Error with network.compress()

arichelle commented 3 years ago

Hi,

I keep running into the same error when using network.compress()

Traceback is as follows:

compress compress_inner cancel_clementine clementine_equality_compression redund with open(matrix_nonredundant_path) as file:

FileNotFoundError: [Errno 2] No such file or directory: 'C:\Users\...\ecmtool\ecmtool\tmp\matrix_nored0.ine'

Any suggestions?

Thank in advance

dhdegroot commented 3 years ago

Hi,

@tjclement can probably help you with this. For now, I know that we have had some problems already with the tmp-folder not being created, but I thought we had solved it before. @arichelle could you check for us if the tmp-folder exists at the reported path?

Best, Daan

arichelle commented 3 years ago

Yes it exits but the only .ine file in it is named "matrix0"

tjclement commented 3 years ago

Hi @arichelle, it seems that the tool we use to removed redundant vectors (called redund) is not writing its nonredundant output file given your input matrix. Could you share your matrix0.ine file with us here, so we can have a look into why redund trips on it?

arichelle commented 3 years ago

Here it goes matrix0.zip

tjclement commented 3 years ago

This is peculiar: I'm not able to reproduce what you're seeing. On Windows, like you're using, running redund on the file you sent seems to result in a reduced matrix just fine.

Can you share more about your environment, like which version of Windows and version of Python are you using, and whether you pip installed or git cloned ecmtool? It would also be very helpful if you could share the network that you're trying to compress.

Thanks!

arichelle commented 3 years ago

Hello, I git cloned the repo, I'm using Spyder as Python environment with Python 3.8. and I've Windows 10 Enterprise. Here the script I try to run

ExampleUseECM.zip

tjclement commented 3 years ago

Hey @arichelle, with Spyder installed on a Windows 10 machine the attached code does not throw the error you're seeing. I did the following:

Git cloned ecmtool
Copied your example script in the top-level directory of the cloned ecmtool repository
Installed Spyder, and set it to use the (3.7) python installation on this system
pip installed ecmtool/requirements.txt
pip installed sympy==1.7.1 (related to the bug in cbmpy mentioned in your other opened issue)
Ran your script

There was a different issue in the script, where making a list of external metabolites went wrong after calculating the ECMs. @dhdegroot fixed that in the script that yours was based on yesterday: https://github.com/SystemsBioinformatics/ecmtool/commit/d5c51920cf792187606a12ce41f12c2e58d4d058.

Regarding the issue you're seeing with removal of redundant vectors, I am not sure how we can best help as we're not able to reproduce it so far. Perhaps it's got something to do with your Python (or anaconda) environment?

arichelle commented 3 years ago

yes it was most likely a problem with my python environment. I was able to run without trouble the example on a VM of Azure.

SystemsBioinformatics / ecmtool

Error with network.compress() #12