Some pytest fixes

[jcermauwedu]

• base.py: Sometimes cfutil is None
• protocols/netcdf.py:
  • Return False right away if content_type is None
  • Support extended type strings: "application/x-netcdf;ver=4"
• suite.py: If text for xml fails, look for netcdf one more time
• Convert suite.run() calls to suite.run_all() calls
• Update hyrax url
• Update thredds url
• Add some development notes for troubleshooting tests with pytest using the vcr feature.

For the SOS test in test_protocols.py, I set that to skip. I searched for awhile for a working SOS service.

Looking forward to seeing #1039 merged.

[jcermauwedu]

pre-commit.ci autofix

[codecov]

Codecov Report

Attention: Patch coverage is 75.00000% with 2 lines in your changes are missing coverage. Please review.

Project coverage is 82.06%. Comparing base (c137e28) to head (b06e777).
Report is 14 commits behind head on develop.

Files	Patch %	Lines
compliance_checker/base.py	66.66%	0 Missing and 1 partial ⚠️
compliance_checker/suite.py	50.00%	0 Missing and 1 partial ⚠️

Additional details and impacted files

@@             Coverage Diff             @@
##           develop    #1056      +/-   ##
===========================================
- Coverage    82.14%   82.06%   -0.08%     
===========================================
  Files           24       24              
  Lines         5170     5175       +5     
  Branches      1242     1245       +3     
===========================================
  Hits          4247     4247              
- Misses         623      626       +3     
- Partials       300      302       +2     

☔ View full report in Codecov by Sentry.
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[ocefpaf]

@jcermauwedu I'm not a compliance-checker expert and I did not look too hard. Can you explain what/when/where cfutil happens to be None? Is that expected or is it an indication of a deeper problem?

[jcermauwedu]

Without the test for None this is the error. Still digging around for this one...

There are still some pkg references kicking around too.

======================================================================================= test session starts ========================================================================================
platform linux -- Python 3.10.14, pytest-8.1.1, pluggy-1.4.0
rootdir: /home/portal/src/compliance-checker
configfile: pyproject.toml
plugins: cov-5.0.0, flake8-1.1.1, requests-mock-1.12.1, vcr-1.0.2, time-machine-2.14.1
collected 235 items                                                                                                                                                                                

compliance_checker/tests/test_acdd.py ................                                                                                                                                       [  6%]
compliance_checker/tests/test_base.py ........                                                                                                                                               [ 10%]
compliance_checker/tests/test_cf.py ...........................................................................................                                                              [ 48%]
compliance_checker/tests/test_cf_integration.py .................                                                                                                                            [ 56%]
compliance_checker/tests/test_cli.py .........                                                                                                                                               [ 60%]
compliance_checker/tests/test_feature_detection.py ...............................                                                                                                           [ 73%]
compliance_checker/tests/test_ioos_profile.py ..........................................                                                                                                     [ 91%]
compliance_checker/tests/test_ioos_sos.py ..                                                                                                                                                 [ 91%]
compliance_checker/tests/test_protocols.py ....s                                                                                                                                             [ 94%]
compliance_checker/tests/test_suite.py .............                                                                                                                                         [ 99%]
compliance_checker/tests/test_util.py .                                                                                                                                                      [100%]

========================================================================================= warnings summary =========================================================================================
compliance_checker/tests/test_cf_integration.py::TestCFIntegration::test_cf_integration[sldmb_43093_agg-expected_messages0]
  /home/portal/src/cc-plugin-ncei/cc_plugin_ncei/util.py:6: DeprecationWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html
    from pkg_resources import resource_filename

compliance_checker/tests/test_cf_integration.py::TestCFIntegration::test_cf_integration[sldmb_43093_agg-expected_messages0]
  /home/portal/miniconda3/envs/py310_dev/lib/python3.10/site-packages/pkg_resources/__init__.py:2832: DeprecationWarning: Deprecated call to `pkg_resources.declare_namespace('sphinxcontrib')`.
  Implementing implicit namespace packages (as specified in PEP 420) is preferred to `pkg_resources.declare_namespace`. See https://setuptools.pypa.io/en/latest/references/keywords.html#keyword-namespace-packages
    declare_namespace(pkg)

-- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html
=========================================================================== 234 passed, 1 skipped, 2 warnings in 24.25s ============================================================================
Exception ignored in: <function BaseCheck.__del__ at 0x702b0dd69fc0>
Traceback (most recent call last):
  File "/home/portal/src/compliance-checker/compliance_checker/base.py", line 198, in __del__
AttributeError: 'NoneType' object has no attribute 'get_geophysical_variables'