Not able to use stereopy after installation

[pratapstat]

I have followed instructions from stereopy instructions page through the following link (https://stereopy.readthedocs.io/en/latest/General/Installation.html) by typing the following commands conda create --name st python=3.8 conda activate st pip install stereopy

After installation, when I was trying to use stereopy by typing the following commands ( shown below) it's giving an error. import warnings warnings.filterwarnings('ignore') import stereo as st

It would be really helpful, if you help on this.

[TheSallyGardens]

@pratapstat Hi! Could you show the error message?

[pratapstat]

@TheSallyGardens Hi, I'm using my mac (mac os: Ventura 13.2.1) and the error message is shown below

ImportError Traceback (most recent call last) Cell In[2], line 1 ----> 1 import stereo as st

File ~/opt/anaconda3/envs/stereo_py/lib/python3.8/site-packages/stereo/init.py:10 8 from . import tools 9 from . import utils ---> 10 from . import plots as plt 11 from . import image

File ~/opt/anaconda3/envs/stereo_py/lib/python3.8/site-packages/stereo/plots/init.py:13 11 from .marker_genes import marker_genes_text, marker_genes_heatmap 12 from .plot_collection import PlotCollection ---> 13 from .interact_plot.spatial_cluster import interact_spatial_cluster 14 from .interact_plot.interactive_scatter import InteractiveScatter 15 from .interact_plot.poly_selection import PolySelection

File ~/opt/anaconda3/envs/stereo_py/lib/python3.8/site-packages/stereo/plots/interact_plot/spatial_cluster.py:8 1 #!/usr/bin/env python3 2 # coding: utf-8 3 """ 4 @author: qindanhua@genomics.cn 5 @time:2021/09/06 6 """ ----> 8 import holoviews as hv 9 import hvplot.pandas 10 import panel as pn

File ~/opt/anaconda3/envs/stereo_py/lib/python3.8/site-packages/holoviews/init.py:12 8 version = str(param.version.Version(fpath=file, archive_commit="$Format:%h$", 9 reponame="holoviews")) 11 from . import util # noqa (API import) ---> 12 from .annotators import annotate # noqa (API import) 13 from .core import archive, config # noqa (API import) 14 from .core.boundingregion import BoundingBox # noqa (API import)

File ~/opt/anaconda3/envs/stereo_py/lib/python3.8/site-packages/holoviews/annotators.py:10 6 from inspect import getmro 8 import param ---> 10 from panel.pane import PaneBase 11 from panel.layout import Row, Tabs 12 from panel.util import param_name

File ~/opt/anaconda3/envs/stereo_py/lib/python3.8/site-packages/panel/init.py:1 ----> 1 from . import layout # noqa 2 from . import links # noqa 3 from . import pane # noqa

File ~/opt/anaconda3/envs/stereo_py/lib/python3.8/site-packages/panel/layout/init.py:1 ----> 1 from .accordion import Accordion # noqa 2 from .base import Column, ListLike, ListPanel, Panel, Row, WidgetBox # noqa 3 from .card import Card # noqa

File ~/opt/anaconda3/envs/stereo_py/lib/python3.8/site-packages/panel/layout/accordion.py:5 1 import param 3 from bokeh.models import Column as BkColumn, CustomJS ----> 5 from .base import NamedListPanel 6 from .card import Card 9 class Accordion(NamedListPanel):

File ~/opt/anaconda3/envs/stereo_py/lib/python3.8/site-packages/panel/layout/base.py:11 7 import param 9 from bokeh.models import Column as BkColumn, Row as BkRow ---> 11 from ..io.model import hold 12 from ..io.state import state 13 from ..reactive import Reactive

File ~/opt/anaconda3/envs/stereo_py/lib/python3.8/site-packages/panel/io/init.py:9 6 import logging 7 import sys ----> 9 from ..config import config 11 from .callbacks import PeriodicCallback # noqa 12 from .embed import embed_state # noqa

File ~/opt/anaconda3/envs/stereo_py/lib/python3.8/site-packages/panel/config.py:20 14 import param 16 from pyviz_comms import ( 17 JupyterCommManager as _JupyterCommManager, extension as _pyviz_extension 18 ) ---> 20 from .io.notebook import load_notebook 21 from .io.state import state 23 version = str(param.version.Version( 24 fpath=file, archive_commit="$Format:%h$", reponame="panel"))

