Harmony v2 version update

[KarlKaise]

Due to updated version of harmony 2 package on cran after installing new harmony v2, there is following issue in CHOIR:

[ERROR] CHOIR clustering failed: 'HarmonyMatrix' is not an exported object from 'namespace:harmony'
Freed choir_input object after CHOIR

Thanks for any help. Love the pipeline.

[KarlKaise]

This worked for me as hot fix:
The harmony 2 fix in one summaryThe problemCHOIR 0.3.0's internal .runDimReduction() calls harmony::HarmonyMatrix() directly when batch_correction_method = "Harmony". But HarmonyMatrix() was removed entirely in harmony 2.0 — only RunHarmony() (with renamed arguments) remains. Your env has harmony 2.0.2, so CHOIR aborted at first contact with:'HarmonyMatrix' is not an exported object from 'namespace:harmony'You ruled out downgrading harmony and ruled out modifying either package on disk. So the fix had to be runtime-only.The first attempt that didn't workThe intuitive fix is to inject a HarmonyMatrix shim into harmony's namespace at runtime. Tried that:rassign("HarmonyMatrix", HarmonyMatrix_shim, envir = asNamespace("harmony"))Failed with cannot add bindings to a locked environment. Reason: when R loads a package, it calls lockEnvironment(ns, bindings = TRUE) on the namespace. Pure R only exposes unlockBinding() (which works on bindings that already exist) — it does not expose any way to unlock the environment itself to allow new bindings. So you cannot add a new symbol to a locked namespace from pure R, full stop.The fix that workedPivot the target. Instead of adding a new binding to harmony, modify an existing binding in CHOIR.CHOIR:::.runDimReduction already exists in CHOIR's namespace. Existing bindings can be unlocked via unlockBinding(). So we:
Read the function out of CHOIR's namespace.
Walk its body recursively. Every time we find a call expression matching harmony::HarmonyMatrix, replace it with an inline forwarder function that calls harmony::RunHarmony() instead — translating the legacy argument names along the way (max.iter.harmony → max_iter, etc.) and forcing return_object = FALSE so CHOIR still receives a plain matrix.
Reinstall the patched function: unlockBinding → assign → lockBinding.