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

pyworkflow/tests/__init__.py

@@ -1,29 +0,0 @@
-#!/usr/bin/env python
-# **************************************************************************
-# *
-# * Authors:     J.M. De la Rosa Trevin (jmdelarosa@cnb.csic.es)
-#                Laura del Cano         (ldelcano@cnb.csic.es)
-# *
-# * Unidad de  Bioinformatica of Centro Nacional de Biotecnologia , CSIC
-# *
-# * 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'
-# *
-# **************************************************************************
-
-from .tests import *

pyworkflow/tests/test_utils.py

@@ -1,25 +0,0 @@
-#!/usr/bin/env python
-# coding: latin-1
-"""
-Created on Mar 25, 2014
-
-@author: airen
-@author: roberto.marabini
-"""
-import time
-
-
-def wait(condition, timeout=30):
-    """ Wait until "condition" returns False or return after timeout (seconds)
-    param"""
-    t0 = time.time()
-
-    while condition():
-        time.sleep(1)
-
-        # Check timeout
-        tDelta = time.time()
-
-        if tDelta - t0 >= timeout:
-            print("Wait timed out after ", timeout, " seconds")
-            return

pyworkflow/tests/tests.py

@@ -1,341 +0,0 @@
-import logging
-logger = logging.getLogger(__name__)
-
-import sys
-import os
-import time
-from traceback import format_exception
-import unittest
-from os.path import join, relpath
-
-import pyworkflow as pw
-import pyworkflow.utils as pwutils
-from pyworkflow.project import Manager
-from pyworkflow.protocol import MODE_RESTART, getProtocolFromDb
-from pyworkflow.object import Set
-
-SMALL = 'small'
-PULL_REQUEST = 'pull'
-DAILY = 'daily'
-WEEKLY = 'weekly'
-
-# Type hint when creating protocols
-from typing import TypeVar
-T = TypeVar('T')
-
-# Procedure to check if a test class has an attribute called _labels and if so
-# then it checks if the class test matches any of the labels in input label parameter.
-def hasLabel(TestClass, labels):
-    # Get _labels attributes in class if any.
-    classLabels = getattr(TestClass, '_labels', None)
-
-    # Check if no label in test class.    
-    return classLabels is not None and any(l in classLabels for l in labels)
-
-
-class DataSet:
-    _datasetDict = {}  # store all created datasets
-
-    def __init__(self, name, folder, files, url=None):
-        """ 
-        Params:
-            
-        #filesDict is dict with key, value pairs for each file
-        """
-        self._datasetDict[name] = self
-        self.folder = folder
-        self.path = join(pw.Config.SCIPION_TESTS, folder)
-        self.filesDict = files
-        self.url = url
-
-    def getFile(self, key):
-        if key in self.filesDict:
-            return join(self.path, self.filesDict[key])
-        return join(self.path, key)
-
-    def getPath(self):
-        return self.path
-
-    @classmethod
-    def getDataSet(cls, name):
-        """
-        This method is called every time the dataset want to be retrieved
-        """
-        assert name in cls._datasetDict, "Dataset: %s dataset doesn't exist." % name
-
-        ds = cls._datasetDict[name]
-        folder = ds.folder
-        url = '' if ds.url is None else ' -u ' + ds.url
-
-        if not pw.Config.SCIPION_TEST_NOSYNC:
-            command = ("%s %s --download %s %s"
-                       % (pw.PYTHON, pw.getSyncDataScript(), folder, url))
-            logger.info(">>>> %s" % command)
-            os.system(command)
-
-        return cls._datasetDict[name]
-
-
-class BaseTest(unittest.TestCase):
-    _labels = [WEEKLY]
-
-    @classmethod
-    def getOutputPath(cls, *filenames):
-        """Return the path to the SCIPION_HOME/tests/output dir
-        joined with filename"""
-        return join(cls.outputPath, *filenames)
-
-    @classmethod
-    def getRelPath(cls, basedir, filename):
-        """Return the path relative to SCIPION_HOME/tests"""
-        return relpath(filename, basedir)
-
-    @classmethod
-    def launchProtocol(cls, prot, **kwargs):
-        """ Launch a given protocol using cls.proj.
-
-        :param wait: if True the function will return after the protocol runs.
-            If not specified, then if waitForOutput is passed, wait is false.
-        :param waitForOutputs: a list of expected outputs, ignored if wait=True
-
-        """
-        wait = kwargs.get('wait', None)
-        waitForOutputs = kwargs.get('waitForOutput', [])
-
-        if wait is None:
-            wait = not waitForOutputs
-
-        if getattr(prot, '_run', True):
-            cls.proj.launchProtocol(prot, wait=wait)
-            if not wait and waitForOutputs:
-                while True:
-                    time.sleep(10)
