`dvc gc` does not remove files under dir.unpacked

[tlouismarie]

Setup is dvc 0.75.0 with the .deb package under Ubuntu 18.04.
Also tested with windows 10 with .exe package. I tried with different configurations for the cache type (default, copy and symlink) and get a similar behavior.

I'm testing DVC and trying to understand how it manages the datasets in its cache.
I initialize an empty repository with dvc init and add data with dvc add data in directory that contains to datasets:

• data/data.json of size 240M
• data/data_1.json of size 65M

I then run a script that produces an output dataset: dvc run -f prepare_data.dvc -d src/prepare_data.py -d data -o output python src prepare_data.py data. It creates: output/prepared_data.npy of size 360M.
The .dvc/cache directory now contains the following files (names are simplified):

• 06/file1 of size 240M at inode 60294316
• 14/file2 of size 360M at inode 60949288
• 20/file3.dir at inode 60294287
• 59/file4 of size 65M at inode 60294327
• dd/file5.dir at inode 60949289

I commit to git and tag it as expe1. I now modify my script and run dvc repro prepare_data.dvc. It produces a new file: output/prepared_data.npy of size 500M. The .dvc/cache directory now contains the following files:

• 06/file1 of size 240M at inode 60294316
• 14/file2 of size 360M at inode 60949288
• 19/file6 of size 500M at inode 60949290
• 20/file3.dir at inode 60294287
• 20/file3.dir.unpacked/data.json of size 240M at inode 60294316
• 20/file3.dir.unpacked/data_1.json of size 65M at inode 60294327
• 22/file7.dir at inode 60294291
• 59/file4 of size 65M at inode 60294327
• dd/file5.dir at inode 60949289
• dd/file5.dir.unpacked/prepared_data.npy of size 360M at inode 60949288

I commit and tag it as expe2. I now want to clean the cache to remove previous outputs from expe1 and run dvc gc. The .dvc/cache directory now contains the following files:

• 06/file1 of size 240M at inode 60294316
• empty directory 14
• 19/file6 of size 500M at inode 60949290
• 20/file3.dir at inode 60294287
• 20/file3.dir.unpacked/data.json of size 240M at inode 60294316
• 20/file3.dir.unpacked/data_1.json of size 65M at inode 60294327
• 22/file7.dir at inode 60294291
• 59/file4 of size 65M at inode 60294327
• dd/file5.dir at inode 60949289
• dd/file5.dir.unpacked/prepared_data.npy of size 360M at inode 60949288

Therefore contrary to what I expect, the previous version of the output file is still present in the cache at dd/file5.dir.unpacked/prepared_data.npy . Is this the expected behavior ?
How can I properly clean the cache ?
It seems that this file is useless as if try to checkout expe1, it raises an error, and I have to reproduce the experiment anyway:

$ git checkout expe1
$ dvc checkout
ERROR: unexpected error - Checkout failed for the following target: 
   output
Did you forget to fetch ?``

[efiop]

Hi @tlouismarie !

Indeed, looks like a bug. That unpacked dirs should indeed be removed by gc, but for now you can simply remove them yourself as a workaround. We'll investigate shortly. Thanks for the feedback!

[efiop]

To fix it, we need to make gc https://github.com/iterative/dvc/blob/0.78.1/dvc/remote/base.py#L694 do check if it is a dir checksum (by .dir suffix, see helpers around there) and then also remove .unpacked dir. Important to note that unpacked optimization is only valid for local path_infos(though need to double-check ssh too), so could consider checking that too.

[efiop]

Here is a reproducer:

#!/bin/bash           
                      
set -e                
set -x                
                      
rm -rf myrepo         
mkdir myrepo          
cd myrepo             
                      
git init              
dvc init              
                      
mkdir data            
echo foo > data/foo   
                      
dvc add data          
                      
tree .dvc/cache       
                      
dvc status            
                      
tree .dvc/cache       
                      
rm data.dvc           
                      
dvc gc -f             
                      
tree .dvc/cache       

[sharidas]

I am having a look into this issue.

[sharidas]

Created PR: #3054

I have tested with the reproduce script suggested #2946 (comment).