Import error can't import name 'Markup' from 'jinja2'

[wh9700]

Hi @albsantosdel

after docker run -d --name ckgapp -p 7474:7474 -p 7687:7687 -p 8090:8090 -p 8050:8050 docker-ckg:latest

cannot import name 'Markup' from 'jinja2' (/usr/local/lib/python3.7/site-packages/jinja2/init.py)

the docker logs

[wh9700]

somebody help me

[Meadunce]

In a closed issue someone proposed a solution ，but now it seems doesn‘t work . ？？？

[wh9700]

thanks

…

------------------ 原始邮件 ------------------ 发件人: ***@***.***>; 发送时间: 2022年4月7日(星期四) 下午4:34 收件人: ***@***.***>; 抄送: ***@***.***>; ***@***.***>; 主题: Re: [MannLabs/CKG] Import error can't import name 'Markup' from 'jinja2' (Issue #83) In a closed issue someone proposed a solution ，but now it seems doesn‘t work . ？？？ — Reply to this email directly, view it on GitHub, or unsubscribe. You are receiving this because you authored the thread.Message ID: ***@***.***>

[rodguinea]

Hi, did someone figure out the solution for this problem?

[kamms]

updating a few python packages fixed this issue for me. Execute
pip install --upgrade Flask werkzeug==2.0.3
in the container's shell.

[roivant-matts]

This can be resolved before building the image by adjusting the following in the requirements.txt:
Update:
Flask==2.0.3

Add:
Werkzeug==2.0.3

Remove:
itsdangerous==2.0.1

[wh9700]

I figured it out, make sure the right version of the enviorment.Jinja2 =3.0.3;werkzeug=2.0.3;pingouin = 0.5.1; pandas=0.24.0

…

------------------ 原始邮件 ------------------ 发件人: "Rodrigo ***@***.***>; 发送时间: 2022年4月19日(星期二) 凌晨2:31 收件人: ***@***.***>; 抄送: ***@***.***>; ***@***.***>; 主题: Re: [MannLabs/CKG] Import error can't import name 'Markup' from 'jinja2' (Issue #83) Hi, did someone figure out the solution for this problem? — Reply to this email directly, view it on GitHub, or unsubscribe. You are receiving this because you authored the thread.Message ID: ***@***.***>

[Mnikley]

What worked for me (applied to the docker image):

docker exec -it ckgapp bash

pip uninstall -y jinja2 werkzeug pingouin pandas importlib-metadata
pip install jinja2==3.0.3 werkzeug==2.0.3 pingouin==0.3.12 pandas==0.24.0 importlib-metadata==4.13.0
exit

docker stop ckgapp && docker start ckgapp

[bolak92]

@Mnikley did you also update Flask before that?

[Mnikley]

Sorry for the late response. Unfortunately I cannot make the container work at the moment and I dont have time to recreate everything from scratch. However, maybe this helps you get on your way regarding the specific Flask issue:

docker exec -it ckgapp bash
python3
>>> from jinja2 import Markup
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
ImportError: cannot import name 'Markup' from 'jinja2' (/usr/local/lib/python3.7/site-packages/jinja2/__init__.py)
>>> quit()

to fix it:

docker exec -it ckgapp bash
pip uninstall -y jinja2 werkzeug pingouin pandas importlib-metadata
pip install jinja2==3.0.3 werkzeug==2.0.3 pingouin==0.3.12 pandas==0.24.0 importlib-metadata==4.13.0
python3
>>> from jinja2 import Markup
>>> quit()

and you will get no error. this is the full Python environment my container uses:

