Remove save() methods for v1.0 - Part 1

package/CHANGELOG

@@ -79,6 +79,8 @@ Enhancements
     convert between a parmed.Structure and MDAnalysis Universe (PR #2404)
 
 Changes
+  * Removes `save()` function from contacts, diffusionmap, hole, LinearDensity,
+    and rms (Issue #1745).
   * Removes; `save_table()` from :class:`HydrogenBondAnalysis`,
     `save_results()` from :class:`HydrogenBondAutoCorrel`, and
     `save_results()`/`filename`/`store` from :class:`PSAnalysis`. Also sets

package/MDAnalysis/analysis/contacts.py

@@ -216,7 +216,7 @@ def is_any_closer(r, r0, dist=2.5):
 
 import MDAnalysis
 import MDAnalysis.lib.distances
-from MDAnalysis.lib.util import openany, deprecate
+from MDAnalysis.lib.util import openany
 from MDAnalysis.analysis.distances import distance_array
 from MDAnalysis.core.groups import AtomGroup
 from .base import AnalysisBase
@@ -370,6 +370,10 @@ class Contacts(AnalysisBase):
     timeseries : list
         list containing *Q* for all refgroup pairs and analyzed frames
 
+    .. versionchanged:: 1.0.0
+       ``save()`` method has been removed. Use ``np.savetxt()`` on
+       :attr:`Contacts.timeseries` instead.
+
     """
     def __init__(self, u, selection, refgroup, method="hard_cut", radius=4.5,
                  kwargs=None, **basekwargs):
@@ -447,20 +451,6 @@ def _single_frame(self):
             self.timeseries[self._frame_index][i] = q
 
 
-    @deprecate(release="0.19.0", remove="1.0.0")
-    def save(self, outfile):
-        """save contacts timeseries
-
-        Parameters
-        ----------
-        outfile : str
-            file to save contacts
-
-        """
-        np.savetxt(outfile, self.timeseries,
-                   header="# q1 analysis\n", comments='')
-
-
 def _new_selections(u_orig, selections, frame):
     """create stand alone AGs from selections at frame"""
     u = MDAnalysis.Universe(u_orig.filename, u_orig.trajectory.filename)

package/MDAnalysis/analysis/diffusionmap.py

@@ -176,7 +176,6 @@
 from MDAnalysis.core.universe import Universe
 from .rms import rmsd
 from .base import AnalysisBase
-from MDAnalysis.lib.util import deprecate
 
 logger = logging.getLogger("MDAnalysis.analysis.diffusionmap")
 
@@ -197,6 +196,10 @@ class DistanceMatrix(AnalysisBase):
         Array of all possible ij metric distances between frames in trajectory.
         This matrix is symmetric with zeros on the diagonal.
 
+    .. versionchanged:: 1.0.0
+       ``save()`` method has been removed. You can use ``np.save()`` on
+       :attr:`DistanceMatrix.dist_matrix` instead.
+
     """
     def __init__(self, u, select='all', metric=rmsd, cutoff=1E0-5,
                  weights=None, **kwargs):
@@ -264,20 +267,6 @@ def _single_frame(self):
     def _conclude(self):
         self._calculated = True
 
-    @deprecate(release="0.19.0", remove="1.0.0",
-               message="Use ``np.save(filename, DistanceMatrix.dist_matrix)`` instead.")
-    def save(self, filename):
-        """save squared distance matrix
-
-        Parameters
-        ----------
-        outfile : str
-            file to save distance matrix
-
-        """
-        np.save(filename, self.dist_matrix)
-        logger.info("Wrote the distance-squared matrix to file %r", filename)
-
 
 class DiffusionMap(object):
     """Non-linear dimension reduction method

package/MDAnalysis/analysis/hole.py

@@ -277,7 +277,7 @@
 from MDAnalysis import Universe
 from MDAnalysis.exceptions import ApplicationError
 from MDAnalysis.lib.util import (which, realpath, asiterable,
-                                 FORTRANReader, deprecate)
+                                 FORTRANReader)
 
 from ..due import due, Doi
 
@@ -387,23 +387,13 @@ def seq2str(v):
 
 
 class BaseHOLE(object):
-    """Baseclass for HOLE analysis, providing plotting and utility functions"""
+    """Baseclass for HOLE analysis, providing plotting and utility functions
 
