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Import failure due to pytorch_lightning.loggers #1772
Comments
can you try installing pytorch lightning 1.7.X? I think this is an issue with 1.6.X |
This worked! But it introduced a different problem with PL (this time, upon training a model, though):
It looks like 'flush_logs_every_n_steps' was deprecated from PL's Trainer here. |
Can you confirm that you have scvi-tools version 0.18? As you can see here: scvi-tools/scvi/train/_trainer.py Line 89 in ea0fd7a
The code looks different than your traceback. |
Well...now I feel stupid. I'm at least 99% positive that it was 0.18 yesterday though...I'm thinking that maybe mamba downgraded it when I upgraded PL. This guess is further supported by the fact that when I create a fresh env, pytorch install goes fine, scanpy install goes fine, and then during scvi install I get hit with this massive list of package incompatibilities due to shared paths (ignore the incorrect scvi size errors): Install/dependency errors (warning: 100+ lines)(scvi-tools) griffen@Griffen-XPS-15:/mnt/c/Users/Griffen/Desktop$ mamba install scvi-tools -c conda-forge
███████████████/ /██/ /██/ /██/ /████████████████████████
█████████████████████████████████████████████████████████████ Looking for: ['scvi-tools'] conda-forge/linux-64 Using cache Pinned packages:
warning libmamba Invalid package cache, file '/home/griffen/miniconda3/pkgs/scvi-tools-0.18.0-pyhd8ed1ab_0/site-packages/scvi/train/_logger.py' has incorrect size Prefix: /home/griffen/miniconda3/envs/scvi-tools Updating specs:
Package Version Build Channel Size
Downgrade:
Summary: Install: 102 packages Total download: 82kB ───────────────────────────────────────────────────────────────────────────────────────────────────── Confirm changes: [Y/n] Y ClobberError: This transaction has incompatible packages due to a shared path. ClobberError: This transaction has incompatible packages due to a shared path. ClobberError: This transaction has incompatible packages due to a shared path. ClobberError: This transaction has incompatible packages due to a shared path. ClobberError: This transaction has incompatible packages due to a shared path. ClobberError: This transaction has incompatible packages due to a shared path. ClobberError: This transaction has incompatible packages due to a shared path. ClobberError: This transaction has incompatible packages due to a shared path. ClobberError: This transaction has incompatible packages due to a shared path. ClobberError: This transaction has incompatible packages due to a shared path. ClobberError: This transaction has incompatible packages due to a shared path. ClobberError: This transaction has incompatible packages due to a shared path. ClobberError: This transaction has incompatible packages due to a shared path. ClobberError: This transaction has incompatible packages due to a shared path. ClobberError: This transaction has incompatible packages due to a shared path. ClobberError: This transaction has incompatible packages due to a shared path. ClobberError: This transaction has incompatible packages due to a shared path. ClobberError: This transaction has incompatible packages due to a shared path. ClobberError: This transaction has incompatible packages due to a shared path. ClobberError: This transaction has incompatible packages due to a shared path. ClobberError: This transaction has incompatible packages due to a shared path. ClobberError: This transaction has incompatible packages due to a shared path. ClobberError: This transaction has incompatible packages due to a shared path. ClobberError: This transaction has incompatible packages due to a shared path. ClobberError: This transaction has incompatible packages due to a shared path. ClobberError: This transaction has incompatible packages due to a shared path. ClobberError: This transaction has incompatible packages due to a shared path. ClobberError: This transaction has incompatible packages due to a shared path. ClobberError: This transaction has incompatible packages due to a shared path. ClobberError: This transaction has incompatible packages due to a shared path. ClobberError: This transaction has incompatible packages due to a shared path. ClobberError: This transaction has incompatible packages due to a shared path. ClobberError: This transaction has incompatible packages due to a shared path. ClobberError: This transaction has incompatible packages due to a shared path. ClobberError: This transaction has incompatible packages due to a shared path. ClobberError: This transaction has incompatible packages due to a shared path. ClobberError: This transaction has incompatible packages due to a shared path. ClobberError: This transaction has incompatible packages due to a shared path. ClobberError: This transaction has incompatible packages due to a shared path. ClobberError: This transaction has incompatible packages due to a shared path. ClobberError: This transaction has incompatible packages due to a shared path. ClobberError: This transaction has incompatible packages due to a shared path. ClobberError: This transaction has incompatible packages due to a shared