Open hossam-zaki opened 3 years ago
Same bug for me.
I re-install pyscenic with version 0.11.1, and downgrade dask==2.30.0
and distributed==2.30.0
, which works for me.
@hossam-zaki ,
I will look further into this but I would suggest using pySCENIC 0.11.1 for now as @eleozzr mentioned.
I got this issue when tryin to do conda install -c bioconda arboreto I got around it by installing pip install pyscenic instead
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
Command run when the error occurred: I ran the following import statements.
Error encountered:
/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'> ...
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 ...