Remove save part2 (#2494)

* Partly addresses #1745 (completes save() removal with PR #2487 and PR #2486 )
* removes save methods
  - removes save method from psa.py
  - also minor change to test_hbonds.py
* deprecates hbond_analysis
  - close #2492
* updates changelog

package/CHANGELOG

@@ -79,6 +79,11 @@ Enhancements
     convert between a parmed.Structure and MDAnalysis Universe (PR #2404)
 
 Changes
+  * Removes; `save_table()` from :class:`HydrogenBondAnalysis`,
+    `save_results()` from :class:`HydrogenBondAutoCorrel`, and
+    `save_results()`/`filename`/`store` from :class:`PSAnalysis`. Also sets
+    the deprecation of `hbonds/hbond_analysis.py` to v1.0 (Issues #1745,
+    #2486, #2487, #2491, #2492).
   * Removes the `format` and `skip` keywords from :meth:`DCDReader.timeseries`
     (Issue #2443)
   * `fullgroup` selection has now been removed (#268)
@@ -89,7 +94,7 @@ Changes
     is "-" (Issue #2448, PR #2457)
 
 Deprecations
-  * analysis.hbonds.HydrogenBondAnalysis will be deprecated in 1.0
+  * analysis.hbonds.HydrogenBondAnalysis is deprecated in 1.0 (remove in 2.0)
 
 09/05/19 IAlibay, richardjgowers
 

package/MDAnalysis/analysis/hbonds/hbond_analysis.py

@@ -30,7 +30,7 @@
 :Copyright: GNU Public License v3
 
 ..Warning:
-    This module will be deprecated in version 1.0.
+    This module is deprecated and will be removed in version 2.0.
     Please use :mod:`MDAnalysis.analysis.hydrogenbonds.hbond_analysis` instead.
 
 Given a :class:`~MDAnalysis.core.universe.Universe` (simulation
@@ -321,7 +321,7 @@ class HydrogenBondAnalysis_OtherFF(HydrogenBondAnalysis):
 """
 from __future__ import division, absolute_import
 import six
-from six.moves import range, zip, map, cPickle
+from six.moves import range, zip
 
 import warnings
 import logging
@@ -334,17 +334,18 @@ class HydrogenBondAnalysis_OtherFF(HydrogenBondAnalysis):
 from MDAnalysis.lib.log import ProgressMeter
 from MDAnalysis.lib.NeighborSearch import AtomNeighborSearch
 from MDAnalysis.lib import distances
-from MDAnalysis.lib.util import deprecate
 
 
 logger = logging.getLogger('MDAnalysis.analysis.hbonds')
 
 warnings.warn(
-            "This module will be deprecated in version 1.0."
+            "This module is deprecated as of MDAnalysis version 1.0."
+            "It will be removed in MDAnalysis version 2.0"
             "Please use MDAnalysis.analysis.hydrogenbonds.hbond_analysis instead.",
             category=DeprecationWarning
         )
 
+
 class HydrogenBondAnalysis(base.AnalysisBase):
     """Perform a hydrogen bond analysis
 
@@ -380,6 +381,10 @@ class HydrogenBondAnalysis(base.AnalysisBase):
     .. versionchanged:: 0.7.6
        DEFAULT_DONORS/ACCEPTORS is now embedded in a dict to switch between
        default values for different force fields.
+
+    .. versionchanged:: 1.0.0
+       ``save_table()`` method has been removed. You can use ``np.save()`` or
+       ``cPickle.dump()`` on :attr:`HydrogenBondAnalysis.table` instead.
     """
 
