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

pyworkflowtests/tests/test_object.py

@@ -1,507 +0,0 @@
-#!/usr/bin/env python
-# -*- coding: utf-8 -*-
-# **************************************************************************
-# *
-# * Authors:     J.M. De la Rosa Trevin (delarosatrevin@scilifelab.se) [1]
-# *
-# * [1] 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, see <https://www.gnu.org/licenses/>.
-# *
-# *  All comments concerning this program package may be sent to the
-# *  e-mail address 'scipion@cnb.csic.es'
-# *
-# **************************************************************************
-import datetime as dt
-try:
-    from datetime import UTC  # python 3.11+
-except ImportError:
-    UTC = dt.timezone.utc
-import os
-from logging import DEBUG, lastResort
-from time import sleep
-
-import pyworkflow.object as pwobj
-import pyworkflow.tests as pwtests
-from pyworkflow.mapper.sqlite import ID, CREATION
-from ..objects import (Complex, MockSetOfImages, MockImage, MockObject,
-                       MockAcquisition, MockMicrograph)
-
-IMAGES_STK = "images.stk"
-
-NUMERIC_ATRIBUTE_NAME = "1"
-
-NUMERIC_ATTRIBUTE_VALUE = "numeric_attribute"
-
-
-class ListContainer(pwobj.Object):
-    def __init__(self, **args):
-        pwobj.Object.__init__(self, **args)
-        self.csv = pwobj.CsvList()
-    
-    
-class TestObject(pwtests.BaseTest):
-    @classmethod
-    def setUpClass(cls):
-        pwtests.setupTestOutput(cls)
-
-    def test_ObjectsDict(self):
-        # Validate that the object dict is populated correctly
-        basicObjNames = [
-            'Scalar', 'Integer', 'Float', 'String', 'Pointer', 'Boolean',
-            'OrderedObject', 'List', 'CsvList', 'PointerList', 'Set'
-        ]
-        self.assertTrue(all(name in pwobj.OBJECTS_DICT
-                            for name in basicObjNames))
-
-    def test_Object(self):
-        value = 2
-        i = pwobj.Integer(value)
-        self.assertEqual(value, i.get())
-        # compare objects
-        i2 = pwobj.Integer(value)
-        self.assertEqual(i, i2)
-        
-        value = 2.
-        f = pwobj.Float(value)
-        self.assertAlmostEqual(value, f.get())
-        
-        f.multiply(5)
-        self.assertAlmostEqual(value*5, f.get())
-        
-        a = pwobj.Integer()
-        self.assertEqual(a.hasValue(), False)
-        c = Complex.createComplex()
-        # Check values are correct
-        self.assertEqual(c.imag.get(), Complex.cGold.imag)
-        self.assertEqual(c.real.get(), Complex.cGold.real)
-        
-        # Test Boolean logic
-        b = pwobj.Boolean(False)
-        self.assertTrue(not b.get())
-
-        b.set('True')
-        self.assertTrue(b.get())
-        
-        b = pwobj.Boolean()
-        b.set(False)
-        self.assertTrue(not b.get())
-        
-        # CsvList should be empty if set to ''
-        l = pwobj.CsvList()
-        l.set('')
-        self.assertEqual(len(l), 0)
-
-        # Test emptiness
-        self.assertIsNotEmpty(b)
-
-    def testWithPointer(self):
-
-        obj = pwobj.Integer(10)
-
-        self.assertFalse(obj.hasPointer(),
-                         "Default instantiation off Integer has a pointer.")
-
-        self.assertEqual(obj.get(), 10, "Integer.get(), without pointer fails.")
-
-        pointee = pwobj.Object()
-        setattr(pointee, "value", pwobj.Integer(20))
-
-        # Set a pointer (not a real case though, but enough here)
-        obj.setPointer(pwobj.Pointer(pointee, extended='value'))
-
-        self.assertEqual(obj.get(), 20, "Integer.get() fails with a pointer.")
-
-    def test_String(self):
-        value = 'thisisastring'
-        s = pwobj.String(value)
-        self.assertEqual(value, s.get())
-        self.assertEqual(s.hasValue(), True)
-        
-        s2 = pwobj.String()
-        # None value is considered empty
-        self.assertTrue(s2.empty(), "s2 string should be empty if None")
-        s2.set(' ')
-        # Only spaces is also empty
-        self.assertTrue(s2.empty(), "s2 string should be empty if only spaces")
-        s2.set('something')
-        # No empty after some value
-        self.assertFalse(s2.empty(),
-                         "s2 string should not be empty after value")
-
-        now = dt.datetime.now()
-        s.set(now)
-        self.assertEqual(now, s.datetime())
-
-        # Ranges and values
-        s2.set("1 2 3 4")
-        self.assertEqual(s2.getListFromValues(caster=float), [1.,2.,3.,4.])
