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95786d1
Initial spatialdata interface
Aug 25, 2026
3fb3775
Use new 'filtered' column and remove faulty min_similarity validators
Aug 25, 2026
29c2011
Make -i/source_path optional; fall back to joining source transcripts…
Aug 25, 2026
4ea4f50
Add example usage to export docstring
Aug 25, 2026
5e71342
Log copy/write start for spatialdata export; check destination existe…
Aug 25, 2026
785fd35
Check spatialdata package is importable before exporting the 'spatial…
Aug 25, 2026
35b7acf
add spatialdata dependency
Aug 26, 2026
18bcc50
Parallelize cell boundary generation across CPUs
Aug 26, 2026
dc9c7d5
Add setuptools dependency to cuda121 env
Tobiaspk Aug 27, 2026
d48625a
Fix parallel boundary generation: list unpacking and worker count
Tobiaspk Aug 27, 2026
d1ec959
Write spatialdata export elements in place, avoid dask-expr crash
Tobiaspk Aug 27, 2026
b0e198c
Thread an optional z coordinate through export and training writers
Tobiaspk Aug 28, 2026
6515b6e
Append segger columns to existing transcripts element instead of a ne…
Tobiaspk Aug 31, 2026
a1e223b
Simplify export.py to rely on the 'filtered' column directly
Tobiaspk Aug 31, 2026
7ec59c1
Take element names as separate args in _check_sdata_elements
Tobiaspk Aug 31, 2026
047716e
Propagate base-element transformations in spatialdata export, merge l…
Tobiaspk Aug 31, 2026
cf3f58e
Fix in-place spatialdata overwrite and drop row_index from transcripts
Tobiaspk Sep 1, 2026
b09195c
Add --min-counts filter and align export table to boundaries
Tobiaspk Sep 1, 2026
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623 changes: 601 additions & 22 deletions pixi.lock

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4 changes: 3 additions & 1 deletion pixi.toml
Original file line number Diff line number Diff line change
Expand Up @@ -37,9 +37,11 @@ cudf-cu12 = "==24.10.*"
cuml-cu12 = "==24.10.*"
cugraph-cu12 = "==24.10.*"
cupy-cuda12x = ">=12.2,<13.0"
spatialdata = ">=0.4.0, <0.5"
setuptools = ">=81.0.0, <82"

[tool.uv.extra-build-dependencies]
torch-scatter = ["torch"]

[environments]
cuda121 = ["cuda121"]
cuda121 = ["cuda121"]
5 changes: 5 additions & 0 deletions src/segger/__init__.py
Original file line number Diff line number Diff line change
@@ -1,6 +1,11 @@
import logging
import os
from pathlib import Path

import dask

dask.config.set({"dataframe.query-planning": False}) # spatialdata doesn't yet support dask-expr; must be set before cudf pulls in dask.dataframe

import cupy as cp
import torch
import rmm
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