Scvelo fails to import with matplotlib==3.4.3 on google cobal

[mxposed]

scVelo fails to import in the google colab notebook like this one: https://colab.research.google.com/github/theislab/scvelo_notebooks/blob/master/DynamicalModeling.ipynb#scrollTo=so7QpP5f2XPz

# code cell 1
!pip install scvelo --upgrade --quiet

# code cell 2
import scvelo as scv

Error output

```pytb KeyError Traceback (most recent call last) in () ----> 1 import scvelo as scv 2 scv.logging.print_version() /usr/local/lib/python3.7/dist-packages/scvelo/__init__.py in () 3 from scanpy import read, read_loom 4 ----> 5 from scvelo import datasets, logging, pl, pp, settings, tl, utils 6 from scvelo.core import get_df 7 from scvelo.plotting.gridspec import GridSpec /usr/local/lib/python3.7/dist-packages/scvelo/pl.py in () ----> 1 from scvelo.plotting import * # noqa /usr/local/lib/python3.7/dist-packages/scvelo/plotting/__init__.py in () 1 from scanpy.plotting import paga_compare, rank_genes_groups 2 ----> 3 from .gridspec import gridspec 4 from .heatmap import heatmap 5 from .paga import paga /usr/local/lib/python3.7/dist-packages/scvelo/plotting/gridspec.py in () 4 5 # todo: auto-complete and docs wrapper ----> 6 from .scatter import scatter 7 from .utils import get_figure_params, hist 8 from .velocity_embedding import velocity_embedding /usr/local/lib/python3.7/dist-packages/scvelo/plotting/scatter.py in () 14 from scvelo.preprocessing.neighbors import get_connectivities 15 from .docs import doc_params, doc_scatter ---> 16 from .utils import * 17 18 /usr/local/lib/python3.7/dist-packages/scvelo/plotting/utils.py in () 17 from matplotlib.gridspec import SubplotSpec 18 from matplotlib.ticker import MaxNLocator ---> 19 from mpl_toolkits.axes_grid1.inset_locator import inset_axes 20 21 from scvelo import logging as logg /usr/local/lib/python3.7/dist-packages/mpl_toolkits/axes_grid1/inset_locator.py in () 135 136 --> 137 class BboxPatch(Patch): 138 @docstring.dedent_interpd 139 def __init__(self, bbox, **kwargs): /usr/local/lib/python3.7/dist-packages/mpl_toolkits/axes_grid1/inset_locator.py in BboxPatch() 136 137 class BboxPatch(Patch): --> 138 @docstring.dedent_interpd 139 def __init__(self, bbox, **kwargs): 140 """ /usr/local/lib/python3.7/dist-packages/matplotlib/docstring.py in dedent_interpd(func) /usr/local/lib/python3.7/dist-packages/matplotlib/docstring.py in __call__(self, func) 38 def __call__(self, func): 39 if func.__doc__: ---> 40 func.__doc__ = inspect.cleandoc(func.__doc__) % self.params 41 return func 42 KeyError: 'Patch_kwdoc' ```

The error is resolved if I first downgrade matplotlib:

!pip install --upgrade matplotlib==3.3.3

I have not tried other versions of matplotlib

[WeilerP]

Hm, strange. Couldn't reproduce this locally. I'll try later on a Linux system. @mxposed, could you please provide the other package versions, i.e. at least the output of scv.logging.print_versions()?

[mxposed]

Well, it's hard to do that since scvelo does not import.

Here's a dump of `pip list`

