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INCATools / ontology-development-kit

Bootstrap an OBO Library ontology
http://incatools.github.io/ontology-development-kit/
BSD 3-Clause "New" or "Revised" License
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The ODK should take care of generating documentation for DOSDP patterns #1101

Closed gouttegd closed 1 month ago

gouttegd commented 1 month ago

The CL custom Makefile includes a rule to generate some documentation pages from the DOSDP patterns:

pattern_docs:
    dosdp document -i ../patterns/dosdp-patterns/ -o ../../docs/patterns/ -d ../patterns/data/matches/

Given that the standard ODK Makefile already contains rule for about every task related to patterns (validation, query, generation), it should also include a rule for generating their documentation, without asking users to create their own rule like CL does above.

gouttegd commented 1 month ago

After toying with this idea a bit, I find that dosdp document crashes on too many pattern files for such a command to be of any use.

balhoff commented 1 month ago

@gouttegd have you tried dosdp-tools docs?

e.g. https://github.com/geneontology/go-ontology/blob/master/docs/patterns/index.md

gouttegd commented 1 month ago

No, because I didn’t know the docs subcommand existed. Thanks!

Copying GO’s full command for reference:

$(DOSDP_TOOLS) docs --obo-prefixes=true --batch-patterns="$(ALL_PATTERN_NAMES)" --template=../design_patterns --outfile=../../docs/patterns --infile=../design_patterns --data-location-prefix='https://github.com/geneontology/go-ontology/tree/master/src/design_patterns/' --ontology=reasoned.owl --catalog=catalog-v001.xml