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theislab / scvelo

RNA Velocity generalized through dynamical modeling
https://scvelo.org
BSD 3-Clause "New" or "Revised" License
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ERROR: XMLRPC request failed [code: -32500] #1117

Closed zhouzhendiao closed 1 month ago

zhouzhendiao commented 1 year ago

Failed running scv.logging.print_versions(), but sc.logging.print_versions() worked fine.

scv.logging.print_versions()
Error output ```pytb scvelo==0.3.0 scanpy==1.9.3 anndata==0.9.2 loompy==3.0.7 numpy==1.24.4 scipy==1.10.1 matplotlib==3.5.3 sklearn==1.1.3 pandas==1.5.3 ERROR: XMLRPC request failed [code: -32500] RuntimeError: PyPI no longer supports 'pip search' (or XML-RPC search). Please use https://pypi.org/search (via a browser) instead. See https://warehouse.pypa.io/api-reference/xml-rpc.html#deprecated-methods for more information. ``` 
sc.logging.print_versions()
Error output ```pytb ----- anndata 0.9.2 scanpy 1.9.3 ----- Cython 0.29.34 PIL 9.5.0 absl NA aiohttp 3.8.4 aiosignal 1.3.1 annotated_types 0.5.0 anyio NA arrow 1.2.3 asttokens NA async_timeout 4.0.2 attr 22.2.0 awkward 2.3.1 awkward_cpp NA babel 2.12.1 backcall 0.2.0 backoff 2.2.1 beta_ufunc NA binom_ufunc NA bottleneck 1.3.7 brotli NA bs4 4.12.2 cairo 1.24.0 certifi 2023.07.22 cffi 1.15.1 charset_normalizer 3.1.0 chex 0.1.7 click 8.1.3 cloudpickle 2.2.1 colorama 0.3.9 comm 0.1.3 contextlib2 NA croniter NA cycler 0.10.0 cython 0.29.34 cython_runtime NA cytoolz 0.12.0 dask 2023.4.1 dateutil 2.8.2 debugpy 1.6.7 decorator 5.1.1 deepdiff 6.3.1 defusedxml 0.7.1 dill 0.3.6 docrep 0.3.2 etils 1.4.1 executing 1.2.0 fastapi 0.101.1 fastjsonschema NA fcsparser 0.2.6 flax 0.7.2 fqdn NA frozenlist 1.4.0 fsspec 2023.4.0 gi 3.44.1 gio NA glib NA gmpy2 2.1.2 gobject NA google NA gtk NA h5py 3.8.0 hypergeom_ufunc NA idna 3.4 igraph 0.10.6 importlib_resources NA invgauss_ufunc NA ipykernel 6.22.0 ipython_genutils 0.2.0 ipywidgets 8.0.6 isal 1.1.0 isoduration NA jax 0.4.14 jaxlib 0.4.14 jaxopt NA jedi 0.18.2 jinja2 3.1.2 joblib 1.2.0 json5 NA jsonpointer 2.0 jsonschema 4.17.3 jupyter_events 0.5.0 jupyter_server 2.5.0 jupyterlab_server 2.22.1 kiwisolver 1.4.4 leidenalg 0.10.0 lightning 2.0.6 lightning_cloud NA lightning_utilities 0.9.0 llvmlite 0.40.1 loompy 3.0.7 louvain 0.8.1 lz4 4.3.2 markupsafe 2.1.2 matplotlib 3.5.3 matplotlib_inline 0.1.6 mellon 1.3.1 ml_collections NA ml_dtypes 0.2.0 mpl_toolkits NA mpmath 1.3.0 msgpack 1.0.5 mudata 0.2.3 multidict 6.0.4 multipart 0.0.6 multipledispatch 0.6.0 natsort 8.4.0 nbformat 5.8.0 nbinom_ufunc NA ncf_ufunc NA nct_ufunc NA ncx2_ufunc NA networkx 3.1 numba 0.57.1 numexpr 2.8.4 numpy 1.24.4 numpy_groupies 0.9.22 numpyro 0.12.1 nvfuser NA opt_einsum v3.3.0 optax 0.1.7 ordered_set 4.1.0 packaging 23.1 palantir 1.3.2 pandas 1.5.3 parso 0.8.3 pexpect 4.8.0 pickleshare 0.7.5 pkg_resources NA platformdirs 3.5.0 progressbar 4.2.0 prometheus_client NA prompt_toolkit 3.0.38 psutil 5.9.5 ptyprocess 0.7.0 pure_eval 0.2.2 pvectorc NA pyarrow 11.0.0 pycparser 2.21 pydantic 2.0.3 pydantic_core 2.3.0 pydev_ipython NA pydevconsole NA pydevd 2.9.5 pydevd_file_utils NA pydevd_plugins NA pydevd_tracing NA pygam 0.8.0 pygments 2.15.1 pyparsing 3.0.9 pyro 1.8.6 pyrsistent NA python_utils NA pythonjsonlogger NA pytz 2023.3 requests 2.29.0 rfc3339_validator 0.1.4 rfc3986_validator 0.1.1 rich NA ruamel NA scipy 1.10.1 scvelo 0.3.0 scvi 1.0.3 send2trash NA session_info 1.0.0 setuptools 68.1.0 setuptools_scm NA six 1.16.0 skewnorm_ufunc NA sklearn 1.1.3 sniffio 1.3.0 socks 1.7.1 soupsieve 2.3.2.post1 sparse 0.14.0 stack_data 0.6.2 starlette 0.27.0 sympy 1.11.1 tblib 1.7.0 texttable 1.6.7 threadpoolctl 3.1.0 tlz 0.12.0 tomli 2.0.1 toolz 0.12.0 torch 2.0.1+cu117 torchmetrics 1.0.3 tornado 6.3 tqdm 4.65.0 traitlets 5.9.0 tree 0.1.8 typing_extensions NA uri_template NA urllib3 1.23 uvicorn 0.23.2 wcwidth 0.2.6 webcolors 1.13 websocket 1.5.1 websockets 11.0.3 wrapt 1.15.0 xarray 2023.7.0 yaml 6.0 yarl 1.9.2 zipp NA zmq 25.0.2 zoneinfo NA zstandard 0.19.0 ----- IPython 8.13.1 jupyter_client 8.2.0 jupyter_core 5.3.0 jupyterlab 3.6.3 notebook 6.5.4 ----- Python 3.10.10 | packaged by conda-forge | (main, Mar 24 2023, 20:08:06) [GCC 11.3.0] Linux-3.10.0-1160.81.1.el7.x86_64-x86_64-with-glibc2.35 ----- Session information updated at 2023-08-22 01:35 /opt/conda/lib/python3.10/site-packages/session_info/main.py:213: DeprecationWarning: Accessing jsonschema.__version__ is deprecated and will be removed in a future release. Use importlib.metadata directly to query for jsonschema's version. mod_version = _find_version(mod.__version__) ```