     # use tuple(set()) here so that one can just copy&paste names from the
@@ -567,7 +572,8 @@ def __init__(self, universe, selection1='protein', selection2='all', selection1_
         super(HydrogenBondAnalysis, self).__init__(universe.trajectory, **kwargs)
 
         warnings.warn(
-            "This class will be deprecated in version 1.0."
+            "This class is deprecated as of MDAnalysis version 1.0 and will "
+            "be removed in version 2.0."
             "Please use MDAnalysis.analysis.hydrogenbonds.hbond_analysis.HydrogenBondAnalysis instead.",
             category=DeprecationWarning
         )
@@ -1120,12 +1126,6 @@ def _reformat_hb(hb, atomformat="{0[0]!s}{0[1]!s}:{0[2]!s}"):
         In 0.16.1, donor and acceptor are stored as a tuple(resname,
         resid, atomid). In 0.16.0 and earlier they were stored as a string.
 
-        .. deprecated:: 1.0
-           This is a compatibility layer so that we can provide the same output
-           in timeseries as before. However, for 1.0 we should make timeseries
-           just return _timeseries, i.e., change the format of timeseries to
-           the un-ambiguous representation provided in _timeseries.
-
         """
         return (hb[:2]
                 + [atomformat.format(hb[2]), atomformat.format(hb[3])]
@@ -1171,33 +1171,6 @@ def generate_table(self):
         self.table = out.view(np.recarray)
         logger.debug("HBond: Stored results as table with %(num_records)d entries.", vars())
 
-    @deprecate(release="0.19.0", remove="1.0.0",
-               message="You can instead use ``np.save(filename, "
-               "HydrogendBondAnalysis.table)``.")
-    def save_table(self, filename="hbond_table.pickle"):
-        """Saves :attr:`~HydrogenBondAnalysis.table` to a pickled file.
-
-        If :attr:`~HydrogenBondAnalysis.table` does not exist yet,
-        :meth:`generate_table` is called first.
-
-        Parameters
-        ----------
-        filename : str (optional)
-             path to the filename
-
-        Example
-        -------
-        Load with ::
-
-           import cPickle
-           table = cPickle.load(open(filename))
-
-        """
-        if self.table is None:
-            self.generate_table()
-        with open(filename, 'w') as f:
-            cPickle.dump(self.table, f, protocol=cPickle.HIGHEST_PROTOCOL)
-
     def _has_timeseries(self):
         has_timeseries = self._timeseries is not None
         if not has_timeseries:

package/MDAnalysis/analysis/hbonds/hbond_autocorrel.py

@@ -215,7 +215,6 @@
 
 from MDAnalysis.lib.log import ProgressMeter
 from MDAnalysis.lib.distances import capped_distance, calc_angles, calc_bonds
-from MDAnalysis.lib.util import deprecate
 from MDAnalysis.core.groups import requires
 
 from MDAnalysis.due import due, Doi
@@ -285,6 +284,11 @@ class HydrogenBondAutoCorrel(object):
         Within each run, the number of frames to analyse [50]
     pbc : bool, optional
         Whether to consider periodic boundaries in calculations [``True``]
+
+    ..versionchanged: 1.0.0
+      ``save_results()`` method was removed. You can instead use ``np.savez()``
+      on :attr:`HydrogenBondAutoCorrel.solution['time']` and
+      :attr:`HydrogenBondAutoCorrel.solution['results']` instead.
     """
 
     def __init__(self, universe,
@@ -426,7 +430,7 @@ def _single_run(self, start, stop):
             # set to above dist crit to exclude
             exclude = np.column_stack((self.exclusions[0], self.exclusions[1]))
             pair = np.delete(pair, np.where(pair==exclude), 0)
-        
+
         hidx, aidx = np.transpose(pair)
 
