Add run and runtmp pytest fixtures. (#1487)

* add 'run' and 'runtmp' test fixtures

* remove unnecessary track_abundance fixture call

* restore original;

tests/conftest.py

@@ -1,14 +1,24 @@
 import os
 
-import matplotlib.pyplot as plt
-plt.rcParams.update({'figure.max_open_warning': 0})
-
 from hypothesis import settings, Verbosity
 import pytest
 
 import matplotlib.pyplot as plt
 plt.rcParams.update({'figure.max_open_warning': 0})
 
+from sourmash_tst_utils import TempDirectory, RunnerContext
+
+
+@pytest.fixture
+def runtmp():
+    with TempDirectory() as location:
+        yield RunnerContext(location)
+
+
+@pytest.fixture
+def run():
+    yield RunnerContext(os.getcwd())
+
 
 @pytest.fixture(params=[True, False])
 def track_abundance(request):

tests/sourmash_tst_utils.py

@@ -1,5 +1,4 @@
 "Various utilities used by sourmash tests."
-
 import sys
 import os
 import tempfile
@@ -12,10 +11,7 @@
 from pkg_resources import Requirement, resource_filename, ResolutionError
 import traceback
 from io import open  # pylint: disable=redefined-builtin
-try:
-    from StringIO import StringIO
-except ImportError:
-    from io import StringIO
+from io import StringIO
 
 
 SIG_FILES = [os.path.join('demo', f) for f in (
@@ -193,6 +189,7 @@ def run_sourmash(self, *args, **kwargs):
             raise ValueError(self)
 
         return self.last_result
+    sourmash = run_sourmash
 
     def run(self, scriptname, *args, **kwargs):
         "Run a script with the given arguments."

tests/test_sourmash.py

@@ -859,15 +859,14 @@ def test_gather_query_db_md5_ambiguous(c):
     assert "Error! Multiple signatures start with md5 '1'" in err
 
 
-@utils.in_tempdir
-def test_gather_lca_db(c):
+def test_gather_lca_db(runtmp):
     # can we do a 'sourmash gather' on an LCA database?
     query = utils.get_test_data('47+63.fa.sig')
     lca_db = utils.get_test_data('lca/47+63.lca.json')
 
-    c.run_sourmash('gather', query, lca_db)
-    print(c)
-    assert 'NC_009665.1 Shewanella baltica OS185' in str(c.last_result.out)
+    runtmp.sourmash('gather', query, lca_db)
+    print(runtmp)
+    assert 'NC_009665.1 Shewanella baltica OS185' in str(runtmp.last_result.out)
 
 
 @utils.in_tempdir
@@ -1443,19 +1442,18 @@ def test_search_containment_s10():
         assert '16.7%' in out
 
 
-@utils.in_thisdir
-def test_search_containment_s10_no_max(c):
+def test_search_containment_s10_no_max(run):
     # check --containment for s10/s10-small
     q1 = utils.get_test_data('scaled/genome-s10.fa.gz.sig')
     q2 = utils.get_test_data('scaled/genome-s10-small.fa.gz.sig')
 
     with pytest.raises(ValueError) as exc:
-        c.run_sourmash('search', q1, q2, '--containment',
+        run.run_sourmash('search', q1, q2, '--containment',
                        '--max-containment')
 
-    print(c.last_result.out)
-    print(c.last_result.err)
-    assert "ERROR: cannot specify both --containment and --max-containment!" in c.last_result.err
+    print(run.last_result.out)
+    print(run.last_result.err)
+    assert "ERROR: cannot specify both --containment and --max-containment!" in run.last_result.err
 
 
 def test_search_max_containment_s10_pairwise():