docker exec ckgapp2 pip list                                                                                                                                                  ─╯
Package                       Version
----------------------------- ------------
alabaster                     0.7.13
alembic                       1.12.1
amqp                          5.2.0
anyio                         3.7.1
appdirs                       1.4.4
argon2-cffi                   23.1.0
argon2-cffi-bindings          21.2.0
async-generator               1.10
async-timeout                 4.0.3
attrs                         23.1.0
autograd                      1.6.2
autograd-gamma                0.5.0
Babel                         2.13.1
backcall                      0.2.0
bcrypt                        3.1.7
beautifulsoup4                4.7.1
billiard                      3.6.4.0
biopython                     1.73
bioservices                   1.11.2
bleach                        6.0.0
Brotli                        1.1.0
cached-property               1.5.2
cattrs                        23.1.2
celery                        5.0.5
certifi                       2023.7.22
certipy                       0.1.3
cffi                          1.15.1
chardet                       3.0.4
chart-studio                  1.0.0
click                         7.1.2
click-didyoumean              0.3.0
click-plugins                 1.1.1
click-repl                    0.3.0
colorama                      0.4.6
colorlog                      6.7.0
combat                        0.2.0
comm                          0.1.4
cryptography                  41.0.5
cvxpy                         1.1.7
cycler                        0.11.0
cyjupyter                     0.2.0
dash                          1.2.0
dash-core-components          1.1.2
dash-cytoscape                0.3.0
dash-html-components          1.0.1
dash-renderer                 1.0.1
dash-table                    4.2.0
debugpy                       1.7.0
decorator                     5.1.1
defusedxml                    0.7.1
dnspython                     2.3.0
docutils                      0.15.2
easydev                       0.12.1
ecos                          2.0.12
entrypoints                   0.4
et-xmlfile                    1.1.0
eventlet                      0.25.1
exceptiongroup                1.1.3
fastjsonschema                2.18.1
Flask                         1.0.3
Flask-Compress                1.14
fonttools                     4.38.0
future                        0.18.3
gevent                        22.10.2
greenlet                      3.0.1
grequests                     0.7.0
gseapy                        0.9.19
h5py                          2.10.0
html5lib                      1.1
idna                          2.8
imagesize                     1.4.1
importlib-metadata            4.13.0
importlib-resources           5.12.0
iniconfig                     2.0.0
ipykernel                     6.16.2
ipython                       7.34.0
ipython-genutils              0.2.0
ipywidgets                    8.1.1
itsdangerous                  2.0.1
jdcal                         1.4.1
jedi                          0.19.1
Jinja2                        3.0.3
joblib                        1.3.2
jsonschema                    4.17.3
jupyter                       1.0.0
jupyter_client                7.4.9
jupyter-console               6.6.3
jupyter_core                  4.12.0
jupyter-server                1.24.0
jupyter-telemetry             0.1.0
jupyterhub                    4.0.2
jupyterlab-pygments           0.2.2
jupyterlab-widgets            3.0.9
kaleido                       0.0.1
kiwisolver                    1.4.5
kmapper                       1.2.0
kombu                         5.2.4
lifelines                     0.23.1
littleutils                   0.2.2
llvmlite                      0.39.1
lxml                          4.3.4
Mako                          1.2.4
MarkupSafe                    2.1.3
matplotlib                    3.5.3
matplotlib-inline             0.1.6
mistune                       3.0.2
monotonic                     1.6
mpmath                        1.2.1
natsort                       6.0.0
nbclassic                     1.0.0
nbclient                      0.7.4
nbconvert                     7.6.0
nbformat                      5.8.0
nbsphinx                      0.9.3
neo4j                         4.2.0
nest-asyncio                  1.5.8
networkx                      2.5
nltk                          3.5
notebook                      6.5.6
notebook_shim                 0.2.3
numba                         0.56.4
numexpr                       2.8.6
numpy                         1.19.5
oauthlib                      3.2.2
obonet                        0.2.5
openpyxl                      3.0.1
osqp                          0.6.3
outdated                      0.2.2
packaging                     23.2
pamela                        1.1.0
pandas                        0.24.0
pandas-flavor                 0.6.0
pandocfilters                 1.5.0
parso                         0.8.3
passlib                       1.7.1
patsy                         0.5.3
pexpect                       4.8.0
pickleshare                   0.7.5
Pillow                        9.5.0
pingouin                      0.3.12
pip                           23.3.1
pkgutil_resolve_name          1.3.10
platformdirs                  3.11.0
plotly                        4.9.0
pluggy                        1.2.0
prometheus-client             0.17.1
prompt-toolkit                3.0.39
psutil                        5.9.6
ptyprocess                    0.7.0
pycparser                     2.21
Pygments                      2.16.1
pynndescent                   0.5.10
pyOpenSSL                     23.3.0
pyparsing                     3.1.1
PyPDF2                        3.0.1
pyrsistent                    0.19.3
pytest                        7.4.3
python-dateutil               2.8.2
python-json-logger            2.0.7
python-louvain                0.13
pytz                          2023.3.post1
pyvis                         0.1.7.0
PyYAML                        5.1.1
pyzmq                         24.0.1
qdldl                         0.1.7.post0
qtconsole                     5.4.4
QtPy                          2.4.1
rarfile                       3.1
redis                         5.0.1
regex                         2023.10.3
reportlab                     3.6.6
requests                      2.22.0
requests-cache                1.1.0
retrying                      1.3.4
rpy2                          3.0.5
rst2pdf                       0.98
ruamel.yaml                   0.18.5
ruamel.yaml.clib              0.2.8
scikit-learn                  1.0.2
scipy                         1.4.1
scs                           3.2.3
seaborn                       0.11.2
Send2Trash                    1.8.2
setuptools                    47.1.0
simplegeneric                 0.8.1
six                           1.16.0
sklearn                       0.0
smartypants                   2.0.1
snfpy                         0.2.2
sniffio                       1.3.0
snowballstemmer               2.2.0
soupsieve                     2.4.1
Sphinx                        2.3.1
sphinxcontrib-applehelp       1.0.2
sphinxcontrib-devhelp         1.0.2
sphinxcontrib-htmlhelp        2.0.0
sphinxcontrib-jsmath          1.0.1
sphinxcontrib-qthelp          1.0.3
sphinxcontrib-serializinghtml 1.1.5
SQLAlchemy                    2.0.23
statsmodels                   0.10.0
suds-community                1.1.2
tables                        3.6.1
tabulate                      0.9.0
tbb                           2021.10.0
terminado                     0.17.1
threadpoolctl                 3.1.0
tinycss2                      1.2.1
tomli                         2.0.1
tornado                       6.2
tqdm                          4.66.1
traitlets                     5.9.0
typing_extensions             4.7.1
tzlocal                       1.5.1
umap-learn                    0.5.4
url-normalize                 1.4.3
urllib3                       1.25.11
uWSGI                         2.0.23
vine                          5.1.0
wcwidth                       0.2.9
webencodings                  0.5.1
websocket-client              1.6.1
webweb                        0.0.37
Werkzeug                      2.0.3
wget                          3.2
wheel                         0.41.3
widgetsnbextension            4.0.9
wordcloud                     1.8.1
wrapt                         1.15.0
xarray                        0.14.1
xhtml2pdf                     0.2.4
xlrd                          1.2.0
xmltodict                     0.13.0
zipp                          3.15.0
zope.event                    5.0
zope.interface                6.1