---
title: "2026-09-18 NanoVirDx scalar samples and conda release"
description: "Refactored NanoVirDx to scalar path-backed samples, isolated DiffSim compatibility, and added internal conda release automation."
image: "https://docs.virdx.dev/img/virdx-social-card.png"
---

> Documentation Index
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# 2026-09-18 NanoVirDx scalar samples and conda release

## Work Done

- Replaced every NanoVirDx `*Batch` struct-of-lists with scalar `*Sample` dataclasses. Predictors now consistently accept and return lists while preserving input order and top-level cardinality.
- Preserved the intentional one-to-many Histo preprocessing relationship as `PreprocessingOutputSample.components: list[WSISample]`.
- Moved fine28 mapping, nine-tissue parameters, sparse Histo v2 region loading, and DiffSim 0.1.100 compatibility into `inference/simulation/_compat.py`. Reduced `diffsim.py` to simulation sequencing and output translation.
- Finished the user's vxData adapter extraction. Both `get_*_by_uid` functions accept an optional client, instantiate their own fallback only for non-empty inputs, preserve requested ordering and duplicates, handle local/S3 paths, and include nuclei maps.
- Added a NanoVirDx conda recipe and manual release workflow. The workflow reads the hardcoded `pyproject.toml` version and uploads only to the internal Artifactory `virdx` channel.
- Removed stale README examples for APIs that are not implemented and documented the list-of-samples contract.
- Validated Ruff, Pyright, compileall, focused mocked contracts, full synthetic fine28 simulation, finite MRI outputs, wheel contents, conda render, actionlint, module boundaries, and diff checks.
- Committed and pushed mono commits `791be45a` and `67a029d2` to `origin/fk/nanovirdx`.
- Added `ISUPGradePredictor` and `PICAIPredictor` placeholder interfaces whose `setup()` and `predict()` methods explicitly raise `NotImplementedError`; pushed mono commit `1d6c28c5`.
- Added Gleason, tissue, and expanded-cell component predictors as projections of the Histo v2 domain pipeline; removed the unsupported `WSIEmbeddingSample` placeholder because Histo has no persisted FeatureGrid contract; pushed mono commit `1b37a2b1`.
- Added `EmbeddingGenerator` writing a slide-level H-optimus token mosaic with valid-core ownership over Histo's super-window lattice; reinstated `WSIEmbeddingSample(path)` as a NanoVirDx-owned Zarr artifact contract; pushed mono commit `26f2a957`. Correction: Histo has a stable in-memory `FeatureGrid` API; only the persisted format was missing.
- Rebuilt Gleason, tissue, and cell predictors on Histo's official head pathways (`load_gleason_head`/`run_gleason_segmentation`, `load_tissue_head`/`run_tissue_segmentation`, `load_cell_head`/`run_cell_detection`) via a shared `WsiHeadSweep` over Histo's super-window lattice; renamed the settings bridge to `_compat_dr_v2_config.yaml`; typed settings as `PipelineSettings`; pushed mono commit `bb61748a`.
- Added explicit `nanovirdx.inference.__init__` exports (`from nanovirdx.inference import DomainRepresentationPredictor, ISUPGradePredictor, ...`) plus empty subpackage `__init__.py` files; heavy runtimes stay lazy in `setup()`; pushed mono commit `0330a4d1`.

## Lessons Learned: Pitfalls

- Running independent workers in one shared worktree requires strict file ownership. The broad sample migration worker therefore produced a read-only design while the other workers owned only new, non-overlapping files.
- Domain-representation downloads need one coherent directory per resource because DiffSim discovers conventionally named maps from a directory. Downloading multiple representations into one flat destination risks collisions.
- Empty predictor inputs should return before model setup; otherwise `predict([])` can needlessly load large Histo or DiffSim state.

## Lessons Learned: Improvements

- Add a small NanoVirDx project/test target so the scalar sample and optional-client contracts run in CI rather than only through focused validation scripts.
- Remove `_compat.py` after DiffSim publishes Cedrik's `region_ids`-aware name mapping support.
- Remove the vendored Histo settings after Histo packages a supported default-settings resource.

Source: https://docs.virdx.dev/knowledge/inbox/2026-09-18-histo-nanovirdx-sample-refactor-release/index.mdx