Merge branch 'develop'

package/CHANGELOG

@@ -13,6 +13,16 @@ The rules for this file:
   * release numbers follow "Semantic Versioning" http://semver.org
 
 ------------------------------------------------------------------------------
+09/05/19 IAlibay, richardjgowers
+
+  * 0.20.1
+
+Fixes
+  * The NetCDF writer now writes `cell_angle` units as `degree` instead of
+    `degrees` in accordance with the AMBER NetCDF convention (Issue #2327).
+  * Fixed installation without Cython (Issue #2337)
+
+
 08/28/19 micaela-matta, xiki-tempula, zemanj, mattwthompson, orbeckst, aliehlen,
          dpadula85, jbarnoud, manuel.nuno.melo, richardjgowers, mattwthompson,
          ayushsuhane, picocentauri, NinadBhat, bieniekmateusz, p-j-smith, Lp0lp,

package/MDAnalysis/coordinates/TRJ.py

@@ -847,10 +847,13 @@ class NCDFWriter(base.WriterBase):
     .. versionchanged:: 0.17.0
        Use fast :mod:`netCDF4` for writing but fall back to slow
        :mod:`scipy.io.netcdf` if :mod:`netCDF4` is not available.
+    .. versionchanged:: 0.20.1
+       Changes the `cell_angles` unit to the AMBER NetCDF convention standard
+       of `degree` instead of the `degrees` written in previous version of
+       MDAnalysis (Issue #2327).
 
     .. TODO:
-       * Change the `cell_angles` units to `degree`, implement `scale_factor`
-         handling (Issue #2327).
+       * Implement `scale_factor` handling (Issue #2327).
 
     """
 
@@ -967,7 +970,7 @@ def _init_netcdf(self, periodic=True):
 
             cell_angles = ncfile.createVariable('cell_angles', 'f8',
                                                 ('frame', 'cell_angular'))
-            setattr(cell_angles, 'units', 'degrees')
+            setattr(cell_angles, 'units', 'degree')
 
             cell_angular = ncfile.createVariable('cell_angular', 'c',
                                                  ('cell_angular', 'label'))

package/MDAnalysis/version.py

@@ -67,4 +67,4 @@
 # e.g. with lib.log
 
 #: Release of MDAnalysis as a string, using `semantic versioning`_.
-__version__ = "0.20.0"  # NOTE: keep in sync with RELEASE in setup.py
+__version__ = "0.20.1"  # NOTE: keep in sync with RELEASE in setup.py

package/setup.py

@@ -73,7 +73,7 @@
     from commands import getoutput
 
 # NOTE: keep in sync with MDAnalysis.__version__ in version.py
-RELEASE = "0.20.0"
+RELEASE = "0.20.1"
 
 is_release = 'dev' not in RELEASE
 
@@ -101,6 +101,7 @@
         print("*** package: Cython not found ***")
         print("MDAnalysis requires cython for development builds")
         sys.exit(1)
+    cython_linetrace = False
 
 
 class Config(object):

testsuite/MDAnalysisTests/__init__.py

@@ -98,7 +98,7 @@
 logger = logging.getLogger("MDAnalysisTests.__init__")
 
 # keep in sync with RELEASE in setup.py
-__version__ = "0.20.0"
+__version__ = "0.20.1"
 
 # Do NOT import MDAnalysis at this level. Tests should do it themselves.
 # If MDAnalysis is imported here coverage accounting might fail because all the import

testsuite/MDAnalysisTests/coordinates/test_netcdf.py

@@ -37,7 +37,7 @@
 
 from MDAnalysisTests.datafiles import (PFncdf_Top, PFncdf_Trj,
                                        GRO, TRR, XYZ_mini,
-                                       PRM_NCBOX, TRJ_NCBOX)
+                                       PRM_NCBOX, TRJ_NCBOX, DLP_CONFIG)
 from MDAnalysisTests.coordinates.test_trj import _TRJReaderTest
 from MDAnalysisTests.coordinates.reference import (RefVGV, RefTZ2)
 from MDAnalysisTests import make_Universe
@@ -875,6 +875,33 @@ def test_write_ts(self, pos, vel, force, tmpdir, ts1, ts2):
         u.trajectory.close()
 
 
+class TestNCDFWriterUnits(object):
+    """Tests that the writer adheres to AMBER convention units"""
+    @pytest.fixture()
+    def outfile(self, tmpdir):
+        return str(tmpdir) + 'ncdf-writer-1.ncdf'
+
+    @pytest.mark.parametrize('var, expected', (
+        ('coordinates', 'angstrom'),
+        ('time', 'picosecond'),
+        ('cell_lengths', 'angstrom'),
+        ('cell_angles', 'degree'),
+        ('velocities', 'angstrom/picosecond'),
+        ('forces', 'kilocalorie/mole/angstrom')
+    ))
+    def test_writer_units(self, outfile, var, expected):
+        trr = mda.Universe(DLP_CONFIG, format='CONFIG')
+
+        with mda.Writer(outfile, trr.trajectory.n_atoms, velocities=True,
+                        forces=True, format='ncdf') as W:
+            for ts in trr.trajectory:
+                W.write_next_timestep(ts)
+
+        with netcdf.netcdf_file(outfile, mode='r') as ncdf:
+            unit = ncdf.variables[var].units.decode('utf-8')
+            assert_equal(unit, expected)
+
+
 class TestNCDFWriterErrors(object):
     @pytest.fixture()
     def outfile(self, tmpdir):

testsuite/setup.py

@@ -88,7 +88,7 @@ def run(self):
 
 if __name__ == '__main__':
     # this must be in-sync with MDAnalysis
-    RELEASE = "0.20.0"
+    RELEASE = "0.20.1"
 
     with open("README") as summary:
         LONG_DESCRIPTION = summary.read()