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Changed scripts to run in Python 3 #2

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Jennie-Martin
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Syntax alteration to work in Python 3. Also updated README and comments in gch_init.py to edit incorrect statements (number of structures in shaketraj.xyz and math error/typo in way --conv argument works) and changed default of -wdir in gch_run to 'tmp' to match new default in gch_init

I'm not sure what's going on with the automatic 'edit detection' for lib_gch.py that appears to suggest I've altered the indentation of lines 681 and 690. If you manually compare my lib_gch.py to the orginal lib_gch.py , this shows that indentation level is unaltered as far as I can tell. These lines had tabs rather than spaces in the original (the rest of the script has spaces) so I think I had to replace tabs with spaces and it should result in the same thing -indented to the same level but you might need to check.

@ceriottm
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Ciao Jenny sorry for the slow response rate. It would help a lot - both me checking this PR and others trying to use this code - if you would add a folder with a mini-example that one can run. Could you try that?

@ceriottm
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ceriottm commented Sep 1, 2022

Hi Jenny, this works well. I would just change the kernel generation routines to start from example_set.xyz, removing the stuff that is specific to the format used in Graeme's group. Then as far as I'm concerned it is good to merge.

@Jennie-Martin
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Hi Michele, I think the kernel generation script should be fixed now

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