Fixes issues 3166 and 3255 (#3256)

* Fixes issues 3166 and 3255

* Add tests

* Changelog and docs

* fix pep8 issue

package/CHANGELOG

@@ -23,6 +23,8 @@ The rules for this file:
   * 2.0.0
 
 Fixes
+  * NCDFReader now defaults to a dt value of 1.0 ps when it cannot estimate
+    it from the first two frames of the file (Issue #3166)
   * Get chi1_selection to match canonical gamma atoms (Issue #2044)
   * ITPParser now accepts relative paths (Issue #3037, PR #3108)
   * Fixed issue with unassigned 'GAP' variable in fasta2algin function when
@@ -214,6 +216,9 @@ Changes
   * `threadpoolctl` is required for installation (Issue #2860)
 
 Deprecations
+  * In 2.1.0 the TRZReader will default to a dt of 1.0 ps when failing to
+    read it from the input TRZ trajectory.
+
 
 06/09/20 richardjgowers, kain88-de, lilyminium, p-j-smith, bdice, joaomcteixeira,
          PicoCentauri, davidercruz, jbarnoud, RMeli, IAlibay, mtiberti, CCook96,

package/MDAnalysis/coordinates/TRJ.py

@@ -454,6 +454,8 @@ class NCDFReader(base.ReaderBase):
     .. versionchanged:: 2.0.0
        Now use a picklable :class:`scipy.io.netcdf.netcdf_file`--
        :class:`NCDFPicklable`.
+       Reading of `dt` now defaults to 1.0 ps if `dt` cannot be extracted from
+       the first two frames of the trajectory.
 
     """
 
@@ -694,8 +696,15 @@ def _read_next_timestep(self, ts=None):
             raise IOError from None
 
     def _get_dt(self):
-        t1 = self.trjfile.variables['time'][1]
-        t0 = self.trjfile.variables['time'][0]
+        """Gets dt based on the time difference between the first and second
+        frame. If missing (i.e. an IndexError is triggered), raises an
+        AttributeError which triggers the default 1 ps return of dt().
+        """
+        try:
+            t1 = self.trjfile.variables['time'][1]
+            t0 = self.trjfile.variables['time'][0]
+        except IndexError:
+            raise AttributeError
         return t1 - t0
 
     def close(self):

package/MDAnalysis/coordinates/TRZ.py

@@ -330,6 +330,9 @@ def _get_dt(self):
             t1 = self.ts.time
             dt = t1 - t0
         except StopIteration:
+            msg = ('dt information could not be obtained, defaulting to 0 ps. '
+                   'Note: in MDAnalysis 2.1.0 this default will change 1 ps.')
+            warnings.warn(msg)
             return 0
         else:
             return dt

testsuite/MDAnalysisTests/coordinates/test_netcdf.py

@@ -594,6 +594,19 @@ def test_program_warn(self, tmpdir, mutation):
                     "attributes are missing")
             assert str(record[0].message.args[0]) == wmsg
 
+    def test_no_dt_warning(self, tmpdir):
+        """Issue 3166 - not being able to call dt should throw a warning.
+        Also at the same time checks that single frame chain reading works"""
+        u = mda.Universe(PFncdf_Top, PFncdf_Trj)
+        with tmpdir.as_cwd():
+            with NCDFWriter('single_frame.nc', u.atoms.n_atoms) as W:
+                W.write(u)
+
+            # Using the ChainReader implicitly calls dt() and thus _get_dt()
+            wmsg = "Reader has no dt information, set to 1.0 ps"
+            with pytest.warns(UserWarning, match=wmsg):
+                u2 = mda.Universe(PFncdf_Top, [PFncdf_Trj, 'single_frame.nc'])
+
 
 class _NCDFWriterTest(object):
     prec = 5
@@ -891,20 +904,16 @@ def test_writer_units(self, outfile, var, expected):
             assert_equal(unit, expected)
 
 
-class TestNCDFWriterErrors(object):
+class TestNCDFWriterErrorsWarnings(object):
     @pytest.fixture()
     def outfile(self, tmpdir):
         return str(tmpdir) + 'out.ncdf'
 
     def test_zero_atoms_VE(self, outfile):
-        from MDAnalysis.coordinates.TRJ import NCDFWriter
-
         with pytest.raises(ValueError):
             NCDFWriter(outfile, 0)
 
     def test_wrong_n_atoms(self, outfile):
-        from MDAnalysis.coordinates.TRJ import NCDFWriter
-
         with NCDFWriter(outfile, 100) as w:
             u = make_Universe(trajectory=True)
             with pytest.raises(IOError):

testsuite/MDAnalysisTests/coordinates/test_trz.py

@@ -194,16 +194,28 @@ class TestTRZWriter2(object):
     def u(self):
         return mda.Universe(two_water_gro)
 
-    def test_writer_trz_from_other(self, u, tmpdir):
-        outfile = os.path.join(str(tmpdir), 'trz-writer-2.trz')
+    @pytest.fixture()
+    def outfile(self, tmpdir):
+        return str(tmpdir.join('/trz-writer-2.trz'))
+
+    def test_writer_trz_from_other(self, u, outfile):
+        with mda.coordinates.TRZ.TRZWriter(outfile, len(u.atoms)) as W:
+            W.write(u)
+
+        u2 = mda.Universe(two_water_gro, outfile)
+
+        assert_almost_equal(u.atoms.positions, u2.atoms.positions, 3)
+
+    def test_no_dt_warning(self, u, outfile):
         with mda.coordinates.TRZ.TRZWriter(outfile, len(u.atoms)) as W:
             W.write(u)
-            W.close()
 
-            u2 = mda.Universe(two_water_gro, outfile)
+        u2 = mda.Universe(two_water_gro, outfile)
 
-            assert_almost_equal(u.atoms.positions,
-                                u2.atoms.positions, 3)
+        wmsg = ('dt information could not be obtained, defaulting to 0 ps. '
+                'Note: in MDAnalysis 2.1.0 this default will change 1 ps.')
+        with pytest.warns(UserWarning, match=wmsg):
+            assert_almost_equal(u2.trajectory.dt, 0)
 
 
 class TestWrite_Partial_Timestep(object):