galaxyproject / galaxyproject/planemo

shed_lint is missing options in lint

Open
#667 1 comment 1 reaction 0 assignees View on GitHub
enhancement linting ux
Dominant language
Python
Stars
110
Forks
102
Avg merge
4d 21h
Merged PRs (30d)
13

Description

```
$ planemo shed_lint --help
Usage: planemo shed_lint [OPTIONS] PROJECT

Check Tool Shed repository for common issues.

With the ``--tools`` flag, this command lints actual Galaxy tools in
addition to tool shed artifacts.

With the ``--urls`` flag, this command searches for
``$URL`` and download actions which specify URLs. Each
of those are accessed individually. By default, this tool requests the
first hundred or so bytes of each listed URL and validates that a 200 OK
was received. In tool XML files, the ``--urls`` option checks through the
help text for mentioned URLs and checks those.

Options:
-r, --recursive Recursively perform command for nested
repository directories.
--fail_fast If multiple repositories are specified and
an error occurs stop immediately instead of
processing remaining repositories.
--report_level [all|warn|error]
--fail_level [warn|error]
--tools Lint tools discovered in the process of
linting repositories.
--xsd / --no_xsd Include tool XSD validation in linting
process.
--ensure_metadata Ensure .shed.yml files contain enough
metadata for each repository to allow
automated creation and/or updates.
--urls Check validity of URLs in XML files
--help Show this message and exit.

```

While this has ``--xsd`` / ``--no_xsd`` and ``--urls``, it is missing ``--dois``, ``--conda_requirements``, ``--biocontainer`` (etc?) from ``planemo lint``.

Checking those currently requires running both ``planemo lint`` and ``planemo shed_lint``, while I would prefer to just run ``planemo shed_lint --tools`` and do it all in one go.

Contributor guide

Open the contributing guide

Assessment

This issue has not been assessed yet.

Get new issues in your inbox

A short digest of beginner-friendly GitHub issues.