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Start backed sparse support for zarr

1

Initial draft of backed sparse array support for zarr. - [ ] I intend to export `sparse_dataset`, `CSRDataset`, and `CSCDataset` class from `experimental`. - [ ] Get tests passing -...

ivirshup

Per element metadata

1

It would be nice to have metadata per element in the anndata object. That is, `X` and each layer could have metadata attached. * All of our on disk formats...

ivirshup

Implement concat with category merging

1

Fixes #756 Performance is suprisingly low. It seems that the type-unstable pandas operation can be quite inefficient. This will provide speedups for mid size datasets with real cell type names,...

ivirshup

Creating AnnCollections from AnnDatas with dataframes in obsm errors

4

Discovered while trying to answer [this discourse question](https://discourse.scverse.org/t/concat-anndata-objects-on-disk/400/2) about concatenating backed `AnnData` objects. Ping @Koncopd ## Example: ```python from pathlib import Path from shutil import rmtree import anndata as ad,...

ivirshup

Calling write_h5ad without converting strings to categoricals

3

Hi AnnData team, It seems I am unable to write to h5ad without having `strings_to_categoricals` be called. https://github.com/theislab/anndata/blob/dad9a085afdfb8d23b30cbbbe890acffdae4d621/anndata/_io/h5ad.py#L85 I am using the output h5ad file in Java, not with scanPy,...

ljjh20

Lambda indexer for anndata

6

With pandas data frames a pattern I use very commonly is ```python df_with_very_long_descriptive_name.loc[lambda x: x["fruit"] == "banana", :] ``` I was wondering if it would be possible to have lambda-based...

grst

When concatenating categoricals whose categories don't match, pandas converts the columns to strings. We should try to avoid this because it's (a) weird and (b) inefficient. A quick proof of...

ivirshup

Unable to `write` in backed mode when `X` doesn't exist

4

Version: 0.8.0rc1 Example: ```python >>> import anndata as ad >>> a = ad.AnnData(shape=(10, 20)) >>> a AnnData object with n_obs × n_vars = 10 × 20 >>> a.write("1.h5ad") >>> b...

kaizhang

Obs reassignment silently allows you to change obs_names

6

When adding a whole obs to adata that already has obs_names the index matching is not checked. I would expect adata to complain if newly assigned obs has different index...

Hrovatin

Improve interpretability of IOSpec errors

4

This adds error messages based on what wasn’t found. There’s 3-4 levels of detail (3 for writing, 4 for reading) 1. Nothing registered for source type (write) / destination type...

flying-sheep