Merge branch 'develop' into fmt-core

testsuite/MDAnalysisTests/import/fork_called.py

@@ -26,6 +26,7 @@
 """Tests whether os.fork() is called as a side effect when importing MDAnalysis.
 See PR #1794 for details."""
 
-with mock.patch('os.fork') as os_dot_fork:
+with mock.patch("os.fork") as os_dot_fork:
     import MDAnalysis
+
     assert not os_dot_fork.called

testsuite/MDAnalysisTests/import/test_import.py

@@ -27,8 +27,10 @@
 
 """Test if importing MDAnalysis has unwanted side effects (PR #1794)."""
 
-@pytest.mark.skipif(os.name == 'nt',
-                    reason="fork-related import checks irrelevant on Windows")
+
+@pytest.mark.skipif(
+    os.name == "nt", reason="fork-related import checks irrelevant on Windows"
+)
 class TestMDAImport(object):
     # Tests concerning importing MDAnalysis.
     def test_os_dot_fork_not_called(self):
@@ -37,7 +39,7 @@ def test_os_dot_fork_not_called(self):
         # no previously imported modules interfere with it. It is therefore
         # offloaded to the script "fork_called.py".
         loc = os.path.dirname(os.path.realpath(__file__))
-        script = os.path.join(loc, 'fork_called.py')
+        script = os.path.join(loc, "fork_called.py")
         encoding = sys.stdout.encoding
         if encoding is None:
             encoding = "utf-8"
@@ -47,16 +49,17 @@ def test_os_dot_fork_not_called(self):
         # CalledProcessError. That error's output member then contains the
         # failed script's stderr and we can print it:
         try:
-            out = subprocess.check_output([sys.executable, script],
-                                          stderr=subprocess.STDOUT)\
-                                         .decode(encoding)
+            out = subprocess.check_output(
+                [sys.executable, script], stderr=subprocess.STDOUT
+            ).decode(encoding)
         except subprocess.CalledProcessError as err:
             print(err.output)
-            raise(err)
+            raise (err)
 
     def test_os_dot_fork_not_none(self):
         # In MDAnalysis.core.universe, os.fork is set to None prior to importing
         # the uuid module and restored afterwards (see PR #1794 for details).
         # This tests asserts that os.fork has been restored.
         import MDAnalysis
+
         assert os.fork is not None

testsuite/MDAnalysisTests/utils/test_authors.py

@@ -24,5 +24,8 @@
 
 import MDAnalysis
 
+
 def test_package_authors():
-    assert len(MDAnalysis.__authors__) > 0, 'Could not find the list of authors'
+    assert (
+        len(MDAnalysis.__authors__) > 0
+    ), "Could not find the list of authors"

testsuite/MDAnalysisTests/utils/test_datafiles.py

@@ -29,10 +29,10 @@ def test_failed_import(monkeypatch):
     # Putting this test first to avoid datafiles already being loaded
     errmsg = "MDAnalysisTests package not installed."
 
-    monkeypatch.setitem(sys.modules, 'MDAnalysisTests.datafiles', None)
+    monkeypatch.setitem(sys.modules, "MDAnalysisTests.datafiles", None)
 
-    if 'MDAnalysis.tests.datafiles' in sys.modules:
-        monkeypatch.delitem(sys.modules, 'MDAnalysis.tests.datafiles')
+    if "MDAnalysis.tests.datafiles" in sys.modules:
+        monkeypatch.delitem(sys.modules, "MDAnalysis.tests.datafiles")
 
     with pytest.raises(ImportError, match=errmsg):
         import MDAnalysis.tests.datafiles
@@ -42,20 +42,35 @@ def test_import():
     try:
         import MDAnalysis.tests.datafiles
     except ImportError:
-        pytest.fail("Failed to 'import MDAnalysis.tests.datafiles --- install MDAnalysisTests")
+        pytest.fail(
+            "Failed to 'import MDAnalysis.tests.datafiles --- install MDAnalysisTests"
+        )
 
 
 def test_all_exports():
     import MDAnalysisTests.datafiles
-    missing = [name for name in dir(MDAnalysisTests.datafiles)
-               if
-               not name.startswith('_') and name not in MDAnalysisTests.datafiles.__all__ and name != 'MDAnalysisTests']
+
+    missing = [
+        name
+        for name in dir(MDAnalysisTests.datafiles)
+        if not name.startswith("_")
+        and name not in MDAnalysisTests.datafiles.__all__
+        and name != "MDAnalysisTests"
+    ]
     assert_equal(missing, [], err_msg="Variables need to be added to __all__.")
 