-    @deprecate(release="0.19.0", remove="1.0.0",
-               message="You can instead use "
-               "``cPickle.dump(HOLE.profiles, open(filename, 'wb'))``.")
-    def save(self, filename="hole.pickle"):
-        """Save :attr:`profiles` as a Python pickle file *filename*.
+    .. versionchanged:: 1.0.0
+       ``save()`` method was removed. You can use ``cPickle.dump()`` on
+       :attr:`BaseHOLE.profiles` instead.
 
-        Load profiles dictionary with ::
-
-           import cPickle
-           profiles = cPickle.load(open(filename))
-
-
-        """
-
-        cPickle.dump(self.profiles, open(filename, "wb"), cPickle.HIGHEST_PROTOCOL)
+    """
 
     def _process_plot_kwargs(self, kwargs):
         kw = {}

package/MDAnalysis/analysis/lineardensity.py

@@ -35,7 +35,6 @@
 import numpy as np
 
 from MDAnalysis.analysis.base import AnalysisBase
-from MDAnalysis.lib.util import deprecate
 
 class LinearDensity(AnalysisBase):
     """Linear density profile
@@ -80,6 +79,11 @@ class LinearDensity(AnalysisBase):
 
     .. versionadded:: 0.14.0
 
+    .. versionchanged:: 1.0.0
+       ``save()`` method was removed, you can use ``np.savetxt()`` or
+       ``np.save()`` on the :attr:`LinearDensity.results` dictionary contents
+       instead.
+
     """
 
     def __init__(self, selection, grouping='atoms', binsize=0.25, **kwargs):
@@ -192,87 +196,6 @@ def _conclude(self):
             self.results[dim]['pos_std'] /= self.results[dim]['slice volume'] * k
             self.results[dim]['char_std'] /= self.results[dim]['slice volume'] * k
 
-    @deprecate(release="0.19.0", remove="1.0.0",
-               message="Instead save the :attr:`results` dictionary directly in "
-               "your favorite format (pickle, json, hdf5, ...).")
-    def save(self, description='', form='txt'):
-        """Save density profile to file
-
-        Allows to save the density profile to either a ASCII txt file or a
-        binary numpy npz file. Output file has extension 'ldens' and begins
-        with the name of the trajectory file.
-
-        Parameters
-        ----------
-        description : str
-          An arbitrary description added to the output filename. Can be useful
-        form : str {'txt', 'npz'}
-          Format of the output. 'txt' will generate an ASCII text file while
-          'npz' will produce a numpy binary file.
-
-        Example
-        -------
-        After initializing and running a `LinearDensity` object, results can be
-        written to file as follows::
-
-          ldens.save(description='mydensprof', form='txt')
-
-        which will output the linear density profiles in a file named
-        `<trajectory_filename>.mydensprof_<grouping>.ldens`.
-
-
-        """
-        # Take root of trajectory filename for output file naming
-        trajname = path.splitext(path.basename(
-            self._universe.trajectory.filename))[0]
-        # additional string for naming the output file
-        description = description + "_" + str(self.grouping)
-        filename = trajname + "." + description + ".ldens"
-
-        if form == 'txt':
-            self._savetxt(filename)
-        elif form == 'npz':
-            self._savez(filename)
-        else:
-            raise ValueError('form argument must be either txt or npz')
-
-    def _savetxt(self, filename):
-        # DEPRECATED: remove in 1.0.0
-        bins = np.linspace(0.0, max(self.dimensions), num=self.nbins)
-
-        # Create list of results which will be output
-        output = [bins]
-
-        for dim in ['x', 'y', 'z']:
-            output.append(self.results[dim]['pos'])
-            output.append(self.results[dim]['pos_std'])
-
-        for dim in ['x', 'y', 'z']:
-            output.append(self.results[dim]['char'])
-            output.append(self.results[dim]['char_std'])
-
-        density = self.totalmass / self.volume
-        header = ("1 coord [Ang] 2-7 mass density (x,sx,y,sz,z,sz) [g/cm^3]"
-                  "8-13 charge density (x,sx,y,sz,z,sz) [e/A^3]\n Average "
-                  "density: {} g/cm3".format(density))
-        np.savetxt(filename,
-                   np.column_stack(output),
-                   fmt='%10.5f',
-                   header=header)
-
-    def _savez(self, filename):
-        # DEPRECATED: remove in 1.0.0
-        bins = np.linspace(0.0, max(self.dimensions), num=self.nbins)
-        dictionary = {'bins': bins}
-
-        for dim in self.results:
-            self.results[dim].pop('dim')
-            self.results[dim].pop('slice volume')
-            for key in self.results[dim]:
-                dictionary[dim + "_" + key] = self.results[dim][key]
-
-        np.savez(filename, **dictionary)
-
     def _add_other_results(self, other):
         # For parallel analysis
         results = self.results

