Finalizing #2537

package/CHANGELOG

@@ -15,7 +15,7 @@ The rules for this file:
 ------------------------------------------------------------------------------
 mm/dd/yy richardjgowers, kain88-de, lilyminium, p-j-smith, bdice, joaomcteixeira,
          PicoCentauri, davidercruz, jbarnoud, RMeli, IAlibay, mtiberti, CCook96,
-         Yuan-Yu, xiki-tempula, orbeckst
+         Yuan-Yu, xiki-tempula, orbeckst, wvandertoorn
 
   * 0.21.0
 
@@ -25,15 +25,15 @@ Fixes
   * Handle exception when PDBWriter is trying to remove an invalid StringIO
     (Issue #2512)
   * Clarifies density_from_Universe docs and adds user warning (Issue #2372)
-  * Fix upstream deprecation of `matplotlib.axis.Tick` attributes in 
+  * Fix upstream deprecation of `matplotlib.axis.Tick` attributes in
     `MDAnalysis.analysis.psa`
   * PDBWriter now uses first character of segid as ChainID (Issue #2224)
   * Adds a more detailed warning when attempting to read chamber-style parm7
     files (Issue #2475)
   * ClusterCollection.get_ids now returns correctly (Issue #2464)
   * Removes files for stubs mainly introduced in 0.11.0 (Issue #2443)
   * Removes support for reading AMBER NetCDF files with `cell_angle` units set
-    to `degrees` instead of the convention agreed `degree` (Issue #2327). 
+    to `degrees` instead of the convention agreed `degree` (Issue #2327).
   * Removes the MassWeight option from gnm (PR #2479).
   * AtomGroup.guess_bonds now uses periodic boundary information when available
     (Issue #2350)
@@ -91,15 +91,15 @@ Changes
     Segment.r1, Universe.s4AKE).  Use select_atoms instead (Issue #1377)
   * Calling Universe() now raises a TypeError advising you to use Universe.empty.
     Universe.empty() now no longer has n_atoms=0 as default. (Issue #2527)
-  * deprecated `start`, `stop`, and `step` keywords have been removed from `__init__` 
-    in :class:`AnalysisBase`. These should now be called in :meth:`AnalysisBase.run` 
+  * deprecated `start`, `stop`, and `step` keywords have been removed from `__init__`
+    in :class:`AnalysisBase`. These should now be called in :meth:`AnalysisBase.run`
     (Issue #1463)
   * Standardize `select` keyword by removing `selection`, `atomselection`
     and `ref_select` (Issue #2461, Issue #2530)
   * Removes support for setting `start`/`stop`/`step` trajecotry slicing
     keywords on :class:`HOLEtraj` construction. Also removes undocumented
     support for passing :class:`HOLE` parameters to :meth:`HOLEtraj.run`
-    (Issue #2513). 
+    (Issue #2513).
   * Removes the `nproc` keyword from
     :class:`Waterdynamics.HydrogenBondLifetimes` as the multiprocessing functionality
     did not work in some cases(Issues #2511).

package/MDAnalysis/analysis/density.py

@@ -1264,6 +1264,9 @@ def Bfactor2RMSF(B):
     ----------
 
     .. [Willis1975]  BTM Willis and AW Pryor. *Thermal vibrations in crystallography*. Cambridge Univ. Press, 1975
+
+
+    .. deprecated:: 1.0.0
     """
     return np.sqrt(3. * B / 8.) / np.pi
 

testsuite/MDAnalysisTests/analysis/test_density.py

@@ -37,6 +37,8 @@
 from MDAnalysis.analysis import density
 
 from MDAnalysisTests.datafiles import TPR, XTC, GRO, PDB_full
+from unittest.mock import Mock, patch
+from MDAnalysisTests.util import block_import
 
 
 class TestDensity(object):
@@ -452,9 +454,34 @@ def test_density_from_PDB(self, sigma, ref_shape, ref_gridsum):
 
         assert isinstance(D, density.Density)
         assert_equal(D.grid.shape, ref_shape)
-        assert_almost_equal(D.grid.sum(), ref_gridsum, decimal=6)
+        assert_almost_equal(D.grid.sum(), ref_gridsum, decimal=5)
 
     def test_has_DeprecationWarning(self):
         with pytest.warns(DeprecationWarning,
                           match="will be removed in release 2.0.0"):
             density.density_from_PDB(PDB_full, delta=5.0, sigma=2)
+
+class TestGridImport(object):
+
+    @block_import('gridData')
+    def test_absence_griddata(self):
+        sys.modules.pop('MDAnalysis.analysis.density', None)
+        # if gridData package is missing an ImportError should be raised
+        # at the module level of MDAnalysis.analysis.density
+        with pytest.raises(ImportError):
+            import MDAnalysis.analysis.density
+
+    def test_presence_griddata(self):
+        sys.modules.pop('MDAnalysis.analysis.density', None)
+        # no ImportError exception is raised when gridData is properly
+        # imported by MDAnalysis.analysis.density
+
+        # mock gridData in case there are testing scenarios where
+        # it is not available
+        mock = Mock()
+        with patch.dict('sys.modules', {'gridData':mock}):
+            try:
+                import MDAnalysis.analysis.density
+            except ImportError:
+                pytest.fail(msg='''MDAnalysis.analysis.density should not raise
+                             an ImportError if gridData is available.''')