Remove ProgressMeter

package/CHANGELOG

@@ -24,6 +24,7 @@ Fixes
 Enhancements
 
 Changes
+  * Removes deprecated ProgressMeter (Issue #2739)
   * Removes deprecated MDAnalysis.units.N_Avogadro (PR #2737)
   * Dropped Python 2 support
 

package/MDAnalysis/analysis/density.py

@@ -191,8 +191,7 @@
 from MDAnalysis import NoDataError, MissingDataWarning
 from .. import units
 from ..lib import distances
-from MDAnalysis.lib.log import ProgressBar 
-from MDAnalysis.lib.log import ProgressMeter   # remove in 2.0
+from MDAnalysis.lib.log import ProgressBar
 from MDAnalysis.lib.util import deprecate
 
 from .base import AnalysisBase

package/MDAnalysis/analysis/hbonds/hbond_analysis.py

@@ -897,8 +897,8 @@ def run(self, start=None, stop=None, step=None, verbose=None, **kwargs):
             read every `step` between `start` (included) and `stop` (excluded),
             ``None`` selects 1. [``None``]
         verbose : bool (optional)
-             toggle progress meter output :class:`~MDAnalysis.lib.log.ProgressMeter`
-             [``True``]
+             toggle progress meter output
+             :class:`~MDAnalysis.lib.log.ProgressBar` [``True``]
         debug : bool (optional)
              enable detailed logging of debugging information; this can create
              *very big* log files so it is disabled (``False``) by default; setting

package/MDAnalysis/lib/log.py

@@ -77,15 +77,18 @@
 Other functions and classes for logging purposes
 ------------------------------------------------
 
+
+.. versionchanged:: 2.0.0
+   Deprecated :class:`MDAnalysis.lib.log.ProgressMeter` has now been removed.
+
 .. autogenerated, see Online Docs
 
 """
-from __future__ import print_function, division, absolute_import
+from __future__ import absolute_import
 
 import sys
 import logging
 import re
-import warnings
 
 from tqdm.auto import tqdm
 
@@ -224,193 +227,6 @@ def _guess_string_format(template):
         return _legacy_format
 
