Can't implicitly convert non-string objects to strings. Bug about tl.filter_rank_genes_groups and tl.rank_genes_groups

[christophechu]

Please make sure these conditions are met

• I have checked that this issue has not already been reported.
• I have confirmed this bug exists on the latest version of anndata.
• (optional) I have confirmed this bug exists on the master branch of anndata.

Report

When I use scanpy
sc.tl.filter_rank_genes_groups or sc.tl.filter_rank_genes_groups, I can not write the result file until I delete the output files stored as adata.uns['rank_genes_groups_filtered'] and adata.uns['rank_genes_groups']

Code:

sc.tl.filter_rank_genes_groups
sc.tl.filter_rank_genes_groups
adata.write
Both default use

Traceback:

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

Versions

-----
anndata             0.9.2
matplotlib          3.6.3
omicverse           1.5.0
scanpy              1.9.5
scib                1.1.4
scvi                1.0.3
seaborn             0.12.2
session_info        1.0.0
-----
Cython                      3.0.2
PIL                         9.3.0
absl                        NA
aiohttp                     3.8.5
aiosignal                   1.3.1
annotated_types             0.5.0
anyio                       NA
arrow                       1.2.3
astor                       0.8.1
asttokens                   NA
async_timeout               4.0.3
attr                        23.1.0
attrs                       23.1.0
autograd                    NA
autograd_gamma              NA
babel                       2.12.1
backcall                    0.2.0
backoff                     2.2.1
boltons                     NA
bs4                         4.12.2
certifi                     2022.12.07
cffi                        1.15.1
charset_normalizer          2.1.1
chex                        0.1.7
click                       8.1.7
cloudpickle                 2.2.1
colorama                    0.4.6
comm                        0.1.4
contextlib2                 NA
croniter                    NA
cycler                      0.10.0
cython                      3.0.2
cython_runtime              NA
cytoolz                     0.12.2
dask                        2023.9.2
datashader                  0.15.2
datashape                   0.5.2
dateutil                    2.8.2
debugpy                     1.8.0
decorator                   5.1.1
deepdiff                    6.5.0
defusedxml                  0.7.1
deprecated                  1.2.14
dill                        0.3.7
docrep                      0.3.2
dot_parser                  NA
etils                       1.4.1
exceptiongroup              1.1.3
executing                   1.2.0
fastapi                     0.103.1
fastjsonschema              NA
filelock                    3.9.0
flax                        0.7.4
fontTools                   4.42.1
formulaic                   0.6.4
fqdn                        NA
frozenlist                  1.4.0
fsspec                      2023.9.1
future                      0.18.3
gdown                       4.7.1
google                      NA
graphlib                    NA
h5py                        3.9.0
hnswlib                     NA
idna                        3.4
igraph                      0.10.8
importlib_metadata          NA
importlib_resources         NA
interface_meta              1.3.0
ipykernel                   6.25.2
ipywidgets                  8.1.1
isoduration                 NA
jax                         0.4.14
jaxlib                      0.4.14
jedi                        0.19.0
jinja2                      3.1.2
joblib                      1.3.2
json5                       NA
jsonpointer                 2.4
jsonschema                  4.19.0
jsonschema_specifications   NA
jupyter_events              0.7.0
jupyter_server              2.7.3
jupyterlab_server           2.25.0
kiwisolver                  1.4.5
lazy_loader                 NA
leidenalg                   0.10.1
lifelines                   0.27.8
lightning                   2.0.9
lightning_cloud             NA
lightning_utilities         0.9.0
llvmlite                    0.40.1
lxml                        4.9.3
markupsafe                  2.1.2
matplotlib_inline           0.1.6
ml_collections              NA
ml_dtypes                   0.2.0
mpl_toolkits                NA
mpmath                      1.2.1
msgpack                     1.0.5
mudata                      0.2.3
multidict                   6.0.4
multipart                   0.0.6
