Upgrading from 0.7.5 to 0.7.6 throws TypeError when saving h5ad

When loading an h5ad and combining it with various annotations, the object is saved as:

mergedData.write(par["output"], compression = "gzip")     

This results in the following exception

Traceback (most recent call last):
  File "/usr/local/lib/python3.8/site-packages/anndata/_io/utils.py", line 209, in func_wrapper
    return func(elem, key, val, *args, **kwargs)
  File "/usr/local/lib/python3.8/site-packages/anndata/_io/h5ad.py", line 270, in write_series
    group.create_dataset(
  File "/usr/local/lib/python3.8/site-packages/h5py/_hl/group.py", line 148, in create_dataset
    dsid = dataset.make_new_dset(group, shape, dtype, data, name, **kwds)
  File "/usr/local/lib/python3.8/site-packages/h5py/_hl/dataset.py", line 140, in make_new_dset
    dset_id.write(h5s.ALL, h5s.ALL, data)
  File "h5py/_objects.pyx", line 54, in h5py._objects.with_phil.wrapper
  File "h5py/_objects.pyx", line 55, in h5py._objects.with_phil.wrapper
  File "h5py/h5d.pyx", line 232, in h5py.h5d.DatasetID.write
  File "h5py/_proxy.pyx", line 145, in h5py._proxy.dset_rw
  File "h5py/_conv.pyx", line 444, in h5py._conv.str2vlen
  File "h5py/_conv.pyx", line 95, in h5py._conv.generic_converter
  File "h5py/_conv.pyx", line 249, in h5py._conv.conv_str2vlen
TypeError: Can't implicitly convert non-string objects to strings

The above exception was the direct cause of the following exception:

Traceback (most recent call last):
  File "/usr/local/lib/python3.8/site-packages/anndata/_io/utils.py", line 209, in func_wrapper
    return func(elem, key, val, *args, **kwargs)
  File "/usr/local/lib/python3.8/site-packages/anndata/_io/h5ad.py", line 263, in write_dataframe
    write_series(group, col_name, series, dataset_kwargs=dataset_kwargs)
  File "/usr/local/lib/python3.8/site-packages/anndata/_io/utils.py", line 212, in func_wrapper
    raise type(e)(
TypeError: Can't implicitly convert non-string objects to strings

Above error raised while writing key 'highly_variable' of <class 'h5py._hl.group.Group'> from /.

The above exception was the direct cause of the following exception:

Traceback (most recent call last):
  File "/tmp/viash-run-mergeabtogex-GbM6xh", line 73, in <module>
    mergedData.write(par["output"], compression = "gzip")     
  File "/usr/local/lib/python3.8/site-packages/anndata/_core/anndata.py", line 1905, in write_h5ad
    _write_h5ad(
  File "/usr/local/lib/python3.8/site-packages/anndata/_io/h5ad.py", line 112, in write_h5ad
    write_attribute(f, "var", adata.var, dataset_kwargs=dataset_kwargs)
  File "/usr/local/lib/python3.8/functools.py", line 875, in wrapper
    return dispatch(args[0].__class__)(*args, **kw)
  File "/usr/local/lib/python3.8/site-packages/anndata/_io/h5ad.py", line 130, in write_attribute_h5ad
    _write_method(type(value))(f, key, value, *args, **kwargs)
  File "/usr/local/lib/python3.8/site-packages/anndata/_io/utils.py", line 212, in func_wrapper
    raise type(e)(
TypeError: Can't implicitly convert non-string objects to strings

Above error raised while writing key 'highly_variable' of <class 'h5py._hl.group.Group'> from /.

Above error raised while writing key 'var' of <class 'h5py._hl.files.File'> from /.

This is specific for version 0.7.6 as the build tests that we perform do work for the same data on 0.7.5. Please note that this also impacts the scirpy package as the following code also returns a similar exception, just on a different column:

import anndata
import scanpy as sc
import scirpy

data = sc.read_h5ad(par["input"])
contigs = scirpy.io.read_10x_vdj(par["input_vdj"])

scirpy.pp.merge_with_ir(data, contigs)

data.write(par["output"], compression = "gzip")

[ddemaeyer]

We are indeed merging different datasets together in this component on the var slot. This results in the following dtypes on the var slots

gene_ids              object
feature_types       category
genome              category
highly_variable       object
means                float64
dispersions          float64
dispersions_norm     float32

The problem is that during the merge we have a var column that does not exist in a dataset. Therefore adding with pandas.concat results in an object type instead of bool. As a quick fix I tried using the convert_dtypes() functionality but this results in setting the boolean dtype which does not solve the issue either.

For the time being I’m going to pin the version of anndata for these components.

[ivirshup]

Closing as duplicate of #504