cleaned up lib.log

- fix #2734
  (docs now build with sphinx 2.3)
- removed unused code from lib.log (left over from ProgressMeter removal)
- explicitly added docs to ProgressMeter
  - avoids sphinx failure due to wrong formatting in tqdm.auto.tqdm
  - add specific example for MDA
  - document our own verbose kwarg
  - improved markup
  - not documented: gui kwarg (discouraged in original docs)

package/MDAnalysis/lib/log.py

@@ -176,57 +176,161 @@ def emit(self, record):
         pass
 
 
-def echo(s='', replace=False, newline=True):
-    r"""Simple string output that immediately prints to the console.
+class ProgressBar(tqdm):
+    r"""Display a visual progress bar and time estimate.
+
+    The :class:`ProgressBar` decorates an iterable object, returning an
+    iterator which acts exactly like the original iterable, but prints a
+    dynamically updating progressbar every time a value is requested. See the
+    example below for how to use it when iterating over the frames of a
+    trajectory.
 
-    The string `s` is modified according to the keyword arguments and then
-    printed to :const:`sys.stderr`, which is immediately flushed.
 
     Parameters
     ----------
-    s : str
-        The string to output.
-    replace : bool
-        If ``True``, the string will be printed on top of the current line. In
-        practice, ``\r`` is added at the beginning of the string.
-    newline : bool
-        If ``True``, a newline is added at the end of the string.
-
-    """
-    if replace:
-        s = '\r' + s
-    if newline:
-        end='\n'
-    else:
-        end=''
-    print(s, file=sys.stderr, end=end)
-    sys.stderr.flush()
-
-
-def _new_format(template, variables):
-    """Format a string that follows the {}-based syntax.
-    """
-    return template.format(**variables)
-
+    iterable  : iterable, optional
+        Iterable to decorate with a progressbar.
+        Leave blank to manually manage the updates.
+    verbose : bool, optional
+        If ``True`` (the default) then show the progress bar, *unless* the
+        `disable` keyword is set to ``True`` (`disable` takes precedence over
+        `verbose`). If `verbose` is set to ``None`` then the progress bar is
+        displayed (like ``True``), *unless* this is a non-TTY output device
+        (see `disable`).
+    desc  : str, optional
+        Prefix for the progressbar.
+    total  : int or float, optional
+        The number of expected iterations. If unspecified,
+        ``len(iterable)`` is used if possible. If ``float("inf")`` or as a last
+        resort, only basic progress statistics are displayed
+        (no ETA, no progressbar).
+    leave  : bool, optional
+        If [default: ``True``], keeps all traces of the progressbar
+        upon termination of iteration.
+        If ``None``, will leave only if `position` is 0.
+    file  : :class:`io.TextIOWrapper` or :class:`io.StringIO`, optional
+        Specifies where to output the progress messages (default:
+        :data:`sys.stderr`). Uses :meth:`file.write` and :meth:`file.flush`
+        methods.  For encoding, see `write_bytes`.
+    ncols  : int, optional
+        The width of the entire output message. If specified,
+        dynamically resizes the progressbar to stay within this bound.
+        If unspecified, attempts to use environment width. The
+        fallback is a meter width of 10 and no limit for the counter and
+        statistics. If 0, will not print any meter (only stats).
+    mininterval  : float, optional
+        Minimum progress display update interval [default: 0.1] seconds.
+    maxinterval  : float, optional
+        Maximum progress display update interval [default: 10] seconds.
+        Automatically adjusts `miniters` to correspond to `mininterval`
+        after long display update lag. Only works if `dynamic_miniters`
+        or monitor thread is enabled.
+    miniters  : int or float, optional
+        Minimum progress display update interval, in iterations.
+        If 0 and `dynamic_miniters`, will automatically adjust to equal
+        `mininterval` (more CPU efficient, good for tight loops).
+        If > 0, will skip display of specified number of iterations.
+        Tweak this and `mininterval` to get very efficient loops.
+        If your progress is erratic with both fast and slow iterations
+        (network, skipping items, etc) you should set miniters=1.
+    ascii  : bool or str, optional
+        If unspecified or ``False``, use unicode (smooth blocks) to fill
+        the meter. The fallback is to use ASCII characters " 123456789#".
