Migrate to pydantic v2

[CasperWA]

Description:

Closes #187

Update to use pydantic v2:

• Upgrade dependencies accordingly.
  • oteapi-core >=0.6.0
  • otelib >=0.4.0
• Use new pydantic v2 model methods throughout.
• Use typing.Annotated throughout as this is recommended.
• Upgrade to use Python 3.9+ format typing throughout (this can also be achieved by running pyupgrade --py39-plus.
• Update tests accordingly.
• Ensure all pydantic v2 warnings are taken care of.
• Ensure tests succeed for all environments in the CI.

Type of change:

• Bug fix.
• New feature.
• Documentation update.

Checklist for the reviewer:

This checklist should be used as a help for the reviewer.

• Is the change limited to one issue?
• Does this PR close the issue?
• Is the code easy to read and understand, including clearly named variables?
• Do all new feature have an accompanying new test?
• Has the documentation been updated as necessary?

[codecov-commenter]

Codecov Report

Attention: Patch coverage is 97.59036% with 2 lines in your changes are missing coverage. Please review.

Project coverage is 89.80%. Comparing base (329a873) to head (6dab541).

Files	Patch %	Lines
oteapi_dlite/strategies/parse_excel.py	94.11%	1 Missing ⚠️
oteapi_dlite/strategies/parse_image.py	83.33%	1 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##           master     #192      +/-   ##
==========================================
+ Coverage   88.67%   89.80%   +1.12%     
==========================================
  Files          15       15              
  Lines         459      451       -8     
==========================================
- Hits          407      405       -2     
+ Misses         52       46       -6     

Flag	Coverage Δ
linux	89.80% <97.59%> (+1.12%)	⬆️
windows	89.80% <97.59%> (+1.12%)	⬆️

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[CasperWA]

This is momentarily put on hold/delayed until its impact on current project deliverables depending on this plugin have been determined and cleared.

[CasperWA]

So I've tested this branch with the TEM demo and found that no changes were really necessary, other than ensuring all dependencies support Pydantic v2. In conclusion, I think there is no issue with merging this PR, other than letting any users know that they should ensure they have the following minimum dependencies:

• oteapi-dlite>0.1.6 (i.e., the next version to be released after this PR has been merged)
• oteapi-core>=0.6
• otelib>=0.4

[CasperWA]

@francescalb Gentle reminder that this has been texted externally and poses no apparent issues - other than assuring the latest versions are used for all OTEAPI-related packages after merging and updating the version. And possibly upgrade plugins as otherwise expected to support pydantic v2 if the depend on oteapi-dlite.

[francescalb]

Looks fine.