Upgrade pip and setuptools in workflow

[hmenager]

fix failing workflows due to:

× Getting requirements to build wheel did not run successfully.
│ exit code: 1
╰─> [20 lines of output]
Traceback (most recent call last):
File "/usr/lib/python3/dist-packages/pip/_vendor/pyproject_hooks/_in_process/_in_process.py", line 353, in <module>
main()
File "/usr/lib/python3/dist-packages/pip/_vendor/pyproject_hooks/_in_process/_in_process.py", line 335, in main
json_out['return_val'] = hook(**hook_input['kwargs'])
^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/python3/dist-packages/pip/_vendor/pyproject_hooks/_in_process/_in_process.py", line 118, in get_requires_for_build_wheel
return hook(config_settings)
^^^^^^^^^^^^^^^^^^^^^
File "/tmp/pip-build-env-2uuifzml/overlay/local/lib/python3.12/dist-packages/setuptools/build_meta.py", line 333, in get_requires_for_build_wheel
return self._get_build_requires(config_settings, requirements=[])
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/tmp/pip-build-env-2uuifzml/overlay/local/lib/python3.12/dist-packages/setuptools/build_meta.py", line 301, in _get_build_requires
self.run_setup()
File "/tmp/pip-build-env-2uuifzml/overlay/local/lib/python3.12/dist-packages/setuptools/build_meta.py", line 520, in run_setup
super().run_setup(setup_script=setup_script)
File "/tmp/pip-build-env-2uuifzml/overlay/local/lib/python3.12/dist-packages/setuptools/build_meta.py", line 317, in run_setup
exec(code, locals())
File "<string>", line 19, in <module>
ModuleNotFoundError: No module named 'pkg_resources'

[sonarqubecloud]

Quality Gate passed

Issues
0 New issues
0 Accepted issues

Measures
0 Security Hotspots
0.0% Coverage on New Code
0.0% Duplication on New Code

See analysis details on SonarQube Cloud

[hmenager]

remaining caseologue CI errors are due to errors in current EDAM, which will be fixed later:

Run cd caseologue_python/

_____________________________________________________________________________________________

The following debug table is archived as an artifact called 'output_caseologue'
_____________________________________________________________________________________________
/home/runner/work/caseologue/caseologue/caseologue_python/caseologue.py:93: DeprecationWarning: ConjunctiveGraph is deprecated, use Dataset instead.

  cls.edam_graph = ConjunctiveGraph()
....F........
======================================================================
FAIL: test_spelling_check (__main__.EdamQueryTest.test_spelling_check)
Uses unix codespell command and custom spelling dictionary to check spelling errors in EDAM.
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/home/runner/work/caseologue/caseologue/caseologue_python/caseologue.py", line 1168, in test_spelling_check
    self.assertEqual(nb_err, 0)
AssertionError: 9 != 0

----------------------------------------------------------------------
Ran 13 tests in 407.690s

FAILED (failures=1)
error = True, essential = True, curation = False

    Test Name                           Time in seconds
--  --------------------------------  -----------------
 0  test_super_class_refers_to_self           0.439643
 1  test_bad_uri_reference                   22.7629
 2  test_empty_property                       1.43686
 3  test_id_unique                            0.0866742
 4  test_spelling_check                       0.394386
 5  test_mandatory_property_missing         312.982
 6  test_deprecated_replacement               0.13786
 7  test_missing_deprecated_property          0.360814
 8  test_next_id_modif                        0.462838
 9  test_subset_id                            0.809666
10  test_object_relation_obsolete             0.0668879
11  test_bad_uri                              0.546318
12  test_duplicate_in_concept                65.4139
    Test Name       Entity    Label    Debug Message
--  --------------  --------  -------  --------------------------------------------------------------------------------------------------------------------------------------------------------------------
 0  spelling_check  Unknown   Unknown  in your EDAM file, line 143, "correspondigly" is suspected to be a spelling error. Could it be "correspondingly" instead? (if exception needed comment in PR ... )
 1  spelling_check  Unknown   Unknown  in your EDAM file, line 2332, "repot" is suspected to be a spelling error. Could it be "report, repost" instead? (if exception needed comment in PR ... )
 2  spelling_check  Unknown   Unknown  in your EDAM file, line 14627, "re-used" is suspected to be a spelling error. Could it be "reused" instead? (if exception needed comment in PR ... )
 3  spelling_check  Unknown   Unknown  in your EDAM file, line 36803, "re-usable" is suspected to be a spelling error. Could it be "reusable" instead? (if exception needed comment in PR ... )
 4  spelling_check  Unknown   Unknown  in your EDAM file, line 37037, "charateristics" is suspected to be a spelling error. Could it be "characteristics" instead? (if exception needed comment in PR ... )
 5  spelling_check  Unknown   Unknown  in your EDAM file, line 40028, "strucural" is suspected to be a spelling error. Could it be "structural" instead? (if exception needed comment in PR ... )
 6  spelling_check  Unknown   Unknown  in your EDAM file, line 48436, "tpyically" is suspected to be a spelling error. Could it be "typically" instead? (if exception needed comment in PR ... )
 7  spelling_check  Unknown   Unknown  in your EDAM file, line 49011, "possiby" is suspected to be a spelling error. Could it be "possibly" instead? (if exception needed comment in PR ... )
 8  spelling_check  Unknown   Unknown  in your EDAM file, line 50003, "Classifiication" is suspected to be a spelling error. Could it be "Classification" instead? (if exception needed comment in PR ... )
<unittest.runner.TextTestResult run=13 errors=0 failures=1>
Error: Process completed with exit code 1.