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Issues list

Broken Link for Enrichment Notebook (Update Documentation)
#842 opened Apr 23, 2025 by wdduncan
chore: update poetry.lock, resolve errors
#841 opened Apr 14, 2025 by sierra-moxon
@sierra-moxon
similarity compare fails on CLI using -set1-file & -set2-file args with complaint about missing @
#840 opened Apr 11, 2025 by kevinschaper
chore: improve dev-testing ergonomics chore Routine maintenance tasks that don't affect application behavior or functionality (e.g., dependency
#838 opened Apr 9, 2025 by sierra-moxon
5 tasks
@sierra-moxon
Broken links to notebooks in documentation
#836 opened Apr 6, 2025 by justaddcoffee
1
switch to standard uv/ruff setup
#834 opened Apr 5, 2025 by cmungall
Broken link in docs
#827 opened Jan 31, 2025 by twhetzel
Update docs on pystow/sqlite cache management
#823 opened Dec 10, 2024 by cmungall
add a matrix view of relationships, like one can get for logical definitions
#822 opened Dec 9, 2024 by turbomam
Extend adapters to support versions
#821 opened Nov 27, 2024 by matentzn
3
Provide simple yaml-based output for release summary in runoak diff
#820 opened Nov 13, 2024 by matentzn
1
requesting a new sqlite:obo:xyz input only says "urllib.error.HTTPError: HTTP Error 404: Not Found" if an ontology with abbreviation xyz can't be found
#813 opened Oct 3, 2024 by turbomam
OAK documentation and command line parsing should differentiate between TSV and CSV
#812 opened Oct 3, 2024 by turbomam
Commands that treat empty lists as "all" should return no lists of a query that has zero results is passed
#811 opened Oct 3, 2024 by cmungall
Consider adding --version option to runoak
#810 opened Oct 3, 2024 by turbomam
Expand documentation on graph projections and allow finer grained control documentation Improvements or additions to documentation
#809 opened Oct 2, 2024 by cmungall
Oaklib annotate function does not return all substring containing values as expected
#805 opened Sep 27, 2024 by bsantan
Making retrieval of axiom annotations for synonyms faster
#767 opened May 16, 2024 by matentzn
Define behavior when conflicting idspaces are specified
#760 opened May 15, 2024 by cmungall
Pin ruff checks and codespell checks
#756 opened May 8, 2024 by cmungall
1
Document instructions for running the obographs-compliance suite documentation Improvements or additions to documentation
#751 opened May 5, 2024 by matentzn
4
Jaccard similarity differences when using information content
#746 opened May 1, 2024 by souzadevinicius
2
Run subset of tests in environment with no extras installed
#745 opened Apr 27, 2024 by cmungall
validate-mappings: NotImplementedError: ... NoneType bug Something isn't working
#742 opened Apr 25, 2024 by joeflack4
ValueSetExpander is too eager in using sqlite:obo as a default resolver
#718 opened Mar 15, 2024 by cmungall
ProTip! What’s not been updated in a month: updated:<2025-04-29.