Deprecate helanal

package/CHANGELOG

@@ -53,6 +53,8 @@ Deprecations
   * core.universe.as_Universe() will be removed in 2.0.0
   * analysis.leaflets.LeafletFinder() will not accept a filename any more,
     only a Universe, in 2.0.0 
+  * analysis.helanal will be removed in 2.0.0 and replaced by
+    analysis.helix_analysis (PR #2622)
 
 
 06/09/20 richardjgowers, kain88-de, lilyminium, p-j-smith, bdice, joaomcteixeira,

package/MDAnalysis/analysis/helanal.py

@@ -30,13 +30,20 @@
 
 
 """
-HELANAL --- analysis of protein helices
-=======================================
+HELANAL (Deprecated) --- analysis of protein helices
+====================================================
 
 :Author:  Benjamin Hall <benjamin.a.hall@ucl.ac.uk>, Oliver Beckstein, Xavier Deupi
 :Year:    2009, 2011, 2013
 :License: GNU General Public License v2 (or higher)
 
+.. note::
+
+    This module was deprecated in 1.0 and will be removed in 2.0.
+    Please use MDAnalysis.analysis.helix_analysis instead
+    (available in 2.0.0).
+
+
 The :mod:`MDAnalysis.analysis.helanal` module is a Python implementation of the
 HELANAL_ algorithm [Bansal2000]_ in `helanal.f`_, which is also available
 through the `HELANAL webserver`_.
@@ -117,20 +124,24 @@
 
 """
 from __future__ import print_function, division, absolute_import
-from six.moves import range, zip
-
 import os
 
 import numpy as np
 
 import MDAnalysis
-from MDAnalysis.lib.log import ProgressBar
-from MDAnalysis.lib import mdamath
+from ..lib.log import ProgressBar
+from ..lib import mdamath, util
 
 import warnings
 import logging
 logger = logging.getLogger("MDAnalysis.analysis.helanal")
 
+warnings.warn("This module is deprecated as of MDAnalysis version 1.0. "
+              "It will be removed in MDAnalysis version 2.0."
+              "Please use (available in 2.0.0) "
+              "MDAnalysis.analysis.helix_analysis instead.",
+              category=DeprecationWarning)
+
 def center(coordinates):
     """Return the geometric center (centroid) of the coordinates.
 
@@ -158,6 +169,9 @@ def mean_abs_dev(a, mean_a=None):
         mean_a = np.mean(a)
     return np.mean(np.fabs(a - mean_a))
 
+
+@util.deprecate(release="1.0.1", remove="2.0",
+                message="In 2.0 use the upcoming helix_analysis module")
 def helanal_trajectory(universe, select="name CA",
                        begin=None, finish=None,
                        matrix_filename="bending_matrix.dat",
@@ -243,7 +257,12 @@ def helanal_trajectory(universe, select="name CA",
 
     .. versionchanged:: 1.0.0
        Changed `selection` keyword to `select`
+
+    .. deprecated:: 1.0.1
+       helanal_trajectory is deprecated and will be removed in 2.0.0.
+       Please use helix_analysis.HELANAL instead (available in 2.0.0).
     """
+
     if ref_axis is None:
         ref_axis = np.array([0., 0., 1.])
     else:
@@ -525,6 +544,8 @@ def stats(some_list):
     return [list_mean, list_sd, list_abdev]
 
 
+@util.deprecate(release="1.0.1", remove="2.0",
+                message="In 2.0 use the upcoming helix_analysis module")
 def helanal_main(pdbfile, select="name CA", ref_axis=None):
     """Simple HELANAL_ run on a single frame PDB/GRO.
 
@@ -581,6 +602,10 @@ def helanal_main(pdbfile, select="name CA", ref_axis=None):
     .. versionchanged:: 1.0.0
        Changed `selection` keyword to `select`
 
+    .. deprecated:: 1.0.1
+       helanal_trajectory is deprecated and will be removed in 2.0.0.
+       Please use helix_analysis.HELANAL instead (available in 2.0.0).
+
     """
 
     universe = MDAnalysis.Universe(pdbfile)

testsuite/MDAnalysisTests/analysis/test_helanal.py

@@ -198,14 +198,13 @@ def test_warnings(tmpdir):
                 u, select="name CA", begin=-1, finish=99999
             )
 
-            assert len(record) == 2
+            assert len(record) == 3
             wmsg1 = ("The input begin time (-1 ps) precedes the starting "
                    "trajectory time --- Setting starting frame to 0".format(
                     -1,0))
-            assert str(record[0].message.args[0]) == wmsg1
+            assert str(record[1].message.args[0]) == wmsg1
             wmsg2 = ("The input finish time ({0} ps) occurs after the end of "
                      "the trajectory ({1} ps). Finish time will be set to "
                      "the end of the trajectory".format(
                       99999,1000.0000762939453))
-            assert str(record[1].message.args[0]) == wmsg2
-
+            assert str(record[2].message.args[0]) == wmsg2