``` Package Version ----------------------------- -------------- absl-py 0.12.0 alabaster 0.7.12 albumentations 0.1.12 altair 4.1.0 anndata 0.7.6 appdirs 1.4.4 argcomplete 1.12.3 argon2-cffi 21.1.0 arviz 0.11.2 astor 0.8.1 astropy 4.3.1 astunparse 1.6.3 atari-py 0.2.9 atomicwrites 1.4.0 attrs 21.2.0 audioread 2.1.9 autograd 1.3 Babel 2.9.1 backcall 0.2.0 beautifulsoup4 4.6.3 bleach 4.1.0 blis 0.4.1 bokeh 2.3.3 Bottleneck 1.3.2 branca 0.4.2 bs4 0.0.1 CacheControl 0.12.6 cached-property 1.5.2 cachetools 4.2.2 catalogue 1.0.0 certifi 2021.5.30 cffi 1.14.6 cftime 1.5.0 chardet 3.0.4 charset-normalizer 2.0.5 clang 5.0 click 7.1.2 cloudpickle 1.3.0 cmake 3.12.0 cmdstanpy 0.9.5 colorcet 2.0.6 colorlover 0.3.0 community 1.0.0b1 contextlib2 0.5.5 convertdate 2.3.2 coverage 3.7.1 coveralls 0.5 crcmod 1.7 cufflinks 0.17.3 cvxopt 1.2.6 cvxpy 1.0.31 cycler 0.10.0 cymem 2.0.5 Cython 0.29.24 daft 0.0.4 dask 2.12.0 datascience 0.10.6 debugpy 1.0.0 decorator 4.4.2 defusedxml 0.7.1 descartes 1.1.0 dill 0.3.4 distributed 1.25.3 dlib 19.18.0 dm-tree 0.1.6 docopt 0.6.2 docutils 0.17.1 dopamine-rl 1.0.5 earthengine-api 0.1.282 easydict 1.9 ecos 2.0.7.post1 editdistance 0.5.3 en-core-web-sm 2.2.5 entrypoints 0.3 ephem 4.0.0.2 et-xmlfile 1.1.0 fa2 0.3.5 fastai 1.0.61 fastdtw 0.3.4 fastprogress 1.0.0 fastrlock 0.6 fbprophet 0.7.1 feather-format 0.4.1 filelock 3.0.12 firebase-admin 4.4.0 fix-yahoo-finance 0.0.22 Flask 1.1.4 flatbuffers 1.12 folium 0.8.3 future 0.16.0 gast 0.4.0 GDAL 2.2.2 gdown 3.6.4 gensim 3.6.0 geographiclib 1.52 geopy 1.17.0 gin-config 0.4.0 glob2 0.7 google 2.0.3 google-api-core 1.26.3 google-api-python-client 1.12.8 google-auth 1.35.0 google-auth-httplib2 0.0.4 google-auth-oauthlib 0.4.6 google-cloud-bigquery 1.21.0 google-cloud-bigquery-storage 1.1.0 google-cloud-core 1.0.3 google-cloud-datastore 1.8.0 google-cloud-firestore 1.7.0 google-cloud-language 1.2.0 google-cloud-storage 1.18.1 google-cloud-translate 1.5.0 google-colab 1.0.0 google-pasta 0.2.0 google-resumable-media 0.4.1 googleapis-common-protos 1.53.0 googledrivedownloader 0.4 graphviz 0.10.1 greenlet 1.1.1 grpcio 1.40.0 gspread 3.0.1 gspread-dataframe 3.0.8 gym 0.17.3 h5py 3.1.0 HeapDict 1.0.1 hijri-converter 2.2.1 holidays 0.10.5.2 holoviews 1.14.5 html5lib 1.0.1 httpimport 0.5.18 httplib2 0.17.4 httplib2shim 0.0.3 humanize 0.5.1 hyperopt 0.1.2 ideep4py 2.0.0.post3 idna 2.10 imageio 2.4.1 imagesize 1.2.0 imbalanced-learn 