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Replace subversion with git --depth 1 for repository checkout #28

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mhalle opened this issue Jul 22, 2023 · 2 comments
Open

Replace subversion with git --depth 1 for repository checkout #28

mhalle opened this issue Jul 22, 2023 · 2 comments

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@mhalle
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mhalle commented Jul 22, 2023

This notebook installs subversion to check out pyplastimatch efficiently.

Instead, use git --depth 1 to create a shallow clone that includes only the last commit.

@fedorov
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fedorov commented Jul 24, 2023

It is actually completely unnecessary in this case at all to even worry about efficient checkout, since that repo is very tiny. But it's a nice trick that I was not aware about - it can be handy in other places.

I can figure out which notebook this is about, but "this notebook" reference is ambiguous, given that this repo contains multiple notebooks.

@mhalle
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mhalle commented Jul 24, 2023

Sorry about that, didn't check that the notebooks weren't in their own repo.

The notebook I was referencing was IDC_segmentation_primer.ipynb , but the specific checkout is pyplastimatch, which is likely used in multiple notebooks:

!svn checkout https://github.com/AIM-Harvard/pyplastimatch/trunk/pyplastimatch tutorial/pyplastimatch

It would be great to avoid some of the ancillary issues like package installs in these demo notebooks if at all possible, if only because they detract from the main task at hand. Sometimes it can't be avoided, though.

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