-                    prot = cls.updateProtocol(prot)
-                    if all(prot.hasAttribute(o) for o in waitForOutputs):
-                        return prot
-
-        if prot.isFailed():
-
-            cls.printLastLogLines(prot)
-            raise Exception("Protocol %s execution failed. See last log lines above for more details." % prot.getRunName())
-
-        if not prot.isFinished() and not prot.useQueue():  # when queued is not finished yet
-
-            cls.printLastLogLines(prot)
-            raise Exception("Protocol %s didn't finish. See last log lines above for more details." % prot.getRunName())
-
-        return prot
-
-    @staticmethod
-    def printLastLogLines(prot):
-        """ Prints the last log lines (50 or  'PROT_LOGS_LAST_LINES' env variable) from stdout and stderr log files
-
-        :param prot: Protocol to take the logs from
-
-        """
-        logs = {"STD OUT": 0, "STD ERR":1}
-
-        lastLines = int(os.environ.get('PROT_LOGS_LAST_LINES', 50))
-
-        # For each log file to print
-        for key in logs:
-
-            logger.info(pwutils.cyanStr("\n*************** last %s lines of %s *********************\n" % (lastLines, key)))
-            logLines = prot.getLogsLastLines(lastLines, logFile=logs[key])
-            for i in range(0, len(logLines)):
-                logger.info(logLines[i])
-            logger.info(pwutils.cyanStr("\n*************** end of %s *********************\n" % key))
-
-            sys.stdout.flush()
-
-    @classmethod
-    def saveProtocol(cls, prot):
-        """ Saves a protocol using cls.proj """
-        cls.proj.saveProtocol(prot)
-
-    @classmethod
-    def _waitOutput(cls, prot, outputAttributeName, sleepTime=20, timeOut=5000):
-        """ Wait until the output is being generated by the protocol. """
-
-        def _loadProt():
-            # Load the last version of the protocol from its own database
-            loadedProt = getProtocolFromDb(prot.getProject().path,
-                                           prot.getDbPath(),
-                                           prot.getObjId())
-            # Close DB connections
-            loadedProt.getProject().closeMapper()
-            loadedProt.closeMappers()
-            return loadedProt
-
-        counter = 1
-        prot2 = _loadProt()
-
-        numberOfSleeps = timeOut/sleepTime
-
-        while (not prot2.hasAttribute(outputAttributeName)) and prot2.isActive():
-            time.sleep(sleepTime)
-            prot2 = _loadProt()
-            if counter > numberOfSleeps:
-                logger.warning("Timeout (%s) reached waiting for %s at %s" % (timeOut, outputAttributeName, prot))
-                break
-            counter += 1
-
-        # Update the protocol instance to get latest changes
-        cls.proj._updateProtocol(prot)
-
-    @classmethod
-    def newProtocol(cls, protocolClass:T, **kwargs)->T:
-        """ Create new protocols instances through the project
-        and return a newly created protocol of the given class
-        """
-        # Try to continue from previous execution
-        if pwutils.envVarOn('SCIPION_TEST_CONTINUE'):
-            candidates = cls.proj.mapper.selectByClass(protocolClass.__name__)
-            if candidates:
-                c = candidates[0]
-                if c.isFinished():
-                    setattr(c, '_run', False)
-                else:
-                    c.runMode.set(MODE_RESTART)
-                return c
-        return cls.proj.newProtocol(protocolClass, **kwargs)
-
-    @classmethod
-    def compareSets(cls, test, set1, set2):
-        """ Iterate the elements of both sets and check
-        that all elements have equal attributes. """
-        for item1, item2 in zip(set1, set2):
-            areEqual = item1.equalAttributes(item2)
-            if not areEqual:
-                logger.info("item 1 and item2 are different: ")
-                item1.printAll()
-                item2.printAll()
-            test.assertTrue(areEqual)
-
-    def compareSetProperties(self, set1:Set, set2:Set, ignore = ["_size", "_mapperPath"]):
-        """ Compares 2 sets' properties"""
-
-        self.assertTrue(set1.equalAttributes(set2, ignore=ignore, verbose=True), "Set1 (%s) properties differs from set2 (%s)." % (set1, set2))
-        self.assertTrue(set2.equalAttributes(set1, ignore=ignore, verbose=True), 'Set2 (%s) has properties that set1 (%s) does not have.' % (set2, set1))
-
-    def assertSetSize(self, setObject, size=None, msg=None, diffDelta=None):
-        """ Check if a pyworkflow Set is not None nor is empty, or of a determined size or
