Error importing add_scenic_metadata; scikit-learn version?[BUG]

[oligomyeggo]

I am working through your "integration with scanpy" notebook, and am running into an issue using from pyscenic.export import export2loom, add_scenic_metadata. I get the following error:

---------------------------------------------------------------------------
ModuleNotFoundError                       Traceback (most recent call last)
<ipython-input-41-7b9ebff39c30> in <module>
     15 from pyscenic.prune import prune2df, df2regulons
     16 from pyscenic.aucell import aucell
---> 17 from pyscenic.export import export2loom, add_scenic_metadata
     18 from pyscenic.utils import load_motifs
     19 from pyscenic.transform import df2regulons

~/.local/share/virtualenvs/li-nAee7qZ4/lib/python3.8/site-packages/pyscenic/export.py in <module>
      5 import pandas as pd
      6 import loompy as lp
----> 7 from sklearn.manifold.t_sne import TSNE
      8 from .aucell import aucell
      9 from .genesig import Regulon

ModuleNotFoundError: No module named 'sklearn.manifold.t_sne'

I am wondering if sklearn.manifold.t_sne is from an older package version, as it looks like version 0.24.1 refers to this as sklearn.manifold.TSNE? If this is the case, what version of scikit-learn should I downgrade to in order to run add_scenic_metadata? Thank you!

Version info:

• pySCENIC version: 0.11.0
• Installation method: Pip
• Run environment: Jupyter notebook
• OS: Mac
• Package versions:

aiohttp==3.7.4.post0
anndata==0.7.6
anndata2ri==1.0.6
appnope==0.1.2
arboreto==0.1.6
argon2-cffi==20.1.0
async-generator==1.10
async-timeout==3.0.1
attrs==20.3.0
backcall==0.2.0
bleach==3.3.0
bokeh==2.3.1
boltons==20.2.1
cellrank==1.3.1
certifi==2020.12.5
cffi==1.14.5
chardet==4.0.0
click==7.1.2
cloudpickle==1.6.0
cycler==0.10.0
cytoolz==0.11.0
dask==2021.4.0
decorator==5.0.6
defusedxml==0.7.1
dill==0.3.3
distributed==2021.4.0
docrep==0.3.2
entrypoints==0.3
frozendict==1.2
fsspec==0.9.0
future==0.18.2
future-fstrings==1.2.0
get-version==2.1
h5py==3.2.1
HeapDict==1.0.1
idna==2.10
interlap==0.2.7
ipykernel==5.5.3
ipython==7.22.0
ipython-genutils==0.2.0
ipywidgets==7.6.3
jedi==0.18.0
Jinja2==2.11.3
joblib==1.0.1
jsonschema==3.2.0
jupyter==1.0.0
jupyter-client==6.1.12
jupyter-console==6.4.0
jupyter-core==4.7.1
jupyterlab-pygments==0.1.2
jupyterlab-widgets==1.0.0
kiwisolver==1.3.1
legacy-api-wrap==1.2
llvmlite==0.36.0
locket==0.2.1
loompy==3.0.6
louvain==0.7.0
MarkupSafe==1.1.1
matplotlib==3.4.1
mistune==0.8.4
msgpack==1.0.2
multidict==5.1.0
multiprocessing-on-dill==3.5.0a4
natsort==7.1.1
nbclient==0.5.3
nbconvert==6.0.7
nbformat==5.1.3
nest-asyncio==1.5.1
networkx==2.5.1
notebook==6.3.0
numba==0.53.1
numexpr==2.7.3
numpy==1.20.2
numpy-groupies==0.9.13
packaging==20.9
pandas==1.2.4
pandocfilters==1.4.3
parso==0.8.2
partd==1.2.0
patsy==0.5.1
pexpect==4.8.0
pickleshare==0.7.5
Pillow==8.2.0
progressbar2==3.53.1
prometheus-client==0.10.1
prompt-toolkit==3.0.18
psutil==5.8.0
ptyprocess==0.7.0
pyarrow==0.16.0
pycparser==2.20
pygam==0.8.0
Pygments==2.8.1
pygpcca==1.0.2
pynndescent==0.5.2
pyparsing==2.4.7
pyrsistent==0.17.3
**pyscenic==0.11.0**
python-dateutil==2.8.1
python-igraph==0.9.1
python-utils==2.5.6
pytz==2021.1
PyYAML==5.4.1
pyzmq==22.0.3
qtconsole==5.0.3
QtPy==1.9.0
requests==2.25.1
rpy2==3.4.3
scanpy==1.7.2
**scikit-learn==0.24.1**
scipy==1.6.2
scvelo==0.2.3
seaborn==0.11.1
Send2Trash==1.5.0
sinfo==0.3.1
six==1.15.0
sortedcontainers==2.3.0
statsmodels==0.12.2
stdlib-list==0.8.0
tables==3.6.1
tblib==1.7.0
terminado==0.9.4
testpath==0.4.4
texttable==1.6.3
threadpoolctl==2.1.0
toolz==0.11.1
tornado==6.1
tqdm==4.60.0
traitlets==5.0.5
typing-extensions==3.7.4.3
tzlocal==2.1
umap-learn==0.5.1
urllib3==1.26.4
wcwidth==0.2.5
webencodings==0.5.1
widgetsnbextension==3.5.1
wrapt==1.12.1
xlrd==1.2.0
yarl==1.6.3
zict==2.0.0

[cflerin]

Thanks @oligomyeggo for reporting this. I will fix the import in the next release or you can downgrade sklearn for now:

pip install scikit-learn==0.21.3

(aertslab/SCENICprotocol/issues/41)

[oligomyeggo]

Great, thanks so much! I appreciate it.