TypeError: No dispatch for <class 'dict'>

[hossam-zaki]

Describe the bug from pyscenic.transform import df2regulons is giving me an error and i'm unable to import it.

Steps to reproduce the behavior

1. Command run when the error occurred: I ran the following import statements.

   from pyscenic.export import export2loom, add_scenic_metadata
   from pyscenic.utils import load_motifs
   from pyscenic.transform import df2regulons
   from pyscenic.aucell import aucell
   from pyscenic.binarization import binarize
   from pyscenic.rss import regulon_specificity_scores
   from pyscenic.plotting import plot_binarization, plot_rss
   ...

2. Error encountered:

   
   TypeError                                 Traceback (most recent call last)
   <ipython-input-2-f00fa4041aff> in <module>
    15 from pyscenic.export import export2loom, add_scenic_metadata
    16 from pyscenic.utils import load_motifs
   ---> 17 from pyscenic.transform import df2regulons
    18 from pyscenic.aucell import aucell
    19 from pyscenic.binarization import binarize

/usr/local/lib/python3.8/site-packages/pyscenic/transform.py in 36 COLUMN_NAME_TYPE = "Type" 37 # TODO: Should actually be a function depending on return_recovery_curves and rank_threshold ---> 38 DF_META_DATA = make_meta( 39 { 40 ('Enrichment', COLUMN_NAME_AUC): np.float64,

/usr/local/lib/python3.8/site-packages/dask/utils.py in call(self, arg, *args, *kwargs) 509 Call the corresponding method based on type of argument. 510 """ --> 511 meth = self.dispatch(type(arg)) 512 return meth(arg, args, **kwargs) 513

/usr/local/lib/python3.8/site-packages/dask/utils.py in dispatch(self, cls) 503 lk[cls] = lk[cls2] 504 return lk[cls2] --> 505 raise TypeError("No dispatch for {0}".format(cls)) 506 507 def call(self, arg, *args, **kwargs):

TypeError: No dispatch for <class 'dict'> ...

**Expected behavior**
It is expected to simply import it without any bug

**Please complete the following information:**
- pySCENIC version: 0.11.2
- Installation method: Pip
- Run environment: Jupyter Notebook
- OS: MacOS
- Package versions: [obtain using `pip freeze`, `conda list`, or skip this if using Docker/Singularity]:
<!-- Put your package version list in this code block (if applicable, else delete the block): -->

absl-py==0.11.0 aiohttp==3.7.4.post0 anndata==0.7.6 appnope==0.1.2 arboreto==0.1.6 argon2-cffi==20.1.0 astunparse==1.6.3 async-generator==1.10 async-timeout==3.0.1 attrs==21.2.0 audible==0.5.3 backcall==0.2.0 beautifulsoup4==4.9.3 bleach==3.3.0 bokeh==2.3.2 boltons==21.0.0 cachetools==4.2.1 certifi==2020.12.5 cffi==1.14.5 chardet==4.0.0 click==7.1.2 cloudpickle==1.6.0 ctxcore==0.1.1 cycler==0.10.0 Cython==0.29.22 cytoolz==0.11.0 dask==2021.5.1 decorator==4.4.2 defusedxml==0.7.1 dill==0.3.3 distributed==2021.5.1 dm-tree==0.1.5 dnspython==1.16.0 entrypoints==0.3 ffprobe-python==1.0.3 Flask==1.1.2 Flask-PyMongo==2.3.0 flatbuffers==1.12 frozendict==2.0.2 fsspec==2021.5.0 gast==0.3.3 get-version==2.2 google-auth==1.27.0 google-auth-oauthlib==0.4.2 google-pasta==0.2.0 grpcio==1.32.0 h11==0.12.0 h5py==2.10.0 HeapDict==1.0.1 httpcore==0.12.3 httpx==0.16.1 idna==2.10 interlap==0.2.7 ipykernel==5.5.5 ipython==7.24.0 ipython-genutils==0.2.0 itsdangerous==1.1.0 jedi==0.18.0 Jinja2==2.11.3 joblib==1.0.1 jsonschema==3.2.0 jupyter-client==6.1.12 jupyter-core==4.7.1 jupyterlab-pygments==0.1.2 Keras-Preprocessing==1.1.2 kiwisolver==1.3.1 legacy-api-wrap==1.2 lineedit==0.1.6 llvmlite==0.36.0 locket==0.2.1 loompy==3.0.6 Markdown==3.3.3 MarkupSafe==1.1.1 matplotlib==3.3.4 matplotlib-inline==0.1.2 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==6.4.0 numba==0.53.1 numexpr==2.7.3 numpy==1.19.5 numpy-groupies==0.9.13 oauthlib==3.1.0 opt-einsum==3.3.0 packaging==20.9 pandas==1.2.2 pandocfilters==1.4.3 parso==0.8.2 partd==1.2.0 patsy==0.5.1 pbkdf2==1.3 pexpect==4.8.0 pickleshare==0.7.5 Pillow==8.1.0 prometheus-client==0.10.1 prompt-toolkit==3.0.18 protobuf==3.15.1 psutil==5.8.0 ptyprocess==0.7.0 pyaes==1.6.1 pyarrow==0.16.0 pyasn1==0.4.8 pyasn1-modules==0.2.8 pycparser==2.20 Pygments==2.8.1 pymongo==3.11.3 pynndescent==0.5.2 pyparsing==2.4.7 pyrsistent==0.17.3 pyscenic==0.11.2 python-dateutil==2.8.1 python-dotenv==0.17.1 pytz==2021.1 PyYAML==5.4.1 pyzmq==22.1.0 quadprog==0.1.8 radian==0.5.10 rchitect==0.3.30 requests==2.25.1 requests-oauthlib==1.3.0 rfc3986==1.4.0 rsa==4.7.1 scanpy==1.7.2 scikit-learn==0.24.1 scipy==1.6.1 seaborn==0.11.1 Send2Trash==1.5.0 sinfo==0.3.4 six==1.15.0 sniffio==1.2.0 sortedcontainers==2.4.0 soupsieve==2.2 statsmodels==0.12.2 stdlib-list==0.8.0 tables==3.6.1 tblib==1.7.0 tensorboard==2.4.1 tensorboard-plugin-wit==1.8.0 tensorflow==2.4.1 tensorflow-estimator==2.4.0 tensorflow-probability==0.12.1 termcolor==1.1.0 terminado==0.10.0 testpath==0.5.0 threadpoolctl==2.1.0 toolz==0.11.1 tornado==6.1 tqdm==4.58.0 traitlets==5.0.5 typing-extensions==3.7.4.3 umap-learn==0.5.1 urllib3==1.26.3 wcwidth==0.2.5 webencodings==0.5.1 Werkzeug==1.0.1 wrapt==1.12.1 xlrd==1.2.0 yarl==1.6.3 zict==2.0.0 ...

[eleozzr]

Same bug for me.

[eleozzr]

I re-install pyscenic with version 0.11.1, and downgrade dask==2.30.0 and distributed==2.30.0, which works for me.

[cflerin]

@hossam-zaki ,

I will look further into this but I would suggest using pySCENIC 0.11.1 for now as @eleozzr mentioned.

[moqri]

I got this issue when tryin to do conda install -c bioconda arboreto I got around it by installing pip install pyscenic instead