From d078bd2653d1d702d54a0ff12f91ef2bd85d8d0e Mon Sep 17 00:00:00 2001 From: Diane Trout Date: Tue, 6 May 2014 16:45:47 -0700 Subject: [PATCH] Change unittest2 back into unittest. Django 1.7 docs pointed out unittest2 was backported into python 2.7, so they dropped their version. --- encode_submission/test_encode_find.py | 6 +++--- encode_submission/test_ucsc_gather.py | 4 ++-- htsworkflow/automation/test/test_runner.py | 6 +++--- htsworkflow/automation/test/test_solexa_utils.py | 6 +++--- htsworkflow/frontend/experiments/test_experiments.py | 4 ++-- htsworkflow/frontend/inventory/test_inventory.py | 4 ++-- htsworkflow/frontend/labels/test_labels.py | 4 ++-- htsworkflow/frontend/samples/test_samples.py | 4 ++-- htsworkflow/pipelines/test/test_alignment_free.py | 6 +++--- htsworkflow/pipelines/test/test_eland.py | 6 +++--- htsworkflow/pipelines/test/test_extract_results.py | 6 +++--- htsworkflow/pipelines/test/test_genome_mapper.py | 6 +++--- htsworkflow/pipelines/test/test_genomemap.py | 6 +++--- htsworkflow/pipelines/test/test_run_xml.py | 6 +++--- htsworkflow/pipelines/test/test_runfolder026.py | 6 +++--- htsworkflow/pipelines/test/test_runfolder030.py | 6 +++--- htsworkflow/pipelines/test/test_runfolder110.py | 6 +++--- htsworkflow/pipelines/test/test_runfolder_casava_1_7.py | 6 +++--- htsworkflow/pipelines/test/test_runfolder_ipar100.py | 6 +++--- htsworkflow/pipelines/test/test_runfolder_ipar130.py | 6 +++--- htsworkflow/pipelines/test/test_runfolder_pair.py | 6 +++--- htsworkflow/pipelines/test/test_runfolder_rta.py | 6 +++--- htsworkflow/pipelines/test/test_runfolder_rta160.py | 6 +++--- htsworkflow/pipelines/test/test_runfolder_rta180.py | 6 +++--- htsworkflow/pipelines/test/test_runfolder_rta1_12.py | 6 +++--- htsworkflow/pipelines/test/test_runfolder_utils.py | 4 ++-- htsworkflow/pipelines/test/test_samplekey.py | 6 +++--- htsworkflow/pipelines/test/test_sequences.py | 6 +++--- htsworkflow/pipelines/test/test_summary.py | 6 +++--- htsworkflow/submission/test/test_condorfastq.py | 4 ++-- htsworkflow/submission/test/test_daf.py | 4 ++-- htsworkflow/submission/test/test_encoded.py | 4 ++-- htsworkflow/submission/test/test_fastqname.py | 6 +++--- htsworkflow/submission/test/test_results.py | 4 ++-- htsworkflow/submission/test/test_submission.py | 4 ++-- htsworkflow/submission/test/test_ucsc.py | 4 ++-- htsworkflow/util/test/test_alphanum.py | 6 +++--- htsworkflow/util/test/test_api.py | 6 +++--- htsworkflow/util/test/test_conversion.py | 6 +++--- htsworkflow/util/test/test_ethelp.py | 6 +++--- htsworkflow/util/test/test_makebed.py | 6 +++--- htsworkflow/util/test/test_queuecommands.py | 6 +++--- htsworkflow/util/test/test_rdfhelp.py | 6 +++--- htsworkflow/util/test/test_rdfinfer.py | 6 +++--- htsworkflow/util/test/test_rdfjsonld.py | 4 ++-- htsworkflow/util/test/test_ucsc.py | 2 +- htsworkflow/util/test/test_url.py | 6 +++--- htsworkflow/util/test/test_validate.py | 6 +++--- htsworkflow/util/test/test_version.py | 6 +++--- test/test_copier.py | 4 ++-- test/test_srf2fastq.py | 6 +++--- 51 files changed, 137 insertions(+), 137 deletions(-) diff --git a/encode_submission/test_encode_find.py b/encode_submission/test_encode_find.py index 77c7585..a81f27a 100644 --- a/encode_submission/test_encode_find.py +++ b/encode_submission/test_encode_find.py @@ -1,7 +1,7 @@ #!/usr/bin/env python from datetime import datetime import os -from unittest2 import TestCase +from unittest import TestCase import RDF @@ -162,12 +162,12 @@ _:bnode120970 '12097') def suite(): - from unittest2 import TestSuite, defaultTestLoader + from unittest import TestSuite, defaultTestLoader suite = TestSuite() suite.addTests(defaultTestLoader.loadTestsFromTestCase(TestEncodeFind)) return suite if __name__ == "__main__": - from unittest2 import main + from unittest import main main() diff --git a/encode_submission/test_ucsc_gather.py b/encode_submission/test_ucsc_gather.py index 6063951..162f56a 100644 --- a/encode_submission/test_ucsc_gather.py +++ b/encode_submission/test_ucsc_gather.py @@ -1,4 +1,4 @@ -from unittest2 import TestCase, TestSuite, defaultTestLoader +from unittest import TestCase, TestSuite, defaultTestLoader import ucsc_gather @@ -11,5 +11,5 @@ def suite(): return suite if __name__ == "__main__": - from unittest2 import main + from unittest import main main(defaultTest='suite') diff --git a/htsworkflow/automation/test/test_runner.py b/htsworkflow/automation/test/test_runner.py index a60c458..22c5b19 100644 --- a/htsworkflow/automation/test/test_runner.py +++ b/htsworkflow/automation/test/test_runner.py @@ -1,4 +1,4 @@ -from unittest2 import TestCase +from unittest import TestCase import os from htsworkflow.automation.solexa import is_runfolder @@ -41,12 +41,12 @@ class testRunner(TestCase): def suite(): - from unittest2 import TestSuite, defaultTestLoader + from unittest import TestSuite, defaultTestLoader suite = TestSuite() suite.addTests(defaultTestLoader.loadTestsFromTestCase(testRunner)) return suite if __name__ == "__main__": - from unittest2 import main + from unittest import main main(defaultTest="suite") diff --git a/htsworkflow/automation/test/test_solexa_utils.py b/htsworkflow/automation/test/test_solexa_utils.py index 210906e..2111406 100644 --- a/htsworkflow/automation/test/test_solexa_utils.py +++ b/htsworkflow/automation/test/test_solexa_utils.py @@ -1,4 +1,4 @@ -from unittest2 import TestCase +from unittest import TestCase from htsworkflow.automation import solexa @@ -24,12 +24,12 @@ class testSolexaRunfolderUtils(TestCase): def suite(): - from unittest2 import TestSuite, defaultTestLoader + from unittest import TestSuite, defaultTestLoader suite = TestSuite() suite.addTests(defaultTestLoader.loadTestsFromTestCase(testSolexaRunfolderUtils)) return suite if __name__ == "__main__": - from unittest2 import main + from unittest import main main(defaultTest="suite") diff --git a/htsworkflow/frontend/experiments/test_experiments.py b/htsworkflow/frontend/experiments/test_experiments.py index fab24cc..b7474d9 100644 --- a/htsworkflow/frontend/experiments/test_experiments.py +++ b/htsworkflow/frontend/experiments/test_experiments.py @@ -678,7 +678,7 @@ class TestSequencer(TestCase): self.assertEqual(len(errmsgs), 0) def suite(): - from unittest2 import TestSuite, defaultTestLoader + from unittest import TestSuite, defaultTestLoader suite = TestSuite() for testcase in [ClusterStationTestCases, SequencerTestCases, @@ -690,5 +690,5 @@ def suite(): return suite if __name__ == "__main__": - from unittest2 import main + from unittest import main main(defaultTest="suite") diff --git a/htsworkflow/frontend/inventory/test_inventory.py b/htsworkflow/frontend/inventory/test_inventory.py index 2456ff3..e3937e1 100644 --- a/htsworkflow/frontend/inventory/test_inventory.py +++ b/htsworkflow/frontend/inventory/test_inventory.py @@ -114,11 +114,11 @@ class InventoryTestCase(TestCase): return flowcells def suite(): - from unittest2 import TestSuite, defaultTestLoader + from unittest import TestSuite, defaultTestLoader suite = TestSuite() suite.addTests(defaultTestLoader.loadTestsFromTestCase(InventoryTestCase)) return suite if __name__ == "__main__": - from unittest2 import main + from unittest import main main(defaultTest="suite") diff --git a/htsworkflow/frontend/labels/test_labels.py b/htsworkflow/frontend/labels/test_labels.py index 29354b2..ca3633b 100644 --- a/htsworkflow/frontend/labels/test_labels.py +++ b/htsworkflow/frontend/labels/test_labels.py @@ -22,11 +22,11 @@ True """} def suite(): - from unittest2 import TestSuite, defaultTestLoader + from unittest import TestSuite, defaultTestLoader suite = TestSuite() suite.addTests(defaultTestLoader.loadTestsFromTestCase(SimpleTest)) return suite if __name__ == "__main__": - from unittest2 import main + from unittest import main main(defaultTest="suite") diff --git a/htsworkflow/frontend/samples/test_samples.py b/htsworkflow/frontend/samples/test_samples.py index 594f281..e700e0e 100644 --- a/htsworkflow/frontend/samples/test_samples.py +++ b/htsworkflow/frontend/samples/test_samples.py @@ -333,7 +333,7 @@ def get_rdf_memory_model(): return model def suite(): - from unittest2 import TestSuite, defaultTestLoader + from unittest import TestSuite, defaultTestLoader suite = TestSuite() suite.addTests(defaultTestLoader.loadTestsFromTestCase(LibraryTestCase)) suite.addTests(defaultTestLoader.loadTestsFromTestCase(SampleWebTestCase)) @@ -341,5 +341,5 @@ def suite(): return suite if __name__ == "__main__": - from unittest2 import main + from unittest import main main(defaultTest="suite") diff --git a/htsworkflow/pipelines/test/test_alignment_free.py b/htsworkflow/pipelines/test/test_alignment_free.py index 700000b..ea6e2de 100644 --- a/htsworkflow/pipelines/test/test_alignment_free.py +++ b/htsworkflow/pipelines/test/test_alignment_free.py @@ -4,7 +4,7 @@ from datetime import datetime, date import os import tempfile import shutil -from unittest2 import TestCase +from unittest import TestCase from htsworkflow.pipelines.test.simulate_runfolder import TESTDATA_DIR @@ -21,12 +21,12 @@ class AlignmentFreeRunfolderTests(TestCase): self.assertEqual(run.runfolder_name, '130508_SN787_0146_BC23KDACXX') def suite(): - from unittest2 import TestSuite, defaultTestLoader + from unittest import TestSuite, defaultTestLoader suite = TestSuite() suite.addTests(defaultTestLoader.loadTestsFromTestCase(AlignmentFreeRunfolderTests)) return suite if __name__ == "__main__": - from unittest2 import main + from unittest import main main(defaultTest="suite") diff --git a/htsworkflow/pipelines/test/test_eland.py b/htsworkflow/pipelines/test/test_eland.py index 57ad62c..f685188 100644 --- a/htsworkflow/pipelines/test/test_eland.py +++ b/htsworkflow/pipelines/test/test_eland.py @@ -2,7 +2,7 @@ """More direct synthetic test cases for the eland output file processing """ from StringIO import StringIO -from unittest2 import TestCase +from unittest import TestCase from htsworkflow.pipelines.eland import ELAND, ElandLane, ElandMatches, \ SampleKey, MatchCodes, MappedReads @@ -276,7 +276,7 @@ class TestElandMatches(TestCase): self.assertEqual(len(em[key11112]), 2) def suite(): - from unittest2 import TestSuite, defaultTestLoader + from unittest import TestSuite, defaultTestLoader suite = TestSuite() suite.addTests(defaultTestLoader.loadTestsFromTestCase(MatchCodeTests)) suite.addTests(defaultTestLoader.loadTestsFromTestCase(TestMappedReads)) @@ -286,5 +286,5 @@ def suite(): if __name__ == "__main__": - from unittest2 import main + from unittest import