[BUG] pyscenic grn ValueError: tuple is not allowed for map key #175
Comments
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Have you tried some of the suggestions in #163 ? |
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Thank you - yes I have tried using I also tried to install
Which versions would you recommend trying? |
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I am using Conda environments, so if you have a .yml file for a Conda environment where pyscenic is working, I could give that a try |
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If none of the dask version tweaks have worked for you, I would then try using the |
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I suggest removing dask from pyscenic. It brings much more difficulties than efficiency boosts. |
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Thank you @cflerin, I have tried using the
I am using a Conda environment containing the following packages: What is this issue related to? Best, |
- Determination of filename extension - Related to #175
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Hi @lc822 , First, this: is a bug in Second, the output you pasted was not from the |
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Thank you - I will update to 0.10.2. This is my command for
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Looks good! |
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Would you mind describing how to get the arboreto_with_multiprocessing script? How do I download it and where should it be stored on my laptop? I have version 0.10.2, but the script doesn't look like it's in my pyscenic package. Also, once I have it, can I import it in a Jupyter notebook? |
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Hi @Annika18, I couldn't find the script within the package either, so I just copied it from the GitHub page. It should then be possible to run the script from your Jupyter Notebook. Best, |
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Hi @Annika18 , You can download the script with wget: You can store it anywhere, but you'll need to have pySCENIC installed to use it. I would recommend running it directly from the command line, then importing the output into a notebook. |
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Thank you. Do you have any advice on picking num_workers? My computer has 4 cores, should I use 4? Why is 20 used in the example in the FAQ? |
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Hi @Annika18, This is likely because most people will be running pySCENIC on a high performance computing cluster. If you only have 4 cores available, then you should go with that. |
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Hi,
I see that this script is no more available at scripts folder. |
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Hello, Why isn't the |
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Hi @davisidarta @saeedfc I reuploaded arboreto_with_multiprocessing.py here: https://github.com/Annika18/arboreto-multi-reupload/blob/master/arboreto_with_multiprocessing.py |
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Hey @saeedfc , @davisidarta , Sorry about that, I moved the script to a different folder because it's now built into the pySCENIC CLI. So if you have pySCENIC |
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Thank you. The |
lucygarner
changed the title
Describe the bug
Error when running pyscenic grn. I am using an older version of dask (1.0.0) as previously suggested.
Steps to reproduce the behavior
Expected behavior
Expected pyscenic grn to produce the output file: filtered_adjacencies.csv
Please complete the following information:
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