Merge branch 'develop' into issue-3386

azure-pipelines.yml

@@ -18,7 +18,7 @@ jobs:
 - job: Windows
   condition: and(succeeded(), ne(variables['Build.SourceBranch'], 'refs/heads/master'))  # skip for PR merges
   pool:
-    vmImage: 'VS2017-Win2016'
+    vmImage: 'windows-2019'
   variables:
     MPLBACKEND: agg
   strategy:

testsuite/MDAnalysisTests/lib/test_augment.py

@@ -20,6 +20,7 @@
 # MDAnalysis: A Toolkit for the Analysis of Molecular Dynamics Simulations.
 # J. Comput. Chem. 32 (2011), 2319--2327, doi:10.1002/jcc.21787
 
+import os
 import pytest
 import numpy as np
 from numpy.testing import assert_almost_equal, assert_equal
@@ -67,6 +68,8 @@
        )
 
 
+@pytest.mark.xfail(os.name == "nt",
+                   reason="see gh-3248")
 @pytest.mark.parametrize('b', (
                          np.array([10, 10, 10, 90, 90, 90], dtype=np.float32),
                          np.array([10, 10, 10, 45, 60, 90], dtype=np.float32)

testsuite/MDAnalysisTests/utils/test_streamio.py

@@ -202,18 +202,15 @@ def test_join(self, tmpdir, funcname="join"):
                      err_msg=("os.path.{0}() does not work with "
                               "NamedStream").format(funcname))
 
-    @pytest.mark.skipif(True, reason='See #1534]')
     def test_expanduser_noexpansion_returns_NamedStream(self):
         ns = self.create_NamedStream("de/zipferlack.txt")  # no tilde ~ in name!
-        reference = ns
+        reference = ns.name
         value = os.path.expanduser(ns)
         assert_equal(value, reference,
                      err_msg=("os.path.expanduser() without '~' did not "
                               "return NamedStream --- weird!!"))
 
-    @pytest.mark.skipif(True, reason='See #1534')
     @pytest.mark.skipif("HOME" not in os.environ, reason='It is needed')
-    @pytest.mark.xfail
     def test_expandvars(self):
         name = "${HOME}/stories/jabberwock.txt"
         ns = self.create_NamedStream(name)
@@ -222,10 +219,9 @@ def test_expandvars(self):
         assert_equal(value, reference,
                      err_msg="os.path.expandvars() did not expand HOME")
 
-    @pytest.mark.skipif(True, reason='See #1534')
     def test_expandvars_noexpansion_returns_NamedStream(self):
         ns = self.create_NamedStream() # no $VAR constructs
-        reference = ns
+        reference = ns.name
         value = os.path.expandvars(ns)
         assert_equal(value, reference,
                      err_msg=("os.path.expandvars() without '$VARS' did not "
@@ -261,8 +257,10 @@ class _StreamData(object):
     }
 
     def __init__(self):
-        self.buffers = {name: "".join(open(fn).readlines())
-                        for name, fn in self.filenames.items()}
+        self.buffers = {}
+        for name, fn in self.filenames.items():
+            with open(fn) as filed:
+                self.buffers[name] = "".join(filed.readlines())
         self.filenames['XYZ_PSF'] = u"bogus/path/mini.psf"
         self.buffers['XYZ_PSF'] = u"""\
 PSF CMAP
@@ -322,45 +320,46 @@ def as_NamedStream(self, name):
         return util.NamedStream(self.as_StringIO(name), self.filenames[name])
 
 
-streamData = _StreamData()
-del _StreamData
+@pytest.fixture(scope='module')
+def streamData():
+    return _StreamData()
 
 
 # possibly add tests to individual readers instead?
 class TestStreamIO(RefAdKSmall):
-    def test_PrimitivePDBReader(self):
+    def test_PrimitivePDBReader(self, streamData):
         u = MDAnalysis.Universe(streamData.as_NamedStream('PDB'))
         assert_equal(u.atoms.n_atoms, self.ref_n_atoms)
 
