`calculate_multifactor_PMD()` adds `int` keys to `.obs` leading to error on `adata.write_h5ad()`

[Moomboh]

Report

pt.tl.Dialogue().calculate_multifactor_PMD() adds MCPs to .obs with int keys instead of str leading to error on adata.write_h5ad():

Traceback (most recent call last):
  File "/Users/eliaskahl/miniconda3/envs/pertpy-apple-silicon/lib/python3.10/site-packages/anndata/_io/utils.py", line 214, in func_wrapper
    return func(elem, key, val, *args, **kwargs)
  File "/Users/eliaskahl/miniconda3/envs/pertpy-apple-silicon/lib/python3.10/site-packages/anndata/_io/specs/registry.py", line 175, in write_elem
    _REGISTRY.get_writer(dest_type, t, modifiers)(f, k, elem, *args, **kwargs)
  File "/Users/eliaskahl/miniconda3/envs/pertpy-apple-silicon/lib/python3.10/site-packages/anndata/_io/specs/registry.py", line 24, in wrapper
    result = func(g, k, *args, **kwargs)
  File "/Users/eliaskahl/miniconda3/envs/pertpy-apple-silicon/lib/python3.10/site-packages/anndata/_io/specs/methods.py", line 499, in write_dataframe
    col_names = [check_key(c) for c in df.columns]
  File "/Users/eliaskahl/miniconda3/envs/pertpy-apple-silicon/lib/python3.10/site-packages/anndata/_io/specs/methods.py", line 499, in <listcomp>
    col_names = [check_key(c) for c in df.columns]
  File "/Users/eliaskahl/miniconda3/envs/pertpy-apple-silicon/lib/python3.10/site-packages/anndata/_io/utils.py", line 109, in check_key
    raise TypeError(f"{key} of type {typ} is an invalid key. Should be str.")
TypeError: 0 of type <class 'int'> is an invalid key. Should be str.

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

Traceback (most recent call last):
  File "/Users/eliaskahl/workspace/github.com/theislab-gobi-sc-dialogue/dialogue-experiments-elias/mre-mcp-str-keys.py", line 19, in <module>
    adata.write_h5ad("data/dialogue-example_pmd.h5ad")
  File "/Users/eliaskahl/miniconda3/envs/pertpy-apple-silicon/lib/python3.10/site-packages/anndata/_core/anndata.py", line 1918, in write_h5ad
    _write_h5ad(
  File "/Users/eliaskahl/miniconda3/envs/pertpy-apple-silicon/lib/python3.10/site-packages/anndata/_io/h5ad.py", line 98, in write_h5ad
    write_elem(f, "obs", adata.obs, dataset_kwargs=dataset_kwargs)
  File "/Users/eliaskahl/miniconda3/envs/pertpy-apple-silicon/lib/python3.10/site-packages/anndata/_io/utils.py", line 220, in func_wrapper
    raise type(e)(
TypeError: 0 of type <class 'int'> is an invalid key. Should be str.

Minimal reproducible example:

import pertpy as pt
import scanpy as sc

import session_info
session_info.show(html=False, dependencies=True)

adata = pt.dt.dialogue_example()
sc.pp.pca(adata)

dl = pt.tl.Dialogue()
adata, mcps, ws, ct_subs = dl.calculate_multifactor_PMD(
    adata,
    sample_id="clinical.status",
    celltype_key="cell.subtypes",
    n_counts_key="nCount_RNA",
    normalize=True,
)

adata.write_h5ad("data/dialogue-example_pmd.h5ad")

Version information

---

pertpy 0.4.0 scanpy 1.9.2 session_info 1.0.0

PIL 9.4.0 PyQt5 NA adjustText NA anndata 0.8.0 arrow 1.2.3 arviz 0.14.0 asttokens NA attr 22.1.0 backcall 0.2.0 certifi 2022.12.07 cffi 1.15.1 cftime 1.6.2 charset_normalizer 3.0.1 comm 0.1.2 custom_inherit 2.4.1 cycler 0.10.0 cython_runtime NA dateutil 2.8.2 decorator 5.1.1 decoupler 1.3.3 defusedxml 0.7.1 entrypoints 0.4 ete3 3.1.2 executing 0.8.3 fontTools 4.38.0 google NA h5py 3.8.0 idna 3.4 igraph 0.10.4 ipykernel 6.19.2 ipython_genutils 0.2.0 ipywidgets 7.6.5 jax 0.4.4 jaxlib 0.4.4 jedi 0.18.1 jinja2 3.1.2 joblib 1.2.0 kiwisolver 1.4.4 leidenalg 0.9.1 llvmlite 0.39.1 markupsafe 2.1.1 matplotlib 3.7.0 mizani 0.8.1 mpl_toolkits NA mudata 0.2.1 multipledispatch 0.6.0 muon 0.1.3 natsort 8.2.0 netCDF4 1.6.2 numba 0.56.4 numpy 1.23.5 numpyro 0.10.1 opt_einsum v3.3.0 packaging 22.0 palettable 3.3.0 pandas 1.5.3 parso 0.8.3 patsy 0.5.3 pexpect 4.8.0 pickleshare 0.7.5 pkg_resources NA platformdirs 2.5.2 plotnine 0.10.1 ply 3.11 png 0.20220715.0 prompt_toolkit 3.0.36 psutil 5.9.0 ptyprocess 0.7.0 pure_eval 0.2.2 pycparser 2.21 pygments 2.11.2 pynndescent 0.5.8 pyomo 6.5.0 pyparsing 3.0.9 pypi_latest 0.1.2 pytz 2022.7 questionary 1.10.0 reportlab 3.6.12 requests 2.28.2 rich NA rpy2 3.5.8 scipy 1.10.1 seaborn 0.11.2 setuptools 65.6.3 sip NA six 1.16.0 sklearn 1.2.1 skmisc 0.1.4 sparsecca 0.3.0 stack_data 0.2.0 statannotations 0.5.0 statsmodels 0.13.5 switchlang 0.1.0 texttable 1.6.7 threadpoolctl 3.1.0 tornado 6.2 toyplot 1.0.3 toytree 2.0.1 tqdm 4.64.1 traitlets 5.7.1 typing_extensions NA tzlocal NA umap 0.5.3 urllib3 1.26.14 wcwidth 0.2.5 xarray 2023.2.0 xarray_einstats 0.5.1 zmq 23.2.0 zoneinfo NA

IPython 8.10.0 jupyter_client 7.4.9 jupyter_core 5.2.0 notebook 6.5.2

Python 3.10.9 | packaged by conda-forge | (main, Feb 2 2023, 20:26:08) [Clang 14.0.6 ] macOS-13.1-arm64-arm-64bit

Session information updated at 2023-03-01 13:34

[Zethson]

Thank you very much for the report!

We've indeed already noticed this and discussed it yesterday @yugeji @tessadgreen . Happy to welcome a PR of we'll fix it very soon ourselves.