path. ClobberError: This transaction has incompatible packages due to a shared path. ClobberError: This transaction has incompatible packages due to a shared path. ClobberError: This transaction has incompatible packages due to a shared path. ClobberError: This transaction has incompatible packages due to a shared path. ClobberError: This transaction has incompatible packages due to a shared path. ClobberError: This transaction has incompatible packages due to a shared path. ClobberError: This transaction has incompatible packages due to a shared path. ClobberError: This transaction has incompatible packages due to a shared path. ClobberError: This transaction has incompatible packages due to a shared path. ClobberError: This transaction has incompatible packages due to a shared path. ClobberError: This transaction has incompatible packages due to a shared path. ClobberError: This transaction has incompatible packages due to a shared path. ClobberError: This transaction has incompatible packages due to a shared path. ClobberError: This transaction has incompatible packages due to a shared path. ClobberError: This transaction has incompatible packages due to a shared path. ClobberError: This transaction has incompatible packages due to a shared path. ClobberError: This transaction has incompatible packages due to a shared path. ClobberError: This transaction has incompatible packages due to a shared path. ClobberError: This transaction has incompatible packages due to a shared path. ClobberError: This transaction has incompatible packages due to a shared path. ClobberError: This transaction has incompatible packages due to a shared path. ClobberError: This transaction has incompatible packages due to a shared path. ClobberError: This transaction has incompatible packages due to a shared path. ClobberError: This transaction has incompatible packages due to a shared path. ClobberError: This transaction has incompatible packages due to a shared path. ClobberError: This transaction has incompatible packages due to a shared path. ClobberError: This transaction has incompatible packages due to a shared path. ClobberError: This transaction has incompatible packages due to a shared path. ClobberError: This transaction has incompatible packages due to a shared path. ClobberError: This transaction has incompatible packages due to a shared path. ClobberError: This transaction has incompatible packages due to a shared path. ClobberError: This transaction has incompatible packages due to a shared path. ClobberError: This transaction has incompatible packages due to a shared path. ClobberError: This transaction has incompatible packages due to a shared path. ClobberError: This transaction has incompatible packages due to a shared path. ClobberError: This transaction has incompatible packages due to a shared path. ClobberError: This transaction has incompatible packages due to a shared path. ClobberError: This transaction has incompatible packages due to a shared path. ClobberError: This transaction has incompatible packages due to a shared path. ClobberError: This transaction has incompatible packages due to a shared path. ClobberError: This transaction has incompatible packages due to a shared path. ClobberError: This transaction has incompatible packages due to a shared path. ClobberError: This transaction has incompatible packages due to a shared path. ClobberError: This transaction has incompatible packages due to a shared path. ClobberError: This transaction has incompatible packages due to a shared path. ClobberError: This transaction has incompatible packages due to a shared path. ClobberError: This transaction has incompatible packages due to a shared path. ClobberError: This transaction has incompatible packages due to a shared path. ClobberError: This transaction has incompatible packages due to a shared path. ClobberError: This transaction has incompatible packages due to a shared path. ClobberError: This transaction has incompatible packages due to a shared path. ClobberError: This transaction has incompatible packages due to a shared path. ClobberError: This transaction has incompatible packages due to a shared path. ClobberError: This transaction has incompatible packages due to a shared path. ClobberError: This transaction has incompatible packages due to a shared path. ClobberError: This transaction has incompatible packages due to a shared path. ClobberError: This transaction has incompatible packages due to a shared path. ClobberError: This transaction has incompatible packages due to a shared path. ClobberError: This transaction has incompatible packages due to a shared path. ClobberError: This transaction has incompatible packages due to a shared path. ClobberError: This transaction has incompatible packages due to a shared path. ClobberError: This transaction has incompatible packages due to a shared path. ClobberError: This transaction has incompatible packages due to a shared path. ClobberError: This transaction has incompatible packages due to a shared path. ClobberError: This transaction has incompatible packages due to a shared path. ClobberError: This transaction has incompatible