========================================
- Hits         4202     4186      -16     
- Misses        427      430       +3     

Flag	Coverage Δ
project	90.68% <99.07%> (-0.10%)	⬇️
validator	90.57% <99.07%> (-0.10%)	⬇️

Flags with carried forward coverage won't be shown. Click here to find out more.

Files	Coverage Δ
optimade/adapters/base.py	96.96% <100.00%> (ø)
optimade/adapters/references/adapter.py	100.00% <100.00%> (ø)
optimade/adapters/structures/adapter.py	100.00% <100.00%> (ø)
optimade/adapters/structures/aiida.py	100.00% <100.00%> (ø)
optimade/adapters/structures/ase.py	98.61% <100.00%> (-0.02%)	⬇️
optimade/adapters/structures/cif.py	84.09% <100.00%> (-0.36%)	⬇️
optimade/adapters/structures/proteindatabank.py	89.28% <100.00%> (-0.13%)	⬇️
optimade/adapters/structures/pymatgen.py	98.50% <100.00%> (ø)
optimade/adapters/structures/utils.py	80.88% <100.00%> (+0.14%)	⬆️
optimade/client/client.py	81.01% <100.00%> (-0.92%)	⬇️
... and 34 more

[JPBergsma]

I think there are still many more locations where we still import the type definitions.
for example: entry_collections/mongo.py
optimade/client/client.py

Should these also be changed?

[ml-evs]

I think there are still many more locations where we still import the type definitions. for example: entry_collections/mongo.py optimade/client/client.py

Should these also be changed?

Do you mean Union, Optional etc? These are still required for Python 3.9 (but not for 3.10). I think the pyupgrade hook dealt with everything we can get away with for now.

[JPBergsma]

Looks like there was an issue with caching. After a reboot, I no longer get any hits when I search for "Tuple".