This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Scalene: An exception of type UnicodeDecodeError occurred. Arguments: | |
('ascii', b'/* PrismJS 1.26.0\nhttps://prismjs.com/download.html#themes=prism&languages=markup+css+clike+javascript+python&plugins=normalize-whitespace */\n/// <reference lib="WebWorker"/>\n\nvar _self =\n typeof window !== "undefined"\n ? window // if in browser\n : typeof WorkerGlobalScope !== "undefined" &&\n self instanceof WorkerGlobalScope\n ? self // if in worker\n : {}; // if in node js\n\n/**\n * Prism: Lightweight, robust, elegant syntax highlighting\n *\n * @license MIT <https://opensource.org/licenses/MIT>\n * @author Lea Verou <https://lea.verou.me>\n * @namespace\n * @public\n */\nvar Prism = (function (_self) {\n // Private helper vars\n var lang = /(?:^|\\s)lang(?:uage)?-([\\w-]+)(?=\\s|$)/i;\n var uniqueId = 0;\n\n // The grammar object for plaintext\n var plainTextGrammar = {};\n\n var _ = {\n /**\n * By default, Prism will attempt to highlight all code elements (by calling {@link Prism.highl |
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
git checkout dask-hvg | |
python run_hvg.py | |
# 544.9354245662689 | |
git checkout dask-hvg-w-pandas | |
python run_hvg.py | |
# 130.07193517684937 |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
# conda deactivate | |
mamba env remove -yn anndata-min-deps-test | |
mamba create -yn anndata-min-deps-test "python=3.9" | |
PACKAGES=`python3 ci/scripts/min-deps.py pyproject.toml --extra dev test` | |
# conda activate anndata-min-deps-test | |
# conda run -n anndata-min-deps-test pip install cupy-cuda12x |
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
import zarr | |
import pandas as pd, numpy as np | |
from anndata.experimental import read_elem, write_elem | |
from anndata._core.sparse_dataset import SparseDataset | |
def _df_index(df: zarr.Group) -> np.ndarray: | |
index_key = df.attrs["_index"] | |
return read_elem(df[index_key]) |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
# Docs: https://docs.h5py.org/en/stable/vds.html | |
import h5py | |
import numpy as np | |
def virtual_concatenate(datasets: list[h5py.Dataset]) -> h5py.VirtualLayout: | |
"""Concatenate datasets along the first axis.""" | |
vds = h5py.VirtualLayout(shape=sum(d.shape[0] for d in datasets), dtype=datasets[0].dtype) | |
offset = 0 | |
for d in datasets: |
NewerOlder