packages due to a shared path. ClobberError: This transaction has incompatible packages due to a shared path. ClobberError: This transaction has incompatible packages due to a shared path. ClobberError: This transaction has incompatible packages due to a shared path. ClobberError: This transaction has incompatible packages due to a shared path. ClobberError: This transaction has incompatible packages due to a shared path. ClobberError: This transaction has incompatible packages due to a shared path. ClobberError: This transaction has incompatible packages due to a shared path. ClobberError: This transaction has incompatible packages due to a shared path. ClobberError: This transaction has incompatible packages due to a shared path. ClobberError: This transaction has incompatible packages due to a shared path. ClobberError: This transaction has incompatible packages due to a shared path. ClobberError: This transaction has incompatible packages due to a shared path. ClobberError: This transaction has incompatible packages due to a shared path. ClobberError: This transaction has incompatible packages due to a shared path. ClobberError: This transaction has incompatible packages due to a shared path. ClobberError: This transaction has incompatible packages due to a shared path. ClobberError: This transaction has incompatible packages due to a shared path. ClobberError: This transaction has incompatible packages due to a shared path. ClobberError: This transaction has incompatible packages due to a shared path. ClobberError: This transaction has incompatible packages due to a shared path. ClobberError: This transaction has incompatible packages due to a shared path. ClobberError: This transaction has incompatible packages due to a shared path. ClobberError: This transaction has incompatible packages due to a shared path. ClobberError: This transaction has incompatible packages due to a shared path. ClobberError: This transaction has incompatible packages due to a shared path. ClobberError: This transaction has incompatible packages due to a shared path. ClobberError: This transaction has incompatible packages due to a shared path. ClobberError: This transaction has incompatible packages due to a shared path. ClobberError: This transaction has incompatible packages due to a shared path. ClobberError: This transaction has incompatible packages due to a shared path. ClobberError: This transaction has incompatible packages due to a shared path. ClobberError: This transaction has incompatible packages due to a shared path. ClobberError: This transaction has incompatible packages due to a shared path. ClobberError: This transaction has incompatible packages due to a shared path. ClobberError: This transaction has incompatible packages due to a shared path. ClobberError: This transaction has incompatible packages due to a shared path. ClobberError: This transaction has incompatible packages due to a shared path. ClobberError: This transaction has incompatible packages due to a shared path. ClobberError: This transaction has incompatible packages due to a shared path. ClobberError: This transaction has incompatible packages due to a shared path. ClobberError: This transaction has incompatible packages due to a shared path. ClobberError: This transaction has incompatible packages due to a shared path. ClobberError: This transaction has incompatible packages due to a shared path. ClobberError: This transaction has incompatible packages due to a shared path. ClobberError: This transaction has incompatible packages due to a shared path. ClobberError: This transaction has incompatible packages due to a shared path. ClobberError: This transaction has incompatible packages due to a shared path. ClobberError: This transaction has incompatible packages due to a shared path. ClobberError: This transaction has incompatible packages due to a shared path. ClobberError: This transaction has incompatible packages due to a shared path. ClobberError: This transaction has incompatible packages due to a shared path. ClobberError: This transaction has incompatible packages due to a shared path. ClobberError: This transaction has incompatible packages due to a shared path. ClobberError: This transaction has incompatible packages due to a shared path. ClobberError: This transaction has incompatible packages due to a shared path. ClobberError: This transaction has incompatible packages due to a shared path. ClobberError: This transaction has incompatible packages due to a shared path. ClobberError: This transaction has incompatible packages due to a shared path. ClobberError: This transaction has incompatible packages due to a shared path. ClobberError: This transaction has incompatible packages due to a shared path. ClobberError: This transaction has incompatible packages due to a shared path. ClobberError: This transaction has incompatible packages due to a shared path. ClobberError: This transaction has incompatible packages due to a shared path. ClobberError: This transaction has incompatible packages due to a shared path. ClobberError: This transaction has incompatible packages due to a shared path. ClobberError: This transaction