 
@@ -481,28 +485,6 @@ def _single_run(self, start, stop):
 
         return results
 
-    @deprecate(release="0.19.0", remove="1.0.0",
-               message="You can instead use "
-               "``np.savez(filename, time=HydrogenBondAutoCorrel.solution['time'], "
-               "results=HydrogenBondAutoCorrel.solution['results'])``.")
-    def save_results(self, filename='hbond_autocorrel'):
-        """Saves the results to a numpy zipped array (.npz, see np.savez)
-
-        This can be loaded using np.load(filename)
-
-        Parameters
-        ----------
-        filename : str, optional
-            The desired filename [hbond_autocorrel]
-
-        """
-        if self.solution['results'] is not None:
-            np.savez(filename, time=self.solution['time'],
-                        results=self.solution['results'])
-        else:
-            raise ValueError(
-                "Results have not been generated, use the run method first")
-
     def solve(self, p_guess=None):
         """Fit results to an multi exponential decay and integrate to find
         characteristic time

package/MDAnalysis/analysis/psa.py

@@ -183,20 +183,14 @@
 
       int, frame index to select frame from :attr:`Path.u_reference`
 
-   .. attribute:: filename
-
-      string, name of file to store calculated distance matrix
-      (:attr:`PSAnalysis.D`)
-
    .. attribute:: paths
 
       list of :class:`numpy.ndarray` objects representing the set/ensemble of
       fitted trajectories
 
    .. attribute:: D
 
-      string, name of file to store calculated distance matrix
-      (:attr:`PSAnalysis.D`)
+      :class:`numpy.ndarray` whichs store calculated distance matrix
 
 
 .. Markup definitions
@@ -1287,6 +1281,10 @@ class PSAnalysis(object):
     alignment of the original trajectories to a reference structure.
 
     .. versionadded:: 0.8
+
+    .. versionchanged:: 1.0.0
+       ``save_result()`` method has been removed. You can use ``np.save()`` on
+       :attr:`PSAnalysis.D` instead.
     """
     def __init__(self, universes, reference=None, ref_select='name CA',
                  ref_frame=0, path_select=None, labels=None,
@@ -1509,31 +1507,15 @@ def run(self, **kwargs):
              ``trajectory[start:stop:step]`` [``None``]
         stop : int
         step : int
-        store : bool
-             if ``True`` then writes :attr:`PSAnalysis.D` to text and
-             compressed npz (numpy) files [``True``]
-
-             .. deprecated:: 0.19.0
-                `store` will be removed together with :meth:`save_results` in 1.0.0.
-
-        filename : str
-             string, filename to save :attr:`PSAnalysis.D`
-
-             .. deprecated:: 0.19.0
-                `filename` will be removed together with :meth:`save_results` in 1.0.0.
 
+        .. versionchanged:: 1.0.0
+           `store` and `filename` have been removed.
 
         """
         metric = kwargs.pop('metric', 'hausdorff')
         start = kwargs.pop('start', None)
         stop = kwargs.pop('stop', None)
         step = kwargs.pop('step', None)
-        # DEPRECATED 0.19.0: remove in 1.0
-        if 'store' in kwargs:
-            warnings.warn("PSAnalysis.run(): 'store' was deprecated in 0.19.0 "
-                          "and will be removed in 1.0",
-                          category=DeprecationWarning)
-        store = kwargs.pop('store', True)
 
         if isinstance(metric, string_types):
             metric_func = get_path_metric_func(str(metric))
@@ -1549,16 +1531,6 @@ def run(self, **kwargs):
                 D[i,j] = metric_func(P, Q)
                 D[j,i] = D[i,j]
         self.D = D
-        if store:
-            # DEPRECATED 0.19.0: remove in 1.0
-            if 'filename' in kwargs:
-                warnings.warn("PSAnalysis.run(): 'filename' was deprecated in "
-                              "0.19.0 and will be removed in 1.0",
-                              category=DeprecationWarning)
-            filename = kwargs.pop('filename', metric)
-            if not isinstance(metric, string_types):
-                filename = 'custom_metric'
-            self.save_result(filename=filename)
 
     def run_pairs_analysis(self, **kwargs):
         """Perform PSA Hausdorff (nearest neighbor) pairs analysis on all unique
@@ -1618,38 +1590,6 @@ def run_pairs_analysis(self, **kwargs):
                     self._HP.append(pp.get_hausdorff_pair())
         self.D = D
 