0.4.3 imblearn 0.0 imgaug 0.2.9 importlib-metadata 4.8.1 importlib-resources 5.2.2 imutils 0.5.4 inflect 2.1.0 iniconfig 1.1.1 intel-openmp 2021.3.0 intervaltree 2.1.0 ipykernel 4.10.1 ipython 5.5.0 ipython-genutils 0.2.0 ipython-sql 0.3.9 ipywidgets 7.6.5 itsdangerous 1.1.0 jax 0.2.19 jaxlib 0.1.70+cuda111 jdcal 1.4.1 jedi 0.18.0 jieba 0.42.1 Jinja2 2.11.3 joblib 1.0.1 jpeg4py 0.1.4 jsonschema 2.6.0 jupyter 1.0.0 jupyter-client 5.3.5 jupyter-console 5.2.0 jupyter-core 4.7.1 jupyterlab-pygments 0.1.2 jupyterlab-widgets 1.0.2 kaggle 1.5.12 kapre 0.3.5 keras 2.6.0 Keras-Preprocessing 1.1.2 keras-vis 0.4.1 kiwisolver 1.3.2 korean-lunar-calendar 0.2.1 librosa 0.8.1 lightgbm 2.2.3 llvmlite 0.34.0 lmdb 0.99 loompy 3.0.6 LunarCalendar 0.0.9 lxml 4.2.6 Markdown 3.3.4 MarkupSafe 2.0.1 matplotlib 3.4.3 matplotlib-inline 0.1.3 matplotlib-venn 0.11.6 missingno 0.5.0 mistune 0.8.4 mizani 0.6.0 mkl 2019.0 mlxtend 0.14.0 more-itertools 8.9.0 moviepy 0.2.3.5 mpmath 1.2.1 msgpack 1.0.2 multiprocess 0.70.12.2 multitasking 0.0.9 murmurhash 1.0.5 music21 5.5.0 natsort 5.5.0 nbclient 0.5.4 nbconvert 5.6.1 nbformat 5.1.3 nest-asyncio 1.5.1 netCDF4 1.5.7 networkx 2.6.3 nibabel 3.0.2 nltk 3.2.5 notebook 5.3.1 numba 0.51.2 numexpr 2.7.3 numpy 1.19.5 numpy-groupies 0.9.14 nvidia-ml-py3 7.352.0 oauth2client 4.1.3 oauthlib 3.1.1 okgrade 0.4.3 opencv-contrib-python 4.1.2.30 opencv-python 4.1.2.30 openpyxl 2.5.9 opt-einsum 3.3.0 osqp 0.6.2.post0 packaging 21.0 palettable 3.3.0 pandas 1.1.5 pandas-datareader 0.9.0 pandas-gbq 0.13.3 pandas-profiling 1.4.1 pandocfilters 1.5.0 panel 0.12.1 param 1.11.1 parso 0.8.2 pathlib 1.0.1 patsy 0.5.1 pep517 0.11.0 pexpect 4.8.0 pickleshare 0.7.5 Pillow 7.1.2 pip 21.1.3 pip-tools 6.2.0 plac 1.1.3 plotly 4.4.1 plotnine 0.6.0 pluggy 0.7.1 pooch 1.5.1 portpicker 1.3.9 prefetch-generator 1.0.1 preshed 3.0.5 prettytable 2.2.0 progressbar2 3.38.0 prometheus-client 0.11.0 promise 2.3 prompt-toolkit 1.0.18 protobuf 3.17.3 psutil 5.4.8 psycopg2 2.7.6.1 ptyprocess 0.7.0 py 1.10.0 pyarrow 3.0.0 pyasn1 0.4.8 pyasn1-modules 0.2.8 pycocotools 2.0.2 pycparser 2.20 pyct 0.4.8 pydata-google-auth 1.2.0 pydot 1.3.0 pydot-ng 2.0.0 pydotplus 2.0.2 PyDrive 1.3.1 pyemd 0.5.1 pyerfa 2.0.0 pyglet 1.5.0 Pygments 2.6.1 pygobject 3.26.1 pymc3 3.11.4 PyMeeus 0.5.11 pymongo 3.12.0 pymystem3 0.2.0 pynndescent 0.5.4 PyOpenGL 3.1.5 pyparsing 2.4.7 pyrsistent 0.18.0 pysndfile 1.3.8 PySocks 1.7.1 