has incompatible packages due to a shared path. ClobberError: This transaction has incompatible packages due to a shared path. ClobberError: This transaction has incompatible packages due to a shared path. ClobberError: This transaction has incompatible packages due to a shared path. ClobberError: This transaction has incompatible packages due to a shared path. ClobberError: This transaction has incompatible packages due to a shared path. ClobberError: This transaction has incompatible packages due to a shared path. ClobberError: This transaction has incompatible packages due to a shared path. ClobberError: This transaction has incompatible packages due to a shared path. ClobberError: This transaction has incompatible packages due to a shared path. ClobberError: This transaction has incompatible packages due to a shared path. ClobberError: This transaction has incompatible packages due to a shared path. ClobberError: This transaction has incompatible packages due to a shared path. ClobberError: This transaction has incompatible packages due to a shared path. ClobberError: This transaction has incompatible packages due to a shared path. ClobberError: This transaction has incompatible packages due to a shared path. ClobberError: This transaction has incompatible packages due to a shared path. ClobberError: This transaction has incompatible packages due to a shared path. ClobberError: This transaction has incompatible packages due to a shared path. ClobberError: This transaction has incompatible packages due to a shared path. ClobberError: This transaction has incompatible packages due to a shared path. ClobberError: This transaction has incompatible packages due to a shared path. ClobberError: This transaction has incompatible packages due to a shared path. ClobberError: This transaction has incompatible packages due to a shared path. ClobberError: This transaction has incompatible packages due to a shared path. ClobberError: This transaction has incompatible packages due to a shared path. ClobberError: This transaction has incompatible packages due to a shared path. ClobberError: This transaction has incompatible packages due to a shared path. ClobberError: This transaction has incompatible packages due to a shared path. ClobberError: This transaction has incompatible packages due to a shared path. ClobberError: This transaction has incompatible packages due to a shared path. ClobberError: This transaction has incompatible packages due to a shared path. ClobberError: This transaction has incompatible packages due to a shared path. ClobberError: This transaction has incompatible packages due to a shared path. ClobberError: This transaction has incompatible packages due to a shared path. ClobberError: This transaction has incompatible packages due to a shared path. ClobberError: This transaction has incompatible packages due to a shared path. ClobberError: This transaction has incompatible packages due to a shared path. ClobberError: This transaction has incompatible packages due to a shared path. ClobberError: This transaction has incompatible packages due to a shared path. ClobberError: This transaction has incompatible packages due to a shared path. ClobberError: This transaction has incompatible packages due to a shared path. ClobberError: This transaction has incompatible packages due to a shared path. ClobberError: This transaction has incompatible packages due to a shared path. ClobberError: This transaction has incompatible packages due to a shared path. ClobberError: This transaction has incompatible packages due to a shared path. ClobberError: This transaction has incompatible packages due to a shared path. ClobberError: This transaction has incompatible packages due to a shared path. ClobberError: This transaction has incompatible packages due to a shared path. ClobberError: This transaction has incompatible packages due to a shared path. ClobberError: This transaction has incompatible packages due to a shared path. ClobberError: This transaction has incompatible packages due to a shared path. ClobberError: This transaction has incompatible packages due to a shared path. ClobberError: This transaction has incompatible packages due to a shared path. ClobberError: This transaction has incompatible packages due to a shared path. ClobberError: This transaction has incompatible packages due to a shared path. ClobberError: This transaction has incompatible packages due to a shared path. ClobberError: This transaction has incompatible packages due to a shared path. ClobberError: This transaction has incompatible packages due to a shared path. ClobberError: This transaction has incompatible packages due to a shared path. ClobberError: This transaction has incompatible packages due to a shared path. ClobberError: This transaction has incompatible packages due to a shared path. ClobberError: This transaction has incompatible packages due to a shared path. ClobberError: This transaction has incompatible packages due to a shared path. ClobberError: This transaction has incompatible packages due to a shared path. ClobberError: This transaction has incompatible packages due to a shared