-    def test_PDBReader(self):
+    def test_PDBReader(self, streamData):
         try:
             u = MDAnalysis.Universe(streamData.as_NamedStream('PDB'))
         except Exception as err:
             raise pytest.fail("StreamIO not supported:\n>>>>> {0}".format(err))
         assert_equal(u.atoms.n_atoms, self.ref_n_atoms)
 
-    def test_CRDReader(self):
+    def test_CRDReader(self, streamData):
         u = MDAnalysis.Universe(streamData.as_NamedStream('CRD'))
         assert_equal(u.atoms.n_atoms, self.ref_n_atoms)
 
-    def test_PSFParser(self):
+    def test_PSFParser(self, streamData):
         u = MDAnalysis.Universe(streamData.as_NamedStream('PSF'))
         assert_equal(u.atoms.n_atoms, self.ref_n_atoms)
 
-    def test_PSF_CRD(self):
+    def test_PSF_CRD(self, streamData):
         u = MDAnalysis.Universe(streamData.as_NamedStream('PSF'),
                                 streamData.as_NamedStream('CRD'))
         assert_equal(u.atoms.n_atoms, self.ref_n_atoms)
 
-    def test_PQRReader(self):
+    def test_PQRReader(self, streamData):
         u = MDAnalysis.Universe(streamData.as_NamedStream('PQR'))
         assert_equal(u.atoms.n_atoms, self.ref_n_atoms)
         assert_almost_equal(u.atoms.total_charge(), self.ref_charmm_totalcharge, 3,
                             "Total charge (in CHARMM) does not match expected value.")
         assert_almost_equal(u.atoms.select_atoms('name H').charges, self.ref_charmm_Hcharges, 3,
                             "Charges for H atoms do not match.")
 
-    def test_PDBQTReader(self):
+    def test_PDBQTReader(self, streamData):
         u = MDAnalysis.Universe(streamData.as_NamedStream('PDBQT'))
         sel = u.select_atoms('backbone')
         assert_equal(sel.n_atoms, 796)
@@ -369,7 +368,7 @@ def test_PDBQTReader(self):
         sel = u.select_atoms('segid B')
         assert_equal(sel.n_atoms, 896, "failed to select segment B")
 
-    def test_GROReader(self):
+    def test_GROReader(self, streamData):
         u = MDAnalysis.Universe(streamData.as_NamedStream('GRO'))
         assert_equal(u.atoms.n_atoms, 6)
         assert_almost_equal(u.atoms[3].position,
@@ -379,14 +378,14 @@ def test_GROReader(self):
                             10. * np.array([0.2519, 0.3140, -0.1734]), 3,  # manually convert nm/ps -> A/ps
                             err_msg="wrong velocity for water 2 OW")
 
-    def test_MOL2Reader(self):
+    def test_MOL2Reader(self, streamData):
         u = MDAnalysis.Universe(streamData.as_NamedStream('MOL2'))
         assert_equal(len(u.atoms), 49)
         assert_equal(u.trajectory.n_frames, 200)
         u.trajectory[199]
         assert_array_almost_equal(u.atoms.positions[0], [1.7240, 11.2730, 14.1200])
 
-    def test_XYZReader(self):
+    def test_XYZReader(self, streamData):
         u = MDAnalysis.Universe(streamData.as_NamedStream('XYZ_PSF'),
                                 streamData.as_NamedStream('XYZ'))
         assert_equal(len(u.atoms), 8)

testsuite/setup.cfg

@@ -11,6 +11,15 @@ filterwarnings=
     ignore:`np.*` is a deprecated alias for the builtin:DeprecationWarning:networkx.*:
     error:Creating an ndarray from ragged nested sequences
     error:invalid escape sequence \\:DeprecationWarning
+    # Ignore frequent errors popping up in our tests
+    # Elements
+    ignore:Element information:UserWarning
+    # Mass
+    ignore:Failed to guess the mass:UserWarning
+    # Coordinates
+    ignore:No coordinate reader found:UserWarning
+    # NamedStream warnings
+    ignore:Constructed NamedStream:RuntimeWarning
 
 # Settings to test for warnings we throw
 # [tool:pytest]