package/MDAnalysis/analysis/rms.py

@@ -87,8 +87,7 @@
               select="backbone",             # superimpose on whole backbone of the whole protein
               groupselections=["backbone and (resid 1-29 or resid 60-121 or resid 160-214)",   # CORE
                                "backbone and resid 122-159",                                   # LID
-                               "backbone and resid 30-59"],                                    # NMP
-              filename="rmsd_all_CORE_LID_NMP.dat")
+                               "backbone and resid 30-59"])                                    # NMP
    R.run()
 
    import matplotlib.pyplot as plt
@@ -147,7 +146,7 @@
 from MDAnalysis.analysis.base import AnalysisBase
 from MDAnalysis.exceptions import SelectionError, NoDataError
 from MDAnalysis.lib.log import ProgressMeter
-from MDAnalysis.lib.util import asiterable, iterable, get_weights, deprecate
+from MDAnalysis.lib.util import asiterable, iterable, get_weights
 
 
 logger = logging.getLogger('MDAnalysis.analysis.rmsd')
@@ -331,11 +330,14 @@ class RMSD(AnalysisBase):
     Run the analysis with :meth:`RMSD.run`, which stores the results
     in the array :attr:`RMSD.rmsd`.
 
+    .. versionchanged:: 1.0.0
+       ``save()`` method was removed, use ``np.savetxt()`` on
+       :attr:`RMSD.rmsd` instead.
+
     """
     def __init__(self, atomgroup, reference=None, select='all',
-                 groupselections=None, filename="rmsd.dat",
-                 weights=None, tol_mass=0.1, ref_frame=0, **kwargs):
-        # DEPRECATION: remove filename kwarg in 1.0
+                 groupselections=None, weights=None, tol_mass=0.1,
+                 ref_frame=0, **kwargs):
         r"""Parameters
         ----------
         atomgroup : AtomGroup or Universe
@@ -379,12 +381,6 @@ def __init__(self, atomgroup, reference=None, select='all',
 
             .. Note:: Experimental feature. Only limited error checking
                       implemented.
-        filename : str (optional)
-            write RMSD into file with :meth:`RMSD.save`
-
-            .. deprecated:; 0.19.0
-               `filename` will be removed together with :meth:`save` in 1.0.
-
         weights : {"mass", ``None``} or array_like (optional)
              choose weights. With ``"mass"`` uses masses as weights; with ``None``
              weigh each atom equally. If a float array of the same length as
@@ -466,8 +462,8 @@ def __init__(self, atomgroup, reference=None, select='all',
         .. versionchanged:: 0.17.0
            removed deprecated `mass_weighted` keyword; `groupselections`
            are *not* rotationally superimposed any more.
-        .. deprecated:: 0.19.0
-           `filename` will be removed in 1.0
+        .. versionchanged:: 1.0.0
+           `filename` keyword was removed.
 