-        self.assertEqual(s2.getListFromRange(), [1, 2, 3, 4])
-
-        # Values ...
-        s2.set("2x4, 4, 7")
-        self.assertEqual(s2.getListFromValues(), [4, 4, 4, 7])
-
-        # Values ...
-        self.assertEqual(s2.getListFromValues(caster=str), ["2x4", "4", "7"])
-
-        # Ranges
-        s2.set("2-8, 1-2, 7")
-        self.assertEqual(s2.getListFromRange(), [2, 3, 4, 5, 6, 7, 8, 1, 2, 7])
-
-    def test_Pointer(self):
-        c = Complex.createComplex()
-        p = pwobj.Pointer()
-        p.set(c)
-        p.setExtended('Name')
-        c.Name = pwobj.String('Paquito')
-
-        self.assertEqual(p.get(), 'Paquito')
-        stackFn = IMAGES_STK
-        mrcsFn = "images.mrcs"
-        fn = self.getOutputPath('test_images.sqlite')
-        imgSet = MockSetOfImages(filename=fn)
-        imgSet.setSamplingRate(1.0)
-        for i in range(10):
-            img = MockImage()
-            img.setLocation(i+1, stackFn)
-            imgSet.append(img)
-
-        imgSet.write()
-
-        # Test that image number 7 is correctly retrieved
-        # from the set
-        img7 = imgSet[7]
-        self.assertEqual(img7.getFileName(), stackFn)
-
-        # Modify some properties of image 7 to test update
-        img7.setFileName(mrcsFn)
-        img7.setSamplingRate(2.0)
-        imgSet.update(img7)
-        # Write changes after the image 7 update
-        imgSet.write()
-
-        # Read again the set to be able to retrieve elements
-        imgSet = MockSetOfImages(filename=fn)
-
-        # Validate that image7 was properly updated
-        img7 = imgSet[7]
-        self.assertEqual(img7.getFileName(), mrcsFn)
-
-        o = MockObject()
-
-        o.pointer = pwobj.Pointer()
-        o.pointer.set(imgSet)
-
-        # This is not true anymore and is allowed unless we see is needed
-        # The main reason is a boost in performance.
-        # o.refC = o.pointer.get()
-        # attrNames = [k for k, a in o.getAttributes()]
-        # # Check that 'refC' should not appear in attributes
-        # # since it is only an "alias" to an existing pointed value
-        # self.assertNotIn('refC', attrNames)
-
-        self.assertFalse(o.pointer.hasExtended(),
-                         'o.pointer should not have extended at this point')
-
-        o.pointer.setExtended(7)
-
-        self.assertTrue(o.pointer.hasExtended())
-        self.assertTrue(o.pointer.hasExtended())
-        self.assertEqual(o.pointer.getExtended(), "7")
-
-        # Check that the Item 7 of the set is properly
-        # retrieved by the pointer after setting the extended to 7
-        self.assertEqual(imgSet[7].getObjId(), o.pointer.get().getObjId())
-
-        # Test the keyword arguments of Pointer constructor
-        # repeat above tests with new pointer
-        ptr = pwobj.Pointer(value=imgSet, extended=7)
-        self.assertTrue(ptr.hasExtended())
-        self.assertTrue(ptr.hasExtended())
-        self.assertEqual(ptr.getExtended(), "7")
-
-        # Check that the Item 7 of the set is properly
-        # retrieved by the pointer after setting the extended to 7
-        self.assertEqual(imgSet[7], ptr.get())
-
-        o2 = pwobj.Object()
-        o2.outputImages = imgSet
-        ptr2 = pwobj.Pointer()
-        ptr2.set(o2)
-        # Test nested extended attributes
-        ptr2.setExtended('outputImages.7')
-        self.assertEqual(imgSet[7], ptr2.get())
-
-        # Same as ptr2, but setting extended in constructor
-        ptr3 = pwobj.Pointer(value=o2, extended='outputImages.7')
-        self.assertEqual(imgSet[7], ptr3.get())
-
-        # Test copy between pointer objects
-        ptr4 = pwobj.Pointer()
-        ptr4.copy(ptr3)
-        self.assertEqual(imgSet[7], ptr4.get())
-        self.assertEqual(ptr4.getExtended(), 'outputImages.7')
-
-        # Test numeric attributes.