+    disable  : bool, optional
+        Whether to disable the entire progressbar wrapper
+        [default: ``False``]. If set to None, disable on non-TTY.
+    unit  : str, optional
+        String that will be used to define the unit of each iteration
+        [default: it].
+    unit_scale  : bool or int or float, optional
+        If 1 or True, the number of iterations will be reduced/scaled
+        automatically and a metric prefix following the
+        International System of Units standard will be added
+        (kilo, mega, etc.) [default: ``False``]. If any other non-zero
+        number, will scale `total` and `n`.
+    dynamic_ncols  : bool, optional
+        If set, constantly alters `ncols` and `nrows` to the
+        environment (allowing for window resizes) [default: ``False``].
+    smoothing  : float, optional
+        Exponential moving average smoothing factor for speed estimates
+        (ignored in GUI mode). Ranges from 0 (average speed) to 1
+        (current/instantaneous speed) [default: 0.3].
+    bar_format  : str, optional
+        Specify a custom bar string formatting. May impact performance.
+        [default: ``'{l_bar}{bar}{r_bar}'``], where ``l_bar='{desc}:
+        {percentage:3.0f}%|'`` and ``r_bar='| {n_fmt}/{total_fmt}
+        [{elapsed}<{remaining}, {rate_fmt}{postfix}]'``
+
+        Possible vars: l_bar, bar, r_bar, n, n_fmt, total, total_fmt,
+        percentage, elapsed, elapsed_s, ncols, nrows, desc, unit,
+        rate, rate_fmt, rate_noinv, rate_noinv_fmt,
+        rate_inv, rate_inv_fmt, postfix, unit_divisor,
+        remaining, remaining_s.
+
+        Note that a trailing ": " is automatically removed after {desc}
+        if the latter is empty.
+    initial  : int or float, optional
+        The initial counter value. Useful when restarting a progress bar
+        [default: 0]. If using :class:`float`, consider specifying ``{n:.3f}``
+        or similar in `bar_format`, or specifying `unit_scale`.
+    position  : int, optional
+        Specify the line offset to print this bar (starting from 0)
+        Automatic if unspecified.
+        Useful to manage multiple bars at once (e.g., from threads).
+    postfix  : dict or \*, optional
+        Specify additional stats to display at the end of the bar.
+        Calls ``set_postfix(**postfix)`` if possible (:class:`dict`).
+    unit_divisor  : float, optional
+        [default: 1000], ignored unless `unit_scale` is ``True``.
+    write_bytes  : bool, optional
+        If (default: ``None``) and `file` is unspecified,
+        bytes will be written in Python 2. If `True` will also write
+        bytes. In all other cases will default to unicode.
+    lock_args  : tuple, optional
+        Passed to `refresh` for intermediate output
+        (initialisation, iterating, and updating).
+    nrows  : int, optional
+        The screen height. If specified, hides nested bars outside this
+        bound. If unspecified, attempts to use environment height.
+        The fallback is 20.
+
+    Returns
+    -------
+    out  : decorated iterator.
+
+    Example
+    -------
+    To get a progress bar when analyzing a trajectory::
+
+      from MDAnalysis.lib.log import ProgressBar
+
+      ...
+
+      for ts in ProgressBar(u.trajectory):
+         # perform analysis
+
+
+    will produce something similar to ::
+
+       30%|███████████                       | 3/10 [00:13<00:30,  4.42s/it]
+
+    in a terminal or Jupyter notebook.
+
+
+    See Also
+    --------
+    The :class:`ProgressBar` is derived from :class:`tqdm.auto.tqdm`; see the
+    `tqdm documentation`_ for further details on how to use it.
+
+
+
+    .. _`tqdm documentation`: https://tqdm.github.io/
 
-def _legacy_format(template, variables):
-    """Format a string that follows the %-based syntax.
     """
-    return template % variables
-
-
-def _guess_string_format(template):
-    """Guess if the template follow {}-based or %-based syntax.
-    """
-    match = re.search(r'%\((step|numsteps|percentage)\)', template)
-    if match is None:
-        return _new_format
-    else:
-        return _legacy_format
-
-
-class ProgressBar(tqdm):
     def __init__(self, *args, **kwargs):
+        """"""
+        # ^^^^ keep the empty doc string to avoid Sphinx doc errors with the
+        # original doc string from tqdm.auto.tqdm
         verbose = kwargs.pop('verbose', True)
         # disable: Whether to disable the entire progressbar wrapper [default: False].
         # If set to None, disable on non-TTY.