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theislab / sfaira

data and model repository for single-cell data
https://sfaira.readthedocs.io
BSD 3-Clause "New" or "Revised" License
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data/d10_1016_j_stem_2018_12_015 #713

Closed irena-starters closed 1 year ago

irena-starters commented 1 year ago

Installed version v0.3.12+52.gf105a1f of sfaira is newer than the latest release 0.3.12! You are running a nightly version and features may break! Run sfaira upgrade to get the latest version. Running loader lint checks ━━━━━━━━━━━━━ 1 of 2 _validate_namespace Running loader lint checks ━━━━━━━━ 1 of 2 _validate_namespace
Running yaml lint checks ━━━━━━━━━━━━━━━━ 2 of 2 _validate_required_attributes

──────────────────────────────── LINT RESULTS ─────────────────────────────────

 [[✔]]    3 tests passed
 [[!]]    0 tests had warnings
 [[✗]]    0 tests failed

────────────────────────────── [[✔]] Tests Passed ────────────────────────────── ╭──────────────────────────────────────────────────────────────────────────────╮ │ Result: Passed required data loader load() namespace checks. │ │ Result: Passed required data loader section checks. │ │ Result: Passed required meta data checks. │ ╰──────────────────────────────────────────────────────────────────────────────╯ Conflicts are not automatically resolved. In case of coflicts, please go back to https://www.ebi.ac.uk/ols/ontologies/cl and add the correct cell ontology class name into the .tsv "target" column. WARNING:nxontology.imports:Cannot add edge: MmusDv:0000000 --> MmusDv:0000038 (mouse life cycle stage --> infant stage): node does not exist in graph: MmusDv:0000038 WARNING:nxontology.imports:Cannot add edge: MmusDv:0000000 --> MmusDv:0000043 (mouse life cycle stage --> immature stage): node does not exist in graph: MmusDv:0000043 WARNING:nxontology.imports:Cannot add edge: MmusDv:0000000 --> MmusDv:0000044 (mouse life cycle stage --> 1-7 days): node does not exist in graph: MmusDv:0000044 WARNING:nxontology.imports:Cannot add edge: MmusDv:0000000 --> MmusDv:0000096 (mouse life cycle stage --> early immature stage): node does not exist in graph: MmusDv:0000096 /lustre/groups/ml01/code/irena.sliskovic/sfaira/sfaira/data/dataloaders/loaders/d10_1016_j_stem_2018_12_015/homosapiens_dorsalplusventralthalamus_2019_10x3v1_xiang_001.py:36: FutureWarning: X.dtype being converted to np.float32 from int64. In the next version of anndata (0.9) conversion will not be automatic. Pass dtype explicitly to avoid this warning. Pass AnnData(X, dtype=X.dtype, ...) to get the future behavour. adata = ad.AnnData( /lustre/groups/ml01/code/irena.sliskovic/sfaira/sfaira/data/dataloaders/loaders/d10_1016_j_stem_2018_12_015/homosapiens_dorsalplusventralthalamus_2019_10x3v1_xiang_001.py:36: FutureWarning: X.dtype being converted to np.float32 from int64. In the next version of anndata (0.9) conversion will not be automatic. Pass dtype explicitly to avoid this warning. Pass AnnData(X, dtype=X.dtype, ...) to get the future behavour. adata = ad.AnnData( /lustre/groups/ml01/code/irena.sliskovic/sfaira/sfaira/data/dataloaders/loaders/d10_1016_j_stem_2018_12_015/homosapiens_dorsalplusventralthalamus_2019_10x3v1_xiang_001.py:36: FutureWarning: X.dtype being converted to np.float32 from int64. In the next version of anndata (0.9) conversion will not be automatic. Pass dtype explicitly to avoid this warning. Pass AnnData(X, dtype=X.dtype, ...) to get the future behavour. adata = ad.AnnData( /lustre/groups/ml01/code/irena.sliskovic/sfaira/sfaira/data/dataloaders/loaders/d10_1016_j_stem_2018_12_015/homosapiens_dorsalplusventralthalamus_2019_10x3v1_xiang_001.py:36: FutureWarning: X.dtype being converted to np.float32 from int64. In the next version of anndata (0.9) conversion will not be automatic. Pass dtype explicitly to avoid this warning. Pass AnnData(X, dtype=X.dtype, ...) to get the future behavour. adata = ad.AnnData( /lustre/groups/ml01/code/irena.sliskovic/sfaira/sfaira/data/dataloaders/loaders/d10_1016_j_stem_2018_12_015/homosapiens_dorsalplusventralthalamus_2019_10x3v1_xiang_001.py:36: FutureWarning: X.dtype being converted to np.float32 from int64. In the next version of anndata (0.9) conversion will not be automatic. Pass dtype explicitly to avoid this warning. Pass AnnData(X, dtype=X.dtype, ...) to get the future behavour. adata = ad.AnnData( transformed feature space on homosapiens_dorsalplusventralthalamus_2019_10x3v1_xiangyangfei_001_d10_1016_j_stem_2018_12_015: log10 total counts 8.05 to 8.05, non-zero features 24836 to 23849 transformed feature space on homosapiens_dorsalplusventralthalamus_2019_10x3v1_xiangyangfei_002_d10_1016_j_stem_2018_12_015: log10 total counts 8.05 to 8.05, non-zero features 24836 to 23849 transformed feature space on homosapiens_dorsalplusventralthalamus_2019_10x3v1_xiangyangfei_003_d10_1016_j_stem_2018_12_015: log10 total counts 8.05 to 8.05, non-zero features 24836 to 23849 transformed feature space on homosapiens_dorsalplusventralthalamus_2019_10x3v1_xiangyangfei_004_d10_1016_j_stem_2018_12_015: log10 total counts 8.05 to 8.05, non-zero features 24836 to 23849 transformed feature space on homosapiens_dorsalplusventralthalamus_2019_10x3v1_xiangyangfei_005_d10_1016_j_stem_2018_12_015: log10 total counts 8.05 to 8.05, non-zero features 24836 to 23849 Completed testing of data loader, the data loader is now ready for use. Sfaira butler: "You data loader is finished!" "Proceed to phase 4 (publish) or use data loader." "Copy the following lines as a post into the pull request:"

Data loader test passed: