Source code for tlo.progressbar

"""Progress bar for visualising progress of simulation runs."""

import html
import os
import platform
import sys
from timeit import default_timer as timer
from typing import Dict, Optional, TextIO, Union

    from IPython import get_ipython
    from IPython.display import display as ipython_display

except ImportError:

def _in_zmq_interactive_shell() -> bool:
    """Check if in interactive ZMQ shell which supports updateable displays"""
        return False
            shell = get_ipython().__class__.__name__
            if shell == "ZMQInteractiveShell":
                return True
            elif shell == "TerminalInteractiveShell":
                return False
                return False
        except NameError:
            return False

def _in_shell_with_ansi_support() -> bool:
    """Check if running in shell with support for ANSI escape characters.

    Based on
    return (
            hasattr(sys.stdout, "isatty")
            and sys.stdout.isatty()
            and platform.system() != 'Windows'
        or os.environ.get('TERM') == "ANSI"
        or os.environ.get('PYCHARM_HOSTED') == "1"

def _create_display(obj):
    """Create an updateable display object.

    :param obj: Initial object to display.
    :return: Object with `update` method to update displayed content.
    if _in_zmq_interactive_shell():
        return ipython_display(obj, display_id=True)
        display = (
            AnsiStreamDisplay() if _in_shell_with_ansi_support()
            else BasicStreamDisplay()
        return display

def _format_time(total_seconds: Union[int, float]) -> str:
    """Format a time interval in seconds as a colon-delimited string [h:]m:s"""
    total_mins, seconds = divmod(int(total_seconds), 60)
    hours, mins = divmod(total_mins, 60)
    if hours != 0:
        return f"{hours:d}:{mins:02d}:{seconds:02d}"
        return f"{mins:02d}:{seconds:02d}"

def _format_stat(stat) -> str:
    """Format numeric stat at fixed precision otherwise convert to string."""
    if isinstance(stat, (int, float)):
        return f"{stat:.4g}"
        return str(stat)

[docs]class ProgressBar: """Iterable object for tracking progress of an iterative task. Implements both string and HTML representations to allow richer display in interfaces which support HTML output, for example Jupyter notebooks or interactive terminals. """ GLYPHS = " ▏▎▍▌▋▊▉█" """Characters used to create string representation of progress bar.""" def __init__( self, n_step: int, description: Optional[str] = None, n_col: int = 10, unit: str = "step", min_refresh_time: float = 1., ): """ :param n_step: Total number of steps in task. :param description: Description of task to prefix progress bar with. :param n_col: Number of columns (characters) to use in string representation of progress bar. :param unit: String describing unit of each step. :param min_referesh_time: Minimum time in seconds between each refresh of progress bar visual representation. """ assert int(n_step) == n_step and n_step > 0, "n_step must be positive integer" self._n_step = int(n_step) self._description = description self._active = False assert int(n_col) == n_col and n_col > 0, "n_col must be positive integer" self._n_col = int(n_col) self._unit = unit self._capitalized_unit = unit.capitalize() self._step = 0 self._start_time = None self._elapsed_time = 0 self._stats_dict = {} assert min_refresh_time >= 0, "min_refresh_time must be non-negative" self._min_refresh_time = min_refresh_time self._display = None @property def n_step(self): """Total number of steps in task.""" return self._n_step @property def description(self): """"Description of task being tracked.""" return self._description @property def step(self): """Progress step count.""" return self._step @step.setter def step(self, value): self._step = max(0, min(value, self.n_step)) @property def prop_complete(self): """Proportion complete (float value in [0, 1]).""" return self.step / self.n_step @property def perc_complete(self): """Percentage complete formatted as string.""" return f"{int(self.prop_complete * 100):3d}%" @property def elapsed_time(self): """Elapsed time formatted as string.""" return _format_time(self._elapsed_time) @property def iter_rate(self): """Mean iteration rate if ≥ 1 `unit/s` or reciprocal `s/unit` as string.""" if self.prop_complete == 0: return "?" else: mean_time = self._elapsed_time / self.step return ( f"{mean_time:.2f}s/{self._unit}" if mean_time > 1 else f"{1/mean_time:.2f}{self._unit}/s" ) @property def est_remaining_time(self): """Estimated remaining time to completion formatted as string.""" if self.prop_complete == 0: return "?" else: return _format_time((1 / self.prop_complete - 1) * self._elapsed_time) @property def n_block_filled(self): """Number of filled blocks in progress bar.""" return int(self._n_col * self.prop_complete) @property def n_block_empty(self): """Number of empty blocks in progress bar.""" return self._n_col - self.n_block_filled @property def prop_partial_block(self): """Proportion filled in partial block in progress bar.""" return self._n_col * self.prop_complete - self.n_block_filled @property def filled_blocks(self): """Filled blocks string.""" return self.GLYPHS[-1] * self.n_block_filled @property def empty_blocks(self): """Empty blocks string.""" if self.prop_partial_block == 0: return self.GLYPHS[0] * self.n_block_empty else: return self.GLYPHS[0] * (self.n_block_empty - 1) @property def partial_block(self): """Partial block character.""" if self.prop_partial_block == 0: return "" else: return self.GLYPHS[int(len(self.GLYPHS) * self.prop_partial_block)] @property def progress_bar(self): """Progress bar string.""" return f"|{self.filled_blocks}{self.partial_block}{self.empty_blocks}|" @property def bar_color(self): """CSS color property for HTML progress bar.""" if self.step == self.n_step: return "var(--jp-success-color1, #4caf50)" elif self._active: return "var(--jp-brand-color1, #2196f3)" else: return "var(--jp-error-color1, #f44336)" @property def stats(self): """Comma-delimited string list of statistic key=value pairs.""" return ", ".join( f"{k}={_format_stat(v)}" for k, v in self._stats_dict.items() ) @property def prefix(self): """Text to prefix progress bar with.""" return ( f'{self.description + ": "if self.description else ""}' f"{self.perc_complete}" ) @property def postfix(self): """Text to postfix progress bar with.""" return ( f"{self._capitalized_unit} {self.step}/{self.n_step} " f"[{self.elapsed_time}<{self.est_remaining_time}, " f"{self.iter_rate}" f'{", " + self.stats if self._stats_dict else ""}]' )
[docs] def reset(self): """Reset progress bar state.""" self._step = 0 self._start_time = timer() self._last_refresh_time = -float("inf") self._stats_dict = {}
[docs] def update( self, step: int, stats_dict: Optional[Dict] = None, refresh: bool = True ): """Update progress bar state. :param step: New value for step counter. :param stats_dict: Dictionary of statistic key-value pairs to use to update postfix stats. :param refresh: Whether to refresh display. """ if step == 0: self.reset() else: self.step = step if stats_dict is not None: self._stats_dict.update(stats_dict) self._elapsed_time = timer() - self._start_time if ( refresh and step == self.n_step or (timer() - self._last_refresh_time > self._min_refresh_time) ): self.refresh() self._last_refresh_time = timer()
[docs] def refresh(self): """Refresh visual display(s) of progress bar.""" self._display.update(self)
[docs] def start(self): """Start tracking progress of task.""" self._active = True self.reset() if self._display is None: self._display = _create_display(self)
[docs] def stop(self): """Stop tracking progress of task.""" self._active = False if self.step != self.n_step: self.refresh() if isinstance(self._display, StreamDisplay): self._display.close()
def __str__(self): return f"{self.prefix}{self.progress_bar}{self.postfix}" def __repr__(self): return self.__str__() def _repr_html_(self): return f""" <div style="line-height: 28px; width: 100%; display: flex; flex-flow: row wrap; align-items: center; position: relative; margin: 2px;"> <label style="margin-right: 8px; flex-shrink: 0; font-size: var(--jp-code-font-size, 13px); font-family: var(--jp-code-font-family, monospace);"> {html.escape(self.prefix).replace(' ', '&nbsp;')} </label> <div role="progressbar" aria-valuenow="{self.prop_complete}" aria-valuemin="0" aria-valuemax="1" style="position: relative; flex-grow: 1; align-self: stretch; margin-top: 4px; margin-bottom: 4px; height: initial; background-color: #eee;"> <div style="background-color: {self.bar_color}; position: absolute; bottom: 0; left: 0; width: {self.perc_complete}; height: 100%;"></div> </div> <div style="margin-left: 8px; flex-shrink: 0; font-family: var(--jp-code-font-family, monospace); font-size: var(--jp-code-font-size, 13px);"> {html.escape(self.postfix)} </div> </div> """
[docs]class StreamDisplay: """Base class for using I/O streams as an updatable display.""" def __init__(self, io: Optional[TextIO] = None): """ :param io: I/O stream to write updates to. Defaults to `sys.stdout` if `None`. """ self._io = io if io is not None else sys.stdout
[docs] def close(self): self._io.write("\n") self._io.flush()
[docs] def update(self, obj): """Update display with string representation of `obj`.""" raise NotImplementedError()
[docs]class AnsiStreamDisplay(StreamDisplay): """Use I/O stream which supports ANSI escape sequences as an updatable display."""
[docs] def update(self, obj): self._io.write("\x1b[2K\r") self._io.write(str(obj)) self._io.flush()
[docs]class BasicStreamDisplay(StreamDisplay): """Use I/O stream without ANSI escape sequence support as an updatable display.""" def __init__(self, io: Optional[TextIO] = None): super().__init__(io) self._last_string_length = 0
[docs] def update(self, obj): string = str(obj) self._io.write(f"\r{string: <{self._last_string_length}}") self._last_string_length = len(string) self._io.flush()