 
 def test_export_variables():
     import MDAnalysisTests.datafiles
     import MDAnalysis.tests.datafiles
-    missing = [name for name in MDAnalysisTests.datafiles.__all__
-               if name not in dir(MDAnalysis.tests.datafiles)]
-    assert_equal(missing, [], err_msg="Variables not exported to MDAnalysis.tests.datafiles")
+
+    missing = [
+        name
+        for name in MDAnalysisTests.datafiles.__all__
+        if name not in dir(MDAnalysis.tests.datafiles)
+    ]
+    assert_equal(
+        missing,
+        [],
+        err_msg="Variables not exported to MDAnalysis.tests.datafiles",
+    )

testsuite/MDAnalysisTests/utils/test_duecredit.py

@@ -35,48 +35,68 @@
 # duecredit itself is not needed in the name space but this is a
 # convenient way to skip all tests if duecredit is not installed
 # (see https://github.com/MDAnalysis/mdanalysis/issues/1906)
-pytest.importorskip('duecredit')
+pytest.importorskip("duecredit")
 
-@pytest.mark.skipif((os.environ.get('DUECREDIT_ENABLE', 'yes').lower()
-                     in ('no', '0', 'false')),
-                    reason=
-                    "duecredit is explicitly disabled with DUECREDIT_ENABLE=no")
+
+@pytest.mark.skipif(
+    (
+        os.environ.get("DUECREDIT_ENABLE", "yes").lower()
+        in ("no", "0", "false")
+    ),
+    reason="duecredit is explicitly disabled with DUECREDIT_ENABLE=no",
+)
 class TestDuecredit(object):
 
     def test_duecredit_active(self):
         assert mda.due.active == True
 
-    @pytest.mark.parametrize("module,path,citekey", [
-        ("MDAnalysis", "MDAnalysis", "10.25080/majora-629e541a-00e"),
-        ("MDAnalysis", "MDAnalysis", "10.1002/jcc.21787"),
-    ])
+    @pytest.mark.parametrize(
+        "module,path,citekey",
+        [
+            ("MDAnalysis", "MDAnalysis", "10.25080/majora-629e541a-00e"),
+            ("MDAnalysis", "MDAnalysis", "10.1002/jcc.21787"),
+        ],
+    )
     def test_duecredit_collector_primary(self, module, path, citekey):
         assert mda.due.citations[(path, citekey)].cites_module == True
 
     # note: citekeys are *all lower case*
-    @pytest.mark.parametrize("module,path,citekey", [
-        ("MDAnalysis.analysis.psa",
-         "pathsimanalysis.psa",
-         "10.1371/journal.pcbi.1004568"),
-        ("MDAnalysis.analysis.hydrogenbonds.hbond_autocorrel",
-         "MDAnalysis.analysis.hydrogenbonds.hbond_autocorrel",
-         "10.1063/1.4922445"),
-        ("MDAnalysis.analysis.leaflet",
-         "MDAnalysis.analysis.leaflet",
-         "10.1002/jcc.21787"),
-        ("MDAnalysis.lib.qcprot",
-         "MDAnalysis.lib.qcprot",
-         "10.1107/s0108767305015266"),
-        ("MDAnalysis.lib.qcprot",
-         "MDAnalysis.lib.qcprot",
-         "qcprot2"),
-        ("MDAnalysis.analysis.encore",
-         "MDAnalysis.analysis.encore",
-         "10.1371/journal.pcbi.1004415"),
-        ("MDAnalysis.analysis.dssp",
-         "MDAnalysis.analysis.dssp",
-         "10.1002/bip.360221211")
-        ])
+    @pytest.mark.parametrize(
+        "module,path,citekey",
+        [
+            (
+                "MDAnalysis.analysis.psa",
+                "pathsimanalysis.psa",
+                "10.1371/journal.pcbi.1004568",
+            ),
+            (
+                "MDAnalysis.analysis.hydrogenbonds.hbond_autocorrel",
+                "MDAnalysis.analysis.hydrogenbonds.hbond_autocorrel",
+                "10.1063/1.4922445",
+            ),
+            (
+                "MDAnalysis.analysis.leaflet",
+                "MDAnalysis.analysis.leaflet",
+                "10.1002/jcc.21787",
+            ),
+            (
+                "MDAnalysis.lib.qcprot",
+                "MDAnalysis.lib.qcprot",
+                "10.1107/s0108767305015266",
+            ),
+            ("MDAnalysis.lib.qcprot", "MDAnalysis.lib.qcprot", "qcprot2"),
+            (
+                "MDAnalysis.analysis.encore",
+                "MDAnalysis.analysis.encore",
+                "10.1371/journal.pcbi.1004415",
+            ),
+            (
+                "MDAnalysis.analysis.dssp",
+                "MDAnalysis.analysis.dssp",
+                "10.1002/bip.360221211",
+            ),
+        ],
+    )
     def test_duecredit_collector_analysis_modules(self, module, path, citekey):
         importlib.import_module(module)
         assert mda.due.citations[(path, citekey)].cites_module == True
@@ -85,17 +105,21 @@ def test_duecredit_mmtf(self):
         # doesn't trigger on import but on use of either parser or reader
         u = mda.Universe(MMTF)
 
