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I am a data scientist and I do a lot of prototyping in jupyterlab. The problem is jupyterlabn autosaves a lot of checkpoint files and when I do git add -A this will rope them in as well forcing me to either add more pointedly (which can be annoying if I've generated a bunch of image files of plots that I want to keep) or to remove them to the commit before running git commit and pushing. How can I add a general block on all file containing this substring .ipynb_checkpoints so for instance none of the checkpoint files will be included in this list:

new file:   .ipynb_checkpoints/High_IEG_expressing_cells-checkpoint.Rmd
#       modified:   DGC_Cck_to_Malat1_BehaviouralAxis.Rmd
#       new file:   EngramCellClassifier/Chen2020_GSE152632/.ipynb_checkpoints/ExcitatorySampleCorrelation-checkpoint.png
#       new file:   EngramCellClassifier/Chen2020_GSE152632/.ipynb_checkpoints/ExcitatorySamplesAllGenesExpression-checkpoint.png
#       new file:   EngramCellClassifier/Chen2020_GSE152632/.ipynb_checkpoints/Filterddata_ExcitatorySampleCorrelation-checkpoint.png
#       modified:   EngramCellClassifier/Chen2020_GSE152632/.ipynb_checkpoints/Pavlab_remotememory_DEG_analysis-checkpoint.ipynb
#       new file:   EngramCellClassifier/Chen2020_GSE152632/.ipynb_checkpoints/RemoteMemoryMarkersExpressionSampleLevel-checkpoint.png
#       new file:   EngramCellClassifier/Chen2020_GSE152632/.ipynb_checkpoints/pseudobulk_sample_corrrealtionmatrix-checkpoint.jpeg
#       new file:   EngramCellClassifier/Chen2020_GSE152632/.ipynb_checkpoints/test-checkpoint.jpg
#       new file:   EngramCellClassifier/Chen2020_GSE152632/ExcitatorySampleCorrelation.png
#       new file:   EngramCellClassifier/Chen2020_GSE152632/ExcitatorySamplesAllGenesExpression.png
#       new file:   EngramCellClassifier/Chen2020_GSE152632/Filterddata_ExcitatorySampleCorrelation.png
#       modified:   EngramCellClassifier/Chen2020_GSE152632/Pavlab_remotememory_DEG_analysis.ipynb
#       new file:   EngramCellClassifier/Chen2020_GSE152632/RemoteMemoryMarkersExpressionSampleLevel.png
#       new file:   EngramCellClassifier/Chen2020_GSE152632/pseudobulk_sample_corrrealtionmatrix.jpeg
#       modified:   High_IEG_expressing_cells.Rmd
Angus Campbell
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1 Answers1

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You first need to create a .gitignore file. Once you have done this you can add .ipynb_checkpoints to the .gitignore.

To do this open Git Bash and navigate to the root folder.

Then use the command touch .gitignore. This creates the .gitignore file.

Once the file has been created open it (it should be a text file) and add the text:

.ipynb_checkpoints

Save the file.

In Git Bash make sure you are in the correct directory, then use the command git add .gitignore. Followed by git commit -m "YOUR COMMENT HERE". Then git push. This should then ignore all files in the .ipynb_checkpoints folder.

To ignore them globally a solution has been posted here.

Hope this helps.

N.B. This is also a helpful article https://www.freecodecamp.org/news/gitignore-file-how-to-ignore-files-and-folders-in-git/

jackdotdi
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