dvc plots show: paths relative to `dvc.yaml` instead of `$PWD` in version 2.12.1 and 2.13.0

Bug Report

Description

In the new release 2.13.0, dvc plots show (or diff) does not work with a setup when the dvc.yaml file is not in the root directory and when the data (for plots) are on a different path relative to the root.

For example with a repo structure like this

.
├── data
├── dvc_plots
├── modules
├── notebooks
├── pipelines

where

pipelines
├── segment_X
│   └── classification
│       ├── product_A
│       │   ├── dvc.lock
│       │   ├── dvc.yaml
│       │   └── params.yaml
│       ├── product_B
│       │   ├── dvc.lock
│       │   ├── dvc.yaml
│       │   └── params.yaml

and

data
├── segment_X
│   ├── classification
│   │   ├── product_A
│   │   │   └── precision_recall_curve.csv
│   │   ├── product_B
│   │   │   └── precision_recall_curve.csv

where in each dvc.yaml file and each stage we have

wdir: ../../../..

(i.e. the working directory is the root of the repo)

you get the following warning when calling dvc plots show

WARNING: 'pipelines/segment_X/classification/product_A/data/segment_X/classification/product_A/precision_recall_curve.csv' was not found in current workspace. 

and similarly with other pipelines and plots. The issue is clearly that dvc seems to use the path to the corresponding dvc.yaml as the working directory (as the path above is indeed not in the workspace since the data directory is in the root directory)

Reproduce

1. Create a pipeline which is structured as above with dvc.yaml in a different directory than the root and outputs in yet another directory.
2. add some plots to a stage in dvc.yaml, the cause might also theoretically come from templating, so try something like

stages:
  plot:
    wdir: ../../../..
    cmd: >-
      python modules/evaluate.py
      --params=${paths.params_file}
    deps: ...
    params:
      - ${paths.params_file}:
          - paths
    metrics: ...
    plots:
      - ${paths.precision_recall_curve}:
          title: "Precision recall curve"
          x: recall
          y: precision

where the params.yaml should be in the same directory as the dvc.yaml and contain the following:

paths:
  params_file: pipelines/segment_X/classification/product_A/params.yaml
  precision_recall_curve: data/segment_X/classification/product_A/precision_recall_curve.csv

1. Call dvc repro to create the precision_recall_curve.csv in the first place
2. Call dvc plots show or dvc plots diff

Expected

The behaviour of dvc up till 2.12.0 where the plot paths are found correctly and relative to the $PWD instead of the directory where the coresponding dvc.yaml is located.

Environment information

Output of dvc doctor:

$ dvc doctor
DVC version: 2.13.0 (pip)
---------------------------------
Platform: Python 3.10.5 on Linux-5.18.7-1-MANJARO-x86_64-with-glibc2.35
Supports:
        azure (adlfs = 2022.4.0, knack = 0.9.0, azure-identity = 1.10.0),
        webhdfs (fsspec = 2022.5.0),
        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/nvme0n1p2
Caches: local
Remotes: azure
Workspace directory: ext4 on /dev/nvme0n1p2
Repo: dvc, git

Additional Information (if any): The new version of dvc has two new dependencies:

• dvc-data-0.0.23
• dvc-objects-0.0.23

I am not sure if either of these two could be the cause, but they were both bumped from version 0.0.16 in dvc 2.13.0

[pared]

Hi @tibor-mach! Should be fixed in next release

[tibor-mach]

@pared Hi, how’s the progress on this one?