GPU accelerated read_mtx #2
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* removed plotting * cunnData deprecated * added anndata and 64 bit support * switch from scanpy_gpu to tools * start to updating docs * update test to work with anndata * swtiched harmony to pp * switched harmony to pp * updated docs * fix docs * added utils * updated documentation * updated docs * move to anndata * updated doc strings * use next anndata * adata version * updated docs * try to fix utils docs * update for dense hvg * added dense normalization test * update and test utils * update test * Update docs/Usage_Principles.md Co-authored-by: Lukas Heumos <[email protected]> * Update docs/Usage_Principles.md Co-authored-by: Lukas Heumos <[email protected]> * Update docs/Usage_Principles.md Co-authored-by: Lukas Heumos <[email protected]> * Update docs/Usage_Principles.md Co-authored-by: Lukas Heumos <[email protected]> * Update docs/Usage_Principles.md Co-authored-by: Lukas Heumos <[email protected]> * Update docs/Usage_Principles.md Co-authored-by: Lukas Heumos <[email protected]> * update api docs * updated docs * test docs * fix docs * added release-notes * updated 0.8.1 * fix for realease-notedocs * fixed links * try to fix release-notes * bumped scanpydoc * test css * make c array safe * enables cunndata to anndata_GPU * update notebooks * updated docs * maybe fix docs * update utils docstring * reset docs * added extlinks * fixes AnnData * update AnnData * added AnnData * updated docs * fixes broken link * test releasenotes * updated conf.py * creates utils in docs * renamed Params Parameters * switched to boolean index * added batching * prepare for transformer API * enhance harmony reproducability * harmony 64 bit * work with dense matrices * added release node * updated ruff * update notebooks * remove cpx raw import * remove cugraph default import * fixed import * make doc-strings pretty * added leiden disclaimer to notebooks * added test for harmonypy * added import test * added profimp for testing * updated anndata-dep --------- Co-authored-by: Lukas Heumos <[email protected]> Co-authored-by: Philipp A <[email protected]>
updates: - [github.com/psf/black: 23.7.0 → 23.9.1](psf/black@23.7.0...23.9.1) - [github.com/astral-sh/ruff-pre-commit: v0.0.287 → v0.0.288](astral-sh/ruff-pre-commit@v0.0.287...v0.0.288) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
* added batchsize for embedding density * adds release note
* adds subclustering to leiden and louvain * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci --------- Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
updates: - [github.com/astral-sh/ruff-pre-commit: v0.0.288 → v0.0.290](astral-sh/ruff-pre-commit@v0.0.288...v0.0.290) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
* updates docs * adds install
* removed small
* Fixes for cupy anndata * added release note * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci --------- Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
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Oh looks like I used the wrong repo, I will open it on scverse |
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I bring my initial implementation of
read_mtx_gpufrom gpu branch of scanpy, now available atrsc.read_mtx! Here are some infos:cudfto load the mtx. There is alsodask-cudfbakend option available as it might help for out of memory loading, but I do not think it is then necessary to includedask-cudfas a pip requirement (but can be otherwise).