Remove writeFasta and processProteinFastaFile - #711
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Both were reachable only by their own test (processProteinFastaFile) or documented example (writeFasta), never from another function or tutorial. Broader audit of every top-level .m file for the same pattern (zero internal callers, zero tutorial reference, zero test, zero doc mention) found no other genuine candidates -- everything else that superficially looked unreferenced is either ledger-tracked with a documented purpose, or an installation/test entry point meant for direct invocation, not something chained from other RAVEN functions. readFasta's now-stale "See also: writeFasta" cross-reference is dropped; the euk_protein.faa fixture, used only by processProteinFastaFile's removed test, goes with it.
Function test results303 tests 276 ✅ 1m 6s ⏱️ Results for commit 4a5a49a. |
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Summary
Both were reachable only by their own test (
processProteinFastaFile) or documented example (writeFasta), never from another function or tutorial.Broader audit of every top-level
.mfile for the same pattern (zero internal callers, zero tutorial reference, zero test, zero doc mention) found no other genuine candidates — everything else that superficially looked unreferenced turned out to be either ledger-tracked with a documented purpose (walkFluxes,getUniProtScores,mapCompartments,predictLocalization) or an installation/test entry point meant for direct invocation (addRavenToUserPath,runRAVENtests), not something chained from other RAVEN functions.readFasta's now-stale "See also: writeFasta" cross-reference is dropped. Theeuk_protein.faafixture, used only byprocessProteinFastaFile's removed test, goes with it.Test plan
tSyntax,tGenomeData,tIO— 20 passed, 0 failed, 1 filtered (unrelated missing dependency)