Update and replace packages

[gmmajal]

Relevant issue: #77

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

• We are using pytest v7.4.4. A new major release is available now and we should update the package.
• ruff as a linting package is reported to be faster than flake8 and it provides similar functionality. We should replace flake8 with ruff. More info here: https://docs.astral.sh/ruff/

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

• Bump version of pytest to v8.3.4 inside the pyproject.toml file.
• Replace flake8 with ruff inside the pyproject.toml file and the .github/workflows/ci.yml file.
• Bumped version of sphinx plugin: sphinx-autodoc-typehints to v3 inside the docs/requirements.txt file.
• Updated poetry.lock file.
• As a consequence of the updated poetry.lock file the package rdflib was bumped to patch release v7.1.2. Unfortunately, this release had some unintended changes on the slicing operator in the package. More info here: Graph.__getitem__ runtime type checking for slices breaks working code RDFLib/rdflib#3037. Therefore, the method extract_relation_by_uri inside the script stwfsapy/thesaurus.py was modified slightly to ensure that the unit tests do not break. Instead of g[:uri:], we use g.subject_objects(uri) The modification can be hopefully reverted once the patch release rdflib v7.1.3 is available.

Added later see below for further changes introduced.

[codecov]

Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 100.00%. Comparing base (f2d6b1a) to head (6f5391e).
Report is 6 commits behind head on master.

Additional details and impacted files

@@            Coverage Diff            @@
##            master       #78   +/-   ##
=========================================
  Coverage   100.00%   100.00%           
=========================================
  Files           16        16           
  Lines          922       922           
=========================================
  Hits           922       922           

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[gmmajal]

Further Changes introduced:

• In the linting task inside github workflows, the check sub-command was required in order to properly perform linting with ruff. This modification was made inside the file .github/workflows/ci.yml

[annakasprzik]

Went through the checks, only found the deprecation warning for safety -- okay.

[gmmajal]

Further changes introduced:

• The poetry.lock file has been refreshed once again. ruff is now at v0.9.2. rdflib is now at v7.1.3.
• The change made in the thesaurus.py script has been reverted. All tests are cleared locally and in the ci pipeline.

[gmmajal]

Further changes introduced:

• The date released and version number inside the CITATION.cff file has been updated.
• The version number given inside the pyproject.toml file has been updated.