KeyError("['popv_onclass_seen'] not in index") when prediction_mode == 'fast'

[axdanbol]

Report

Problem Description

I get a KeyError when running popv with prediction_mode set to fast.
If needed I can provide links to public h5ad I've used (HuBMAP)

Solution

I suspect the problem is this line:
adata.obs["onclass_seen"] = pred_label_str in _onclass.py which should be changed to
adata.obs[self.seen_result_key] = pred_label_str like in the non-fast prediction mode path

Stacktrace

File "/usr/local/lib/python3.11/dist-packages/popv/annotation.py", line 75, in annotate_data
    compute_consensus(adata, all_prediction_keys_seen)
File "/usr/local/lib/python3.11/dist-packages/popv/annotation.py", line 119, in compute_consensus
    consensus_prediction = adata.obs[prediction_keys].apply(_utils.majority_vote, axis=1)
                           ~~~~~~~~~^^^^^^^^^^^^^^^^^
File "/usr/local/lib/python3.11/dist-packages/pandas/core/frame.py", line 3813, in __getitem__
    indexer = self.columns._get_indexer_strict(key, "columns")[1]
              ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/local/lib/python3.11/dist-packages/pandas/core/indexes/base.py", line 6070, in _get_indexer_strict
    self._raise_if_missing(keyarr, indexer, axis_name)
File "/usr/local/lib/python3.11/dist-packages/pandas/core/indexes/base.py", line 6133, in _raise_if_missing
    raise KeyError(f"{not_found} not in index")

Version information

---

popv 0.4.2
session_info 1.0.0

97d2165b493fecec79c65b5c6254dffd4e375528 NA
OnClass NA
PIL 10.2.0
absl NA
anndata 0.10.6
annoy NA
astunparse 1.6.3
attr 23.2.0
celltypist 1.6.2
certifi 2024.02.02
charset_normalizer 3.3.2
chex 0.1.85
contextlib2 NA
cycler 0.12.1
cython_runtime NA
dateutil 2.9.0.post0
docrep 0.3.2
etils 1.7.0
fbpca NA
filelock 3.13.1
flatbuffers 24.3.7
flax 0.8.1
fontTools 4.49.0
fsspec 2024.2.0
gast 0.5.4
google NA
h5py 3.10.0
harmony 0.1.8
huggingface_hub 0.21.4
idna 3.6
igraph 0.11.4
importlib_resources NA
intervaltree NA
jax 0.4.25
jaxlib 0.4.25
joblib 1.3.2
keras 3.0.5
kiwisolver 1.4.5
leidenalg 0.10.2
lightning 2.1.4
lightning_utilities 0.10.1
llvmlite 0.42.0
matplotlib 3.8.3
ml_collections NA
ml_dtypes 0.3.2
mpl_toolkits NA
msgpack 1.0.8
mudata 0.2.3
multipledispatch 0.6.0
namex NA
natsort 8.4.0
networkx 3.2.1
numba 0.59.0
numpy 1.26.4
numpyro 0.14.0
obonet 1.0.0
opt_einsum v3.3.0
optax 0.2.1
packaging 24.0
pandas 1.5.3
patsy 0.5.6
pkg_resources NA
psutil 5.9.8
pybind11_abseil NA
pygments 2.17.2
pynndescent 0.5.11
pyparsing 3.1.2
pyro 1.9.0
pytz 2024.1
regex 2.5.140
requests 2.31.0
rich NA
scanorama 1.7.4
scanpy 1.9.8
scipy 1.12.0
scvi 1.1.2
seaborn 0.13.2
setuptools 69.1.1
sitecustomize NA
six 1.16.0
sklearn 1.1.3
socks 1.7.1
sortedcontainers 2.4.0
statsmodels 0.14.1
tensorflow 2.16.1
termcolor NA
texttable 1.7.0
threadpoolctl 3.3.0
tokenizers 0.15.2
toolz 0.12.1
torch 2.2.1+cu121
torchgen NA
torchmetrics 1.3.1
tqdm 4.66.2
transformers 4.38.2
tree 0.1.8
typing_extensions NA
urllib3 2.2.1
wrapt 1.16.0
yaml 6.0.1
zoneinfo NA

Python 3.11.0rc1 (main, Aug 12 2022, 10:02:14) [GCC 11.2.0]
Linux-5.10.102.1-microsoft-standard-WSL2-x86_64-with-glibc2.35

Session information updated at 2024-03-25 20:15

[canergen]

Thanks for reporting. Fixed with #50 .