ImportError

[cellphys]

Hi there,

I tried to run minian after installation and encountered ImportError. It occurs on my two computers. Can anyone tell me what happens and what I should do? Thanks!

ImportError Traceback (most recent call last)
Input In [3], in <cell line: 31>()
23 from minian.preprocessing import denoise, remove_background
24 from minian.utilities import (
25 TaskAnnotation,
26 get_optimal_chk,
(...)
29 save_minian,
30 )
---> 31 from minian.visualization import (
32 CNMFViewer,
33 VArrayViewer,
34 generate_videos,
35 visualize_gmm_fit,
36 visualize_motion,
37 visualize_preprocess,
38 visualize_seeds,
39 visualize_spatial_update,
40 visualize_temporal_update,
41 write_video,
42 )

File ~\Documents\CellPhys\miniscope\minian-master\minian\visualization.py:16, in
14 import numpy as np
15 import pandas as pd
---> 16 import panel as pn
17 import param
18 import scipy.sparse as scisps

File ~.conda\envs\minian\lib\site-packages\panel_init_.py:5, in
1 from future import absolute_import, division, unicode_literals
3 import param as _param
----> 5 from . import layout # noqa
6 from . import links # noqa
7 from . import pane # noqa

File ~.conda\envs\minian\lib\site-packages\panel\layout.py:22, in
19 from bokeh.models.widgets import Tabs as BkTabs, Panel as BkPanel
21 from .util import param_name, param_reprs
---> 22 from .viewable import Layoutable, Reactive
24 _row = namedtuple("row", ["children"])
25 _col = namedtuple("col", ["children"])

File ~.conda\envs\minian\lib\site-packages\panel\viewable.py:21, in
17 from functools import partial
19 import param
---> 21 from bokeh.document.document import Document as _Document, _combine_document_events
22 from bokeh.document.events import ModelChangedEvent
23 from bokeh.io import curdoc as _curdoc

File ~.conda\envs\minian\lib\site-packages\bokeh\document_init_.py:43, in
33 all = (
34 'DEFAULT_TITLE',
35 'Document',
36 'without_document_lock',
37 )
39 #-----------------------------------------------------------------------------
40 # General API
41 #-----------------------------------------------------------------------------
---> 43 from .document import DEFAULT_TITLE ; DEFAULT_TITLE
44 from .document import Document ; Document
45 from .locking import without_document_lock ; without_document_lock

File ~.conda\envs\minian\lib\site-packages\bokeh\document\document.py:49, in
47 from ..core.json_encoder import serialize_json
48 from ..core.query import find
---> 49 from ..core.templates import FILE
50 from ..core.validation import check_integrity
51 from ..events import Event

File ~.conda\envs\minian\lib\site-packages\bokeh\core\templates.py:43, in
40 import sys
42 # External imports
---> 43 from jinja2 import Environment, Markup, FileSystemLoader
45 # Bokeh imports
46
47 #-----------------------------------------------------------------------------
48 # Globals and constants
49 #-----------------------------------------------------------------------------
51 all = (
52 'AUTOLOAD_JS',
53 'AUTOLOAD_NB_JS',
(...)
65 'SCRIPT_TAG',
66 )

ImportError: cannot import name 'Markup' from 'jinja2' (C:\Users\user.conda\envs\minian\lib\site-packages\jinja2_init_.py)

[mberensc]

see this reply in issues #195 (comment)

The issue is with the versions of Bokeh, Jinja2, and markupsafe