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Python3 fixes#92
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jmchilton merged 2 commits intogalaxyproject:masterfrom Feb 26, 2018
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Fix `planemo lint --conda_requirements`, see the following test
traceback:
```
======================================================================
FAIL: test_lint_dependencies_okay (tests.test_lint.LintTestCase)
----------------------------------------------------------------------
Traceback (most recent call last):
File "/home/travis/build/galaxyproject/planemo/tests/test_lint.py", line 101, in test_lint_dependencies_okay
self._check_exit_code(lint_cmd)
File "/home/travis/build/galaxyproject/planemo/tests/test_utils.py", line 100, in _check_exit_code
raise AssertionError(message)
nose.proxy.AssertionError: Planemo command [lint --conda_requirements /home/travis/build/galaxyproject/planemo/tests/../project_templates/seqtk_complete/seqtk_seq.xml] resulted in unexpected exit code [-1], expected exit code [0]]. Command output [Linting tool /home/travis/build/galaxyproject/planemo/project_templates/seqtk_complete/seqtk_seq.xml
...
Traceback (most recent call last):
File "/home/travis/build/galaxyproject/planemo/.tox/py34/lib/python3.4/site-packages/click/testing.py", line 279, in invoke
prog_name=self.get_default_prog_name(cli), **extra)
File "/home/travis/build/galaxyproject/planemo/.tox/py34/lib/python3.4/site-packages/click/core.py", line 697, in main
rv = self.invoke(ctx)
File "/home/travis/build/galaxyproject/planemo/.tox/py34/lib/python3.4/site-packages/click/core.py", line 1066, in invoke
return _process_result(sub_ctx.command.invoke(sub_ctx))
File "/home/travis/build/galaxyproject/planemo/.tox/py34/lib/python3.4/site-packages/click/core.py", line 895, in invoke
return ctx.invoke(self.callback, **ctx.params)
File "/home/travis/build/galaxyproject/planemo/.tox/py34/lib/python3.4/site-packages/click/core.py", line 535, in invoke
return callback(*args, **kwargs)
File "/home/travis/build/galaxyproject/planemo/.tox/py34/lib/python3.4/site-packages/click/decorators.py", line 64, in new_func
return ctx.invoke(f, obj, *args[1:], **kwargs)
File "/home/travis/build/galaxyproject/planemo/.tox/py34/lib/python3.4/site-packages/click/core.py", line 535, in invoke
return callback(*args, **kwargs)
File "/home/travis/build/galaxyproject/planemo/planemo/cli.py", line 177, in handle_blended_options
return f(*args, **kwds)
File "/home/travis/build/galaxyproject/planemo/planemo/commands/cmd_lint.py", line 58, in cli
recursive=kwds["recursive"]
File "/home/travis/build/galaxyproject/planemo/planemo/tool_lint.py", line 31, in lint_tools_on_path
if not lint_tool_source(tool_xml, **lint_args):
File "/home/travis/build/galaxyproject/planemo/.tox/py34/lib/python3.4/site-packages/galaxy/tools/lint.py", line 17, in lint_tool_source
lint_tool_source_with(lint_context, tool_source, extra_modules)
File "/home/travis/build/galaxyproject/planemo/.tox/py34/lib/python3.4/site-packages/galaxy/tools/lint.py", line 53, in lint_tool_source_with
lint_context.lint(name, value, tool_source)
File "/home/travis/build/galaxyproject/planemo/.tox/py34/lib/python3.4/site-packages/galaxy/tools/lint.py", line 81, in lint
lint_func(lint_target, self)
File "/home/travis/build/galaxyproject/planemo/planemo/linters/conda_requirements.py", line 18, in lint_requirements_in_conda
(best_hit, exact) = best_practice_search(conda_target)
File "/home/travis/build/galaxyproject/planemo/planemo/conda.py", line 155, in best_practice_search
return conda_util.best_search_result(conda_target, conda_context=conda_context, channels_override=BEST_PRACTICE_CHANNELS, offline=offline)
File "/home/travis/build/galaxyproject/planemo/.tox/py34/lib/python3.4/site-packages/galaxy/tools/deps/conda_util.py", line 462, in best_search_result
hits = json.loads(res).get(conda_target.package, [])
File "/usr/lib/python3.4/json/__init__.py", line 312, in loads
s.__class__.__name__))
TypeError: the JSON object must be str, not 'bytes'
```
Member
|
Thanks a million, you are awesome! I've published 18.1.0 that includes this to help with galaxyproject/planemo#774. |
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xref. galaxyproject/planemo#774