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take advantage of absolute_import to simplify import statements
author
Diane Trout
<diane@ghic.org>
Mon, 2 Feb 2015 22:54:28 +0000
(14:54 -0800)
committer
Diane Trout
<diane@ghic.org>
Mon, 2 Feb 2015 22:54:28 +0000
(14:54 -0800)
16 files changed:
encode_submission/test_ucsc_gather.py
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htsworkflow/pipelines/test/test_alignment_free.py
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htsworkflow/pipelines/test/test_extract_results.py
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htsworkflow/pipelines/test/test_run_xml.py
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htsworkflow/pipelines/test/test_runfolder026.py
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htsworkflow/pipelines/test/test_runfolder110.py
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htsworkflow/pipelines/test/test_runfolder_casava_1_7.py
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htsworkflow/pipelines/test/test_runfolder_ipar100.py
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htsworkflow/pipelines/test/test_runfolder_ipar130.py
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htsworkflow/pipelines/test/test_runfolder_pair.py
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htsworkflow/pipelines/test/test_runfolder_rta.py
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htsworkflow/pipelines/test/test_runfolder_rta160.py
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htsworkflow/pipelines/test/test_runfolder_rta180.py
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htsworkflow/pipelines/test/test_runfolder_rta1_12.py
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htsworkflow/pipelines/test/test_summary.py
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htsworkflow/submission/test/test_results.py
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diff --git
a/encode_submission/test_ucsc_gather.py
b/encode_submission/test_ucsc_gather.py
index 162f56ad4d6730b13cbb41915b723371828f7cf3..9baf16031aa125735f8799f428db2ff24db0e3cd 100644
(file)
--- a/
encode_submission/test_ucsc_gather.py
+++ b/
encode_submission/test_ucsc_gather.py
@@
-1,6
+1,8
@@
+from __future__ import absolute_import
+
from unittest import TestCase, TestSuite, defaultTestLoader
from unittest import TestCase, TestSuite, defaultTestLoader
-import ucsc_gather
+
from .
import ucsc_gather
class testUCSCGather(TestCase):
pass
class testUCSCGather(TestCase):
pass
diff --git
a/htsworkflow/pipelines/test/test_alignment_free.py
b/htsworkflow/pipelines/test/test_alignment_free.py
index ea6e2def0bb71cc2ff65d1a59f497b0a2e251c12..adbe33ae8872bfcf5cc74d26af5765612916e19e 100644
(file)
--- a/
htsworkflow/pipelines/test/test_alignment_free.py
+++ b/
htsworkflow/pipelines/test/test_alignment_free.py
@@
-1,4
+1,5
@@
#!/usr/bin/env python
#!/usr/bin/env python
+from __future__ import absolute_import
from datetime import datetime, date
import os
from datetime import datetime, date
import os
diff --git
a/htsworkflow/pipelines/test/test_extract_results.py
b/htsworkflow/pipelines/test/test_extract_results.py
index 29ab3fddd71d7f7af123fc882adec7657f8d8e54..0d96a4553858d4aaa7e3b9aec3a66eb4414c2986 100644
(file)
--- a/
htsworkflow/pipelines/test/test_extract_results.py
+++ b/
htsworkflow/pipelines/test/test_extract_results.py
@@
-1,4
+1,5
@@
#!/usr/bin/env python
#!/usr/bin/env python
+from __future__ import absolute_import
from datetime import datetime, date
import logging
from datetime import datetime, date
import logging
@@
-15,7
+16,7
@@
from htsworkflow.pipelines import gerald
from htsworkflow.pipelines import runfolder
from htsworkflow.pipelines import ElementTree
from htsworkflow.pipelines import runfolder
from htsworkflow.pipelines import ElementTree
-from
htsworkflow.pipelines.test
.simulate_runfolder import *
+from .simulate_runfolder import *
logging.basicConfig(level=logging.ERROR)
logging.basicConfig(level=logging.ERROR)
diff --git
a/htsworkflow/pipelines/test/test_run_xml.py
b/htsworkflow/pipelines/test/test_run_xml.py
index 9ef8dd08882b1df30a118d9aeb6a06eb2e2a03b8..b311df212ef4755b4fef19e5a866811ecd53e953 100644
(file)
--- a/
htsworkflow/pipelines/test/test_run_xml.py
+++ b/
htsworkflow/pipelines/test/test_run_xml.py
@@
-1,8
+1,10
@@
+from __future__ import absolute_import
+
import os
from unittest import TestCase
from six.moves import StringIO
import os
from unittest import TestCase
from six.moves import StringIO
-from simulate_runfolder import TESTDATA_DIR
+from
.