main main(defaultTest="suite") diff --git a/htsworkflow/pipelines/test/test_extract_results.py b/htsworkflow/pipelines/test/test_extract_results.py index 7381d8c..29ab3fd 100644 --- a/htsworkflow/pipelines/test/test_extract_results.py +++ b/htsworkflow/pipelines/test/test_extract_results.py @@ -6,7 +6,7 @@ import os import tempfile import shutil import sys -from unittest2 import TestCase +from unittest import TestCase from htsworkflow.pipelines import eland from htsworkflow.pipelines import ipar @@ -81,13 +81,13 @@ class RunfolderExtractTests(TestCase): def suite(): - from unittest2 import TestSuite, defaultTestLoader + from unittest import TestSuite, defaultTestLoader suite = TestSuite() suite.addTests(defaultTestLoader.loadTestsFromTestCase(RunfolderExtractTests)) return suite if __name__ == "__main__": - from unittest2 import main + from unittest import main main(defaultTest="suite") diff --git a/htsworkflow/pipelines/test/test_genome_mapper.py b/htsworkflow/pipelines/test/test_genome_mapper.py index 1101305..d71755c 100644 --- a/htsworkflow/pipelines/test/test_genome_mapper.py +++ b/htsworkflow/pipelines/test/test_genome_mapper.py @@ -1,4 +1,4 @@ -from unittest2 import TestCase +from unittest import TestCase from StringIO import StringIO from htsworkflow.pipelines import genome_mapper @@ -27,12 +27,12 @@ class testGenomeMapper(TestCase): def suite(): - from unittest2 import TestSuite, defaultTestLoader + from unittest import TestSuite, defaultTestLoader suite = TestSuite() suite.addTests(defaultTestLoader.loadTestsFromTestCase(testGenomeMapper)) return suite if __name__ == "__main__": - from unittest2 import main + from unittest import main main(defaultTest="suite") diff --git a/htsworkflow/pipelines/test/test_genomemap.py b/htsworkflow/pipelines/test/test_genomemap.py index 7195d0f..7640910 100644 --- a/htsworkflow/pipelines/test/test_genomemap.py +++ b/htsworkflow/pipelines/test/test_genomemap.py @@ -5,7 +5,7 @@ import os from StringIO import StringIO import shutil import tempfile -from unittest2 import TestCase +from unittest import TestCase from htsworkflow.pipelines import ElementTree from htsworkflow.pipelines import genomemap @@ -77,12 +77,12 @@ class TestGenomeMap(TestCase): def suite(): - from unittest2 import TestSuite, defaultTestLoader + from unittest import TestSuite, defaultTestLoader suite = TestSuite() suite.addTests(defaultTestLoader.loadTestsFromTestCase(TestGenomeMap)) return suite if __name__ == "__main__": - from unittest2 import main + from unittest import main main(defaultTest="suite") diff --git a/htsworkflow/pipelines/test/test_run_xml.py b/htsworkflow/pipelines/test/test_run_xml.py index 8b28b9e..42dedf9 100644 --- a/htsworkflow/pipelines/test/test_run_xml.py +++ b/htsworkflow/pipelines/test/test_run_xml.py @@ -1,5 +1,5 @@ import os -from unittest2 import TestCase +from unittest import TestCase from StringIO import StringIO from simulate_runfolder import TESTDATA_DIR @@ -97,12 +97,12 @@ class testLoadRunXML(TestCase): def suite(): - from unittest2 import TestSuite, defaultTestLoader + from unittest import TestSuite, defaultTestLoader suite = TestSuite() suite.addTests(defaultTestLoader.loadTestsFromTestCase(testLoadRunXML)) return suite if __name__ == "__main__": - from unittest2 import main + from unittest import main main(defaultTest="suite") diff --git a/htsworkflow/pipelines/test/test_runfolder026.py b/htsworkflow/pipelines/test/test_runfolder026.py index de68a25..fe52a62 100644 --- a/htsworkflow/pipelines/test/test_runfolder026.py +++ b/htsworkflow/pipelines/test/test_runfolder026.py @@ -4,7 +4,7 @@ from datetime import datetime, date import os import tempfile import shutil -from unittest2 import TestCase +from unittest import TestCase from htsworkflow.pipelines import firecrest from htsworkflow.pipelines import bustard @@ -471,12 +471,12 @@ class RunfolderTests(TestCase): def suite(): - from unittest2 import TestSuite, defaultTestLoader + from unittest import TestSuite, defaultTestLoader suite = TestSuite() suite.addTests(defaultTestLoader.loadTestsFromTestCase(RunfolderTests)) return suite if __name__ == "__main__": - from unittest2 import main + from unittest import main main(defaultTest="suite") diff --git a/htsworkflow/pipelines/test/test_runfolder030.py b/htsworkflow/pipelines/test/test_runfolder030.py index cd631bf..323d7da 100644 --- a/htsworkflow/pipelines/test/test_runfolder030.py +++ b/htsworkflow/pipelines/test/test_runfolder030.py @@ -4,7 +4,7 @@ from datetime import datetime, date import os import tempfile import shutil -from unittest2 import TestCase +from unittest import TestCase from htsworkflow.pipelines import firecrest from htsworkflow.pipelines import bustard @@ -895,11 +895,11 @@ class RunfolderTests(TestCase): def suite(): - from unittest2 import TestSuite, defaultTestLoader + from unittest import TestSuite, defaultTestLoader suite = TestSuite() suite.addTests(defaultTestLoader.loadTestsFromTestCase(RunfolderTests)) return suite if __name__ == "__main__": - from unittest2 import main + from unittest import main main(defaultTest="suite") diff --git a/htsworkflow/pipelines/test/test_runfolder110.py b/htsworkflow/pipelines/test/test_runfolder110.py index 27e6649..bc2b3a6 100644 --- a/htsworkflow/pipelines/test/test_runfolder110.py +++ b/htsworkflow/pipelines/test/test_runfolder110.py @@ -4,7 +4,7 @@ from datetime import datetime, date import os import tempfile import shutil -from unittest2 import TestCase +from unittest import TestCase from htsworkflow.pipelines import firecrest from htsworkflow.pipelines import bustard @@ -300,12 +300,12 @@ class RunfolderTests(TestCase): def suite(): - from unittest2 import TestSuite, defaultTestLoader + from unittest import TestSuite, defaultTestLoader suite = TestSuite() suite.addTests(defaultTestLoader.loadTestsFromTestCase(RunfolderTests)) return suite if __name__ == "__main__": - from unittest2 import main + from unittest import main main(defaultTest="suite") diff --git a/htsworkflow/pipelines/test/test_runfolder_casava_1_7.py b/htsworkflow/pipelines/test/test_runfolder_casava_1_7.py index 96a5bcf..9936420 100644 --- a/htsworkflow/pipelines/test/test_runfolder_casava_1_7.py +++ b/htsworkflow/pipelines/test/test_runfolder_casava_1_7.py @@ -5,7 +5,7 @@ import glob import os import tempfile import shutil -from unittest2 import TestCase +from unittest import TestCase from htsworkflow.pipelines import bustard from htsworkflow.pipelines import eland @@ -300,12 +300,12 @@ class RunfolderTests(TestCase): def suite(): - from unittest2 import TestSuite, defaultTestLoader + from unittest import TestSuite, defaultTestLoader suite = TestSuite() suite.addTests(defaultTestLoader.loadTestsFromTestCase(RunfolderTests)) return suite if __name__ == "__main__": - from unittest2 import main + from unittest import main main(defaultTest="suite") diff --git a/htsworkflow/pipelines/test/test_runfolder_ipar100.py b/htsworkflow/pipelines/test/test_runfolder_ipar100.py index 34a9c8a..9de3653 100644 --- a/htsworkflow/pipelines/test/test_runfolder_ipar100.py +++ b/htsworkflow/pipelines/test/test_runfolder_ipar100.py @@ -4,7 +4,7 @@ from datetime import datetime, date import os import tempfile import shutil -from unittest2 import TestCase +from unittest import TestCase from htsworkflow.pipelines import ipar from htsworkflow.pipelines import bustard @@ -299,12 +299,12 @@ class RunfolderTests(TestCase): def suite(): - from unittest2 import TestSuite, defaultTestLoader + from unittest import TestSuite, defaultTestLoader suite = TestSuite() suite.addTests(defaultTestLoader.loadTestsFromTestCase(RunfolderTests)) return suite if __name__ == "__main__": - from unittest2 import main + from unittest import main main(defaultTest="suite") diff --git a/htsworkflow/pipelines/test/test_runfolder_ipar130.py b/htsworkflow/pipelines/test/test_runfolder_ipar130.py index c23ed97..366f588 100644 --- a/htsworkflow/pipelines/test/test_runfolder_ipar130.py +++ b/htsworkflow/pipelines/test/test_runfolder_ipar130.py @@ -4,7 +4,7 @@ from datetime import datetime, date import os import tempfile import shutil -from unittest2 import TestCase +from unittest import TestCase from htsworkflow.pipelines import eland from htsworkflow.pipelines import ipar @@ -337,12 +337,12 @@ class RunfolderTests(TestCase): def suite(): - from unittest2 import TestSuite, defaultTestLoader + from unittest import TestSuite, defaultTestLoader suite = TestSuite() suite.addTests(defaultTestLoader.loadTestsFromTestCase(RunfolderTests)) return suite if __name__ == "__main__": - from unittest2 import main + from unittest import main main(defaultTest="suite") diff --git a/htsworkflow/pipelines/test/test_runfolder_pair.py b/htsworkflow/pipelines/test/test_runfolder_pair.py index dce0788..355765e 100644 --- a/htsworkflow/pipelines/test/test_runfolder_pair.py +++ b/htsworkflow/pipelines/test/test_runfolder_pair.py @@ -4,7 +4,7 @@ from datetime import datetime, date import os import tempfile import shutil -from unittest2 import TestCase +from unittest import TestCase from htsworkflow.pipelines import firecrest from htsworkflow.pipelines import bustard @@ -325,12 +325,12 @@ class RunfolderTests(TestCase): def suite(): - from unittest2 import TestSuite, defaultTestLoader + from unittest import TestSuite, defaultTestLoader suite = TestSuite() suite.addTests(defaultTestLoader.loadTestsFromTestCase(RunfolderTests)) return suite if __name__ == "__main__": - from unittest2 import main + from unittest import main main(defaultTest="suite") diff --git a/htsworkflow/pipelines/test/test_runfolder_rta.py b/htsworkflow/pipelines/test/test_runfolder_rta.py index 497fe7b..9c2a3d1 100644 --- a/htsworkflow/pipelines/test/test_runfolder_rta.py +++ b/htsworkflow/pipelines/test/test_runfolder_rta.py @@ -4,7 +4,7 @@ from datetime import datetime, date import os import tempfile import shutil -from unittest2 import TestCase +from unittest import TestCase from htsworkflow.pipelines import eland from htsworkflow.pipelines import ipar @@ -299,12 +299,12 @@ class RunfolderTests(TestCase): def suite(): - from unittest2 import TestSuite, defaultTestLoader + from unittest import TestSuite, defaultTestLoader suite = TestSuite() suite.addTests(defaultTestLoader.loadTestsFromTestCase(RunfolderTests)) return suite if __name__ == "__main__": - from unittest2 import main + from unittest import main main(defaultTest="suite") diff --git a/htsworkflow/pipelines/test/test_runfolder_rta160.py b/htsworkflow/pipelines/test/test_runfolder_rta160.py index 8d8f2f1..19b0cfa 100644 --- a/htsworkflow/pipelines/test/test_runfolder_rta160.py +++ b/htsworkflow/pipelines/test/test_runfolder_rta160.py @@ -4,7 +4,7 @@ from datetime import datetime, date import os import tempfile import shutil -from unittest2 import TestCase +from unittest import TestCase from htsworkflow.pipelines import eland from htsworkflow.pipelines import ipar @@ -276,12 +276,12 @@ class RunfolderTests(TestCase): def suite(): - from unittest2 import TestSuite, defaultTestLoader + from unittest import TestSuite, defaultTestLoader suite = TestSuite() suite.addTests(defaultTestLoader.loadTestsFromTestCase(RunfolderTests)) return suite if __name__ == "__main__": - from unittest2 import main + from unittest import main main(defaultTest="suite") diff --git a/htsworkflow/pipelines/test/test_runfolder_rta180.py b/htsworkflow/pipelines/test/test_runfolder_rta180.py index 2817328..312d92f 100644 --- a/htsworkflow/pipelines/test/test_runfolder_rta180.py +++ b/htsworkflow/pipelines/test/test_runfolder_rta180.py @@ -4,7 +4,7 @@ from datetime import datetime, date import os import tempfile import shutil -from unittest2 import TestCase +from unittest import TestCase from htsworkflow.pipelines import eland from htsworkflow.pipelines import ipar @@ -287,12 +287,12 @@ class RunfolderTests(TestCase): def suite(): - from unittest2 import TestSuite, defaultTestLoader + from unittest import TestSuite, defaultTestLoader suite = TestSuite() suite.addTests(defaultTestLoader.loadTestsFromTestCase(RunfolderTests)) return suite if __name__ == "__main__": - from unittest2 import main + from unittest import main main(defaultTest="suite") diff --git a/htsworkflow/pipelines/test/test_runfolder_rta1_12.py b/htsworkflow/pipelines/test/test_runfolder_rta1_12.py index 8396bd0..c22535b 100644 --- a/htsworkflow/pipelines/test/test_runfolder_rta1_12.py +++ b/htsworkflow/pipelines/test/test_runfolder_rta1_12.py @@ -5,7 +5,7 @@ import logging import os import tempfile import shutil -from unittest2 import TestCase +from unittest import TestCase from htsworkflow.pipelines import eland from htsworkflow.pipelines.samplekey import SampleKey @@ -275,12 +275,12 @@ class RunfolderTests(TestCase): self.failIfEqual(r2.gerald, None) def suite(): - from unittest2 import TestSuite, defaultTestLoader + from unittest import TestSuite, defaultTestLoader suite = TestSuite() suite.addTests(defaultTestLoader.loadTestsFromTestCase(RunfolderTests)) return suite if __name__ == "__main__": - from unittest2 import main + from unittest import main main(defaultTest="suite") diff --git a/htsworkflow/pipelines/test/test_runfolder_utils.py b/htsworkflow/pipelines/test/test_runfolder_utils.py index e7c0c38..5471c18 100644 --- a/htsworkflow/pipelines/test/test_runfolder_utils.py +++ b/htsworkflow/pipelines/test/test_runfolder_utils.py @@ -1,4 +1,4 @@ -from unittest2 import TestCase, TestSuite, defaultTestLoader +from unittest import TestCase, TestSuite, defaultTestLoader from htsworkflow.pipelines import runfolder class TestRunfolderUtilities(TestCase): @@ -32,5 +32,5 @@ def suite(): return suite if __name__ == "__main__": - from unittest2 import main + from unittest import main main(defaultTest="suite") diff --git a/htsworkflow/pipelines/test/test_samplekey.py b/htsworkflow/pipelines/test/test_samplekey.py index ecd273d..7861a58 100644 --- a/htsworkflow/pipelines/test/test_samplekey.py +++ b/htsworkflow/pipelines/test/test_samplekey.py @@ -2,7 +2,7 @@ """More direct synthetic test cases for the eland output file processing """ from StringIO import StringIO -from unittest2 import TestCase +from unittest import TestCase from htsworkflow.pipelines.samplekey import SampleKey @@ -44,12 +44,12 @@ class TestSampleKey(TestCase): self.assertTrue(k3.matches(q3)) def suite(): - from unittest2 import TestSuite, defaultTestLoader + from unittest import TestSuite, defaultTestLoader suite = TestSuite() suite.addTests(defaultTestLoader.loadTestsFromTestCase(TestSampleKey)) return suite if __name__ == "__main__": - from unittest2 import main + from unittest import main main(defaultTest="suite") diff --git a/htsworkflow/pipelines/test/test_sequences.py b/htsworkflow/pipelines/test/test_sequences.py index 522a9aa..cd2b852 100644 --- a/htsworkflow/pipelines/test/test_sequences.py +++ b/htsworkflow/pipelines/test/test_sequences.py @@ -2,7 +2,7 @@ import os import shutil import tempfile -from unittest2 import TestCase +from unittest import TestCase import RDF @@ -612,12 +612,12 @@ class SimulateSimpleTree(SimulateTree): def suite(): - from unittest2 import TestSuite, defaultTestLoader + from unittest import TestSuite, defaultTestLoader suite = TestSuite() suite.addTests(defaultTestLoader.loadTestsFromTestCase(SequenceFileTests)) return suite if __name__ == "__main__": - from unittest2 import main + from unittest import main main(defaultTest="suite") diff --git a/htsworkflow/pipelines/test/test_summary.py b/htsworkflow/pipelines/test/test_summary.py index 1f7e461..fbc025b 100644 --- a/htsworkflow/pipelines/test/test_summary.py +++ b/htsworkflow/pipelines/test/test_summary.py @@ -1,7 +1,7 @@ #!