Fix #85

CHANGELOG.md

@@ -15,6 +15,7 @@
 ### Linting
 
 * Adjusted linting to enable `patch` branches from being tested
+* Warn if pipeline name contains upper case letters or non alphabetical characters [#85](https://github.com/nf-core/tools/issues/85)
 
 ### Template
 

docs/lint_errors.md

@@ -236,3 +236,7 @@ This lint test runs through all files in the pipeline and searches for these lin
 ## Error #11 - Singularity file found ##{#11}
 
 As we are relying on [Docker Hub](https://https://hub.docker.com/) instead of Singularity and all containers are automatically pulled from there, repositories should not have a `Singularity` file present.
+
+## Error #12 - Pipeline name ## {#12}
+
+In order to ensure consistent naming, pipeline names should contain only lower case, alphabetical characters. Otherwise a warning is displayed.

nf_core/lint.py

@@ -172,7 +172,8 @@ def lint_pipeline(self, release_mode=False):
             'check_readme',
             'check_conda_env_yaml',
             'check_conda_dockerfile',
-            'check_pipeline_todos'
+            'check_pipeline_todos',
+            'check_pipeline_name'
         ]
         if release_mode:
             self.release_mode = True
@@ -333,6 +334,7 @@ def check_nextflow_config(self):
         and print all config variables.
         NB: Does NOT parse contents of main.nf / nextflow script
         """
+
         # Fail tests if these are missing
         config_fail = [
             'manifest.name',
@@ -802,6 +804,18 @@ def check_pipeline_todos(self):
                                 l = '{}..'.format(l[:50-len(fname)])
                             self.warned.append((10, "TODO string found in '{}': {}".format(fname,l)))
 
+    def check_pipeline_name(self):
+        """Check whether pipeline name adheres to lower case/no hyphen naming convention"""
+
+        if self.pipeline_name.islower() and self.pipeline_name.isalpha():
+            self.passed.append((12, "Name adheres to nf-core convention"))
+        if not self.pipeline_name.islower():
+            self.warned.append((12, "Naming does not adhere to nf-core conventions: Contains uppercase letters"))
+        if not self.pipeline_name.isalpha():
+            self.warned.append((12, "Naming does not adhere to nf-core conventions: Contains non alphabetical characters"))
+
+
+
     def print_results(self):
         # Print results
         rl = "\n  Using --release mode linting tests" if self.release_mode else ''

tests/test_bump_version.py

@@ -8,7 +8,7 @@
 import nf_core.lint, nf_core.bump_version
 
 WD = os.path.dirname(__file__)
-PATH_WORKING_EXAMPLE = os.path.join(WD, 'lint_examples/minimal_working_example')
+PATH_WORKING_EXAMPLE = os.path.join(WD, 'lint_examples/minimalworkingexample')
 
 
 @pytest.mark.datafiles(PATH_WORKING_EXAMPLE)

tests/test_download.py

@@ -16,7 +16,7 @@
 import tempfile
 import unittest
 
-PATH_WORKING_EXAMPLE = os.path.join(os.path.dirname(__file__), 'lint_examples/minimal_working_example')
+PATH_WORKING_EXAMPLE = os.path.join(os.path.dirname(__file__), 'lint_examples/minimalworkingexample')
 
 class DownloadTest(unittest.TestCase):
 

tests/test_lint.py

@@ -32,13 +32,13 @@ def pf(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')
-PATH_WORKING_EXAMPLE = pf(WD, 'lint_examples/minimal_working_example')
+PATH_WORKING_EXAMPLE = pf(WD, 'lint_examples/minimalworkingexample')
 PATH_MISSING_LICENSE_EXAMPLE = pf(WD, 'lint_examples/missing_license_example')
 PATHS_WRONG_LICENSE_EXAMPLE = [pf(WD, 'lint_examples/wrong_license_example'),
     pf(WD, 'lint_examples/license_incomplete_example')]
 
 # The maximum sum of passed tests currently possible
-MAX_PASS_CHECKS = 61
+MAX_PASS_CHECKS = 62
 # The additional tests passed for releases
 ADD_PASS_RELEASE = 1
 
@@ -423,3 +423,20 @@ def test_pip_dependency_fails(self):
         lint_obj.check_conda_env_yaml()
         expectations = {"failed": 1, "warned": 0, "passed": 2}
         self.assess_lint_status(lint_obj, **expectations)
+
+    def test_pipeline_name_pass(self):
+        """Tests pipeline name good pipeline example: lower case, no punctuation"""
+        #good_lint_obj = nf_core.lint.run_linting(PATH_WORKING_EXAMPLE)
+        good_lint_obj = nf_core.lint.PipelineLint(PATH_WORKING_EXAMPLE)
+        good_lint_obj.pipeline_name = 'tools'
+        good_lint_obj.check_pipeline_name()
+        expectations = {"failed": 0, "warned": 0, "passed": 1}
+        self.assess_lint_status(good_lint_obj, **expectations)
+
+    def test_pipeline_name_critical(self):
+        """Tests that warning is returned for pipeline not adhering to naming convention"""
+        critical_lint_obj = nf_core.lint.PipelineLint(PATH_WORKING_EXAMPLE)
+        critical_lint_obj.pipeline_name = 'Tools123'
+        critical_lint_obj.check_pipeline_name()
+        expectations = {"failed": 0, "warned": 2, "passed": 0}
+        self.assess_lint_status(critical_lint_obj, **expectations)