 
-class ProgressMeter(object):
-    r"""Simple progress meter (Deprecated)
-
-    ..Warning:
-    This class is deprecated and will be removed in version 2.0.
-    Please use :class:`MDAnalysis.lib.log.ProgressBar` instead.
-
-    The :class:`ProgressMeter` class can be used to show running progress such
-    as frames processed or percentage done to give the user feedback on the
-    duration and progress of a task. It is structures as a class that is
-    customized on instantation (e.g., using a custom `format` string and the
-    expected total number of frames to be processed). Within a processing loop,
-    call :meth:`echo` with the current frame number to print the output to
-    stderr.
-
-    Parameters
-    ----------
-    numsteps: int
-        total number of steps
-    interval: int
-        only calculate and print progress every `interval` steps [10]
-    format: str
-        a format string with Python variable interpolation. Allowed
-        values:
-
-        * *step*: current step
-        * *numsteps*: total number of steps as supplied in *numsteps*
-        * *percentage*: percentage of total
-
-        The last call to :meth:`ProgressMeter.print` will automatically
-        issue a newline ``\n``.
-
-        If *format* is ``None`` then the default is used::
-
-            Step {step:5d}/{numsteps} [{percentage:5.1f}%]
-
-    offset: int
-        number to add to *step*; e.g. if *step* is 0-based (as in MDAnalysis)
-        then one should set *offset* = 1; for 1-based steps, choose 0. [1]
-    verbose: bool
-        If ``False``, disable all output, ``True`` print all messages as
-        specified, [``True``]
-    dynamic: bool
-        If ``True``, each line will be printed on top of the previous one.
-        This is done by prepedind the format with ``\r``. [``True``]
-    format_handling: str
-        how to handle the format string. Allowed values are:
-
-        * *new*: the format string uses {}-based formating
-        * *legacy*: the format string uses %-basedd formating
-        * *auto*: default, try to guess how the format string should be
-          handled
-
-
-    Examples
-    --------
-    The typical use case is to show progress as frames of a trajectory are
-    processed::
-
-       u = Universe(PSF, DCD)
-       pm = ProgressMeter(u.trajectory.n_frames, interval=100)
-       for ts in u.trajectory:
-           pm.echo(ts.frame)
-           ...
-
-    For a trajectory with 10000 frames this will produce output such
-    as ::
-
-       Step   100/10000 [  1.0%]
-       Step   200/10000 [  2.0%]
-       ...
-
-    The default *format* string is::
-
-        Step {step:5d}/{numsteps} [{percentage:5.1f}%]
-
-    By default, each line of the progress meter is displayed on top of the
-    previous one. To prevent this behaviour, set the `dynamic` keyword to
-    ``False``.
-
-    It is possible to embed (almost) arbitrary additional data in the
-    format string, for example a current RMSD value::
-
-        format_line = "RMSD {rmsd:5.2f} at {step:5d}/{numsteps} [{percentage:5.1f}%]"
-        pm = ProgressMeter(u.trajectory.n_frames,
-                           interval=100, format=format_line)
-        for ts in u.trajectory:
-           pm.echo(ts.frame, rmsd=current_rmsd)
-           ...
-
-    This will print something like::
-
-       RMSD   1.02 at  100/10000 [  1.0%]
-       RMSD   1.89 at  200/10000 [  2.0%]
-       ...
-
-    .. versionchanged:: 0.8
-       Keyword argument *quiet* was added.
-
-    .. versionchanged:: 0.16
-       Keyword argument *dynamic* replaces ``\r`` in the format.
-
-    .. deprecated:: 0.16
-       Keyword argument *quiet* is deprecated in favor of *verbose*.
-
-    .. deprecated:: 1.0
-       This class is deprecated in favor of *ProgressBar*.
-
-    """
-
-    def __init__(self, numsteps, format=None, interval=10, offset=1,
-                 verbose=True, dynamic=True,
-                 format_handling='auto'):
-        warnings.warn(
-            "This class is deprecated as of MDAnalysis version 1.0. "
-            "It will be removed in MDAnalysis version 2.0. "
-            "Please use MDAnalysis.lib.log.ProgressBar instead.",
-            category=DeprecationWarning
-            )
-        self.numsteps = numsteps
-        self.interval = int(interval)
-        self.offset = int(offset)
-        self.verbose = verbose
-        self.dynamic = dynamic
-        self.numouts = -1
-
-        if format is None:
-            format = "Step {step:5d}/{numsteps} [{percentage:5.1f}%]"
-            self.format_handler = _new_format
-        else:
-            if format_handling == 'auto':
-                self.format_handler = _guess_string_format(format)
-            else:
-                self.format_handler = {'new': _new_format,
-                                       'legacy': _legacy_format}[format_handling]
-        self.format = format
-        self.step = 0
-        self.percentage = 0.0
-        assert numsteps > 0, "numsteps step must be >0"
-        assert interval > 0, "interval step must be >0"
-
-    def update(self, step, **kwargs):
-        """Update the state of the ProgressMeter.
-
-        *kwargs* are additional attributes that can be references in
-        the format string.
-        """
-        self.step = step + self.offset
-        self.percentage = 100. * self.step / self.numsteps
-        for k, v in kwargs.items():
-            setattr(self, k, v)
-
-        self.numouts += 1
-
-    def echo(self, step, **kwargs):
-        """Print the state to stderr, but only every *interval* steps.
-
-        1) calls :meth:`~ProgressMeter.update`
-        2) writes step and percentage to stderr with :func:`echo`,
-           using the format string (in :attr:`ProgressMeter.format`)
-
-        The last step is always shown, even if not on an *interval*, and a
-        carriage return is replaced with a new line for a cleaner display.
-
-        *kwargs* are additional attributes that can be references in
-        the format string.
-
-        .. Note:: If *verbose* = ``False`` has been set in the
-                  constructor or if :attr:`ProgressMeter.verbose` has
-                  been set to ``False``, then no messages will be
-                  printed.
-        """
-        if not self.verbose:
-            return
-        self.update(step, **kwargs)
-        format = self.format
-        newline = not self.dynamic
-        if self.step == self.numsteps:
-            newline = True
-        elif self.numouts % self.interval == 0:
-            pass
-        else:
-            return
-        echo(self.format_handler(format, vars(self)),
-             replace=self.dynamic, newline=newline)
-
-
 class ProgressBar(tqdm):
     def __init__(self, *args, **kwargs):
         verbose = kwargs.pop('verbose', True)

testsuite/MDAnalysisTests/lib/test_log.py

@@ -25,32 +25,9 @@
 import warnings
 import pytest
 
-from MDAnalysis.lib.log import ProgressMeter, ProgressBar
+from MDAnalysis.lib.log import ProgressBar
 