         """
         super(RMSD, self).__init__(atomgroup.universe.trajectory,
@@ -481,7 +477,6 @@ def __init__(self, atomgroup, reference=None, select='all',
         self.weights = weights
         self.tol_mass = tol_mass
         self.ref_frame = ref_frame
-        self.filename = filename   # DEPRECATED in 0.19.0, remove in 1.0.0
 
         self.ref_atoms = self.reference.select_atoms(*select['reference'])
         self.mobile_atoms = self.atomgroup.select_atoms(*select['mobile'])
@@ -556,10 +551,6 @@ def __init__(self, atomgroup, reference=None, select='all',
                              "weights=None or weights='mass', not a weight "
                              "array.")
 
-        # initialized to note for testing the save function
-        self.rmsd = None
-
-
     def _prepare(self):
         self._n_atoms = self.mobile_atoms.n_atoms
 
@@ -653,27 +644,6 @@ def _single_frame(self):
 
         self._pm.rmsd = self.rmsd[self._frame_index, 2]
 
-    @deprecate(release="0.19.0", remove="1.0.0",
-               message="You can instead use "
-               "``np.savetxt(filename, RMSD.rmsd)``.")
-    def save(self, filename=None):
-        """Save RMSD from :attr:`RMSD.rmsd` to text file *filename*.
-
-        Parameters
-        ----------
-        filename : str (optional)
-            if no filename is given the default provided to the constructor is
-            used.
-
-        """
-        filename = filename or self.filename
-        if filename is not None:
-            if self.rmsd is None:
-                raise NoDataError("rmsd has not been calculated yet")
-            np.savetxt(filename, self.rmsd)
-            logger.info("Wrote RMSD timeseries  to file %r", filename)
-        return filename
-
 
 class RMSF(AnalysisBase):
     r"""Calculate RMSF of given atoms across a trajectory.

testsuite/MDAnalysisTests/analysis/test_contacts.py

@@ -302,16 +302,6 @@ def test_non_callable_method(self, universe):
         with pytest.raises(ValueError):
             self._run_Contacts(universe, method=2, stop=2)
 
-    def test_save(self, universe):
-        with tempdir.in_tempdir():
-            ca = self._run_Contacts(universe)
-            ca.save('testfile.npy')
-            saved = np.genfromtxt('testfile.npy')
-            assert_array_almost_equal(ca.timeseries, saved)
-            # check the header was written correctly
-            with open('testfile.npy', 'r') as fin:
-                assert fin.readline().strip() == '# q1 analysis'
-
 
 def test_q1q2():
     u = mda.Universe(PSF, DCD)

testsuite/MDAnalysisTests/analysis/test_rms.py

@@ -221,20 +221,15 @@ def test_rmsd_single_frame(self, universe):
                             err_msg="error: rmsd profile should match" +
                             "test values")
 
-    def test_mass_weighted_and_save(self, universe, outfile, correct_values):
+    def test_mass_weighted(self, universe, correct_values):
         # mass weighting the CA should give the same answer as weighing
         # equally because all CA have the same mass
         RMSD = MDAnalysis.analysis.rms.RMSD(universe, select='name CA',
                                             weights='mass').run(step=49)
-        RMSD.save(outfile)
 
         assert_almost_equal(RMSD.rmsd, correct_values, 4,
                             err_msg="error: rmsd profile should match"
                             "test values")
-        saved = np.loadtxt(outfile)
-        assert_almost_equal(RMSD.rmsd, saved, 4,
-                            err_msg="error: rmsd profile should match "
-                            "saved test values")
 
     def test_custom_weighted(self, universe, correct_values_mass):
         RMSD = MDAnalysis.analysis.rms.RMSD(universe, weights="mass").run(step=49)
@@ -324,11 +319,6 @@ def test_group_selections_unequal_len(self, universe):
                                                 groupselections=
                                                 ['resname MET','type NH3'])
 
-    def test_save_before_run(self, universe):
-        with pytest.raises(NoDataError):
-            RMSD = MDAnalysis.analysis.rms.RMSD(universe)
-            RMSD.save('blah')
-
 
 class TestRMSF(object):
     @pytest.fixture()