simulate_runfolder import TESTDATA_DIR
from htsworkflow.pipelines.runfolder import load_pipeline_run_xml
from htsworkflow.pipelines.eland import SampleKey
from htsworkflow.pipelines.runfolder import load_pipeline_run_xml
from htsworkflow.pipelines.eland import SampleKey
diff --git
a/htsworkflow/pipelines/test/test_runfolder026.py
b/htsworkflow/pipelines/test/test_runfolder026.py
index fe52a62060fda3b50d815eaae35c0e3d4fb04d8e..dcdd36517e49f0605548ac04f546cf8fe1e0c1e5 100644
(file)
--- a/
htsworkflow/pipelines/test/test_runfolder026.py
+++ b/
htsworkflow/pipelines/test/test_runfolder026.py
@@
-1,4
+1,5
@@
#!/usr/bin/env python
#!/usr/bin/env python
+from __future__ import absolute_import
from datetime import datetime, date
import os
from datetime import datetime, date
import os
@@
-12,7
+13,7
@@
from htsworkflow.pipelines import gerald
from htsworkflow.pipelines import runfolder
from htsworkflow.pipelines import ElementTree
from htsworkflow.pipelines import runfolder
from htsworkflow.pipelines import ElementTree
-from
htsworkflow.pipelines.test
.simulate_runfolder import *
+from .simulate_runfolder import *
def make_summary_htm(gerald_dir):
def make_summary_htm(gerald_dir):
diff --git
a/htsworkflow/pipelines/test/test_runfolder110.py
b/htsworkflow/pipelines/test/test_runfolder110.py
index bc2b3a60d3ff3d779d290c6a2b18a477ddbd35ce..266fcfdd3ddee9768b3f9f0f8d3e79b02a443748 100644
(file)
--- a/
htsworkflow/pipelines/test/test_runfolder110.py
+++ b/
htsworkflow/pipelines/test/test_runfolder110.py
@@
-1,4
+1,5
@@
#!/usr/bin/env python
#!/usr/bin/env python
+from __future__ import absolute_import
from datetime import datetime, date
import os
from datetime import datetime, date
import os
@@
-12,7
+13,7
@@
from htsworkflow.pipelines import gerald
from htsworkflow.pipelines import runfolder
from htsworkflow.pipelines import ElementTree
from htsworkflow.pipelines import runfolder
from htsworkflow.pipelines import ElementTree
-from
htsworkflow.pipelines.test
.simulate_runfolder import *
+from .simulate_runfolder import *
def make_runfolder(obj=None):
def make_runfolder(obj=None):
diff --git
a/htsworkflow/pipelines/test/test_runfolder_casava_1_7.py
b/htsworkflow/pipelines/test/test_runfolder_casava_1_7.py
index 99364205c7f1412a38a1b60c0b292a8894bd753f..bb9ae5af2ee64c044c8b9187c7afdee63559f136 100644
(file)
--- a/
htsworkflow/pipelines/test/test_runfolder_casava_1_7.py
+++ b/
htsworkflow/pipelines/test/test_runfolder_casava_1_7.py
@@
-1,4
+1,5
@@
#!/usr/bin/env python
#!/usr/bin/env python
+from __future__ import absolute_import
from datetime import datetime, date
import glob
from datetime import datetime, date
import glob
@@
-15,7
+16,7
@@
from htsworkflow.pipelines import runfolder
from htsworkflow.pipelines import srf
from htsworkflow.pipelines import ElementTree
from htsworkflow.pipelines import srf
from htsworkflow.pipelines import ElementTree
-from
htsworkflow.pipelines.test
.simulate_runfolder import *
+from .simulate_runfolder import *
FCID = 'AA01AAABXX'
RUN_NAME = '110420_SN787_0069_%s' %( FCID,)
FCID = 'AA01AAABXX'
RUN_NAME = '110420_SN787_0069_%s' %( FCID,)
diff --git
a/htsworkflow/pipelines/test/test_runfolder_ipar100.py
b/htsworkflow/pipelines/test/test_runfolder_ipar100.py
index 9de36535e2bd3cff21809570c794b525b719f62f..054fbc79e71add360b5c9c107bea87f9758ddd00 100644
(file)
--- a/
htsworkflow/pipelines/test/test_runfolder_ipar100.py
+++ b/
htsworkflow/pipelines/test/test_runfolder_ipar100.py
@@
-1,4
+1,5
@@
#!/usr/bin/env python
#!/usr/bin/env python
+from __future__ import absolute_import
from datetime import datetime, date
import os
from datetime import datetime, date
import os
@@
-12,7
+13,7
@@
from htsworkflow.pipelines import gerald
from htsworkflow.pipelines import runfolder
from htsworkflow.pipelines import ElementTree
from htsworkflow.pipelines import runfolder