/usr/bin/env python import os from StringIO import StringIO -from unittest2 import TestCase +from unittest import TestCase from htsworkflow.pipelines import summary from simulate_runfolder import TESTDATA_DIR @@ -36,12 +36,12 @@ class SummaryTests(TestCase): def suite(): - from unittest2 import TestSuite, defaultTestLoader + from unittest import TestSuite, defaultTestLoader suite = TestSuite() suite.addTests(defaultTestLoader.loadTestsFromTestCase(SummaryTests)) return suite if __name__ == "__main__": - from unittest2 import main + from unittest import main main(defaultTest="suite") diff --git a/htsworkflow/submission/test/test_condorfastq.py b/htsworkflow/submission/test/test_condorfastq.py index 1e1c2d9..2d23271 100644 --- a/htsworkflow/submission/test/test_condorfastq.py +++ b/htsworkflow/submission/test/test_condorfastq.py @@ -681,11 +681,11 @@ class TestCondorFastq(TestCase): def suite(): - from unittest2 import TestSuite, defaultTestLoader + from unittest import TestSuite, defaultTestLoader suite = TestSuite() suite.addTests(defaultTestLoader.loadTestsFromTestCase(TestCondorFastq)) return suite if __name__ == "__main__": - from unittest2 import main + from unittest import main main(defaultTest='suite') diff --git a/htsworkflow/submission/test/test_daf.py b/htsworkflow/submission/test/test_daf.py index 082c4ab..5bc9014 100644 --- a/htsworkflow/submission/test/test_daf.py +++ b/htsworkflow/submission/test/test_daf.py @@ -4,7 +4,7 @@ import os from StringIO import StringIO import shutil import tempfile -from unittest2 import TestCase, TestSuite, defaultTestLoader +from unittest import TestCase, TestSuite, defaultTestLoader from htsworkflow.submission import daf, results from htsworkflow.util.rdfhelp import \ @@ -338,5 +338,5 @@ def suite(): if __name__ == "__main__": logging.basicConfig(level=logging.DEBUG) - from unittest2 import main + from unittest import main main(defaultTest='suite') diff --git a/htsworkflow/submission/test/test_encoded.py b/htsworkflow/submission/test/test_encoded.py index 31a551d..a1b22a0 100644 --- a/htsworkflow/submission/test/test_encoded.py +++ b/htsworkflow/submission/test/test_encoded.py @@ -1,7 +1,7 @@ import json import os from pprint import pprint -from unittest2 import TestCase, TestSuite, defaultTestLoader, skip +from unittest import TestCase, TestSuite, defaultTestLoader, skip from htsworkflow.submission.encoded import (ENCODED, ENCODED_CONTEXT, @@ -185,5 +185,5 @@ def suite(): return suite if __name__ == "__main__": - from unittest2 import main + from unittest import main main(defaultTest='suite') diff --git a/htsworkflow/submission/test/test_fastqname.py b/htsworkflow/submission/test/test_fastqname.py index 56c094e..c84599d 100644 --- a/htsworkflow/submission/test/test_fastqname.py +++ b/htsworkflow/submission/test/test_fastqname.py @@ -1,4 +1,4 @@ -from unittest2 import TestCase +from unittest import TestCase from htsworkflow.submission.fastqname import FastqName class TestFastqName(TestCase): @@ -123,11 +123,11 @@ class TestFastqName(TestCase): def suite(): - from unittest2 import TestSuite, defaultTestLoader + from unittest import TestSuite, defaultTestLoader suite = TestSuite() suite.addTests(defaultTestLoader.loadTestsFromTestCase(TestFastqName)) return suite if __name__ == "__main__": - from unittest2 import main + from unittest import main main(defaultTest='suite') diff --git a/htsworkflow/submission/test/test_results.py b/htsworkflow/submission/test/test_results.py index ee207cf..08bb413 100644 --- a/htsworkflow/submission/test/test_results.py +++ b/htsworkflow/submission/test/test_results.py @@ -3,7 +3,7 @@ from pprint import pprint import shutil -from unittest2 import TestCase, defaultTestLoader +from unittest import TestCase, defaultTestLoader from htsworkflow.submission.results import ResultMap from submission_test_common import * @@ -91,5 +91,5 @@ def suite(): if __name__ == "__main__": import logging logging.basicConfig(level=logging.DEBUG) - from unittest2 import main + from unittest import main main(defaultTest='suite') diff --git a/htsworkflow/submission/test/test_submission.py b/htsworkflow/submission/test/test_submission.py index e441f20..0c4e087 100644 --- a/htsworkflow/submission/test/test_submission.py +++ b/htsworkflow/submission/test/test_submission.py @@ -3,7 +3,7 @@ import os from StringIO import StringIO import shutil import tempfile -from unittest2 import TestCase, TestSuite, defaultTestLoader +from unittest import TestCase, TestSuite, defaultTestLoader from htsworkflow.submission import daf, results from htsworkflow.util.rdfhelp import \ @@ -170,5 +170,5 @@ def suite(): return suite if __name__ == "__main__": - from unittest2 import main + from unittest import main main(defaultTest='suite') diff --git a/htsworkflow/submission/test/test_ucsc.py b/htsworkflow/submission/test/test_ucsc.py index fad690e..b4cb2d8 100644 --- a/htsworkflow/submission/test/test_ucsc.py +++ b/htsworkflow/submission/test/test_ucsc.py @@ -1,4 +1,4 @@ -from unittest2 import TestCase, TestSuite, defaultTestLoader +from unittest import TestCase, TestSuite, defaultTestLoader from StringIO import StringIO from htsworkflow.submission import ucsc @@ -26,5 +26,5 @@ def suite(): return suite if __name__ == "__main__": - from unittest2 import main + from unittest import main main(defaultTest='suite') diff --git a/htsworkflow/util/test/test_alphanum.py b/htsworkflow/util/test/test_alphanum.py index 29a5385..a47e682 100644 --- a/htsworkflow/util/test/test_alphanum.py +++ b/htsworkflow/util/test/test_alphanum.py @@ -1,6 +1,6 @@ import copy import os -from unittest2 import TestCase +from unittest import TestCase from htsworkflow.util.alphanum import alphanum @@ -42,12 +42,12 @@ class testAlphanum(TestCase): def suite(): - from unittest2 import TestSuite, defaultTestLoader + from unittest import TestSuite, defaultTestLoader suite = TestSuite() suite.addTests(defaultTestLoader.loadTestsFromTestCase(testAlphanum)) return suite if __name__ == "__main__": - from unittest2 import main + from unittest import main main(defaultTest="suite") diff --git a/htsworkflow/util/test/test_api.py b/htsworkflow/util/test/test_api.py index dadd6af..4d50457 100644 --- a/htsworkflow/util/test/test_api.py +++ b/htsworkflow/util/test/test_api.py @@ -1,6 +1,6 @@ import copy import os -from unittest2 import TestCase +from unittest import TestCase from htsworkflow.util import api @@ -14,12 +14,12 @@ class testApi(TestCase): self.failUnless(k1 != k2) def suite(): - from unittest2 import TestSuite, defaultTestLoader + from unittest import TestSuite, defaultTestLoader suite = TestSuite() suite.addTests(defaultTestLoader.loadTestsFromTestCase(TestApi)) return suite if __name__ == "__main__": - from unittest2 import main + from unittest import main main(defaultTest="suite") diff --git a/htsworkflow/util/test/test_conversion.py b/htsworkflow/util/test/test_conversion.py index 4919e56..6eb1589 100644 --- a/htsworkflow/util/test/test_conversion.py +++ b/htsworkflow/util/test/test_conversion.py @@ -1,6 +1,6 @@ #!/usr/bin/env python -from unittest2 import TestCase +from unittest import TestCase from htsworkflow.util import conversion @@ -15,12 +15,12 @@ class TestConversion(TestCase): self.failUnlessEqual(s.stop, 2) def suite(): - from unittest2 import TestSuite, defaultTestLoader + from unittest import TestSuite, defaultTestLoader suite = TestSuite() suite.addTests(defaultTestLoader.loadTestsFromTestCase(TestConversion)) return suite if __name__ == "__main__": - from unittest2 import main + from unittest import main main(defaultTest="suite") diff --git a/htsworkflow/util/test/test_ethelp.py b/htsworkflow/util/test/test_ethelp.py index 461a564..379dd9e 100644 --- a/htsworkflow/util/test/test_ethelp.py +++ b/htsworkflow/util/test/test_ethelp.py @@ -1,5 +1,5 @@ import os -from unittest2 import TestCase +from unittest import TestCase try: from xml.etree import ElementTree @@ -25,12 +25,12 @@ class testETHelper(TestCase): self.failUnless(flatten(self.foo_tree), 'asdf') def suite(): - from unittest2 import TestSuite, defaultTestLoader + from unittest import TestSuite, defaultTestLoader suite = TestSuite() suite.addTests(defaultTestLoader.loadTestsFromTestCase(testETHelper)) return suite if __name__ == "__main__": - from unittest2 import main + from unittest import main main(defaultTest="suite") diff --git a/htsworkflow/util/test/test_makebed.py b/htsworkflow/util/test/test_makebed.py index af815b6..50d2c64 100644 --- a/htsworkflow/util/test/test_makebed.py +++ b/htsworkflow/util/test/test_makebed.py @@ -1,6 +1,6 @@ import os from StringIO import StringIO -from unittest2 import TestCase +from unittest import TestCase from htsworkflow.util import makebed @@ -47,12 +47,12 @@ class testMakeBed(TestCase): def suite(): - from unittest2 import TestSuite, defaultTestLoader + from unittest import TestSuite, defaultTestLoader suite = TestSuite() suite.addTests(defaultTestLoader.loadTestsFromTestCase(testMakeBed)) return suite if __name__ == "__main__": - from unittest2 import main + from unittest import main main(defaultTest="suite") diff --git a/htsworkflow/util/test/test_queuecommands.py b/htsworkflow/util/test/test_queuecommands.py index 5885f73..e320819 100644 --- a/htsworkflow/util/test/test_queuecommands.py +++ b/htsworkflow/util/test/test_queuecommands.py @@ -1,7 +1,7 @@ import os import logging import time -from unittest2 import TestCase +from unittest import TestCase from htsworkflow.util.queuecommands import QueueCommands @@ -44,12 +44,12 @@ class testQueueCommands(TestCase): def suite(): - from unittest2 import TestSuite, defaultTestLoader + from unittest import TestSuite, defaultTestLoader suite = TestSuite() suite.addTests(defaultTestLoader.loadTestsFromTestCase(testQueueCommands)) return suite if __name__ == "__main__": - from unittest2 import main + from unittest import main main(defaultTest="suite") diff --git a/htsworkflow/util/test/test_rdfhelp.py b/htsworkflow/util/test/test_rdfhelp.py index 2f14190..9694c37 100644 --- a/htsworkflow/util/test/test_rdfhelp.py +++ b/htsworkflow/util/test/test_rdfhelp.py @@ -1,6 +1,6 @@ import os import types -from unittest2 import TestCase +from unittest import TestCase from datetime import datetime @@ -265,7 +265,7 @@ except ImportError, e: print "Unable to test rdfhelp" def suite(): - from unittest2 import TestSuite, defaultTestLoader + from unittest import TestSuite, defaultTestLoader suite = TestSuite() suite.addTests(defaultTestLoader.loadTestsFromTestCase(TestRDFHelp)) suite.addTests(defaultTestLoader.loadTestsFromTestCase(TestRDFSchemas)) @@ -273,5 +273,5 @@ def suite(): if __name__ == "__main__": - from unittest2 import main + from unittest import main main(defaultTest="suite") diff --git a/htsworkflow/util/test/test_rdfinfer.py b/htsworkflow/util/test/test_rdfinfer.py index c6164fa..417218e 100644 --- a/htsworkflow/util/test/test_rdfinfer.py +++ b/htsworkflow/util/test/test_rdfinfer.py @@ -1,4 +1,4 @@ -from unittest2 import TestCase +from unittest import TestCase import RDF @@ -229,12 +229,12 @@ class TestInfer(TestCase): def suite(): - from unittest2 import TestSuite, defaultTestLoader + from unittest import TestSuite, defaultTestLoader suite = TestSuite() suite.addTests(defaultTestLoader.loadTestsFromTestCase(TestInfer)) return suite if __name__ == "__main__": - from unittest2 import main + from unittest import main main(defaultTest="suite") diff --git a/htsworkflow/util/test/test_rdfjsonld.py b/htsworkflow/util/test/test_rdfjsonld.py index 8e501ba..dd9ea37 100644 --- a/htsworkflow/util/test/test_rdfjsonld.py +++ b/htsworkflow/util/test/test_rdfjsonld.py @@ -1,4 +1,4 @@ -from unittest2 import TestCase, TestSuite, defaultTestLoader, skip +from unittest import TestCase, TestSuite, defaultTestLoader, skip from htsworkflow.util.rdfjsonld import load_into_model, to_node, triple_to_statement from htsworkflow.util.rdfhelp import get_model @@ -52,5 +52,5 @@ def suite(): return suite if __name__ == "__main__": - from unittest2 import main + from unittest import main main(defaultTest='suite') diff --git a/htsworkflow/util/test/test_ucsc.py b/htsworkflow/util/test/test_ucsc.py index 2b2e976..35c7388 100644 --- a/htsworkflow/util/test/test_ucsc.py +++ b/htsworkflow/util/test/test_ucsc.py @@ -1,7 +1,7 @@ """Test wrappers around ucsc file formats """ import os -from unittest2 import TestCase +from unittest import TestCase from htsworkflow.util.test import TEST_DATA_DIR from htsworkflow.util.ucsc import bigWigInfo diff --git a/htsworkflow/util/test/test_url.py b/htsworkflow/util/test/test_url.py index 979e144..0d2c3a0 100644 --- a/htsworkflow/util/test/test_url.py +++ b/htsworkflow/util/test/test_url.py @@ -1,4 +1,4 @@ -from unittest2 import TestCase +from unittest import TestCase from htsworkflow.util.url import normalize_url, parse_ssh_url @@ -36,11 +36,11 @@ class TestURLUtilities(TestCase): self.assertRaises(ValueError, parse_ssh_url, 'hello') def suite(): - from unittest2 import TestSuite, defaultTestLoader + from unittest import TestSuite, defaultTestLoader suite = TestSuite() suite.addTests(defaultTestLoader.loadTestsFromTestCase(TestURLUtilities)) return suite if __name__ == '__main__': - from unittest2 import main + from unittest import main main(defaultTest="suite") diff --git a/htsworkflow/util/test/test_validate.py b/htsworkflow/util/test/test_validate.py index cc05f3c..c906cd5 100644 --- a/htsworkflow/util/test/test_validate.py +++ b/htsworkflow/util/test/test_validate.py @@ -1,6 +1,6 @@ import os from StringIO import StringIO -from unittest2 import TestCase +from unittest import TestCase from htsworkflow.util import validate @@ -47,12 +47,12 @@ class TestValidate(TestCase): def suite(): - from unittest2 import TestSuite, defaultTestLoader + from unittest import TestSuite, defaultTestLoader suite = TestSuite() suite.addTests(defaultTestLoader.loadTestsFromTestCase(testValidate)) return suite if __name__ == "__main__": - from unittest2 import main + from unittest import main main(defaultTest="suite") diff --git a/htsworkflow/util/test/test_version.py b/htsworkflow/util/test/test_version.py index 212f124..f1e4db0 100644 --- a/htsworkflow/util/test/test_version.py +++ b/htsworkflow/util/test/test_version.py @@ -1,4 +1,4 @@ -from unittest2 import TestCase +from unittest import TestCase from htsworkflow.util import version @@ -11,11 +11,11 @@ class TestVersion(TestCase): def suite(): - from unittest2 import TestSuite, defaultTestLoader + from unittest import TestSuite, defaultTestLoader suite = TestSuite() suite.addTest(defaultTestLoader.loadTestsFromTestCase(TestVersion)) return suite if __name__ == "__main__": - from unittest2 import main + from unittest import main main(defaultTest="suite") diff --git a/test/test_copier.py b/test/test_copier.py index a2dd5d7..52bd8e2 100644 --- a/test/test_copier.py +++ b/test/test_copier.py @@ -82,12 +82,12 @@ notify_users: user3@example.fake def suite(): - from unittest2 import TestSuite, defaultTestLoader + from unittest import TestSuite, defaultTestLoader suite = TestSuite() suite.addTests(defaultTestLoader.loadTestsFromTestCase(testCopier)) return suite if __name__ == "__main__": - from unittest2 import main + from unittest import main main(defaultTest="suite") diff --git a/test/test_srf2fastq.py b/test/test_srf2fastq.py index 9185fff..e06ec82 100644 --- a/test/test_srf2fastq.py +++ b/test/test_srf2fastq.py @@ -1,7 +1,7 @@ import os from StringIO import StringIO import sys -from unittest2 import TestCase +from unittest import TestCase _module_path, _module_name = os.path.split(__file__) sys.path.append(os.path.join(_module_path, '..', 'scripts')) @@ -137,12 +137,12 @@ IIIIB+++ def suite(): - from unittest2 import TestSuite, defaultTestLoader + from unittest import TestSuite, defaultTestLoader suite = TestSuite() suite.addTests(defaultTestLoader.loadTestsFromTestCase(testSrf2Fastq)) return suite if __name__ == "__main__": - from unittest2 import main + from unittest import main main(defaultTest="suite") -- 2.30.2