Add more digits to the delta of openDX (#89)

- fix #88 
- write out OpeDX delta with 7 significant figures
- add test
- update CHANGES and AUTHORS

Author: xiki-tempula

AUTHORS

@@ -22,3 +22,4 @@ Contributors:
 * Lily Wang <lilyminium>
 * Josh Vermaas <jvermaas>
 * Irfan Alibay <IAlibay>
+* Zhiyi Wu <xiki-tempula>

CHANGELOG

@@ -21,6 +21,7 @@ The rules for this file:
 
   * Allow parsing/writing gzipped DX files
   * Update doc theme to use sphinx-rtd-theme (#80)
+  * Delta of OpenDX writes 7 significant figures (#89)
 
   Fixes
 

doc/source/conf.py

@@ -61,7 +61,8 @@
 # General information about the project.
 project = u'GridDataFormats'
 authors = (u'Oliver Beckstein, Jan Domanski, Jesse Johnson, Max Linke, Tyler Luchko, '
-           u'Dominik Mierzejewski, Giacomo Fiorin, Lily Wang, Josh Vermaas, Irfan Alibay')
+           u'Dominik Mierzejewski, Giacomo Fiorin, Lily Wang, Josh Vermaas, '
+           u'Irfan Alibay，Zhiyi Wu')
 copyright = u'2007-2021, ' + authors
 
 # The version info for the project you're documenting, acts as replacement for

gridData/OpenDX.py

@@ -55,6 +55,11 @@
 Known issues for writing OpenDX files
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 
+* APBS require the delta to be written to the seventh significant figure.
+  The delta is now written to reflect this increase in precision.
+
+  .. versionchanged:: 0.6.0
+
 * PyMOL_ requires OpenDX files with the type specification "double" in
   the `class array` section (see issue `#35`_). By default (since
   release 0.4.0), the type is set to the one that most closely
@@ -241,7 +246,9 @@ def write(self, stream):
         self._write_line(stream, 'origin %f %f %f\n' % tuple(self.origin))
         for delta in self.delta:
             self._write_line(
-                stream, ('delta '+self.ndformat(' %f')+'\n') % tuple(delta))
+                stream, ('delta ' +
+                         self.ndformat(' {:.7g}').format(*delta) +
+                         '\n'))
 
     def edges(self):
         """Edges of the grid cells, origin at centre of 0,0,..,0 grid cell.

gridData/tests/test_dx.py

@@ -80,3 +80,15 @@ def test_write_dx_ValueError(tmpdir, nptype, outfile, counts=100, ndim=3):
         with tmpdir.as_cwd():
             g.export(outfile)
 
+
+def test_delta_precision(tmpdir):
+    '''Test if the delta has been written to the 7th significant figure.'''
+    g = Grid(datafiles.DX)
+    g.delta = np.array([90, 90, 150]) / 257
+    with tmpdir.as_cwd():
+        g.export("grid.dx")
+        g2 = Grid("grid.dx")
+    assert_almost_equal(
+        g.delta, g2.delta,
+        decimal=7,
+        err_msg="deltas of written grid do not match original")