data/10_1038_s41380_020_0844_z

[irena-starters]

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_1038_s41380_020_0844_z/homosapiens_brain_2020_quartzseq_sawada_001.py:23: 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. temp = ad.AnnData(X=scipy.sparse.csr_matrix(d), /lustre/groups/ml01/code/irena.sliskovic/sfaira/sfaira/data/dataloaders/loaders/d10_1038_s41380_020_0844_z/homosapiens_brain_2020_quartzseq_sawada_001.py:23: 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. temp = ad.AnnData(X=scipy.sparse.csr_matrix(d), /lustre/groups/ml01/code/irena.sliskovic/sfaira/sfaira/data/dataloaders/loaders/d10_1038_s41380_020_0844_z/homosapiens_brain_2020_quartzseq_sawada_001.py:23: 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. temp = ad.AnnData(X=scipy.sparse.csr_matrix(d), /lustre/groups/ml01/code/irena.sliskovic/sfaira/sfaira/data/dataloaders/loaders/d10_1038_s41380_020_0844_z/homosapiens_brain_2020_quartzseq_sawada_001.py:23: 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. temp = ad.AnnData(X=scipy.sparse.csr_matrix(d), /lustre/groups/ml01/code/irena.sliskovic/sfaira/sfaira/data/dataloaders/loaders/d10_1038_s41380_020_0844_z/homosapiens_brain_2020_quartzseq_sawada_001.py:23: 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. temp = ad.AnnData(X=scipy.sparse.csr_matrix(d), /lustre/groups/ml01/code/irena.sliskovic/sfaira/sfaira/data/dataloaders/loaders/d10_1038_s41380_020_0844_z/homosapiens_brain_2020_quartzseq_sawada_001.py:23: 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. temp = ad.AnnData(X=scipy.sparse.csr_matrix(d), /lustre/groups/ml01/code/irena.sliskovic/sfaira/sfaira/data/dataloaders/loaders/d10_1038_s41380_020_0844_z/homosapiens_brain_2020_quartzseq_sawada_001.py:23: 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. temp = ad.AnnData(X=scipy.sparse.csr_matrix(d), /lustre/groups/ml01/code/irena.sliskovic/sfaira/sfaira/data/dataloaders/loaders/d10_1038_s41380_020_0844_z/homosapiens_brain_2020_quartzseq_sawada_001.py:23: 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. temp = ad.AnnData(X=scipy.sparse.csr_matrix(d), /home/icb/irena.sliskovic/miniconda3/envs/sfaira/lib/python3.10/site-packages/anndata/_core/anndata.py:1828: UserWarning: Observation names are not unique. To make them unique, call .obs_names_make_unique. utils.warn_names_duplicates("obs") transformed feature space on homosapiens_brain_2020_quartzseq_sawadatomoyo_001_d10_1038_s41380_020_0844_z: log10 total counts 7.79 to 7.58, non-zero features 34980 to 23802 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:

• homosapiens_brain_2020_quartzseq_sawadatomoyo_001_d10_1038_s41380_020_0844_z