Merge pull request #69 from sjanssen2/use_flake8

fixing minor code style issues + activating flake8 for travis

.travis.yml

@@ -31,6 +31,6 @@ install:
 script:
   - COVERAGE_FILE=.coverage coverage run -p --concurrency=multiprocessing --rcfile .coveragerc setup.py nosetests -w test/unittest/
   - coverage combine
-  #- flake8 micronota setup.py
+  - flake8 run_tipp.py setup.py run_abundance.py split_sequences.py run_tipp_tool.py distribute_setup.py run_ensemble.py run_sepp.py run_upp.py merge_script.py test/unittest/ sepp/
 after_success:
   - coveralls

sepp/exhaustive_tipp.py

@@ -188,7 +188,8 @@ def perform(self):
                 baseAlignment.write_to_path(pj.backbone_alignment_file)
 
             elif self.placer == "epa":
-                assert isinstance(pj, EPAJob)
+                # assert isinstance(pj, EPAJob)
+                raise ValueError("EPA Currently not supported")
 
                 # Write out the extended alignments in phylip for EPA
                 fullExtendedAlignment.write_to_path(
@@ -371,8 +372,8 @@ def build_jobs(self):
                         placement_problem, self.options.info_file, i)
                 elif self.placer == "epa":
                     raise ValueError("EPA Currently not supported")
-                    #pj = EPAJob()
-                    #pj.partial_setup_for_subproblem(
+                    # pj = EPAJob()
+                    # pj.partial_setup_for_subproblem(
                     #    placement_problem, self.molecule, i)
 
                 placement_problem.add_job(get_placement_job_name(i), pj)

test/unittest/testConfig.py

@@ -155,6 +155,7 @@ def testLog(self):
         sepp._DEBUG = sdb
         sepp.reset_loggers()
 
+
 if __name__ == "__main__":
     # import sys;sys.argv = ['', 'Test.testConfigFile']
     unittest.main()

test/unittest/testMidpoint.py

@@ -73,5 +73,6 @@ def test_diamCent(self):
         self.x.run()
         self.assertTrue(self.x.results is not None)
 
+
 if __name__ == "__main__":
     unittest.main()