path. ClobberError: This transaction has incompatible packages due to a shared path. ClobberError: This transaction has incompatible packages due to a shared path. ClobberError: This transaction has incompatible packages due to a shared path. ClobberError: This transaction has incompatible packages due to a shared path. ClobberError: This transaction has incompatible packages due to a shared path. ClobberError: This transaction has incompatible packages due to a shared path. ClobberError: This transaction has incompatible packages due to a shared path. ClobberError: This transaction has incompatible packages due to a shared path. ClobberError: This transaction has incompatible packages due to a shared path. ClobberError: This transaction has incompatible packages due to a shared path. ClobberError: This transaction has incompatible packages due to a shared path. ClobberError: This transaction has incompatible packages due to a shared path. ClobberError: This transaction has incompatible packages due to a shared path. ClobberError: This transaction has incompatible packages due to a shared path. ClobberError: This transaction has incompatible packages due to a shared path. ClobberError: This transaction has incompatible packages due to a shared path. ClobberError: This transaction has incompatible packages due to a shared path. ClobberError: This transaction has incompatible packages due to a shared path. ClobberError: This transaction has incompatible packages due to a shared path. ClobberError: This transaction has incompatible packages due to a shared path. ClobberError: This transaction has incompatible packages due to a shared path. ClobberError: This transaction has incompatible packages due to a shared path. ClobberError: This transaction has incompatible packages due to a shared path. ClobberError: This transaction has incompatible packages due to a shared path. ClobberError: This transaction has incompatible packages due to a shared path. ClobberError: This transaction has incompatible packages due to a shared path. ClobberError: This transaction has incompatible packages due to a shared path. ClobberError: This transaction has incompatible packages due to a shared path. ClobberError: This transaction has incompatible packages due to a shared path. ClobberError: This transaction has incompatible packages due to a shared path. ClobberError: This transaction has incompatible packages due to a shared path. ClobberError: This transaction has incompatible packages due to a shared path. ClobberError: This transaction has incompatible packages due to a shared path. ClobberError: This transaction has incompatible packages due to a shared path. ClobberError: This transaction has incompatible packages due to a shared path. ClobberError: This transaction has incompatible packages due to a shared path. ClobberError: This transaction has incompatible packages due to a shared path. ClobberError: This transaction has incompatible packages due to a shared path. ClobberError: This transaction has incompatible packages due to a shared path. ClobberError: This transaction has incompatible packages due to a shared path. ClobberError: This transaction has incompatible packages due to a shared path. ClobberError: This transaction has incompatible packages due to a shared path. ClobberError: This transaction has incompatible packages due to a shared path. ClobberError: This transaction has incompatible packages due to a shared path. ClobberError: This transaction has incompatible packages due to a shared path. ClobberError: This transaction has incompatible packages due to a shared path. ClobberError: This transaction has incompatible packages due to a shared path. ClobberError: This transaction has incompatible packages due to a shared path. ClobberError: This transaction has incompatible packages due to a shared path. ClobberError: This transaction has incompatible packages due to a shared path. ClobberError: This transaction has incompatible packages due to a shared path. ClobberError: This transaction has incompatible packages due to a shared path. ClobberError: This transaction has incompatible packages due to a shared path. ClobberError: This transaction has incompatible packages due to a shared path. done I'm guessing that I probably just need a fresh conda install at this point? |
New conda install seems reasonable to me, we prefer mambaforge |
Another issue might be that we used to upload to the bioconda channel but for the last few months have moved to conda-forge |
I'll probably just go with this then. Hopefully it fixes it (I'm guessing that it will). Thanks for all the help. |
Just to let anyone else know who has the same/similar problems--completely removing and reinstalling mamba/conda fixed this for me. Be sure to backup your conda environments first though. |
On attempting import scvi-tools 0.18.0 I get the following:
When I check pytorch_lightning itself, python is correct. There is indeed no 'Logger' in _loggers.py:
Not sure if I have the wrong version of pytorch_lightning? Or something else entirely.
Any help would be much appreciated.
Thanks,
GW
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