galaxyproject / galaxyproject/planemo

`planemo lint` false positive warning about `HelpInvalidRST` when using local images?

Open
#1,589 1 comment 0 reactions 0 assignees View on GitHub
Dominant language
Python
Stars
110
Forks
102
Avg merge
4d 21h
Merged PRs (30d)
13

Description

In [this tool wrapper XML](https://github.com/BMCV/galaxy-image-analysis/blob/cb6024de5269d57dc5565a62ba34e7f6be88242b/tools/color_deconvolution/color_deconvolution.xml#L174) we have the following block of RST code within the `help` tag:
```rst
.. image:: he.png
:width: 434px
:scale: 50%
```

Doing a `planemo lint` gives a warning:

> .. WARNING (HelpInvalidRST): Invalid reStructuredText found in help - [:: (WARNING/2) Problem reading image file: [Errno 2] No such file or directory: 'he.png'
> ].

However, the RST code is in accordance with the best practices https://galaxyproject.org/defining-images-in-tool-configs:

> The previously required $PATH_TO_IMAGES is now deprecated, and is ignored if used. The "best practice" for including image files within the repository is to place them in the directory path /static/images within the repository hierarchy in the tool shed.
>
> .. image:: \

It also works when served on Galaxy Europe:

https://usegalaxy.eu/root?tool_id=toolshed.g2.bx.psu.edu/repos/imgteam/color_deconvolution/ip_color_deconvolution/0.9+galaxy0

So is this a false positive warning?

Contributor guide

Open the contributing guide

Research direction

Start by running `planemo lint` against the referenced color_deconvolution.xml example and inspect how the `help` block handles its local image reference. Compare the warning with the documented `/static/images` layout and the behavior on Galaxy Europe; done means the lint result correctly distinguishes valid repository-local images from missing files.

Written by the indexing model from the issue text.

Assessment

Tech stack
python
Domain
cli
Issue type
Bug
Difficulty
3/5
Estimated time
1-2 days
Activity status
Stale
Clarity
Mostly clear
Newbie friendliness
35/100

Get new issues in your inbox

A short digest of beginner-friendly GitHub issues.