write seems to be broken on master

adata = sc.datasets.pbmc3k() adata.write('test.h5ad') sc.read('test.h5ad') and after trying to read i get

Error

--------------------------------------------------------------------------- AttributeError Traceback (most recent call last) <ipython-input-11-ea34a1ff06f9> in <module> ----> 1 sc.read('test.h5ad')

~\Apps\Miniconda3\envs\work38\lib\site-packages\scanpy\readwrite.py in read(filename, backed, sheet, ext, delimiter, first_column_names, backup_url, cache, cache_compression, **kwargs) 110 filename = Path(filename) # allow passing strings 111 if is_valid_filename(filename): –> 112 return _read( 113 filename, 114 backed=backed,

~\Apps\Miniconda3\envs\work38\lib\site-packages\scanpy\readwrite.py in _read(filename, backed, sheet, ext, delimiter, first_column_names, backup_url, cache, cache_compression, suppress_cache_warning, **kwargs) 711 if ext in {‘h5’, ‘h5ad’}: 712 if sheet is None: –> 713 return read_h5ad(filename, backed=backed) 714 else: 715 logg.debug(f’reading sheet {sheet} from file {filename}')

~\Apps\Miniconda3\envs\work38\lib\site-packages\anndata_io\h5ad.py in read_h5ad(filename, backed, as_sparse, as_sparse_fmt, chunk_size) 236 elif k in {“obs”, “var”}: 237 # Backwards compat –> 238 d[k] = read_dataframe(f[k]) 239 else: # Base case 240 d[k] = read_elem(f[k])

~\Apps\Miniconda3\envs\work38\lib\site-packages\anndata_io\h5ad.py in read_dataframe(group) 301 return read_dataframe_legacy(group) 302 else: –> 303 return read_elem(group) 304 305

~\Apps\Miniconda3\envs\work38\lib\site-packages\anndata_io\specs\registry.py in read_elem(elem, modifiers) 178 def read_elem(elem, modifiers: frozenset(str) = frozenset()): 179 “”“Read an element from an on disk store.”“” –> 180 return _REGISTRY.get_reader(type(elem), get_spec(elem), frozenset(modifiers))(elem) 181 182

~\Apps\Miniconda3\envs\work38\lib\site-packages\anndata_io\specs\methods.py in read_dataframe(elem) 520 df = pd.DataFrame( 521 {k: read_elem(elem[k]) for k in columns}, –> 522 index=read_elem(elem[idx_key]), 523 columns=list(columns), 524 )

~\Apps\Miniconda3\envs\work38\lib\site-packages\anndata_io\specs\registry.py in read_elem(elem, modifiers) 178 def read_elem(elem, modifiers: frozenset(str) = frozenset()): 179 “”“Read an element from an on disk store.”“” –> 180 return _REGISTRY.get_reader(type(elem), get_spec(elem), frozenset(modifiers))(elem) 181 182

~\Apps\Miniconda3\envs\work38\lib\site-packages\anndata_io\specs\methods.py in read_string_array(d) 323 @_REGISTRY.register_read(H5Array, IOSpec(“string-array”, “0.2.0”)) 324 def read_string_array(d): –> 325 return read_array(d.asstr()) 326 327

AttributeError: ‘Dataset’ object has no attribute ‘asstr’

Versions

PIL 8.1.2 absl NA anndata 0.7.7.dev20+g286bc7f autoreload NA backcall 0.2.0 brotli NA cairo 1.20.0 certifi 2021.05.30 cffi 1.14.5 chardet 4.0.0 cloudpickle 1.6.0 colorama 0.4.4 cycler 0.10.0 cython_runtime NA cytoolz 0.11.0 dask 2021.03.0 dateutil 2.8.1 decorator 4.4.2 deprecate 0.3.0 docrep 0.3.2 fsspec 2021.11.0 google NA h5py 2.10.0 idna 2.10 igraph 0.8.3 ipykernel 5.3.4 ipython_genutils 0.2.0 ipywidgets 7.6.3 jedi 0.17.0 joblib 1.0.1 kiwisolver 1.3.1 leidenalg 0.8.3 llvmlite 0.35.0 louvain 0.7.0 matplotlib 3.3.4 mkl 2.3.0 mpl_toolkits NA natsort 7.1.1 nt NA ntsecuritycon NA numba 0.52.0 numexpr 2.7.3 numpy 1.19.2 opt_einsum v3.1.0 packaging 20.9 pandas 1.2.3 parso 0.8.1 pickleshare 0.7.5 pkg_resources NA prompt_toolkit 3.0.8 psutil 5.8.0 pycparser 2.20 pygments 2.8.1 pyparsing 2.4.7 pyro 1.6.0 pythoncom NA pytorch_lightning 1.3.8 pytz 2021.1 pywintypes NA regex 2.5.91 requests 2.25.1 rich NA scanpy 1.8.0.dev65+g0712d9ab scarches 0.4.1 scipy 1.6.1 scvi 0.14.3 seaborn 0.11.1 setuptools_scm NA sinfo 0.3.1 six 1.15.0 sklearn 0.24.1 socks 1.7.1 sphinxcontrib NA statsmodels 0.12.2 storemagic NA tables 3.6.1 tblib 1.7.0 tensorboard 2.4.1 texttable 1.6.3 threadpoolctl 2.1.0 tlz 0.11.0 toolz 0.11.1 torch 1.8.0 torchmetrics 0.6.0 torchvision 0.9.0 tornado 6.1 tqdm 4.59.0 traitlets 5.0.5 typing_extensions NA urllib3 1.26.4 wcwidth 0.2.5 win32api NA win32com NA win32security NA yaml 5.4.1 zmq 20.0.0 zope NA ----- IPython 7.21.0 jupyter_client 6.1.7 jupyter_core 4.7.1 notebook 6.2.0 ----- Python 3.8.8 (default, Feb 24 2021, 15:54:32) [MSC v.1928 64 bit (AMD64)] Windows-10-10.0.19041-SP0 8 logical CPU cores, Intel64 Family 6 Model 142 Stepping 12, GenuineIntel

Reading adata files written with older versions is fine. I am on 0.8.0.dev0 now and it is fine.