fix doctests

docs/conf.py

@@ -51,34 +51,38 @@
 ]
 
 doctest_global_setup = '''
+import os
 import sys
 assert sys.version_info[0] > 2, "Tests in docs are for Python 3 only"
+disabled_features = []
 try:
     import numpy
 except ImportError:
-    print('Tests that use NumPy are disabled.', file=sys.stderr)
+    disabled_features.append('NumPy')
     numpy = None
 try:
     import pandas
 except ImportError:
-    print('Tests that use pandas are disabled.', file=sys.stderr)
+    disabled_features.append('pandas')
     pandas = None
 try:
     import networkx
 except ImportError:
-    print('Tests that use networkx are disabled.', file=sys.stderr)
+    disabled_features.append('networkx')
     networkx = None
 try:
     import pynauty
 except ImportError:
-    print('Tests that use pynauty are disabled.', file=sys.stderr)
+    disabled_features.append('pynauty')
     pynauty = None
-import os
 mdm2_unmerged_mtz_path = os.getenv('CCP4')
 if mdm2_unmerged_mtz_path:
-    mdm2_unmerged_mtz_path += '/share/ccp4i2/demo_data/mdm2/mdm2_unmerged.mtz'
+    mdm2_unmerged_mtz_path += ('/lib/python3.7/site-packages/' +
+                               'ccp4i2/demo_data/mdm2/mdm2_unmerged.mtz')
     if not os.path.isfile(mdm2_unmerged_mtz_path):
         mdm2_unmerged_mtz_path = None
+if mdm2_unmerged_mtz_path is None:
+    disabled_features.append('$CCP4')
 '''
 
 def setup(app):

docs/grid.rst

@@ -302,6 +302,7 @@ Unlike array slicing, these functions are aware of the cell repeat
 (PBC) -- the block area is not limited by the unit cell boundaries.
 
 .. doctest::
+  :skipif: numpy is None
 
   >>> sub = gr.get_subarray(start=[3,3,3], shape=[2,3,4])
   >>> sub.shape
@@ -443,6 +444,7 @@ as in NumPy MaskedArray.
 The primary use for MaskedGrid is working with asymmetric unit (asu) only:
 
 .. doctest::
+  :skipif: numpy is None
 
   >>> asu = grid.masked_asu()
   >>> asu  # doctest: +ELLIPSIS

docs/hkl.rst

@@ -321,10 +321,10 @@ but they can be accessed directly if needed:
 .. doctest::
   :skipif: mdm2_unmerged_mtz_path is None
 
-  >>> batch.ints
+  >>> list(batch.ints)
   [185, 29, 156, 0, -1, 1, -1, 0, 0, 0, 0, 0, 1, 0, 2, 1, 0, 1, 0, 1, 2, 0, 0, 0, 0, 0, 0, 0, 0]
-  >>> batch.floats[36:38]  # start and end of phi
-  [80.0, 80.5]
+  >>> batch.floats[36], batch.floats[37]  # start and end of phi
+  (80.0, 80.5)
 
 One peculiarity of the MTZ format is that instead of the original Miller
 indices it stores indices of the equivalent reflection in the ASU
@@ -1797,6 +1797,7 @@ The coefficients can be used to directly calculate the sum of Gaussians --
 the structure factor contribution:
 
 .. doctest::
+  :skipif: numpy is None
 
   >>> fe_coef.calculate_sf(stol2=0.4)  # argument: (sin(theta)/lambda)^2
   9.303602485040315
@@ -1808,6 +1809,7 @@ In the simplest case, the atom's contribution to the electron density at a grid
 point can be calculated as:
 
 .. doctest::
+  :skipif: numpy is None
 
   >>> # arguments are distance^2 and isotropic ADP
   >>> fe_coef.calculate_density_iso(r2=2.3, B=50)
@@ -1973,7 +1975,7 @@ SpaceGroup because UnitCell already contains a list of symmetry operations).
 Now we can compute structure factors from Model for any (hkl):
 
 .. doctest::
-  :skipif: sys.platform == 'win32'
+  :skipif: sys.platform == 'win32' or numpy is None
 
   >>> calc_e.calculate_sf_from_model(st[0], (3,4,5))
   (54.50873699946033+53.39498671218277j)

docs/mol.rst

@@ -805,6 +805,8 @@ that has properties listed in the C++ section above. Examples:
   import gemmi
   output_path = 'out.pdb'
   structure = gemmi.read_pdb('../tests/1orc.pdb')
+  print('Running doctest. Disabled features:',
+        ', '.join(disabled_features) or 'none', file=sys.stderr)
 
 .. testcode::