Compared NanoVirDx’s 503-line DiffSim wrapper with the breaking DiffSim sequence rewrite released in 0.1.99 and republished with relaxed dependencies as 0.1.100.
Confirmed that SimCfg, run_simulation, TissueCharacteristics, and the old idealised sequence types were removed. The replacement public surface includes domain_from_histo, Tissues, Scanner, SimState.with_walkers_sampled, packed sequences, simulate, and US-spelled idealized sequence types.
Found that the repository’s apps/gen4ve2e runner owns output persistence and postprocessing but is not included in the installed DiffSim package. The package itself does not write NIfTIs, derive ADC, or expose a high-level result contract.
Opened DiffSim PR #738 to relax virdx-ome to >=0.0.19,<0.1. The resulting 0.1.100 package resolved successfully with Histo and virdx-ome 0.0.24.
Ran pixi upgrade diffsim in NanoVirDx, installed and imported DiffSim 0.1.100, verified domain_from_histo and simulate, lock-checked the environment, then committed and pushed c0e41b83 to origin/fk/nanovirdx.
Replaced the 503-line NanoVirDx wrapper with a 195-line adapter using the 0.1.100 public APIs. DiffSim now owns domain loading, tissue construction, walker sampling, sequence packing, simulation, and magnetization capture. NanoVirDx retains only protocol constants, NIfTI persistence, and ADC derivation so BPMRIBatch remains unchanged.
Removed local cache manifests, retry/downsampling fallback, duplicate metadata, state cache, segmentation loading, device validation, noise/smoothing, and foreground-mask persistence. Removed the now-unused direct SciPy dependency.
Validated a complete synthetic 13-class Histo-domain simulation on Metal with T2, high-b DWI, and finite ADC NIfTIs, then committed and pushed 39aa23a5 to origin/fk/nanovirdx.
Lessons Learned: Pitfalls
DiffSim 0.1.99 was a large breaking API rewrite under a patch version and originally constrained virdx-ome to the incompatible 0.0.19 patch series.
The earlier recommendation to simplify through SimCfg.run() was stale: SimCfg was removed in 0.1.99.
The current BPMRIBatch contract requires derived ADC, while DiffSim’s native/reference outputs do not include ADC. Preserving that contract keeps a small ADC calculation in NanoVirDx.
The reference gen4ve2e app targets the current 13-class Histo domain schema. An older 40-class fixture with grade labels encoded at 128-139 cannot pass DiffSim domain_from_histo’s mapping-length contract and is not supported by the simplified adapter.
The simplified outputs are native magnitude T2/high-b images plus derived ADC. The prior wrapper’s synthetic smoothing/noise and explicit foreground-mask files were removed rather than duplicated outside DiffSim.
The high-level gen4ve2e implementation looks reusable but is application code outside the built wheel, so NanoVirDx cannot delegate to it through the packaged dependency.
Lessons Learned: Improvements
Promote a stable high-level generation runner and result type from apps/gen4ve2e into src/diffsim before reducing NanoVirDx to a Histo-style thin adapter.
If native DiffSim output becomes a reusable product boundary, introduce DiffsimOutputBatch and move ADC derivation into a separate transformer. For now, the small ADC calculation preserves BPMRIBatch without a public output change.
Treat package release notes or compatibility declarations as necessary for breaking internal API changes even before semantic version 1.0.
