Drop support for python 3.9

[gmmajal]

Relevant issue: #53

Background info: # any relevant background info for additional context, references to documentations etc.

• The EOL for python v3.9 is Oct 2025. We should look to drop its support and add support for pythonv3.13
• Some other packages like black, ruff and scipy should be updated as well.

Changes introduced: # list changes to the code repo made in this pull request

• Change range of supported python versions in the pyproject.toml file and the *.yaml files found in the .github/workflows/ folder.
• Update python image being used in the Dockerfile.
• Update versions of black, pre-commit, ruff, safety , scipy, pytest and its associated pluggins. In particular for the newer version of ruff it is necessary to add the target-version key. See notes here: https://github.com/astral-sh/ruff/blob/main/BREAKING_CHANGES.md#0110.
• The .pre-commit.yaml has been updated.
• A new poetry.lock file has been added.

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Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 100.00%. Comparing base (1210b8d) to head (f9a4f0d).

Additional details and impacted files

@@            Coverage Diff            @@
##            master       #54   +/-   ##
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  Coverage   100.00%   100.00%           
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  Files           22        22           
  Lines          905       905           
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  Hits           905       905           

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[gmmajal]

More changes introduced:

• The versions of rdflib and pydantic-settings have been bumped.

[gmmajal]

More changes introduced:

• The version and date-released keys have been updated inside the CITATION.cff file.
• The version key has been updated inside the pyproject.toml file.