 
-class TestProgressMeter(object):
-
-    def test_deprecated(self, capsys):
-        with warnings.catch_warnings(record=True) as w:
-            # Cause all warnings to always be triggered.
-            warnings.simplefilter("always")
-            # Trigger a warning.
-            pm = ProgressMeter(10)
-            # Verify the warning
-            assert len(w) == 1
-            assert issubclass(w[-1].category, DeprecationWarning)
-            assert "MDAnalysis.lib.log.ProgressBar" in str(w[-1].message)
-
-    def test_output(self, capsys):
-        pm = ProgressMeter(10, interval=1)
-        for i in range(10):
-            pm.echo(i)
-        out, err = capsys.readouterr()
-        expected = 'Step    10/10 [100.0%]'
-        actual = err.strip().split('\r')[-1]
-        assert actual == expected
-
-
 class TestProgressBar(object):
 
     def test_output(self, capsys):

testsuite/MDAnalysisTests/utils/test_log.py

@@ -72,74 +72,3 @@ def buffer():
 def _assert_in(output, string):
     assert string in output, "Output '{0}' does not match required format '{1}'.".format(output.replace('\r', '\\r'), string.replace('\r', '\\r'))
 
-
-def test_default_ProgressMeter(buffer, n=101, interval=10):
-    template = "Step {step:5d}/{numsteps} [{percentage:5.1f}%]"
-    with RedirectedStderr(buffer):
-        pm = MDAnalysis.lib.log.ProgressMeter(n, interval=interval)
-        for frame in range(n):
-            pm.echo(frame)
-    buffer.seek(0)
-    output = "".join(buffer.readlines())
-    _assert_in(output, ('\r' + template).format(**{'step': 1, 'numsteps': n, 'percentage': 100./n}))
-    # last line always ends with \n!
-    _assert_in(output,
-                    ('\r' + template + '\n').format(**{'step': n, 'numsteps': n,
-                                              'percentage': 100.}))
-
-
-def test_custom_ProgressMeter(buffer, n=51, interval=7):
-    template = "RMSD {rmsd:5.2f} at {step:03d}/{numsteps:4d} [{percentage:5.1f}%]"
-    with RedirectedStderr(buffer):
-        pm = MDAnalysis.lib.log.ProgressMeter(n, interval=interval,
-                                              format=template, offset=1)
-        for frame in range(n):
-            # n+1/n correction for 0-based frame vs 1-based counting
-            rmsd = 0.02 * frame * (n+1)/ n
-            pm.echo(frame, rmsd=rmsd)
-    buffer.seek(0)
-    output = "".join(buffer.readlines())
-    _assert_in(output,
-                    ('\r' + template).format(**{'rmsd': 0.0, 'step': 1,
-                                     'numsteps': n, 'percentage': 100./n}))
-    # last line always ends with \n!
-    _assert_in(output,
-                    ('\r' + template + '\n').format(
-                        **{'rmsd': 0.02*n, 'step': n,
-                           'numsteps': n, 'percentage': 100.0}))
-
-
-def test_legacy_ProgressMeter(buffer, n=51, interval=7):
-    template = "RMSD %(rmsd)5.2f at %(step)03d/%(numsteps)4d [%(percentage)5.1f%%]"
-    with RedirectedStderr(buffer):
-        pm = MDAnalysis.lib.log.ProgressMeter(n, interval=interval,
-                                              format=template, offset=1)
-        for frame in range(n):
-            # n+1/n correction for 0-based frame vs 1-based counting
-            rmsd = 0.02 * frame * (n+1)/ n
-            pm.echo(frame, rmsd=rmsd)
-    buffer.seek(0)
-    output = "".join(buffer.readlines())
-    _assert_in(output,
-                    ('\r' + template) % {'rmsd': 0.0, 'step': 1,
-                                       'numsteps': n, 'percentage': 100./n})
-    # last line always ends with \n!
-    _assert_in(output,
-                    ('\r' + template + '\n') % {'rmsd': 0.02*n, 'step': n,
-                                              'numsteps': n, 'percentage': 100.0})
-
-
-@pytest.mark.parametrize('step, percentage', [
-    (1, 100./51),
-    (51, 100.)
-])
-def test_not_dynamic_ProgressMeter(buffer, step, percentage, n=51, interval=10):
-    template = "Step {step:5d}/{numsteps} [{percentage:5.1f}%]"
-    with RedirectedStderr(buffer):
-        pm = MDAnalysis.lib.log.ProgressMeter(n, interval=interval,
-                                              dynamic=False)
-        for frame in range(n):
-            pm.echo(frame)
-    buffer.seek(0)
-    output = "".join(buffer.readlines())
-    _assert_in(output, (template + '\n').format(**{'step': step, 'numsteps': n, 'percentage': percentage}))