scipion-pyworkflow 3.10.6__py3-none-any.whl → 3.11.0__py3-none-any.whl

pyworkflow/utils/profiler.py

@@ -1,92 +0,0 @@
-
-import time
-instances = {}
-elapsedTime = {}
-
-
-def getInstancesCount():
-    return instances
-
-
-def instanceCreated(cls):
-    instances[cls] = instances.get(cls, 0) + 1
-
-
-def instanceDestroyed(cls):
-    instances[cls] = instances.get(cls, 0) - 1
-
-
-def printInstances():
-    for k, v in instances.items():
-        print("%s: %d", k, v)
-
-
-def waitForDebugger(seconds=20):
-    print("Waiting for debugger %d seconds." % seconds)
-    from pyworkflow.utils import printTraceBack
-    printTraceBack()
-
-    while seconds > 0:
-        time.sleep(1)
-        # Set seconds to 0:
-        # Execute this in the debugger:  seconds = 0
-        print(str(seconds) + " seconds left.")
-        seconds -= 1
-
-
-# From: https://www.huyng.com/posts/python-performance-analysis
-
-
-class Timer(object):
-    indentation = 0
-    blackList = []
-    whiteList = []
-    minms = 1
-
-    def __init__(self, name=None, verbose=True):
-        self.verbose = verbose
-        self.name = name
-        Timer.indentation += 1
-
-    def __enter__(self):
-        self.start = time.time()
-        return self
-
-    def __exit__(self, *args):
-        self.end = time.time()
-        self.secs = self.end - self.start
-        self.msecs = self.secs * 1000  # millisecs
-        Timer.indentation -= 1
-
-        toPrint = (len(Timer.whiteList) == 0)
-
-        if any(self.name.startswith(s) for s in Timer.blackList):
-            toPrint = False
-
-        if any(self.name.startswith(s) for s in Timer.whiteList):
-            toPrint = True
-
-        if self.verbose and toPrint and self.msecs > Timer.minms:
-            print('{0}{1:10.0f}\tms\t{2}'.format('\t' * Timer.indentation, self.msecs, self.name))
-
-# To monitor memory leaks:
-# 1.- Check you have installed pympler: scipion run pip install pympler
-# 2.- Uncomment lines below
-# 3.- Add a with statement like:
-#     with monitor.MemoryMonitor():
-#         <code to analyze>
-# from pympler.tracker import SummaryTracker
-#
-#
-# class MemoryMonitor(object):
-#
-#     def __init__(self):
-#         self.tracker = None
-#
-#     def __enter__(self):
-#         self.tracker = SummaryTracker()
-#         self.tracker.print_diff()
-#         return self
-#
-#     def __exit__(self, *args):
-#         self.tracker.print_diff()

