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@Intron7 Intron7 commented Sep 11, 2025

This for now is a test with precompiled cuda extensions.

@Intron7 Intron7 added the run-gpu-ci runs GPU CI label Sep 11, 2025
@Intron7 Intron7 marked this pull request as draft September 11, 2025 19:02
@github-actions github-actions bot removed the run-gpu-ci runs GPU CI label Sep 11, 2025
@Intron7 Intron7 added the run-gpu-ci runs GPU CI label Sep 11, 2025
@github-actions github-actions bot removed the run-gpu-ci runs GPU CI label Sep 11, 2025
@Intron7 Intron7 added the run-gpu-ci runs GPU CI label Sep 11, 2025
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@Intron7 Intron7 added the run-gpu-ci runs GPU CI label Sep 12, 2025
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Oh wow, that looks super cool! Addresses all my previous concerns about manual specification of magic numbers for chunking, repetitive kernel wrapper code, and so on!

from rapids_singlecell._cuda import _qc_cuda as _qc

if sparse.isspmatrix_csr(X):
_qc.sparse_qc_csr(
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ditto, for all of these

@Intron7 Intron7 added the run-gpu-ci runs GPU CI label Jan 19, 2026
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@Intron7 Intron7 added the run-gpu-ci runs GPU CI label Jan 19, 2026
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@Intron7 Intron7 added the run-gpu-ci runs GPU CI label Jan 19, 2026
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@Intron7 Intron7 added the run-gpu-ci runs GPU CI label Jan 19, 2026
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looks awesome, the module exports are much nicer now!

This is missing stub generation, otherwise really nice!

Comment on lines 34 to 39
static inline void launch_auc(std::uintptr_t ranks, int R, int C, std::uintptr_t cnct,
std::uintptr_t starts, std::uintptr_t lens, int n_sets, int n_up,
std::uintptr_t max_aucs, std::uintptr_t es, cudaStream_t stream) {
static inline void launch_auc(const int* ranks, int R, int C, const int* cnct, const int* starts,
const int* lens, int n_sets, int n_up, const float* max_aucs,
float* es, cudaStream_t stream) {
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why do these stop being a pointer sized non-nullable ints and become a 🤷-sized signed ints? (same in many other places)

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because they are now typed by feeding them through nanobind

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so nanobind creates all this? then this shouldn’t be checked into Git and just be part of the build system.

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@Intron7 Intron7 Jan 26, 2026

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no this has to be specifically written for each function. I dont know if there is an abstraction that auto creates this in the build system

@Intron7 Intron7 added the run-gpu-ci runs GPU CI label Jan 29, 2026
@github-actions github-actions bot removed the run-gpu-ci runs GPU CI label Jan 29, 2026
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codecov-commenter commented Jan 29, 2026

Codecov Report

❌ Patch coverage is 75.18248% with 68 lines in your changes missing coverage. Please review.
✅ Project coverage is 84.12%. Comparing base (2fdb84f) to head (b9a0721).

Files with missing lines Patch % Lines
...apids_singlecell/preprocessing/_harmony/_helper.py 67.85% 9 Missing ⚠️
src/rapids_singlecell/preprocessing/_qc.py 69.23% 8 Missing ⚠️
src/rapids_singlecell/get/_aggregated.py 58.82% 7 Missing ⚠️
src/rapids_singlecell/squidpy_gpu/_gearysc.py 44.44% 5 Missing ⚠️
src/rapids_singlecell/squidpy_gpu/_moransi.py 44.44% 5 Missing ⚠️
...apids_singlecell/pertpy_gpu/_metrics/_edistance.py 75.00% 4 Missing ⚠️
src/rapids_singlecell/preprocessing/_scale.py 78.94% 4 Missing ⚠️
src/rapids_singlecell/preprocessing/_normalize.py 86.95% 3 Missing ⚠️
...inglecell/preprocessing/_sparse_pca/_sparse_pca.py 50.00% 3 Missing ⚠️
src/rapids_singlecell/squidpy_gpu/_co_oc.py 82.35% 3 Missing ⚠️
... and 9 more
Additional details and impacted files
@@            Coverage Diff             @@
##             main     #455      +/-   ##
==========================================
- Coverage   85.98%   84.12%   -1.87%     
==========================================
  Files         107       88      -19     
  Lines        6688     6148     -540     
==========================================
- Hits         5751     5172     -579     
- Misses        937      976      +39     
Files with missing lines Coverage Δ
src/rapids_singlecell/_cuda/__init__.py 100.00% <100.00%> (ø)
...rapids_singlecell/preprocessing/_harmony/_fuses.py 100.00% <ø> (ø)
...glecell/preprocessing/_kernels/_mean_var_kernel.py 100.00% <ø> (ø)
...ecell/preprocessing/_neighbors/_helper/__init__.py 80.55% <100.00%> (-1.03%) ⬇️
src/rapids_singlecell/squidpy_gpu/_ligrec.py 82.59% <100.00%> (-1.31%) ⬇️
src/rapids_singlecell/tools/_rank_gene_groups.py 90.29% <85.71%> (+0.10%) ⬆️
src/rapids_singlecell/decoupler_gpu/_helper/_pv.py 62.06% <77.77%> (-0.59%) ⬇️
.../rapids_singlecell/decoupler_gpu/_method_aucell.py 89.79% <60.00%> (-3.96%) ⬇️
...inglecell/preprocessing/_hvg/_pearson_residuals.py 92.22% <91.66%> (-2.29%) ⬇️
...c/rapids_singlecell/preprocessing/_hvg/_poisson.py 91.17% <71.42%> (-2.77%) ⬇️
... and 14 more

... and 3 files with indirect coverage changes

@Intron7 Intron7 added the run-gpu-ci runs GPU CI label Jan 29, 2026
@github-actions github-actions bot removed the run-gpu-ci runs GPU CI label Jan 29, 2026
@Intron7 Intron7 added the run-gpu-ci runs GPU CI label Jan 30, 2026
@github-actions github-actions bot removed the run-gpu-ci runs GPU CI label Jan 30, 2026
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4 participants