Running the google colab version, I am getting a type error at step 3 when importing dandelion as ddl

[savitaj]

Hi Dr. Tuong,

Thanks for the tool. I am getting error while using google colab at step 3

import and show versions

import dandelion as ddl
ddl.logging.print_header()

---

TypeError Traceback (most recent call last)
in <cell line: 2>()
1 # import and show versions
----> 2 import dandelion as ddl
3 ddl.logging.print_header()

7 frames
/usr/local/lib/python3.10/site-packages/scanpy/plotting/_utils.py in
33
34
---> 35 class _AxesSubplot(Axes, axes.SubplotBase, ABC):
36 """Intersection between Axes and SubplotBase: Has methods of both"""
37

TypeError: metaclass conflict: the metaclass of a derived class must be a (non-strict) subclass of the metaclasses of all its bases

Could you please advise. Thanks in advance.

[zktuong]

hi @savitaj, thank you for alerting me to this. can you try replace the step 2 with just
!pip install -q sc-dandelion scanpy[leiden]

[zktuong]

forgot about the networkx patch #258

so until i update the pypi version, the full installation line should be

!pip install -q sc-dandelion scanpy[leiden] networkx==2.7

[zktuong]

hi @savitaj, i'm closing this issue as the new notebook link has incorporated the changes to make it work again. thanks again for letting me know.

[savitaj]

Thanks a lot Dr. Tuong. It is working now. Really appreciate it.

I am also trying to run Dandelion separately on Jupyter notebook after installing all the required packages listed . Facing some version conflict issues with python packages there as well. I will raise a different ticket for that. Thanks again.

Best regards,
Savita