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|
--- a/test/test_automated_analysis.py
+++ b/test/test_automated_analysis.py
@@ -11,8 +11,7 @@
import collections
import functools
-from nose import SkipTest
-from nose.plugins.attrib import attr
+#from nose2 import SkipTest
import yaml
@@ -31,19 +30,19 @@
finally:
os.chdir(orig_dir)
-def expected_failure(test):
- """Small decorator to mark tests as expected failure.
- Useful for tests that are work-in-progress.
- """
- @functools.wraps(test)
- def inner(*args, **kwargs):
- try:
- test(*args, **kwargs)
- except Exception:
- raise SkipTest
- else:
- raise AssertionError('Failure expected')
- return inner
+#def expected_failure(test):
+# """Small decorator to mark tests as expected failure.
+# Useful for tests that are work-in-progress.
+# """
+# @functools.wraps(test)
+# def inner(*args, **kwargs):
+# try:
+# test(*args, **kwargs)
+# except Exception:
+# raise SkipTest
+# else:
+# raise AssertionError('Failure expected')
+# return inner
class AutomatedAnalysisTest(unittest.TestCase):
"""Setup a full automated analysis and run the pipeline.
@@ -65,8 +64,6 @@
shutil.move(os.path.basename(dirname), dirname)
os.remove(os.path.basename(url))
- @attr(complete=True)
- @attr(cluster=True)
def test_srnaseq_cluster(self):
"""Run cluster analysis
"""
@@ -88,8 +85,9 @@
print(" ".join(cl))
subprocess.check_call(cl)
- @attr(complete=True)
- @attr(miraligner=True)
+ test_srnaseq_cluster.complete = True
+ test_srnaseq_cluster.cluster = True
+
def test_srnaseq_miraligner(self):
"""Run miraligner analysis
"""
@@ -105,3 +103,5 @@
"../../data/examples/miraligner/sim_isomir.fa"]
print(" ".join(cl))
# subprocess.check_call(cl)
+ test_srnaseq_miraligner.complete = True
+ test_srnaseq_miraligner.miraligner = True
--- a/test/test_database.py
+++ b/test/test_database.py
@@ -11,7 +11,6 @@
from seqcluster.libs.read import load_data
from seqcluster.db import make_database
from seqcluster.libs.logger import initialize_logger
-from nose.plugins.attrib import attr
@contextlib.contextmanager
def make_workdir():
@@ -30,7 +29,6 @@
class TestDatabase(TestCase):
- @attr(database=True)
def test_database(self):
if find_cmd("sqlite3"):
with make_workdir() as workdir:
@@ -44,3 +42,4 @@
logger.info("Create database")
make_database(data)
# self.assertTrue()
+ test_database.database = True
--- a/test/test_preparedata.py
+++ b/test/test_preparedata.py
@@ -5,11 +5,9 @@
import inspect
from seqcluster.prepare_data import _read_fastq_files, _create_matrix_uniq_seq
import seqcluster
-from nose.plugins.attrib import attr
class TestPreparedata(TestCase):
- @attr(collapse=True)
def test_preparedata(self):
out_dir = "test/test_out_prepare"
if os.path.exists(out_dir):
@@ -26,7 +24,8 @@
if os.path.exists(out_dir):
shutil.rmtree(out_dir)
- @attr(umis=True)
+ test_preparedata.collapse = True
+
def test_umis(self):
from seqcluster.libs.fastq import collapse, write_output
umis = collapse(os.path.abspath("data/examples/umis/sample.fastq"))
@@ -37,3 +36,5 @@
shutil.rmtree(out_dir)
os.mkdir(out_dir)
write_output(os.path.join(out_dir, "umis.fastq"), umis)
+
+ test_umis.umis = True
|