-        setattr(o2, NUMERIC_ATRIBUTE_NAME, NUMERIC_ATTRIBUTE_VALUE)
-        ptr5 = pwobj.Pointer(value=o2, extended=NUMERIC_ATRIBUTE_NAME)
-        self.assertEqual(NUMERIC_ATTRIBUTE_VALUE, ptr5.get())
-
-    def test_Sets(self):
-        stackFn = IMAGES_STK
-        fn = self.getOutputPath('test_images2.sqlite')
-
-        imgSet = MockSetOfImages(filename=fn)
-
-        halfTimeStamp = None
-
-        for i in range(10):
-            img = MockImage()
-            img.setLocation(i + 1, stackFn)
-            img.setSamplingRate(i % 3)
-            imgSet.append(img)
-            if i == 4:
-                sleep(1)
-                halfTimeStamp = dt.datetime.now(UTC).replace(microsecond=0)
-        imgSet.write()
-
-        # Test size is 10
-        self.assertSetSize(imgSet, 10)
-
-        # Test hasChangedSince
-        timeStamp = dt.datetime.now()
-        self.assertFalse(imgSet.hasChangedSince(timeStamp), "Set.hasChangedSince returns true when it hasn't changed.")
-        # Remove 10 seconds
-        self.assertTrue(imgSet.hasChangedSince(timeStamp-dt.timedelta(0,10)), "Set.hasChangedSince returns false when it has changed.")
-
-        # PERFORMANCE functionality
-        def checkSetIteration(limit, skipRows=None):
-
-            expectedId = 1 if skipRows is None else skipRows+1
-            index = 0
-            for item in imgSet.iterItems(limit=(limit, skipRows)):
-                self.assertEqual(item.getIndex(), expectedId+index,
-                                 "Wrong item in set when using limits.")
-                index += 1
-
-            self.assertEqual(index, limit,
-                             "Number of iterations wrong with limits")
-
-        # Check iteration with limit
-        checkSetIteration(2)
-
-        # Check iteration with limit and skip rows
-        checkSetIteration(3, 2)
-
-        # Tests unique method
-        # Requesting 1 unique value as string
-        result = imgSet.getUniqueValues("_samplingRate")
-        self.assertEqual(len(result), 3, "Unique values wrong for 1 attribute and 3 value")
-
-        # Requesting 1 unique value as list
-        result = imgSet.getUniqueValues(["_samplingRate"])
-        self.assertEqual(len(result), 3, "Unique values wrong for 1 attribute and one value as list")
-        
-        # Requesting several unique values as string
-        result = imgSet.getUniqueValues("_index")
-        self.assertEqual(len(result), 10, "Unique values wrong for id attribute")
-
-        # Requesting several unique values with several columns
-        result = imgSet.getUniqueValues(["_filename", "_samplingRate"])
-        # Here we should have 2 keys containing 2 list
-        self.assertEqual(len(result), 2, "Unique values dictionary length wrong")
-        self.assertEqual(len(result["_filename"]), 3, "Unique values dict item size wrong")
-
-        # Requesting unique values with where
-        result = imgSet.getUniqueValues("_index",where="_samplingRate = 2")
-        # Here we should have 2 values
-        self.assertEqual(len(result), 3, "Unique values with filter not working")
-
-        # Request id list
-        result = imgSet.getUniqueValues(ID)
-        # Here we should have 10 values
-        self.assertEqual(len(result), 10, "Unique values with ID")
-
-        # Use creation timestamp
-        # Request id list
-        result = imgSet.getUniqueValues(ID, where="%s>=%s" % (CREATION, imgSet.fmtDate(halfTimeStamp)))
-        self.assertEqual(len(result), 5, "Unique values after a time stamp does not work")
-
-        # Test getIdSet
-        ids = imgSet.getIdSet()
-        self.assertIsInstance(ids, set, "getIdSet does not return a set")
-        self.assertIsInstance(next(iter(ids)), int, "getIdSet items are not integer")
-        self.assertEqual(len(ids), 10, "getIdSet does not return 10 items")
-
-        # Request item by id
-        item = imgSet[1]
-        self.assertEqual(item.getObjId(), 1, "Item accessed by [] and id does not work")
-
-        # Request item by field
-        item = imgSet.getItem("id", 2)
-        self.assertEqual(item.getObjId(), 2, "Item accessed field id does not work")
-
-        # Test load properties queries
-        from pyworkflow.mapper.sqlite_db import logger
-        logger.setLevel(DEBUG)
-        lastResort.setLevel(DEBUG)
-        imgSetVerbose = MockSetOfImages(filename=fn)
-        imgSetVerbose.loadAllProperties()
-
-        # Compare sets are "equal"
-        self.compareSetProperties(imgSet, imgSetVerbose, ignore=[])
-
-
-    def test_copyAttributes(self):
-        """ Check that after copyAttributes, the values
-        were properly copied.
