switched to py.test, closes #12

conftest.py

@@ -0,0 +1,10 @@
+import py.test
+
+def pytest_addoption(parser):
+    parser.addoption('--slow', action='store_true', default=False,
+                      help='Also run slow tests')
+
+def pytest_runtest_setup(item):
+    """Skip tests if they are marked as slow and --slow is not given"""
+    if getattr(item.obj, 'slow', None) and not item.config.getvalue('slow'):
+        py.test.skip('slow tests not requested')

requirements.txt

@@ -1,4 +1,4 @@
-nose
+pytest
 click
 pyfaidx
 norns>0.1.1

setup.cfg

@@ -1,5 +1,5 @@
 [metadata]
 description-file = README.md
 
-[nosetests]
+[pytest]
 attr=!slow

setup.py

@@ -32,7 +32,7 @@
 }
 
 requires = [
-    'nose',
+    'pytest',
     'click',
     'pyfaidx',
     'norns>0.1.1',

tests/test_annotation.py

@@ -1,4 +1,3 @@
-from nose.tools import *
 from tempfile import mkdtemp, NamedTemporaryFile
 import genomepy
 import shutil

tests/test_gaps.py

@@ -1,4 +1,3 @@
-from nose.tools import *
 from tempfile import mkdtemp, NamedTemporaryFile
 from genomepy.utils import generate_gap_bed
 import shutil
@@ -11,13 +10,7 @@
 except NameError:
     FileNotFoundError = IOError
 
-def setup():
-    pass
-
-def teardown():
-    pass
-
-def test_annotation():
+def test_gaps():
     infa = "tests/data/gap.fa"
     outbed = "tests/data/gap.bed" 
 

tests/genomepy_tests.py → tests/test_genomepy.py

@@ -1,31 +1,26 @@
-from nose.tools import *
 from tempfile import mkdtemp, NamedTemporaryFile
 import genomepy
 import shutil
+import pytest
 
 # Python 2
 try:
     FileNotFoundError
 except NameError:
     FileNotFoundError = IOError
 
-def setup():
-    print("SETUP!")
-
-def teardown():
-    print("TEAR DOWN!")
-
 def test_basic():
     cfg = genomepy.functions.config
+    print(cfg)
     assert 2 == len(cfg.keys())
 
-@raises(FileNotFoundError)
 def test_genome_dir_not_found():
-    genomepy.Genome("unknown", "unknown")
+    with pytest.raises(FileNotFoundError):
+        genomepy.Genome("unknown", "unknown")
 
-@raises(FileNotFoundError)
 def test_no_fasta_files():
-    genomepy.Genome("empty", "tests/data/genome")
+    with pytest.raises(FileNotFoundError):
+        genomepy.Genome("empty", "tests/data/genome")
 
 def test_ucsc_genome(): 
     """Test UCSC.
@@ -66,6 +61,7 @@ def test_ncbi_genome():
     assert str(seq).upper() == "TTTGCAACAGCTGCCGCAGTGTGACCGTTGTACTG"
     shutil.rmtree(tmp)
 
+@pytest.mark.slow
 def test_ucsc_human(): 
     """Test UCSC.
    
@@ -79,6 +75,7 @@ def test_ucsc_human():
     assert str(seq) == "CCTCCTCGCTCTCTT"
     shutil.rmtree(tmp)
 
+@pytest.mark.slow
 def test_ensembl_human(): 
     """Test Ensembl.
     
@@ -92,6 +89,7 @@ def test_ensembl_human():
     assert str(seq) == "CCTCCTCGCTCTCTT"
     shutil.rmtree(tmp)
 
+@pytest.mark.slow
 def test_ncbi_human(): 
     """Test NCBI.
     
@@ -124,7 +122,3 @@ def test_regexp_filter():
         fa = genomepy.utils.filter_fasta(
                 fname, tmpfa, regex=regex, v=True, force=True)
         assert len(fa.keys()) == no_match
-
-test_ncbi_human.slow = 1
-test_ensembl_human.slow = 1
-test_ucsc_human.slow = 1