-        assert mda.due.citations[('MDAnalysis.coordinates.MMTF',
-                                  '10.1371/journal.pcbi.1005575')].cites_module
-        assert mda.due.citations[('MDAnalysis.topology.MMTFParser',
-                                  '10.1371/journal.pcbi.1005575')].cites_module
+        assert mda.due.citations[
+            ("MDAnalysis.coordinates.MMTF", "10.1371/journal.pcbi.1005575")
+        ].cites_module
+        assert mda.due.citations[
+            ("MDAnalysis.topology.MMTFParser", "10.1371/journal.pcbi.1005575")
+        ].cites_module
 
     @pytest.mark.skipif(not HAS_H5PY, reason="h5py not installed")
     def test_duecredit_h5md(self):
         # doesn't trigger on import but on use of either reader or writer
         u = mda.Universe(TPR_xvf, H5MD_xvf)
 
-        assert mda.due.citations[('MDAnalysis.coordinates.H5MD',
-                                  '10.25080/majora-1b6fd038-005')].cites_module
-        assert mda.due.citations[('MDAnalysis.coordinates.H5MD',
-                                  '10.1016/j.cpc.2014.01.018')].cites_module
+        assert mda.due.citations[
+            ("MDAnalysis.coordinates.H5MD", "10.25080/majora-1b6fd038-005")
+        ].cites_module
+        assert mda.due.citations[
+            ("MDAnalysis.coordinates.H5MD", "10.1016/j.cpc.2014.01.018")
+        ].cites_module

testsuite/MDAnalysisTests/utils/test_failure.py

@@ -24,9 +24,10 @@
 
 
 def test_failure():
-    """Fail if the MDA_FAILURE_TEST environment variable is set.
-    """
-    if u'MDA_FAILURE_TEST' in os.environ:
+    """Fail if the MDA_FAILURE_TEST environment variable is set."""
+    if "MDA_FAILURE_TEST" in os.environ:
         # Have a file open to trigger an output from the open_files plugin.
-        f = open('./failure.txt', 'w')
-        raise AssertionError("the MDA_FAILURE_TEST environment variable is set")
+        f = open("./failure.txt", "w")
+        raise AssertionError(
+            "the MDA_FAILURE_TEST environment variable is set"
+        )

testsuite/MDAnalysisTests/utils/test_imports.py

@@ -29,11 +29,11 @@
 
 path_to_testing_modules = MDAnalysisTests.__path__[0]
 # Exclusion path relative to MDAnalysisTests
-exclusions = ['/plugins', '/data']
+exclusions = ["/plugins", "/data"]
 
 
 def is_excluded(path):
-    leaf = path[len(path_to_testing_modules):]
+    leaf = path[len(path_to_testing_modules) :]
     return leaf in exclusions
 
 
@@ -42,20 +42,26 @@ def get_file_paths():
     for dirpath, dirnames, files in os.walk(path_to_testing_modules):
         if is_excluded(dirpath):
             continue
-        for f in filter(lambda x: x.endswith('.py'), files):
+        for f in filter(lambda x: x.endswith(".py"), files):
             fpath = os.path.join(dirpath, f)
             if is_excluded(fpath):
                 continue
             paths.append(fpath)
     return paths
 
 
-@pytest.mark.parametrize('testing_module', get_file_paths())
+@pytest.mark.parametrize("testing_module", get_file_paths())
 def test_relative_import(testing_module):
-    with open(testing_module, 'r') as test_module_file_object:
+    with open(testing_module, "r") as test_module_file_object:
         for lineno, line in enumerate(test_module_file_object, start=1):
-            if 'from .' in line and 'import' in line \
-                    and not 'test_imports' in testing_module:
+            if (
+                "from ." in line
+                and "import" in line
+                and not "test_imports" in testing_module
+            ):
                 raise AssertionError(
                     "A relative import statement was found in "
-                    "module {testing_module} at linenumber {lineno}.".format(**vars()))
+                    "module {testing_module} at linenumber {lineno}.".format(
+                        **vars()
+                    )
+                )

testsuite/MDAnalysisTests/utils/test_log.py

@@ -68,5 +68,8 @@ def buffer():
 
 
 def _assert_in(output, string):
-    assert string in output, "Output '{0}' does not match required format '{1}'.".format(output.replace('\r', '\\r'), string.replace('\r', '\\r'))
-
+    assert (
+        string in output
+    ), "Output '{0}' does not match required format '{1}'.".format(
+        output.replace("\r", "\\r"), string.replace("\r", "\\r")
+    )