Make every benchmark mode run - #122
Merged
Merged
Conversation
The subcommand was shipped in --help and failed in all five modes. Pairwise modes cast the signature set to an int before a lookup keyed on strings, so a valid set was reported as missing from a list that visibly contained it. Multiple modes used i, signature_names and W, which are only assigned in the pairwise branch, so they raised NameError; multiple_gen was a bare pass that then ran the aggregation anyway. --root and --signatures were accepted and then ignored by the multiple modes, which wrote to a hardcoded data/benchmark/multiple. Three library calls had drifted: write_decomposition lost the arguments the benchmark passed and now takes a mapping keyed by sample, decompose_mutational_profile_counts lost debug, and _get_stats had a branch for a plain exposure vector that set only h and then read two names it never bound, so it raised UnboundLocalError every time that documented path was taken. The deconstructSigs modes now say Rscript is missing instead of failing inside a worker, and --replicates and --processes make the generators testable. Closes #114
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
1 participant
Add this suggestion to a batch that can be applied as a single commit.This suggestion is invalid because no changes were made to the code.Suggestions cannot be applied while the pull request is closed.Suggestions cannot be applied while viewing a subset of changes.Only one suggestion per line can be applied in a batch.Add this suggestion to a batch that can be applied as a single commit.Applying suggestions on deleted lines is not supported.You must change the existing code in this line in order to create a valid suggestion.Outdated suggestions cannot be applied.This suggestion has been applied or marked resolved.Suggestions cannot be applied from pending reviews.Suggestions cannot be applied on multi-line comments.Suggestions cannot be applied while the pull request is queued to merge.Suggestion cannot be applied right now. Please check back later.
mutagene benchmarkis in--helpand failed in all five modes.intbefore a lookup keyed on stringsi,signature_names,Wfrom the pairwise branch →NameError;--root/--signaturesignored for a hardcoded pathwrite_decomposition(lost args, now takes a mapping),decompose_mutational_profile_counts(lostdebug), and_get_stats, whose plain-vector branch set onlyhthen read two unbound names_dsmodes now report missingRscriptup front.--replicates/--processesadded so the generators are testable.6 tests covering all five modes. Closes #114.