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(atlas-anndata) yalan@C02WL01MHV2Q anndata_test % make_bundle_from_anndata --anndata-file human_fetus_immune.h5ad E-ANND-5 init --droplet
..Checking for gene_meta gene_name
..Checking for gene_meta index
Validating config against /Users/yalan/opt/miniconda3/envs/atlas-anndata/lib/python3.8/site-packages/atlas_anndata/config_schema.yaml
WARNING: FILL ME fields are present in the config. Please make sure this is resolved before running this script for the final time.
Config YAML file successfully validated
Now checking config against anndata file
..Checking for matrices X
..Checking for cell_meta n_counts
..Checking for cell_meta n_genes
..Checking for cell_meta file
..Checking for cell_meta mito
..Checking for cell_meta doublet_scores
..Checking for cell_meta predicted_doublets
..Checking for cell_meta old_annotation_uniform
..Checking for cell_meta organ
..Checking for cell_meta Sort_id
..Checking for cell_meta age
..Checking for cell_meta method
..Checking for cell_meta donor
..Checking for cell_meta sex
..Checking for cell_meta Sample
..Checking for cell_meta scvi_clusters
..Checking for cell_meta is_maternal_contaminant
..Checking for cell_meta anno_lvl_2_final_clean
..Checking for cell_meta celltype_annotation
..Checking for dimension_reductions X_scvi
..Checking for dimension_reductions X_umap
..Checking for matrices FILL ME with a string
..Checking for gene_meta index
..Checking for gene_meta FILL ME with a string
..Checking for cell_meta FILL ME with a string
annData file successfully validated against config /Users/yalan/Documents/curation_work/anndata_test/E-ANND-5/anndata-config.yaml
Writing var(gene) metadata
Writing obs metadata of kind: curation
Extracting metadata from annData object...
...deriving runs and barcodes by parsing cell IDs
..extracting metadata consistent within samples
..assigning other metadata as cell_specific
Writing annData file
/Users/yalan/opt/miniconda3/envs/atlas-anndata/lib/python3.8/site-packages/anndata/_core/anndata.py:1228: FutureWarning: The `inplace` parameter in pandas.Categorical.reorder_categories is deprecated and will be removed in a future version. Reordering categories will always return a new Categorical object.
  c.reorder_categories(natsorted(c.categories), inplace=True)
... storing 'sample' as categorical

(atlas-anndata) yalan@C02WL01MHV2Q anndata_test % make_bundle_from_anndata E-ANND-5 init_magetab 
Validating config against /Users/yalan/opt/miniconda3/envs/atlas-anndata/lib/python3.8/site-packages/atlas_anndata/config_schema.yaml
WARNING: FILL ME fields are present in the config. Please make sure this is resolved before running this script for the final time.
Config YAML file successfully validated
Now checking config against anndata file
..Checking for matrices X
..Checking for cell_meta n_counts
..Checking for cell_meta n_genes
..Checking for cell_meta file
..Checking for cell_meta mito
..Checking for cell_meta doublet_scores
..Checking for cell_meta predicted_doublets
..Checking for cell_meta old_annotation_uniform
..Checking for cell_meta organ
..Checking for cell_meta Sort_id
..Checking for cell_meta age
..Checking for cell_meta method
..Checking for cell_meta donor
..Checking for cell_meta sex
..Checking for cell_meta Sample
..Checking for cell_meta scvi_clusters
..Checking for cell_meta is_maternal_contaminant
..Checking for cell_meta anno_lvl_2_final_clean
..Checking for cell_meta celltype_annotation
..Checking for dimension_reductions X_scvi
..Checking for dimension_reductions X_umap
..Checking for matrices FILL ME with a string
..Checking for gene_meta GeneID
..Checking for gene_meta GeneName
..Checking for cell_meta file
annData file successfully validated against config /Users/yalan/Documents/curation_work/anndata_test/E-ANND-5/anndata-config.yaml
Writing cell/library mapping for a droplet experiment
Writing var(gene) metadata
Writing obs metadata of kind: curation
Extracting metadata from annData object...
...deriving runs using supplied sample ID column file
..extracting metadata consistent within samples
..assigning other metadata as cell_specific
Writing obs (unsupervised clusterings)
Writing markers and statistics
No cell groupings have markers specified, skipping writing of markers and stats
Writing dimension reductions
.. Writing dimension reduction from slot: X_scvi
.. Writing dimension reduction from slot: X_umap
Writing annData file

$ make_bundle_from_anndata --scxa-metadata-branch gtex_sc E-ANND-2 inject_magetab

    from conda.common.compat import ensure_text_type, init_std_stream_encoding
ImportError: cannot import name 'init_std_stream_encoding' from 'conda.common.compat' (/hps/software/users/ma/fg_atlas/miniconda3/lib/python3.9/site-packages/conda/common/compat.py)

$ conda install -c conda-forge mamba