refactor: move non-download functionalities out of PODPDownloader - _run_bigscape

[gcroci2]

• _run_bigscape method has been moved to src/nplinker/pairedomics/runbigscape.py as a function and it is now called podp_run_bigscape
• src/nplinker/pairedomics/downloader.py now uses podp_run_bigscape
• Type hints in src/nplinker/pairedomics/runbigscape.py have been added

[gcroci2]

In src/nplinker/pairedomics/runbigscape.py, run_bigscape takes as input extra_params, which to me appears to be a string. But then in the if __name__ == "__main__": statement, cutoffs=[0.3] is passed as extra_params parameter. Prospector indeed classifies it as an error, because it doesn't expect a cutoffs parameter.

[CunliangGeng]

In src/nplinker/pairedomics/runbigscape.py, run_bigscape takes as input extra_params, which to me appears to be a string. But then in the if __name__ == "__main__": statement, cutoffs=[0.3] is passed as extra_params parameter. Prospector indeed classifies it as an error, because it doesn't expect a cutoffs parameter.

Indeed, the extra_params is a string with space as separator.

[CunliangGeng]

Ideally the download and run logics should be independent. To move run_bigscape out of PODPDownloader, we have to move the run logics to a higher level (i.e. to loader.py). Let's keep it as it is and really move it out when refactoring the loader part.

[gcroci2]

Ideally the download and run logics should be independent. To move run_bigscape out of PODPDownloader, we have to move the run logics to a higher level (i.e. to loader.py). Let's keep it as it is and really move it out when refactoring the loader part.

Sounds good, I mentioned it in the DataLoader issue #145