File ~/opt/anaconda3/envs/stereo_py/lib/python3.8/site-packages/panel/io/notebook.py:14 11 from six import string_types 13 import bokeh ---> 14 import bokeh.embed.notebook 16 from bokeh.core.json_encoder import serialize_json 17 from bokeh.core.templates import MACROS

File ~/opt/anaconda3/envs/stereo_py/lib/python3.8/site-packages/bokeh/embed/init.py:23 16 log = logging.getLogger(name) 18 #----------------------------------------------------------------------------- 19 # Imports 20 #----------------------------------------------------------------------------- 21 22 # Bokeh imports ---> 23 from .server import server_document, server_session 24 from .standalone import autoload_static, components, file_html, json_item 26 #----------------------------------------------------------------------------- 27 # Globals and constants 28 #-----------------------------------------------------------------------------

File ~/opt/anaconda3/envs/stereo_py/lib/python3.8/site-packages/bokeh/embed/server.py:25 22 from urllib.parse import quote_plus, urlparse 24 # Bokeh imports ---> 25 from ..core.templates import AUTOLOAD_REQUEST_TAG, FILE 26 from ..resources import DEFAULT_SERVER_HTTP_URL 27 from ..util.serialization import make_id

File ~/opt/anaconda3/envs/stereo_py/lib/python3.8/site-packages/bokeh/core/templates.py:41 38 from os.path import dirname, join 40 # External imports ---> 41 from jinja2 import Environment, FileSystemLoader 43 #----------------------------------------------------------------------------- 44 # Globals and constants 45 #----------------------------------------------------------------------------- 47 all = ( 48 'AUTOLOAD_JS', 49 'AUTOLOAD_NB_JS', (...) 62 'SCRIPT_TAG', 63 )

File ~/opt/anaconda3/envs/stereo_py/lib/python3.8/site-packages/jinja2/init.py:12 10 from .bccache import FileSystemBytecodeCache 11 from .bccache import MemcachedBytecodeCache ---> 12 from .environment import Environment 13 from .environment import Template 14 from .exceptions import TemplateAssertionError

File ~/opt/anaconda3/envs/stereo_py/lib/python3.8/site-packages/jinja2/environment.py:25 23 from .compiler import CodeGenerator 24 from .compiler import generate ---> 25 from .defaults import BLOCK_END_STRING 26 from .defaults import BLOCK_START_STRING 27 from .defaults import COMMENT_END_STRING

File ~/opt/anaconda3/envs/stereo_py/lib/python3.8/site-packages/jinja2/defaults.py:3 1 # -- coding: utf-8 -- 2 from ._compat import range_type ----> 3 from .filters import FILTERS as DEFAULT_FILTERS # noqa: F401 4 from .tests import TESTS as DEFAULT_TESTS # noqa: F401 5 from .utils import Cycler

File ~/opt/anaconda3/envs/stereo_py/lib/python3.8/site-packages/jinja2/filters.py:13 11 from markupsafe import escape 12 from markupsafe import Markup ---> 13 from markupsafe import soft_unicode 15 from ._compat import abc 16 from ._compat import imap

ImportError: cannot import name 'soft_unicode' from 'markupsafe' (/Users/pratap/opt/anaconda3/envs/stereo_py/lib/python3.8/site-packages/markupsafe/init.py)

[TheSallyGardens]

@pratapstat Hi! Sorry, Stereopy does not support the mac system at present.

[pratapstat]

@TheSallyGardens thanks. Is there any docker or container available for mac ?

[TheSallyGardens]

Currently, it supports linux and window, and plans to support mac in the future.

[junhouhui]

hi，we already push the stereopy (version: 0.6.0) image to Dockerhub, please visit stereopy_docker

[junhouhui]

docker execute command: docker run -p 8888:8888 -it bgi-research/stereopy:1.0 /bin/bash -c "jupyter lab --JupyterApp.config_file='/home/stereonote/jupyter_notebook_config.py' --allow-root --ip=0.0.0.0 --NotebookApp.passwd=''"

[junhouhui]

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