planemo shed_lint --fail_fast broken?

[peterjc]

Using peterjc/pico_galaxy@4a83837 as an example, with planemo as of f88f055

$ planemo --version
planemo, version 0.28.0.dev0

Sample output:

$ planemo shed_lint tools/ -r --fail_fast ; echo "Return code $?"
...
Linting repository /Volumes/Hitachi-3TB-mirrored/repositories/pico_galaxy/tools/mira3
Applying linter expansion... WARNING
.. WARNING: Failed to expand inclusions [{u'source': u'../../tools/mira3/mira.py', u'strip_components': 2}, {u'source': u'../../tools/mira3/mira.xml', u'strip_components': 2}, {u'source': u'../../tools/mira3/tool_dependencies.xml', u'strip_components': 2}]
Applying linter tool_dependencies_xsd... CHECK
.. INFO: No tool_dependencies.xml, skipping.
Applying linter tool_dependencies_actions... CHECK
.. INFO: No tool_dependencies.xml, skipping.
Applying linter repository_dependencies... CHECK
.. INFO: No repository_dependencies.xml, skipping.
Applying linter shed_yaml... CHECK
.. INFO: .shed.yml found and appears to be valid YAML.
Applying linter readme... CHECK
.. INFO: README found containing valid reStructuredText.
Failed linting
Linting repository /Volumes/Hitachi-3TB-mirrored/repositories/pico_galaxy/tools/mira4_0
Applying linter expansion... WARNING
.. WARNING: Failed to expand inclusions [{u'source': u'../../tools/mira4_0/mira4.py', u'strip_components': 2}, {u'source': u'../../tools/mira4_0/mira4_bait.py', u'strip_components': 2}, {u'source': u'../../tools/mira4_0/mira4_convert.py', u'strip_components': 2}, {u'source': u'../../tools/mira4_0/mira4_de_novo.xml', u'strip_components': 2}, {u'source': u'../../tools/mira4_0/mira4_make_bam.py', u'strip_components': 2}, {u'source': u'../../tools/mira4_0/mira4_mapping.xml', u'strip_components': 2}, {u'source': u'../../tools/mira4_0/mira4_validator.py', u'strip_components': 2}, {u'source': u'../../tools/mira4_0/repository_dependencies.xml', u'strip_components': 2}, {u'source': u'../../tools/mira4_0/tool_dependencies.xml', u'strip_components': 2}]
Applying linter tool_dependencies_xsd... CHECK
.. INFO: No tool_dependencies.xml, skipping.
Applying linter tool_dependencies_actions... CHECK
.. INFO: No tool_dependencies.xml, skipping.
Applying linter repository_dependencies... CHECK
.. INFO: No repository_dependencies.xml, skipping.
Applying linter shed_yaml... CHECK
.. INFO: .shed.yml found and appears to be valid YAML.
Applying linter readme... CHECK
.. INFO: README found containing valid reStructuredText.
Failed linting
Linting repository /Volumes/Hitachi-3TB-mirrored/repositories/pico_galaxy/tools/mira4_9
Applying linter expansion... WARNING
.. WARNING: Failed to expand inclusions [{u'source': u'../../tools/mira4_9/mira_4_9_bait.xml', u'strip_components': 2}, {u'source': u'../../tools/mira4_9/repository_dependencies.xml', u'strip_components': 2}, {u'source': u'../../tools/mira4_9/tool_dependencies.xml', u'strip_components': 2}]
Applying linter tool_dependencies_xsd... CHECK
.. INFO: No tool_dependencies.xml, skipping.
Applying linter tool_dependencies_actions... CHECK
.. INFO: No tool_dependencies.xml, skipping.
Applying linter repository_dependencies... CHECK
.. INFO: No repository_dependencies.xml, skipping.
Applying linter shed_yaml... CHECK
.. INFO: .shed.yml found and appears to be valid YAML.
Applying linter readme... CHECK
.. INFO: README found containing valid reStructuredText.
Failed linting
...
Linting repository /Volumes/Hitachi-3TB-mirrored/repositories/pico_galaxy/tools/venn_list
Applying linter expansion... CHECK
.. INFO: Included files all found.
Applying linter tool_dependencies_xsd... CHECK
.. INFO: tool_dependencies.xml found and appears to be valid XML
Applying linter tool_dependencies_actions... CHECK
.. INFO: Parsed tool dependencies.
Applying linter repository_dependencies... CHECK
.. INFO: No repository_dependencies.xml, skipping.
Applying linter shed_yaml... CHECK
.. INFO: .shed.yml found and appears to be valid YAML.
Applying linter readme... CHECK
.. INFO: README found containing valid reStructuredText.
Return code 1

Despite failing relatively early on, planemo shed_lint continued and linted all the folders.

By using --fail_fast I expected planemo to abort after the first failure.

[nsoranzo]

@peterjc I've seen this one too, thanks for opening the issue!

[jmchilton]

This was not quite the kind of error fail_fast detects but from the outside the behavior described here seems the most obvious and most desirable. So its a bug, but it isn't a regression I guess - it never did this. I think I have a fix for this though...