pyworkflow/utils/progressbar.py

@@ -1,154 +0,0 @@
-# **************************************************************************
-# *
-# * Authors:      Roberto Marabini (roberto@cnb.csic.es) [1]
-# *               J.M. De la Rosa Trevin (delarosatrevin@scilifelab.se) [2]
-# *
-# * [1] Unidad de  Bioinformatica of Centro Nacional de Biotecnologia , CSIC
-# * [2] SciLifeLab, Stockholm University
-# *
-# * This program is free software; you can redistribute it and/or modify
-# * it under the terms of the GNU General Public License as published by
-# * the Free Software Foundation; either version 3 of the License, or
-# * (at your option) any later version.
-# *
-# * This program is distributed in the hope that it will be useful,
-# * but WITHOUT ANY WARRANTY; without even the implied warranty of
-# * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-# * GNU General Public License for more details.
-# *
-# * You should have received a copy of the GNU General Public License
-# * along with this program; if not, write to the Free Software
-# * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA
-# * 02111-1307  USA
-# *
-# *  All comments concerning this program package may be sent to the
-# *  e-mail address 'scipion@cnb.csic.es'
-# *
-# **************************************************************************
-
-
-import sys
-import re
-
-
-class ProgressBar(object):
-    """ Text progress bar class for Python.
-
-    A text progress bar is typically used to display the progress of a long-running
-    operation, providing a visual cue that processing is underway.
-
-    Example::
-
-        N = 1000
-        pb = ProgressBar(N, fmt=ProgressBar.FULL)
-        pb.start()
-        for x in range(N):
-            pb.update(x+1)
-            sleep(0.1)
-        pb.finish()
-
-    Optionally you can pass a step param (default to 10000) and call increase in each loop. Only when the step is reached, the progress is printed.
-    """
-    DEFAULT = 'Progress: %(bar)s %(percent)3d%%'
-    FULL = '%(bar)s %(current)d/%(total)d (%(percent)3d%%) %(remaining)d to go'
-    # scipion uses variable fonts so the bar size changes
-    # since the space width is different from the = width
-    NOBAR = '%(current)d/%(total)d (%(percent)3d%%) %(remaining)d to go'
-    OBJID = '%(bar)s %(current)d/%(total)d (%(percent)3d%%) (objectId=%(objectId)d)'
-    DOT = '.'
-
-    def __init__(self, total, width=40, fmt=DEFAULT, symbol='=',
-                 output=None, extraArgs=None, step=10000):
-        """
-        Create a new ProgressBar object.
-
-        :param total: The total amount that will be running the progress bar.
-            The value in the update() method can no go greater than this value.
-        :param width: progress bar width (without the percentage and number of
-            iterations loop)
-        :param fmt: predefined format string, so far DEFAULT, FULL, OBJID and
-            DOT are defined.
-        :param symbol: progress bar is made with this symbol
-        :param output:
-        :param extraArgs: Additional arguments that can be passed to be used
-            the fmt format. (e.g extraArgs={'objectId': 1} for fmt=OBJID
-        :param step: interval between printing progress. Use in combination with "increase"
-        """
-        if len(symbol) != 1:
-            raise Exception("Symbol should be only 1 character length. ")
-
-        self._total = total
-        self._width = width
-        self._symbol = symbol
-        self._output = output or sys.stdout
-        self._current = -1
-        self._extraArgs = extraArgs or {}
-        self._fmt = fmt
-        self._directPrint = fmt == self.DOT
-        self.step = step
-
-        if not self._directPrint:
-            # This line computes the number of digits
-            # in total and rewrites the fmt string
-            # so if total = 100, %d is converted to %3d
-            self._fmt = re.sub(r'(?P<name>%\(.+?\))d',
-                               r'\g<name>%dd' % len(str(total)), fmt)
-
-    def __getStr(self):
-        """ Internal function to return the current string value.
-        It should be called after the value has being set.
-        """
-        if self._directPrint:  # print just a dot
-            return self._fmt if self._current else ''
-
-        percent = self._current / float(self._total)
-        size = int(self._width * percent)
-        remaining = self._total - self._current
-        bar = '[' + self._symbol * size + ' ' * (self._width - size) + ']'
-
-        args = {
-            'total': self._total,
-            'bar': bar,
-            'current': self._current,
-            'percent': percent * 100,
-            'remaining': remaining,
-        }
-        args.update(self._extraArgs)
-
-        return '\r' + self._fmt % args
-
-    def start(self):
-        """ Print empty progress bar. """
-        self.update(0)
-
-    def update(self, value):
-        """
-        Update the current value and print the progress.
-
-        :param value: New value, should be greater than the previous
-            value and less or equal the total value
-        :return:
-        """
-        if value < 0 or value <= self._current or value > self._total:
-            raise Exception("Incorrect value provided. It should be greater "
-                            "than previous value and between 0 and total. ")
-        self._current = value
-        self._output.write(self.__getStr())
-        self._output.flush()
-
-    def increase(self):
-        """ Increase the value by 1. Is new value matches the step. update is called"""
-        nextValue = self._current + 1
-        if (nextValue) % self.step == 0:
-            self.update(nextValue)
-        else:
-            self._current=nextValue
-
-    def finish(self, printNewLine=True):
-        """ Finalize the progress and
-        print last update with 100% complete message """
-        if self._current < self._total:
-            self.update(self._total)
-        # print a new line
-        if printNewLine:
-            self._output.write("\n")