pystan 2.19.1.1 pytest 3.6.4 python-apt 0.0.0 python-chess 0.23.11 python-dateutil 2.8.2 python-louvain 0.15 python-slugify 5.0.2 python-utils 2.5.6 pytz 2018.9 pyviz-comms 2.1.0 PyWavelets 1.1.1 PyYAML 3.13 pyzmq 22.2.1 qdldl 0.1.5.post0 qtconsole 5.1.1 QtPy 1.11.1 regex 2019.12.20 requests 2.23.0 requests-oauthlib 1.3.0 resampy 0.2.2 retrying 1.3.3 rpy2 3.4.5 rsa 4.7.2 scanpy 1.8.1 scikit-image 0.16.2 scikit-learn 0.22.2.post1 scipy 1.4.1 screen-resolution-extra 0.0.0 scs 2.1.4 scvelo 0.2.4 seaborn 0.11.2 semver 2.13.0 Send2Trash 1.8.0 setuptools 57.4.0 setuptools-git 1.2 Shapely 1.7.1 simplegeneric 0.8.1 sinfo 0.3.4 six 1.15.0 sklearn 0.0 sklearn-pandas 1.8.0 smart-open 5.2.1 snowballstemmer 2.1.0 sortedcontainers 2.4.0 SoundFile 0.10.3.post1 spacy 2.2.4 Sphinx 1.8.5 sphinxcontrib-serializinghtml 1.1.5 sphinxcontrib-websupport 1.2.4 SQLAlchemy 1.4.23 sqlparse 0.4.2 srsly 1.0.5 statsmodels 0.10.2 stdlib-list 0.8.0 sympy 1.7.1 tables 3.4.4 tabulate 0.8.9 tblib 1.7.0 tensorboard 2.6.0 tensorboard-data-server 0.6.1 tensorboard-plugin-wit 1.8.0 tensorflow 2.6.0 tensorflow-datasets 4.0.1 tensorflow-estimator 2.6.0 tensorflow-gcs-config 2.6.0 tensorflow-hub 0.12.0 tensorflow-metadata 1.2.0 tensorflow-probability 0.13.0 termcolor 1.1.0 terminado 0.12.1 testpath 0.5.0 text-unidecode 1.3 textblob 0.15.3 Theano-PyMC 1.1.2 thinc 7.4.0 tifffile 2021.8.30 toml 0.10.2 tomli 1.2.1 toolz 0.11.1 torch 1.9.0+cu102 torchsummary 1.5.1 torchtext 0.10.0 torchvision 0.10.0+cu102 tornado 5.1.1 tqdm 4.62.2 traitlets 5.1.0 tweepy 3.10.0 typeguard 2.7.1 typing-extensions 3.7.4.3 tzlocal 1.5.1 umap-learn 0.5.1 uritemplate 3.0.1 urllib3 1.24.3 vega-datasets 0.9.0 wasabi 0.8.2 wcwidth 0.2.5 webencodings 0.5.1 Werkzeug 1.0.1 wheel 0.37.0 widgetsnbextension 3.5.1 wordcloud 1.5.0 wrapt 1.12.1 xarray 0.18.2 xgboost 0.90 xkit 0.0.0 xlrd 1.1.0 xlwt 1.3.0 yellowbrick 0.9.1 zict 2.0.0 zipp 3.5.0 ```

[WeilerP]

Well, it's hard to do that since scvelo does not import.

Oh yes, you're right. Sorry, I didn't think of that. 😅 . Thanks for the pip list. I'll look into it.

[Zethson]

@WeilerP I could reproduce it. Accidentally ran into it when preparing some exercise sheet for students.

[WeilerP]

@Zethson, thanks for putting this on my radar again. I think this is the same issue as reported in theislab/cellrank#770. @mxposed, sorry didn't get a chance to investigate and fix this yet.

[WeilerP]

Closing as stale.