```dvc exp run --queue```: deleting file 'params.yaml' for each command call

Bug Report

dvc exp run --queue: deleting file ‘params.yaml’ for each command call

Description

dvc exp run --queue deletes file ‘params.yaml’ for each trial to add a new experiment and the experiment don’t put into queue. It works correctly only if command git add params.yaml was called before.

Reproduce

Example files: test.py

import numpy as np
import json
import yaml

params = yaml.safe_load(open('params.yaml'))["test"]

precision = np.random.random()
recall = params['value']
accuracy = np.random.random()

rows = {'precision': precision,
        'recall': recall,
        'accuracy': accuracy}

with open(params['metrics_path'], 'w') as outfile:
    json.dump(rows, outfile)

fpr = 10*np.random.random((1,10)).tolist()
tpr = 10*np.random.random((1,10)).tolist()

with open('plot.json', 'w') as outfile2:
    json.dump(
      {
        "roc": [ {"fpr": f, "tpr": t} for f, t in zip(fpr, tpr) ]
      }, 
      outfile2
      )

params.yaml

test:
  metrics_path: scores.json
  value: 2

dvc.yaml

stages:
  test:
    cmd: python test.py
    deps:
    - test.py
    params:
    - test.metrics_path
    - test.value
    metrics:
    - scores.json:
        cache: false
    plots:
    - plot.json:
        cache: false
        x: fpr
        y: tpr

1. dvc exp run --queue -S test.value=101

Expected

New experiments adds to queue without ‘params.yaml’ deleting.

Environment information

Ubuntu 20.04

Output of dvc doctor:

$ dvc doctor

DVC version: 2.10.2 (pip)
---------------------------------
Platform: Python 3.9.7 on Linux-5.13.0-40-generic-x86_64-with-glibc2.31
Supports:
        webhdfs (fsspec = 2022.3.0),
        http (aiohttp = 3.8.1, aiohttp-retry = 2.4.6),
        https (aiohttp = 3.8.1, aiohttp-retry = 2.4.6)
Cache types: hardlink, symlink
Cache directory: ext4 on /dev/nvme0n1p6
Caches: local
Remotes: None
Workspace directory: ext4 on /dev/nvme0n1p6
Repo: dvc, git

Additional Information (if any):

[behrica]

I stumbled over this today and found it at least “unexpected” and did not know how to fix it, until I came here.

[pmrowla]

Applying the merge on the workspace isn’t the correct behavior, that would put -S modified params into the workspace and not the original params file.

I think the fix for this should just be to use stash_workspace(include_untracked=True) here https://github.com/iterative/dvc/blob/55b16166c852a72e8dd47d4e32090063d27497e4/dvc/repo/experiments/queue/base.py#L320

When we leave that context it is supposed to restore the workspace to the state before any DVC exp related changes/operations were done. include_untracked was omitted because we aren’t supposed to be touching untracked files at all in exps, but the bug is we actually can modify untracked files in the params file case.