Implement shed_lint.

[jmchilton]

Lint a shed repository instead of just tools. This is a meta-issue to track 4 issues open by @peterjc.

• Check sample files linting: Check sample loc files exist under tool-data/ #96.
• Check for a README linting: Check for suitable README file #89.
• Check rst in any .rst files linting: Check reStructuredText markup in any .rst files #91.
• Lint tool_dependencies.xml.
• Cross reference tool_dependencies.xml with tools linting: Check tool_dependencies.xml consistent with requirement tags #90.
• Lint .shed.yml
• Lint repository_dependencies.xml.
• Check that packages belong only to the category Tool Dependency Packages. 8c2a45a
• Check tool dependency actions that are difficult to verify with XSD. 8117e03
• Check for required type based on repository type. planemo shed_lint and tool_dependency_definition #156
• Check for changeset and tool shed attributes in tool_dependencies.xml files. (Remove hardcoded changesets tools-iuc#149 (comment))

[hexylena]

How would you feel about checking for .shed.yml?
http://galaxy-iuc-standards.readthedocs.org/en/latest/best_practices/shed_yml.html

[jmchilton]

Some initial work here #130 addressing linting tool_dependencies.xml, repository_dependencies.xml and .shed.yml but not the rest of this - but there is at least a spot for it now.

[peterjc]

@erasche did you mean finding a .shed.yml means the folder is a Tool Shed repository? Or when checking a folder thought to be a Tool Shed repository, it ought to have a .shed.yml? This is important for recursion - how should planemo shed_list -r ... decide what to look at?

[hexylena]

@peterjc nmo, I meant checking that a .shed.yml file was present in what looks like a tool folder/maybe validating the contents of it. See #130 and "Bare minimum to lint .shed.yml files."

[peterjc]

Thanks for the clarification @erasche - basic linting of .shed.yml is happening now (ticked on the TODO list here), but I agree that can probably be more through.

See also #156 for dependency packages.

[hexylena]

#96 would've caught galaxyproject/tools-iuc#148

[hexylena]

planemo shed_lint --tools --ensure_metadata --urls --report_level warn --fail_level error tools/jq
Linting repository /home/hxr/work/tools-iuc/tools/jq
+Linting tool /home/hxr/work/tools-iuc/tools/jq/jq.xml
Applying linter citations... WARNING
.. WARNING: No citations found, consider adding citations to your tool.
Applying linter shed_metadata... WARNING
.. WARNING: Missing shed metadata field [description] for repository
.. WARNING: Missing shed metadata field [long_description] for repository
.. WARNING: Missing shed metadata field [remote_repository_url] for repository
.. WARNING: Missing shed metadata field [homepage_url] for repository
.. WARNING: Missing shed metadata field [categories] for repository

I think a missing .shed.yml file should be an error. Some of the metadata fields like homepage_url are nice-to-haves and thus are fine being warnings, but a missing .shed.yml is a problem, and we missed it during the JQ merge. Someone (i.e. myself, whenever I find five seconds amongst packing for my move) should PR this change.

xref galaxyproject/tools-iuc#1402