[MRG] replace utils.TempDirectory with run tmp (#1502)

* replaced utils.TempDirectory with run tmp

* added runner context run.tmp

* updated test_import_mash_csv_to_sig with runtmp fixture

* replaced "runner context" w runtmp

* updated runner context and working

* added runtmp to test_linear_index_save, wrking

* added runtmp to test_linear_index_save_load, wrkng

Co-authored-by: C. Titus Brown <titus@idyll.org>

tests/test_cmd_signature.py

@@ -1588,27 +1588,18 @@ def test_import_export_2(c):
     assert imported.minhash == compare.minhash
 
 
-def test_import_mash_csv_to_sig():
+def test_import_mash_csv_to_sig(runtmp):
     # test copied over from 'sourmash import_csv'.
-    with utils.TempDirectory() as location:
-        testdata1 = utils.get_test_data('short.fa.msh.dump')
-        testdata2 = utils.get_test_data('short.fa')
-
-        status, out, err = utils.runscript('sourmash', ['sig', 'import',
-                                                        '--csv',
-                                                        testdata1,
-                                                        '-o', 'xxx.sig'],
-                                           in_directory=location)
-
-        status, out, err = utils.runscript('sourmash',
-                                           ['compute', '-k', '31',
-                                            '-n', '970', testdata2],
-                                           in_directory=location)
-
-        status, out, err = utils.runscript('sourmash',
-                                           ['search', '-k', '31',
-                                            'short.fa.sig', 'xxx.sig'],
-                                           in_directory=location)
-        print(status, out, err)
-        assert '1 matches:' in out
-        assert '100.0%       short.fa' in out
+    testdata1 = utils.get_test_data('short.fa.msh.dump')
+    testdata2 = utils.get_test_data('short.fa')
+
+    runtmp.sourmash('sig', 'import', '--csv', testdata1, '-o', 'xxx.sig')
+
+    runtmp.sourmash('compute', '-k', '31', '-n', '970', testdata2)
+
+    runtmp.sourmash('search', '-k', '31', 'short.fa.sig', 'xxx.sig')
+
+    print("RUNTEMP", runtmp)
+
+    assert '1 matches:' in runtmp.last_result.out
+    assert '100.0%       short.fa' in runtmp.last_result.out

tests/test_index.py

@@ -410,7 +410,7 @@ def test_linear_index_search_abund_subj_flat():
     assert "'search_abund' requires subject signatures with abundance information" in str(exc.value)
 
 
-def test_linear_index_save():
+def test_linear_index_save(runtmp):
     sig2 = utils.get_test_data('2.fa.sig')
     sig47 = utils.get_test_data('47.fa.sig')
     sig63 = utils.get_test_data('63.fa.sig')
@@ -424,24 +424,23 @@ def test_linear_index_save():
     linear.insert(ss47)
     linear.insert(ss63)
 
-    with utils.TempDirectory() as location:
-        filename = os.path.join(location, 'foo')
-        linear.save(filename)
+    filename = runtmp.output('foo')
+    linear.save(filename)
 
-        si = set(sourmash.load_file_as_signatures(filename))
+    si = set(sourmash.load_file_as_signatures(filename))
 
     x = {ss2, ss47, ss63}
 
     print(len(si))
     print(len(x))
 
-    print(si)
-    print(x)
+    print('si: ', si)
+    print('x: ', x)
 
     assert si == x, si
 
 
-def test_linear_index_load():
+def test_linear_index_load(runtmp):
     sig2 = utils.get_test_data('2.fa.sig')
     sig47 = utils.get_test_data('47.fa.sig')
     sig63 = utils.get_test_data('63.fa.sig')
@@ -450,21 +449,20 @@ def test_linear_index_load():
     ss47 = sourmash.load_one_signature(sig47)
     ss63 = sourmash.load_one_signature(sig63)
 
-    with utils.TempDirectory() as location:
-        from sourmash import save_signatures
-
-        filename = os.path.join(location, 'foo')
-        with open(filename, 'wt') as fp:
-            sourmash.save_signatures([ss2, ss47, ss63], fp)
+    from sourmash import save_signatures
+
+    filename = runtmp.output('foo')
+    with open(filename, 'wt') as fp:
+        sourmash.save_signatures([ss2, ss47, ss63], fp)
 
-        linear = LinearIndex.load(filename)
+    linear = LinearIndex.load(filename)
 
     x = {ss2, ss47, ss63}
     assert set(linear.signatures()) == x, linear.signatures
     assert linear.location == filename
 
 
-def test_linear_index_save_load():
+def test_linear_index_save_load(runtmp):
     sig2 = utils.get_test_data('2.fa.sig')
     sig47 = utils.get_test_data('47.fa.sig')
     sig63 = utils.get_test_data('63.fa.sig')
@@ -477,11 +475,10 @@ def test_linear_index_save_load():
     linear.insert(ss2)
     linear.insert(ss47)
     linear.insert(ss63)
-
-    with utils.TempDirectory() as location:
-        filename = os.path.join(location, 'foo')
-        linear.save(filename)
-        linear2 = LinearIndex.load(filename)
+
+    filename = runtmp.output('foo')
+    linear.save(filename)
+    linear2 = LinearIndex.load(filename)
 
     # now, search for sig2
     sr = linear2.search(ss2, threshold=1.0)