from htsworkflow.pipelines import ElementTree
-from
htsworkflow.pipelines.test
.simulate_runfolder import *
+from .simulate_runfolder import *
def make_runfolder(obj=None):
def make_runfolder(obj=None):
diff --git
a/htsworkflow/pipelines/test/test_runfolder_ipar130.py
b/htsworkflow/pipelines/test/test_runfolder_ipar130.py
index 366f588b8b4472d5248a23ca777195ae656625d2..5fe62219a82e36b8caedcfcaf5dc78097ede97de 100644
(file)
--- a/
htsworkflow/pipelines/test/test_runfolder_ipar130.py
+++ b/
htsworkflow/pipelines/test/test_runfolder_ipar130.py
@@
-1,4
+1,5
@@
#!/usr/bin/env python
#!/usr/bin/env python
+from __future__ import absolute_import
from datetime import datetime, date
import os
from datetime import datetime, date
import os
@@
-13,7
+14,7
@@
from htsworkflow.pipelines import gerald
from htsworkflow.pipelines import runfolder
from htsworkflow.pipelines import ElementTree
from htsworkflow.pipelines import runfolder
from htsworkflow.pipelines import ElementTree
-from
htsworkflow.pipelines.test
.simulate_runfolder import *
+from .simulate_runfolder import *
def make_runfolder(obj=None):
def make_runfolder(obj=None):
diff --git
a/htsworkflow/pipelines/test/test_runfolder_pair.py
b/htsworkflow/pipelines/test/test_runfolder_pair.py
index 355765e6f26e852522d3895df85db61afd38ef6e..4f4976e5caa3a71b31e58d772757fdfaea266966 100644
(file)
--- a/
htsworkflow/pipelines/test/test_runfolder_pair.py
+++ b/
htsworkflow/pipelines/test/test_runfolder_pair.py
@@
-1,4
+1,5
@@
#!/usr/bin/env python
#!/usr/bin/env python
+from __future__ import absolute_import
from datetime import datetime, date
import os
from datetime import datetime, date
import os
@@
-13,7
+14,7
@@
from htsworkflow.pipelines.eland import SampleKey
from htsworkflow.pipelines import runfolder
from htsworkflow.pipelines import ElementTree
from htsworkflow.pipelines import runfolder
from htsworkflow.pipelines import ElementTree
-from
htsworkflow.pipelines.test
.simulate_runfolder import *
+from .simulate_runfolder import *
def make_runfolder(obj=None):
def make_runfolder(obj=None):
diff --git
a/htsworkflow/pipelines/test/test_runfolder_rta.py
b/htsworkflow/pipelines/test/test_runfolder_rta.py
index 9c2a3d1ac88c7d28a30415a78cf643abc5ced9ed..371a49b699479bd35a63067e05e91c0893c27184 100644
(file)
--- a/
htsworkflow/pipelines/test/test_runfolder_rta.py
+++ b/
htsworkflow/pipelines/test/test_runfolder_rta.py
@@
-1,4
+1,5
@@
#!/usr/bin/env python
#!/usr/bin/env python
+from __future__ import absolute_import
from datetime import datetime, date
import os
from datetime import datetime, date
import os
@@
-14,7
+15,7
@@
from htsworkflow.pipelines import runfolder
from htsworkflow.pipelines.samplekey import SampleKey
from htsworkflow.pipelines import ElementTree
from htsworkflow.pipelines.samplekey import SampleKey
from htsworkflow.pipelines import ElementTree
-from
htsworkflow.pipelines.test
.simulate_runfolder import *
+from .simulate_runfolder import *
def make_runfolder(obj=None):
def make_runfolder(obj=None):
diff --git
a/htsworkflow/pipelines/test/test_runfolder_rta160.py
b/htsworkflow/pipelines/test/test_runfolder_rta160.py
index 19b0cfad384bf8edd96edf47ec2835f7f8eb2937..621f32d9a187bad6f8bdfa3851b81cfa6edda808 100644
(file)
--- a/
htsworkflow/pipelines/test/test_runfolder_rta160.py
+++ b/
htsworkflow/pipelines/test/test_runfolder_rta160.py
@@
-1,4
+1,5
@@
#!/usr/bin/env python
#!/usr/bin/env python
+from __future__ import absolute_import
from datetime import datetime, date
import os
from datetime import datetime, date
import os
@@
-14,7
+15,7
@@
from htsworkflow.pipelines import runfolder
from htsworkflow.pipelines.samplekey import SampleKey
from htsworkflow.pipelines import ElementTree
from htsworkflow.pipelines.samplekey import SampleKey
from htsworkflow.pipelines import ElementTree
