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YosefLab / scib-metrics

Accelerated, Python-only, single-cell integration benchmarking metrics
https://scib-metrics.readthedocs.io/
BSD 3-Clause "New" or "Revised" License
49 stars 11 forks source link

progress bar not moving #175

Closed Flu09 closed 2 months ago

Flu09 commented 3 months ago

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bm = Benchmarker( ... obj, ... batch_key="dataset", ... label_key="celltypes, ... embedding_obsm_keys=["unintegrated", "cca", "rpca", "harmony", "scvi"], ... n_jobs=29, ... ) bm.benchmark() Computing neighbors: 100%|██████████| 5/5 [41:56<00:00, 503.33s/it] Embeddings: 0%| | 0/5 [00:00<?, ?it/s] Metrics: 0%| | 0/10 [00:00<?, ?it/s] Metrics: 0%| | 0/10 [00:00<?, ?it/s, Bio conservation: isolated_labels]

It has been like that for 12 hours now. I am not sure how long it is supposed to take. The cells are 1.3 million. I will appreciate it if you can help. Also how to import seurat v5 cca embedding into the adata object please ?

Version information

scib-metrics: 0.5.1 anndata: 0.10.8 chex: 0.1.85 igraph: 0.10.8 jax: 0.4.25 jaxlib: 0.4.25 matplotlib: 3.8.3 numpy: 1.26.4 pandas: 2.2.1 plottable: 0.1.5 pynndescent: 0.5.11 rich: 13.7.1 scanpy: 1.9.8 scikit-learn: 1.4.1.post1 scipy: 1.11.4 tqdm: 4.66.2 umap-learn: 0.5.5 texttable: 1.7.0 get-annotations: 0.1.2 h5py: 3.10.0 joblib: 1.3.2 natsort: 8.4.0 networkx: 3.2.1 numba: 0.59.0 packaging: 23.2 patsy: 0.5.6 seaborn: 0.13.2 session-info: 1.0.0 statsmodels: 0.14.1 array-api-compat: 1.4.1 exceptiongroup: 1.2.0 contourpy: 1.2.0 cycler: 0.12.1 fonttools: 4.49.0 kiwisolver: 1.4.5 pillow: 10.2.0 pyparsing: 3.1.2 python-dateutil: 2.9.0.post0 importlib-resources: 6.1.2 pytz: 2024.1 tzdata: 2024.1 threadpoolctl: 3.3.0 llvmlite: 0.42.0 absl-py: 2.1.0 typing-extensions: 4.10.0 toolz: 0.12.1 ml-dtypes: 0.3.2 opt-einsum: 3.3.0 importlib-metadata: 6.11.0 markdown-it-py: 3.0.0 pygments: 2.17.2 zipp: 3.17.0 mdurl: 0.1.2 six: 1.16.0 stdlib-list: 0.10.0

canergen commented 2 months ago

Hi, see my response on discourse.