-        """
-        c1 = Complex(imag=10., real=11.)
-        c2 = Complex(imag=0., real=1.0001)
-        
-        # Float values are different, should not be equal
-        self.assertFalse(c1.equalAttributes(c2))
-        c2.copyAttributes(c1, 'imag', 'real')
-        
-        self.assertTrue(c1.equalAttributes(c2), 
-                        'Complex c1 and c2 have not equal attributes'
-                        '\nc1: %s\nc2: %s\n' % (c1, c2))
-
-        c1.score = pwobj.Float(1.)
-
-        # If we copyAttributes again, score dynamic attribute should
-        # be set in c2
-        c2.copyAttributes(c1, 'score')
-        self.assertTrue(hasattr(c2, 'score'))
-        
-    def test_equalAttributes(self):
-        """ Check that equal attributes function behaves well
-        to compare floats with a given precision.
-        """
-        c1 = Complex(imag=0., real=1.)
-        c2 = Complex(imag=0., real=1.0001)
-        
-        # Since Float precision is 0.001, now c1 and c2
-        # should have equal attributes
-        self.assertTrue(c1.equalAttributes(c2))
-        # Now if we set a more restrictive precision
-        # c1 and c2 are not longer equals
-        pwobj.Float.setPrecision(0.0000001)
-        self.assertFalse(c1.equalAttributes(c2))
-
-    def test_formatString(self):
-        """ Test that Scalar objects behave well
-        when using string formatting such as: %f or %d
-        """
-        i = pwobj.Integer(10)
-        f = pwobj.Float(3.345)
-        
-        s1 = "i = %d, f = %0.3f" % (i, f)
-        
-        self.assertEqual(s1, "i = 10, f = 3.345")
-
-    def test_getObjDict(self):
-        """ Test retrieving an object dictionary with its attribute values."""
-        acq1 = MockAcquisition(magnification=50000,
-                               voltage=200,
-                               sphericalAberration=2.7,
-                               dosePerFrame=1)
-        m1 = MockMicrograph(
-            'my_movie.mrc', objId=1, objLabel='test micrograph',
-            objComment='Testing store and retrieve from dict.')
-        m1.setSamplingRate(1.6)
-        m1.setAcquisition(acq1)
-        m1Dict = m1.getObjDict(includeBasic=True)
-
-        goldDict1 = dict([
-            ('object.id', 1),
-            ('object.label', 'test micrograph'),
-            ('object.comment', 'Testing store and retrieve from dict.'),
-            ('_index', 0),
-            ('_filename', 'my_movie.mrc'),
-            ('_samplingRate', 1.6),
-            ('_micName', None),
-            ('_acquisition', None),
-            ('_acquisition._magnification', 50000.0),
-            ('_acquisition._voltage', 200.0),
-            ('_acquisition._sphericalAberration', 2.7),
-            ('_acquisition._amplitudeContrast', None),
-            ('_acquisition._doseInitial', 0.0),
-            ('_acquisition._dosePerFrame', 1.0),
-             ])
-
-        self.assertEqual(goldDict1, m1Dict)
-
-    def test_Dict(self):
-        d = pwobj.Dict(default='missing')
-        d.update({1: 'one', 2: 'two'})
-
-        # Return default value for any non-present key
-        self.assertEqual('missing', d[10])
-
-        # Return true for any 'contains' query
-        self.assertTrue(100 in d)
-        
-
-class TestUtils(pwtests.BaseTest):
-
-    @classmethod
-    def setUpClass(cls):
-        pwtests.setupTestOutput(cls)
-            
-    def test_ListsFunctions(self):
-        """ Test of some methods that retrieve lists from string. """
-        from pyworkflow.utils import getListFromValues, getFloatListFromValues,\
-            getBoolListFromValues
-        
-        results = [('2x1 2x2 4 5', getListFromValues, ['2x1', '2x2', '4', '5'], None),
-                   ('2x1 2x2 4 5', getFloatListFromValues, [1., 1., 2., 2., 4., 5.],None),
