deprecate CCP4 module (remove in 0.8.0)

- deprecation warning raised
- test for warning
- add deprecation to docs

CHANGELOG

@@ -24,8 +24,7 @@ The rules for this file:
 
   Deprecations
 
-  * The CCP4 module will be removed in 0.8.0 and files will only be
-    read with mrc.
+  * The CCP4 module (replaced by mrc) will be removed in 0.8.0.
 
 
 10/10/2021 eloyfelix, renehamburger1993, lilyminium, jvermaas, xiki-tempula,

gridData/CCP4.py

@@ -6,11 +6,14 @@
 # Copyright Science and Technologies Facilities Council, 2015.
 
 """
-:mod:`CCP4` --- the CCP4 volumetric data format
-===============================================
+:mod:`CCP4` --- the CCP4 volumetric data format (DEPRECATED)
+============================================================
 
 .. versionadded:: 0.3.0
 
+.. deprecated:: 0.7.0 The CCP4 module is replaced by :mod:`gridData.mrc` and
+   will be removed in 0.8.0.
+
 .. _CCP4: http://www.ccp4.ac.uk/html/maplib.html#description
 
 The module provides a simple implementation of a reader for CCP4_
@@ -160,6 +163,9 @@ class CCP4(object):
        * symmetry records
        * index ordering besides standard column-major and row-major
        * non-standard fields, such any in filed in future use block
+
+    .. deprecated:: 0.7.0
+       Use :class:`gridData.mrc.MRC` instead. This class will be removed in 0.8.0.
     """
 
     _axis_map = {1: 'x', 2: 'y', 3: 'z'}
@@ -196,6 +202,10 @@ def __init__(self, filename=None):
         if filename is not None:
             self.read(filename)
 
+        warnings.warn("CCP4.CCP4 is being replaced by mrc.MRC and will be removed "
+                      "in release 0.8.0",
+                      category=DeprecationWarning)
+
     def read(self, filename):
         """Populate the instance from the ccp4 file *filename*."""
         if filename is not None:

gridData/__init__.py

@@ -93,16 +93,8 @@
 Formats
 -------
 
-The following formats are available (:ref:`supported-file-formats`):
-
-   :mod:`~gridData.OpenDX`
-        IBM's Data Explorer, http://www.opendx.org/
-   :mod:`~gridData.gOpenMol`
-        http://www.csc.fi/gopenmol/
-   :mod:`~gridData.CCP4`
-        CCP4 format http://www.ccp4.ac.uk/html/maplib.html#description
-   pickle
-        python pickle file (:mod:`pickle`)
+For the available file formats see :ref:`supported-file-formats`.
+
 
 
 """

gridData/mrc.py

@@ -22,10 +22,11 @@
 
 .. [Burnley2017] Burnley T, Palmer C and Winn M (2017) Recent
                  developments in the CCP-EM software suite. *Acta
-                 Cryst.* D73:469–477. doi: `10.1107/S2059798317007859`_
+                 Cryst.* D73:469-477. doi: `10.1107/S2059798317007859`_
 
 
 .. _`10.1107/S2059798317007859`: https://doi.org/10.1107/S2059798317007859
+
 Classes
 -------
 

gridData/tests/test_ccp4.py

@@ -12,7 +12,9 @@
 
 @pytest.fixture(scope="module")
 def g():
-    ccp4 = CCP4.CCP4()
+    with pytest.warns(DeprecationWarning,
+                      match="CCP4.CCP4 is being replaced by mrc.MRC and will be removed"):
+        ccp4 = CCP4.CCP4()
     ccp4.read(datafiles.CCP4)
     grid, edges = ccp4.histogramdd()
     return Grid(grid=grid, edges=edges)
@@ -27,7 +29,10 @@ def test_ccp4(g):
 
 @pytest.fixture(scope="module")
 def ccp4data():
-    return CCP4.CCP4(datafiles.CCP4_1JZV)
+    with pytest.warns(DeprecationWarning,
+                      match="CCP4.CCP4 is being replaced by mrc.MRC and will be removed"):
+        ccp4 = CCP4.CCP4(datafiles.CCP4_1JZV)
+    return ccp4
 
 @pytest.mark.parametrize('name,value', [
     ('nc', 96),