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Conda tutorial fixes. Enable ``--conda_use_local`` option for ``planemo test`` #876

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merged 8 commits into from Nov 15, 2018

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nsoranzo commented Oct 14, 2018

See individual commits for details.

@nsoranzo nsoranzo force-pushed the nsoranzo:tutorial_fixes branch from e991523 to 6452d91 Oct 14, 2018

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nsoranzo commented Oct 14, 2018

The remaining test failures seem unrelated.

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mvdbeek commented Oct 14, 2018

Yes, I think I fixed them in #874.

@nsoranzo nsoranzo force-pushed the nsoranzo:tutorial_fixes branch 2 times, most recently from 6fd3be7 to 077af1a Oct 18, 2018

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nsoranzo commented Oct 18, 2018

Rebased and green too!

@@ -1,4 +1,7 @@
<tool id="fleeqtk_seq" name="Convert to FASTA (fleeqtk)" version="0.1.0">
<requirements>
<requirement type="package" version="1.3">fleeqtk</requirement>
</requirements>

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But this is part of the exercise right? Maybe make that more clear in the exercise written description?

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It is not mentioned anywhere in https://planemo.readthedocs.io/en/latest/writing_advanced.html#exercise-build-a-recipe , it's more of a surprise egg...
How to add a requirement was already explained for seqtk_seq using planemo tool_init in https://planemo.readthedocs.io/en/latest/writing_standalone.html#the-basics, it is not clear at all why it's removed here for fleeqtk_seq, unless the goal is to confuse people.

@nsoranzo nsoranzo force-pushed the nsoranzo:tutorial_fixes branch from 077af1a to 9e8adb3 Nov 14, 2018

@nsoranzo nsoranzo force-pushed the nsoranzo:tutorial_fixes branch from 9de55f8 to 48f28e3 Nov 14, 2018

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nsoranzo commented Nov 15, 2018

galaxyproject/galaxy#7013 should help for the failing tests.

Fix locally test
Fix the following traceback:

```
======================================================================
FAIL: Test training_generate_from_wf command with workflow on running instance.
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/usr/users/ga002/soranzon/software/nsoranzo_planemo/tests/test_cmd_training_generate_from_wf.py", line 77, in test_training_generate_from_wf_command_remote_wf
    self._check_exit_code(training_init_command, exit_code=1)
  File "/usr/users/ga002/soranzon/software/nsoranzo_planemo/tests/test_utils.py", line 105, in _check_exit_code
    return check_exit_code(self._runner, command_list, exit_code=exit_code)
  File "/usr/users/ga002/soranzon/software/nsoranzo_planemo/tests/test_utils.py", line 310, in check_exit_code
    raise AssertionError(message)
AssertionError: Planemo command [training_generate_from_wf --topic_name test --tutorial_name test --workflow_id ID] resulted in unexpected exit code [-1], expected exit code [1]]. Command output [] Exception [The topic test does not exists. It should be created], Traceback [['Traceback (most recent call last):\n', '  File "/usr/users/ga002/soranzon/software/nsoranzo_planemo/.venv3/lib/python3.5/site-packages/click/testing.py", line 279, in invoke\n    prog_name=self.get_default_prog_name(cli), **extra)\n', '  File "/usr/users/ga002/soranzon/software/nsoranzo_planemo/.venv3/lib/python3.5/site-packages/click/core.py", line 697, in main\n    rv = self.invoke(ctx)\n', '  File "/usr/users/ga002/soranzon/software/nsoranzo_planemo/.venv3/lib/python3.5/site-packages/click/core.py", line 1066, in invoke\n    return _process_result(sub_ctx.command.invoke(sub_ctx))\n', '  File "/usr/users/ga002/soranzon/software/nsoranzo_planemo/.venv3/lib/python3.5/site-packages/click/core.py", line 895, in invoke\n    return ctx.invoke(self.callback, **ctx.params)\n', '  File "/usr/users/ga002/soranzon/software/nsoranzo_planemo/.venv3/lib/python3.5/site-packages/click/core.py", line 535, in invoke\n    return callback(*args, **kwargs)\n', '  File "/usr/users/ga002/soranzon/software/nsoranzo_planemo/.venv3/lib/python3.5/site-packages/click/decorators.py", line 64, in new_func\n    return ctx.invoke(f, obj, *args[1:], **kwargs)\n', '  File "/usr/users/ga002/soranzon/software/nsoranzo_planemo/.venv3/lib/python3.5/site-packages/click/core.py", line 535, in invoke\n    return callback(*args, **kwargs)\n', '  File "/usr/users/ga002/soranzon/software/nsoranzo_planemo/planemo/cli.py", line 195, in handle_blended_options\n    return f(*args, **kwds)\n', '  File "/usr/users/ga002/soranzon/software/nsoranzo_planemo/planemo/commands/cmd_training_generate_from_wf.py", line 19, in cli\n    training.generate_tuto_from_wf(ctx)\n', '  File "/usr/users/ga002/soranzon/software/nsoranzo_planemo/planemo/training/__init__.py", line 86, in generate_tuto_from_wf\n    self.check_topic_init_tuto()\n', '  File "/usr/users/ga002/soranzon/software/nsoranzo_planemo/planemo/training/__init__.py", line 45, in check_topic_init_tuto\n    raise Exception("The topic %s does not exists. It should be created" % self.topic.name)\n', 'Exception: The topic test does not exists. It should be created\n']]
```

@jmchilton jmchilton merged commit 5810ce8 into galaxyproject:master Nov 15, 2018

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@nsoranzo nsoranzo deleted the nsoranzo:tutorial_fixes branch Jan 30, 2019

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