-        of a determined size with a percentage (base 1) of difference"""
-        self.assertIsNotNone(setObject, msg)
-        setObjSize = setObject.getSize()
-
-        if size is None:
-            # Test is not empty
-            self.assertNotEqual(setObjSize, 0, msg)
-        else:
-            if diffDelta:
-                self.assertLessEqual(abs(setObjSize - size), round(diffDelta * size), msg)
-            else:
-                self.assertEqual(setObjSize, size, msg)
-
-    def assertIsNotEmpty(self, setObject, msg=None):
-        """ Check if the pyworkflow object is not None nor is empty"""
-        self.assertIsNotNone(setObject, msg)
-
-        self.assertIsNotNone(setObject.get(), msg)
-
-    @classmethod
-    def setupTestOutput(cls):
-        setupTestOutput(cls)
-
-
-def setupTestOutput(cls):
-    """ Create the output folder for a give Test class. """
-    cls.outputPath = join(pw.Config.SCIPION_TESTS_OUTPUT, cls.__name__)
-    pwutils.cleanPath(cls.outputPath)
-    pwutils.makePath(cls.outputPath)
-
-
-def setupTestProject(cls, writeLocalConfig=False):
-    """ Create and setup a Project for a give Test class. """
-    projName = cls.__name__
-    hostsConfig = None
-
-    if writeLocalConfig:
-        hostsConfig = '/tmp/hosts.conf'
-        logger.info("Writing local config: %s" % hostsConfig)
-        import pyworkflow.protocol as pwprot
-        pwprot.HostConfig.writeBasic(hostsConfig)
-
-    if os.environ.get('SCIPION_TEST_CONTINUE', None) == '1':
-        proj = Manager().loadProject(projName)
-    else:
-        proj = Manager().createProject(projName, hostsConf=hostsConfig)
-
-    cls.outputPath = proj.path
-    # Create project does not change the working directory anymore
-    os.chdir(cls.outputPath)
-    cls.projName = projName
-    cls.proj = proj
-
-
-class GTestResult(unittest.TestResult):
-    """ Subclass TestResult to output tests results with colors
-    (green for success and red for failure)
-    and write a report on an .xml file. 
-    """
-    xml = None
-    testFailed = 0
-    numberTests = 0
-
-    def __init__(self):
-        unittest.TestResult.__init__(self)
-        self.startTimeAll = time.time()
-
-    def openXmlReport(self, classname, filename):
-        pass
-
-    def doReport(self):
-        secs = time.time() - self.startTimeAll
-        logger.info("\n%s run %d tests (%0.3f secs)\n" %
-                         (pwutils.greenStr("[==========]"),
-                          self.numberTests, secs))
-        if self.testFailed:
-            logger.info("%s %d tests\n"
-                             % (pwutils.redStr("[  FAILED  ]"),
-                                self.testFailed))
-        logger.info("%s %d tests\n"
-                         % (pwutils.greenStr("[  PASSED  ]"),
-                            self.numberTests - self.testFailed))
-
-    def tic(self):
-        self.startTime = time.time()
-
-    def toc(self):
-        return time.time() - self.startTime
-
-    def startTest(self, test):
-        self.tic()
-        self.numberTests += 1
-
-    @staticmethod
-    def getTestName(test):
-        parts = str(test).split()
-        name = parts[0]
-        parts = parts[1].split('.')
-        classname = parts[-1].replace(")", "")
-        return "%s.%s" % (classname, name)
-
-    def addSuccess(self, test):
-        secs = self.toc()
-        logger.info("%s %s (%0.3f secs)\n" %
-                         (pwutils.greenStr('[ RUN   OK ]'),
-                          self.getTestName(test), secs))
-
-    def reportError(self, test, err):
-        logger.info("%s %s\n" % (pwutils.redStr('[   FAILED ]'),
-                                      self.getTestName(test)))
-        logger.info("\n%s"
-                         % pwutils.redStr("".join(format_exception(*err))))
-        self.testFailed += 1
-
-    def addError(self, test, err):
-        self.reportError(test, err)
-
-    def addFailure(self, test, err):
-        self.reportError(test, err)

pyworkflow/utils/__init__.py

@@ -1,38 +0,0 @@
-# **************************************************************************
-# *
-# * Authors:     J.M. De la Rosa Trevin (jmdelarosa@cnb.csic.es)
-# *
-# * Unidad de  Bioinformatica of Centro Nacional de Biotecnologia , CSIC
-# *
-# * 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'
-# *
-# **************************************************************************
-"""
-This module contains utilities functions and classes.
-"""
-
-from .utils import *
-from .path import *
-from .process import *
-from .which import *
-from .graph import *
-from .reflection import *
-from .log import *
-from .properties import *
-from .progressbar import ProgressBar