multipledispatch            0.6.0
multiprocess                0.70.15
natsort                     8.4.0
nbformat                    5.9.2
networkx                    3.0
numba                       0.57.1
numpy                       1.23.5
numpyro                     0.13.0
nvfuser                     NA
opt_einsum                  v3.3.0
optax                       0.1.7
ordered_set                 4.1.0
overrides                   NA
packaging                   23.1
pandas                      1.5.3
param                       1.13.0
parso                       0.8.3
patsy                       0.5.3
pexpect                     4.8.0
pickleshare                 0.7.5
pkg_resources               NA
platformdirs                3.10.0
progressbar                 4.2.0
prometheus_client           NA
prompt_toolkit              3.0.39
psutil                      5.9.5
ptyprocess                  0.7.0
pure_eval                   0.2.2
pyarrow                     13.0.0
pycparser                   2.21
pyct                        0.5.0
pydantic                    2.1.1
pydantic_core               2.4.0
pydev_ipython               NA
pydevconsole                NA
pydevd                      2.9.5
pydevd_file_utils           NA
pydevd_plugins              NA
pydevd_tracing              NA
pydot                       1.4.2
pygam                       0.8.0
pygments                    2.16.1
pynndescent                 0.5.10
pyparsing                   3.1.1
pyro                        1.8.6
python_utils                NA
pythonjsonlogger            NA
pytz                        2023.3.post1
pywt                        1.4.1
referencing                 NA
requests                    2.31.0
rfc3339_validator           0.1.4
rfc3986_validator           0.1.1
rich                        NA
rpds                        NA
scipy                       1.11.2
send2trash                  NA
setuptools                  68.2.2
six                         1.16.0
skimage                     0.21.0
sklearn                     1.3.0
skmisc                      0.3.0
sniffio                     1.3.0
socks                       1.7.1
soupsieve                   2.5
sparse                      0.14.0
stack_data                  0.6.2
starlette                   0.27.0
statsmodels                 0.14.0
sympy                       1.11.1
tensorboard                 2.14.0
termcolor                   NA
texttable                   1.6.7
threadpoolctl               3.2.0
tlz                         0.12.2
tomli                       2.0.1
toolz                       0.12.0
torch                       2.0.1+cu118
torchaudio                  2.0.2+cu118
torchmetrics                1.1.2
torchvision                 0.15.2+cu118
tornado                     6.3.3
tqdm                        4.66.1
traitlets                   5.10.0
tree                        0.1.8
typing_extensions           NA
umap                        0.5.4
uri_template                NA
urllib3                     1.26.13
uvicorn                     0.23.2
wcwidth                     0.2.6
webcolors                   1.13
websocket                   1.6.3
websockets                  11.0.3
wrapt                       1.15.0
xarray                      2023.8.0
yaml                        6.0.1
yarl                        1.9.2
zipp                        NA
zmq                         25.1.1
zoneinfo                    NA
zope                        NA
-----
IPython             8.15.0
jupyter_client      8.3.1
jupyter_core        5.3.1
jupyterlab          4.0.6
notebook            7.0.3
-----
Python 3.9.18 | packaged by conda-forge | (main, Aug 30 2023, 03:49:32) [GCC 12.3.0]
Linux-5.4.0-131-generic-x86_64-with-glibc2.27
-----
Session information updated at 2023-09-17 16:35

[c-westhoven]

I have the same issue, although without the use sc.tl.filter_rank_genes_groups

I tried downgrading h5py from 3.9.0 to 3.7.0, and the issue still persists.
Anndata version: 0.9.2

In general, if there are dtypes as objects in .obs or .var or other layers, a similar type error seems to pop up.

TypeError: Can't implicitly convert non-string objects to strings

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

[flying-sheep]

This is probably a duplicate of #1068 (which comes with a reproducer). If not, we need more information to know what’s different. I’m going to close this, feel free to provide more info if you think that wasn’t the right thing to do.