-    @deprecate(release="0.19.0", remove="1.0.0",
-               message="You can save the distance matrix :attr:`D` to a numpy "
-               "file with ``np.save(filename, PSAnalysis.D)``.")
-    def save_result(self, filename=None):
-        """Save distance matrix :attr:`PSAnalysis.D` to a numpy compressed npz
-        file and text file.
-
-        The data are saved with :func:`numpy.savez_compressed` and
-        :func:`numpy.savetxt` in the directory specified by
-        :attr:`PSAnalysis.targetdir`.
-
-        Parameters
-        ----------
-        filename : str
-             specifies filename [``None``]
-
-        Returns
-        -------
-        filename : str
-
-        """
-        filename = filename or 'psa_distances'
-        head = os.path.join(self.targetdir, self.datadirs['distance_matrices'])
-        outfile = os.path.join(head, filename)
-        if self.D is None:
-            raise NoDataError("Distance matrix has not been calculated yet")
-        np.save(outfile + '.npy', self.D)
-        np.savetxt(outfile + '.dat', self.D)
-        logger.info("Wrote distance matrix to file %r.npz", outfile)
-        logger.info("Wrote distance matrix to file %r.dat", outfile)
-        return filename
-
 
     def save_paths(self, filename=None):
         """Save fitted :attr:`PSAnalysis.paths` to numpy compressed npz files.
@@ -1756,7 +1696,7 @@ def plot(self, filename=None, linkage='ward', count_sort=False,
 
         if self.D is None:
             raise ValueError(
-                "No distance data; do 'PSAnalysis.run(store=True)' first.")
+                "No distance data; do 'PSAnalysis.run()' first.")
         npaths = len(self.D)
         dist_matrix = self.D
 
@@ -1907,7 +1847,7 @@ def plot_annotated_heatmap(self, filename=None, linkage='ward',             \
 
         if self.D is None:
             raise ValueError(
-                "No distance data; do 'PSAnalysis.run(store=True)' first.")
+                "No distance data; do 'PSAnalysis.run()' first.")
         dist_matrix = self.D
 
         Z, dgram = self.cluster(method=linkage,                                 \
@@ -2215,8 +2155,7 @@ def get_pairwise_distances(self, vectorform=False, checks=False):
 
         Note
         ----
-        Must run :meth:`PSAnalysis.run` with ``store=True`` prior to
-        calling this method.
+        Must run :meth:`PSAnalysis.run` prior to calling this method.
 
         Parameters
         ----------
@@ -2234,7 +2173,7 @@ def get_pairwise_distances(self, vectorform=False, checks=False):
         """
         if self.D is None:
             raise ValueError(
-                "No distance data; do 'PSAnalysis.run(store=True)' first.")
+                "No distance data; do 'PSAnalysis.run()' first.")
         if vectorform:
             return spatial.distance.squareform(self.D, force='tovector',
                                                checks=checks)

testsuite/MDAnalysisTests/analysis/test_hbonds.py

@@ -20,6 +20,8 @@
 # MDAnalysis: A Toolkit for the Analysis of Molecular Dynamics Simulations.
 # J. Comput. Chem. 32 (2011), 2319--2327, doi:10.1002/jcc.21787
 #
+# Note: to be removed with MDAnalysis.analysis.hbonds.hbond_analysis in 2.0
+
 from __future__ import print_function, absolute_import
 
 
@@ -78,7 +80,6 @@ def h(self, universe):
         kw = self.kwargs.copy()
         # kw.update(kwargs)
         h = MDAnalysis.analysis.hbonds.HydrogenBondAnalysis(universe, **kw)
-        # remove in 1.0
         if kw['detect_hydrogens'] == 'heuristic':
             with pytest.warns(DeprecationWarning):
                 h.run(verbose=False)