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Merged
ewels merged 3 commits into from
Feb 15, 2018
Merged

Started with implementing unittests for lint #1

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7b9ca7c
Remove redundant entry for nextflow.config
sven1103 Feb 14, 2018
f2e9533
Add click pkg as requirement
sven1103 Feb 14, 2018
860a66c
Start implementing unittests
sven1103 Feb 14, 2018
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1 change: 0 additions & 1 deletion nf_core/lint.py
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Original file line number Diff line number Diff line change
Expand Up @@ -60,7 +60,6 @@ def check_files_exist (self):
files_fail = [
'LICENSE',
'README.md',
'nextflow.config',
'Dockerfile',
'docs/README.md',
'nextflow.config'
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1 change: 1 addition & 0 deletions requirements.txt
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@@ -0,0 +1 @@
click
Empty file added tests/lint_examples/critical_example/LICENSE
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Empty file added tests/lint_examples/failing_example/main.nf
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Empty file added tests/lint_examples/failing_example/nextflow.config
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40 changes: 40 additions & 0 deletions tests/test_lint.py
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@@ -0,0 +1,40 @@
#!/usr/bin/env python
"""Some tests covering the linting code.
Provide example wokflow directory contents like:

--tests
|--lint_examples
| |--missing_license
| | |...<files here>
| |--missing_config
| | |....<files here>
| |...
|--test_lint.py
"""
import os
import unittest
import nf_core.lint
from nose.tools import raises

def pf(wd, path):
return os.path.join(wd, path)

WD = os.path.dirname(__file__)
PATH_CRITICAL_EXAMPLE = pf(WD, 'lint_examples/critical_example')
PATH_FAILING_EXAMPLE = pf(WD, 'lint_examples/failing_example')

class TestLint(unittest.TestCase):
"""Class for lint tests"""

@raises(AssertionError)
def test_critical_example(self):
"""Tests for missing nextflow config and main.nf files"""
lint_obj = nf_core.lint.PipelineLint(PATH_CRITICAL_EXAMPLE)
lint_obj.lint_pipeline()

def test_failing_example(self):
"""Tests for missing files like Dockerfile or LICENSE"""
lint_obj = nf_core.lint.PipelineLint(PATH_FAILING_EXAMPLE)
lint_obj.lint_pipeline()
assert len(lint_obj.failed) == 4, "Expected 6 files missing, but found %r" % len(lint_obj.failed)
assert len(lint_obj.passed) == 2, "Expected 6 files missing, but found %r" % len(lint_obj.passed)