Update dependencies and pre-commit

[CasperWA]

Updating dependencies according to @dependabot PRs.
Update setup.py accordingly.

Also, run pre-commit autoupdate to update the versions of the pre-commit tasks and subsequenctly run pre-commit for all files, resulting in the updated black version removing some white space in function doc-strings, which in turn updated the descriptions in the OpenAPI JSON.

I also took the liberty to fix some doc-string Returns:, removing the written type, making sure it was instead defined in the function definition using ... -> return_type:.

[codecov]

Codecov Report

Merging #477 into master will not change coverage.
The diff coverage is 100.00%.

@@           Coverage Diff           @@
##           master     #477   +/-   ##
=======================================
  Coverage   91.65%   91.65%           
=======================================
  Files          60       60           
  Lines        2828     2828           
=======================================
  Hits         2592     2592           
  Misses        236      236           

Flag	Coverage Δ
#unittests	91.65% <100.00%> (ø)

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

Impacted Files	Coverage Δ
optimade/adapters/structures/aiida.py	100.00% <ø> (ø)
optimade/adapters/structures/ase.py	100.00% <ø> (ø)
optimade/adapters/structures/cif.py	100.00% <ø> (ø)
optimade/adapters/structures/jarvis.py	100.00% <ø> (ø)
optimade/adapters/structures/proteindatabank.py	100.00% <ø> (ø)
optimade/adapters/structures/pymatgen.py	100.00% <ø> (ø)
optimade/filtertransformers/elasticsearch.py	87.82% <ø> (ø)
optimade/filtertransformers/mongo.py	97.15% <ø> (ø)
optimade/models/optimade_json.py	96.51% <ø> (ø)
optimade/models/references.py	97.67% <ø> (ø)
... and 9 more

---

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[ml-evs]

Thanks for this @CasperWA, I tidied up a few docstrings on the way through my review too. I like the new features in black, it sounds like they're getting close to stable release now.

I notice that we still don't validate properly according to swagger (see recent issue on the spec repo)...

https://validator.swagger.io/validator/debug?url=https://raw.githubusercontent.com/Materials-Consortia/optimade-python-tools/a6926f53263fcabc91523e974c4d4b5bbe5bc9f1/openapi/openapi.json

[CasperWA]

I notice that we still don't validate properly according to swagger (see recent issue on the spec repo)...

https://validator.swagger.io/validator/debug?url=https://raw.githubusercontent.com/Materials-Consortia/optimade-python-tools/a6926f53263fcabc91523e974c4d4b5bbe5bc9f1/openapi/openapi.json

Hmm. Yeah that is a bit weird still. I am not completely sure about what to do about it?

[CasperWA]

I notice that we still don't validate properly according to swagger (see recent issue on the spec repo)...
https://validator.swagger.io/validator/debug?url=https://raw.githubusercontent.com/Materials-Consortia/optimade-python-tools/a6926f53263fcabc91523e974c4d4b5bbe5bc9f1/openapi/openapi.json

Hmm. Yeah that is a bit weird still. I am not completely sure about what to do about it?

Okay, I think I may have found the issue here.
According to the OpenAPI specification the items property of a Schema Object MUST be an object. But for dimension_types, it's an array.

Furthermore, I found that type is not listed as "required" for a StructureResource. Also, the constant value of "structures" is not provided in the specification. We could force this through the pattern property, e.g.? I even think this should be contributed upstream to FastAPI.

Edit: The issue is also mentioned in pydantic's documentation here (see in the table for Tuple).

[ml-evs]

I notice that we still don't validate properly according to swagger (see recent issue on the spec repo)...
https://validator.swagger.io/validator/debug?url=https://raw.githubusercontent.com/Materials-Consortia/optimade-python-tools/a6926f53263fcabc91523e974c4d4b5bbe5bc9f1/openapi/openapi.json

Hmm. Yeah that is a bit weird still. I am not completely sure about what to do about it?

Okay, I think I may have found the issue here.
According to the OpenAPI specification the items property of a Schema Object MUST be an object. But for dimension_types, it's an array.

Furthermore, I found that type is not listed as "required" for a StructureResource. Also, the constant value of "structures" is not provided in the specification. We could force this through the pattern property, e.g.? I even think this should be contributed upstream to FastAPI.

Edit: The issue is also mentioned in pydantic's documentation here (see in the table for Tuple).

Ah nice one, I got nowhere when I was trying to figure this out. Do you want to add a comment over at the spec issue and we can work on fixing it? I'm happy to raise the issue for the changes we need to make, unless you want to do so (will do it in 10 mins if I don't see one from you)

[ml-evs]

Found one more docstring tweak, but will accept here. Either force merge as an admin after committing it, or ping me to re-review and I can do it asap.

[ml-evs]

Thanks @CasperWA!