[REF] Upgrade codebase to Pydantic>2

[alyssadai]

• Closes Migrate to Pydantic v2 #180

Changes proposed in this pull request:

• Bump Pydantic to latest version (2.9.2) and upgrade dependencies
• Replace deprecated Pydantic model, field configuration, and validation method names/syntax
  • Add type annotation to all fields as now required
• Refactor generate_context() using more standard methods to accommodate changes to Pydantic internals
• Replace deprecated DataFrame.applymap to suppress deprecation warnings
• Remove Python 3.9 and added 3.11 to the test runner matrix (3.9 is no longer compatible with the dependency updates introduced in this PR using pip-compile)
  • see also Add python version runners for 3.11 and 3.12 planning#23

Checklist

This section is for the PR reviewer

• PR has an interpretable title with a prefix ([ENH], [FIX], [REF], [TST], [CI], [MNT], [INF], [MODEL], [DOC]) (see our Contributing Guidelines for more info)
• PR has a label for the release changelog or skip-release (to be applied by maintainers only)
• PR links to GitHub issue with mention Closes #XXXX
• Tests pass
• Checks pass

For new features:

• Tests have been added

For bug fixes:

• There is at least one test that would fail under the original bug conditions.

[codecov]

Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 98.36%. Comparing base (3156101) to head (0147316).
Report is 7 commits behind head on main.

Additional details and impacted files

@@            Coverage Diff             @@
##             main     #389      +/-   ##
==========================================
- Coverage   98.36%   98.36%   -0.01%     
==========================================
  Files          21       18       -3     
  Lines         980      977       -3     
==========================================
- Hits          964      961       -3     
  Misses         16       16              

☔ View full report in Codecov by Sentry.
📢 Have feedback on the report? Share it here.

---

🚨 Try these New Features:

• Flaky Tests Detection - Detect and resolve failed and flaky tests

[coveralls]

Pull Request Test Coverage Report for Build 11849787896

Details

• 51 of 51 (100.0%) changed or added relevant lines in 6 files are covered.
• No unchanged relevant lines lost coverage.
• Overall coverage decreased (-0.005%) to 98.362%

---

Totals
Change from base Build 11812239829:	-0.005%
Covered Lines:	961
Relevant Lines:	977

---

💛 - Coveralls

[surchs]

Thanks @alyssadai, that's awesome. Very nice that we can finally close this!

Everything looks nice, left some comments, but 🧑‍🍳

[neurobagel-bot]

🚀 PR was released in v0.3.4 🚀