hunter-moseley
commented
1 year ago Just include both versions of the option in the docstring. It is the safest and easiest.
Just indicate in the description that the underscore option is identical to the dashed option and indicate it will be deprecated in the future.
On Thu, Jul 6, 2023 at 10:24 AM ptth222 @.***> wrote:
I have ran into more of an issue than I expected trying to implement this. Basically, since docopt is used for the interface the only way to allow both the underscore version and the hyphen version of an option is to add them into the usage. There is no concept of aliases or hidden options to docopt. The interface would have to look like:
Usage: academic_tracker author_search
[--test --prev_pub= --no_GoogleScholar --no-GoogleScholar --no_ORCID --no-ORCID --no_Crossref --no-Crossref --no_PubMed --no-PubMed --verbose --silent] academic_tracker reference_search [--test --prev_pub= --prev-pub= --PMID_reference --PMID-reference --MEDLINE_reference --MEDLINE-reference --no_Crossref --no-Crossref --no_PubMed --no-PubMed --verbose --silent] academic_tracker find_ORCID [--verbose --silent] academic_tracker find_Google_Scholar [--verbose --silent] academic_tracker add_authors [--verbose --silent] academic_tracker tokenize_reference [--MEDLINE_reference --MEDLINE-reference --verbose --silent] academic_tracker gen_reports_and_emails_auth [--test --verbose --silent] academic_tracker gen_reports_and_emails_ref [--test --prev_pub= --prev-pub= --MEDLINE_reference --MEDLINE-reference --verbose --silent] Options: -h --help Show this screen. -v --version Show version. --verbose Print hidden error messages. --silent Do not print anything to the screen. --test Generate pubs and email texts, but do not send emails. --prev_pub=
Filepath to json or csv with publication ids to ignore. Enter "ignore" for the to not look for previous publications.json files in tracker directories. --prev-pub= Filepath to json or csv with publication ids to ignore. Enter "ignore" for the to not look for previous publications.json files in tracker directories. Reference Type Options: --PMID_reference Indicates that the reference_file is a PMID file and only PubMed info will be returned. --PMID-reference Indicates that the reference_file is a PMID file and only PubMed info will be returned. --MEDLINE_reference Indicates that the reference_file is a MEDLINE file. --MEDLINE-reference Indicates that the reference_file is a MEDLINE file.
Search Options: --no_GoogleScholar Don't search Google Scholar. --no-GoogleScholar Don't search Google Scholar. --no_ORCID Don't search ORCID. --no-ORCID Don't search ORCID. --no_Crossref Don't search Crossref. --no-Crossref Don't search Crossref. --no_PubMed Don't search PubMed. --no-PubMed Don't search PubMed.
It looks like I could overwrite docopt's function and get around this without too much difficulty, but I don't really like doing that if I don't have to because it's fragile to breaking if the underlying package changes. docopt hasn't changed since 2014 though, so it is probably one of the safest packages to do this with. What do you think?
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-- Hunter Moseley, Ph.D. -- Univ. of Kentucky Professor, Dept. of Molec. & Cell. Biochemistry / Markey Cancer Center / Institute for Biomedical Informatics / UK Superfund Research Center Not just a scientist, but a fencer as well. My foil is sharp, but my mind sharper still.
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ptth222
I have ran into more of an issue than I expected trying to implement this. Basically, since docopt is used for the interface the only way to allow both the underscore version and the hyphen version of an option is to add them into the usage. There is no concept of aliases or hidden options to docopt. The interface would have to look like:
It looks like I could overwrite docopt's function and get around this without too much difficulty, but I don't really like doing that if I don't have to because it's fragile to breaking if the underlying package changes. docopt hasn't changed since 2014 though, so it is probably one of the safest packages to do this with. What do you think?