Remove some TODOs #455

Job	Run time
Build-environments (jupyter-book/introduction/analysis_tools.yml)	55s
Build-environments (jupyter-book/preprocessing_visualization/preprocessing.yml)	1m 46s
Build-environments (jupyter-book/cellular_structure/clustering.yml)	1m 8s
Build-environments (jupyter-book/cellular_structure/annotation.yml)	2m 53s
Build-environments (jupyter-book/cellular_structure/integration.yml)	2m 22s
Build-environments (jupyter-book/conditions/compositional.yml)	3m 15s
Build-environments (jupyter-book/conditions/gsea_pathway.yml)	2m 9s
Build-environments (jupyter-book/conditions/perturbation_modeling.yml)	4m 45s
Build-environments (jupyter-book/conditions/differential_gene_expression.yml)	3m 30s
Build-environments (jupyter-book/trajectories/lineage_tracing.yml)	2m 25s
Build-environments (jupyter-book/trajectories/pseudotemporal.yml)	59s
Build-environments (jupyter-book/mechanisms/cell_cell_communication.yml)	1m 55s
Build-environments (jupyter-book/spatial/spatial.yml)	2m 50s
Build-environments (jupyter-book/surface_protein/surface_protein.yml)	2m 41s
Build-environments (jupyter-book/multimodal_integration/paired_integration.yml)	1s
Build-environments (jupyter-book/multimodal_integration/advanced_integration.yml)	3m 43s
	37m 17s

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