Allow to disable Entrez search result limit

[jonasfreimuth]

Fixes the limit on max_results for EntrezAPI.search() and adds an option to ignore all similar limits.

Should pretty much close #16, at least for my purposes.

Note: Running pytest on commit 3c2b396 resulted in the following output once, but the error disappeared after I ran it again without changing anything, the programmers dream nightmare.

(.venv) jfreige@sl-akali-p-cs1:easy-entrez (16-entrez-result-limit)$ pytest
============================================================================================== test session starts ===============================================================================================
platform linux -- Python 3.10.12, pytest-7.4.2, pluggy-1.3.0
rootdir: /data/local/jfreige/geo-mining/easy-entrez
plugins: cov-4.1.0
collected 15 items                                                                                                                                                                                               

tests/test_api.py ..F                                                                                                                                                                                      [ 20%]
tests/test_parsing.py ....                                                                                                                                                                                 [ 46%]
tests/test_queries.py ........                                                                                                                                                                             [100%]

==================================================================================================== FAILURES ====================================================================================================
___________________________________________________________________________________________________ test_fetch ___________________________________________________________________________________________________

    def test_fetch():
        result = entrez_api.fetch(['4'], max_results=1, database='snp')
        assert is_response_for(result, FetchQuery)
        assert not is_response_for(result, SearchQuery)
        snp = result.data[0]
        namespaces = {'ns0': 'https://www.ncbi.nlm.nih.gov/SNP/docsum'}
>       chromosome = snp.find('.//ns0:CHR', namespaces).text
E       AttributeError: 'NoneType' object has no attribute 'text'

tests/test_api.py:38: AttributeError
================================================================================================ warnings summary ================================================================================================
tests/test_parsing.py:39
  /data/local/jfreige/geo-mining/easy-entrez/tests/test_parsing.py:39: PytestUnknownMarkWarning: Unknown pytest.mark.optional - is this a typo?  You can register custom marks to avoid this warning - for details, see https://docs.pytest.org/en/stable/how-to/mark.html
    @pytest.mark.optional

tests/test_parsing.py:78
  /data/local/jfreige/geo-mining/easy-entrez/tests/test_parsing.py:78: PytestUnknownMarkWarning: Unknown pytest.mark.optional - is this a typo?  You can register custom marks to avoid this warning - for details, see https://docs.pytest.org/en/stable/how-to/mark.html
    @pytest.mark.optional

tests/test_parsing.py:89
  /data/local/jfreige/geo-mining/easy-entrez/tests/test_parsing.py:89: PytestUnknownMarkWarning: Unknown pytest.mark.optional - is this a typo?  You can register custom marks to avoid this warning - for details, see https://docs.pytest.org/en/stable/how-to/mark.html
    @pytest.mark.optional

-- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html
============================================================================================ short test summary info =============================================================================================
FAILED tests/test_api.py::test_fetch - AttributeError: 'NoneType' object has no attribute 'text'
==================================================================================== 1 failed, 14 passed, 3 warnings in 4.47s ====================================================================================```

[jonasfreimuth]

Ok hold on while I sign my commits...

[jonasfreimuth]

Also, yes, I've noticed the error above is different to the one mentioned in #19, and will be looking into if this is a problem.

[jonasfreimuth]

I don't think the readthedocs fail has anything to do with this PR, right?

[krassowski]

Hi @jonasfreimuth thank you for this!

Can you please merge with the main branch which now includes a fix for the docs (#20) so that we can see if they build properly?

[jonasfreimuth]

Will do, hang on.

[jonasfreimuth]

Ok it's merged. @krassowski you might have to manually allow the other checks to run again...

[krassowski]

Thank you @jonasfreimuth