-from
htsworkflow.pipelines.test
.simulate_runfolder import *
+from .simulate_runfolder import *
def make_runfolder(obj=None):
def make_runfolder(obj=None):
diff --git
a/htsworkflow/pipelines/test/test_runfolder_rta180.py
b/htsworkflow/pipelines/test/test_runfolder_rta180.py
index 312d92fbbdf5e5b933fb6521ee497ae3445653fb..df57cf4ce3a944be5dbbec6933faaea607ef316d 100644
(file)
--- a/
htsworkflow/pipelines/test/test_runfolder_rta180.py
+++ b/
htsworkflow/pipelines/test/test_runfolder_rta180.py
@@
-1,4
+1,5
@@
#!/usr/bin/env python
#!/usr/bin/env python
+from __future__ import absolute_import
from datetime import datetime, date
import os
from datetime import datetime, date
import os
@@
-14,7
+15,7
@@
from htsworkflow.pipelines import runfolder
from htsworkflow.pipelines.samplekey import SampleKey
from htsworkflow.pipelines import ElementTree
from htsworkflow.pipelines.samplekey import SampleKey
from htsworkflow.pipelines import ElementTree
-from
htsworkflow.pipelines.test
.simulate_runfolder import *
+from .simulate_runfolder import *
def make_runfolder(obj=None):
def make_runfolder(obj=None):
diff --git
a/htsworkflow/pipelines/test/test_runfolder_rta1_12.py
b/htsworkflow/pipelines/test/test_runfolder_rta1_12.py
index c22535b6bcbf7da056d621e92bc4b9bce1c750d1..c1a33143c4a01df3ee70094b6a19b5cc0f96b575 100644
(file)
--- a/
htsworkflow/pipelines/test/test_runfolder_rta1_12.py
+++ b/
htsworkflow/pipelines/test/test_runfolder_rta1_12.py
@@
-1,4
+1,5
@@
#!/usr/bin/env python
#!/usr/bin/env python
+from __future__ import absolute_import
from datetime import datetime, date
import logging
from datetime import datetime, date
import logging
@@
-15,7
+16,7
@@
from htsworkflow.pipelines import gerald
from htsworkflow.pipelines import runfolder
from htsworkflow.pipelines import ElementTree
from htsworkflow.pipelines import runfolder
from htsworkflow.pipelines import ElementTree
-from
htsworkflow.pipelines.test
.simulate_runfolder import *
+from .simulate_runfolder import *
def make_runfolder(obj=None):
def make_runfolder(obj=None):
diff --git
a/htsworkflow/pipelines/test/test_summary.py
b/htsworkflow/pipelines/test/test_summary.py
index 835d2069d22d714c2185cef8ae821648782fb70d..98b4fd0fe528a829ca41d3896451568ba6bab47c 100644
(file)
--- a/
htsworkflow/pipelines/test/test_summary.py
+++ b/
htsworkflow/pipelines/test/test_summary.py
@@
-1,10
+1,12
@@
#!/usr/bin/env python
#!/usr/bin/env python
+from __future__ import absolute_import
+
import os
from six.moves import StringIO
from unittest import TestCase
from htsworkflow.pipelines import summary
import os
from six.moves import StringIO
from unittest import TestCase
from htsworkflow.pipelines import summary
-from simulate_runfolder import TESTDATA_DIR
+from
.
simulate_runfolder import TESTDATA_DIR
class SummaryTests(TestCase):
"""Test elements of the summary file parser
class SummaryTests(TestCase):
"""Test elements of the summary file parser
diff --git
a/htsworkflow/submission/test/test_results.py
b/htsworkflow/submission/test/test_results.py
index 08bb413ce49208dafde2e226e23e44f12554ba6f..a755f6c0e39fe3161b105c24cd6d48ab77b36b47 100644
(file)
--- a/
htsworkflow/submission/test/test_results.py
+++ b/
htsworkflow/submission/test/test_results.py
@@
-1,4
+1,5
@@
#!/usr/bin/env python
#!/usr/bin/env python
+from __future__ import absolute_import
from pprint import pprint
import shutil
from pprint import pprint
import shutil
@@
-6,7
+7,7
@@
import shutil
from unittest import TestCase, defaultTestLoader
from htsworkflow.submission.results import ResultMap
from unittest import TestCase, defaultTestLoader
from htsworkflow.submission.results import ResultMap
-from submission_test_common import *
+from
.
submission_test_common import *
class TestResultMap(TestCase):
def setUp(self):
class TestResultMap(TestCase):
def setUp(self):