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Merged
Claptar merged 1 commit into from
Nov 2, 2026
Merged

Release 0.17.5 #119

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14 changes: 13 additions & 1 deletion STATUS.md
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Expand Up @@ -7,6 +7,7 @@ moves; the plan of record for the current item is in the section below.

| Version | What | Issues |
|---|---|---|
| 0.17.5 | Audit fixes, wave 2 (fidelity): scanpy's marker genes and anndata 0.7 files survive every copy, data held outside an h5ad refused; subset/split keep every named row and subset every element as anndata; concat takes any number of inputs in anndata's order; 10x, MTX, Parse, CellBender, loom, SCope and MuData fixes; release pipeline hardened, image non-root; zarr >= 3.2 | #93, #94, #95, #99, #100, #102 |
| 0.17.4 | Audit fixes, wave 1 (data safety): every writer staged and checked, close errors fail the command, `--chunk` at least 1, a free-space check; text/MTX/dense imports refuse what they cannot read; concat refuses repeated var names and keeps missing values and dtypes; import/export type values as pandas does; Pillow 13 | #89, #90, #91, #92, #98 |
| 0.17.3 | Space Ranger's analysis (clusters, UMAP, PCA) for Visium spots and HD bins; `convert` works on fresh installs (broken since 0.7.0) | #85, #88 |
| 0.17.2 | Visium HD segmented cells (Space Ranger 4): centroids, areas and Space Ranger's analysis | #83 |
Expand Down Expand Up @@ -51,11 +52,22 @@ Decisions:
Steps:
- [x] B0: `convert` on fresh installs (#88), in 0.17.3
- [x] Wave 1, then 0.17.4
- [ ] Wave 2, then 0.17.5
- [x] Wave 2, then 0.17.5
- [ ] Waves 3 and 4, then 0.17.6

## Follow-ups noticed

- From wave 2 of the audit fixes:
- CI: a Python 3.14 leg; Dependabot for the pinned actions, uv and base
image (the pinned actions run on Node 20, which GitHub is retiring); the
base image to Debian trixie; a Codecov token (B9).
- Repository settings: the default workflow token can write, and the
`pypi` environment has no protection rules (B9).
- Zarr stores need a counterpart to the HDF5 hardening in 0.17.5, outside
that fix's scope (B5).
- Flex's `target_sets` group is not carried, and `--make-unique` names
export with their suffixes (B8a).
- A numeric `in` list with thousands of values is slow (B4).
- From wave 1 of the audit fixes:
- `core/csr_build.py`'s on-disk sort makes many small appends, slow for
a Zarr scratch at small budgets; buffer bucket writes in
Expand Down
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