🧬 helanal refactor 🧬

package/CHANGELOG

@@ -39,6 +39,8 @@ Fixes
     empty AtomGroup (Issue #2848)
 
 Enhancements
+  * Refactored analysis.helanal into analysis.helix_analysis
+    (Issue #2452, PR #2622)
   * Improved MSD code to accept `AtomGroup` and reject `UpdatingAtomGroup`
     and improved docs (Issue #2784)
   * Added the RDKitParser which creates a `core.topology.Topology` object from
@@ -276,6 +278,7 @@ Changes
     function calls. (Issue #782)
 
 Deprecations
+  * analysis.helanal is deprecated in 1.0 (remove in 2.0)
   * analysis.hole is deprecated in 1.0 (remove in 2.0)
   * analysis.hbonds.HydrogenBondAnalysis is deprecated in 1.0 (remove in 2.0)
   * analysis.density.density_from_Universe() (remove in 2.0)

package/MDAnalysis/analysis/helanal.py

@@ -30,13 +30,19 @@
 
 
 """
-HELANAL --- analysis of protein helices
-=======================================
+HELANAL (Deprecated) --- analysis of protein helices
+====================================================
 
 :Author:  Benjamin Hall <[email protected]>, 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.
+
+
 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`_.
@@ -128,6 +134,11 @@
 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 MDAnalysis.analysis.helix_analysis instead.",
+              category=DeprecationWarning)
+
 def center(coordinates):
     """Return the geometric center (centroid) of the coordinates.
 
@@ -241,6 +252,12 @@ def helanal_trajectory(universe, select="name CA",
     .. versionchanged:: 1.0.0
        Changed `selection` keyword to `select`
     """
+
+    warnings.warn("This function is deprecated as of MDAnalysis version 1.0. "
+                  "It will be removed in MDAnalysis version 2.0. Please use "
+                  "MDAnalysis.analysis.helix_analysis.HELANAL instead.",
+                  category=DeprecationWarning)
+
     if ref_axis is None:
         ref_axis = np.array([0., 0., 1.])
     else:
@@ -580,6 +597,12 @@ def helanal_main(pdbfile, select="name CA", ref_axis=None):
 
     """
 
+    warnings.warn("This function is deprecated as of MDAnalysis version 1.0. "
+                  "It will be removed in MDAnalysis version 2.0. Please use "
+                  "MDAnalysis.analysis.helix_analysis.helix_analysis on "
+                  "a Universe instead.",
+                  category=DeprecationWarning)
+
     universe = MDAnalysis.Universe(pdbfile)
     ca = universe.select_atoms(select)