-                   ('1 2 3x3 0.5', getFloatListFromValues, [1., 2., 3., 3., 3., 0.5, 0.5, 0.5], 8),
-                   ('3x1 3x0 1', getBoolListFromValues, [True, True, True, False, False, False, True, True],8),
-                   ]
-
-        for s, func, goldList, length in results:
-
-            l = func(s, length=length)
-            for i in range(0,len(goldList)):
-                self.assertEqual(l[i], goldList[i])
-
-            self.assertEqual(len(goldList), len(l), )
-                
-    def test_Environ(self):
-        """ Test the Environ class with its utilities. """
-        from pyworkflow.utils import Environ
-        env = Environ({'PATH': '/usr/bin:/usr/local/bin',
-                       'LD_LIBRARY_PATH': '/usr/lib:/usr/lib64'
-                       })
-        env1 = Environ(env)
-        env1.set('PATH', '/usr/local/xmipp')
-        self.assertEqual(env1['PATH'], '/usr/local/xmipp')
-        self.assertEqual(env1['LD_LIBRARY_PATH'], env['LD_LIBRARY_PATH'])
-        
-        env2 = Environ(env)
-        env2.set('PATH', '/usr/local/xmipp', position=Environ.BEGIN)
-        self.assertEqual(env2['PATH'], '/usr/local/xmipp' + os.pathsep +
-                         env['PATH'])
-        self.assertEqual(env2['LD_LIBRARY_PATH'], env['LD_LIBRARY_PATH'])
-        
-        env3 = Environ(env)
-        env3.update({'PATH': '/usr/local/xmipp', 
-                     'LD_LIBRARY_PATH': '/usr/local/xmipp/lib'},
-                    position=Environ.END)
-        self.assertEqual(env3['PATH'], env['PATH'] + os.pathsep +
-                         '/usr/local/xmipp')
-        self.assertEqual(env3['LD_LIBRARY_PATH'], env['LD_LIBRARY_PATH'] +
-                         os.pathsep + '/usr/local/xmipp/lib')

pyworkflowtests/tests/test_project.py

@@ -1,42 +0,0 @@
-#!/usr/bin/env python
-# **************************************************************************
-# *
-# * Authors:     Pablo Conesa (pconesa@cnb.csic.es) [1]
-# *
-# * [1] 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, see <https://www.gnu.org/licenses/>.
-# *
-# *  All comments concerning this program package may be sent to the
-# *  e-mail address 'scipion@cnb.csic.es'
-# *
-# **************************************************************************
-
-from pyworkflow.project.project import Project
-from unittest import TestCase
-from unittest.mock import patch
-
-
-# NOTE: This test as it is might serve as a skeleton for future testing the fixLinks
-# but as it is now it does not test anything at all. I leave it as an example of using patch (mock testing)
-class TestProject(TestCase):
-
-    def test_fixlinks(self):
-        """ Test fixlinks call."""
-
-        with patch("pyworkflow.project.Project.getRuns") as getruns:
-
-            getruns.return_value = []
-            proj = Project("domain", "path")
-            proj.fixLinks("foo")

pyworkflowtests/tests/test_protocol_execution.py

@@ -1,142 +0,0 @@
-# -*- coding: utf-8 -*-
-# **************************************************************************
-# *
-# * Authors:     J.M. De la Rosa Trevin (delarosatrevin@scilifelab.se) [1]
-# *
-# * [1] 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, see <https://www.gnu.org/licenses/>.
-# *
-# *  All comments concerning this program package may be sent to the
-# *  e-mail address 'scipion@cnb.csic.es'
-# *
-# **************************************************************************
-import threading
-
-import pyworkflow.tests as pwtests
-import pyworkflow.mapper as pwmapper
-import pyworkflow.protocol as pwprot
-from pyworkflow.project import Project
-from pyworkflow.protocol.constants import VOID_GPU
-
-
-# TODO: this test seems not to be finished.
-from pyworkflowtests.protocols import SleepingProtocol
-from pyworkflowtests import Domain
-
-
-class TestProtocolExecution(pwtests.BaseTest):
-    
-    @classmethod
-    def setUpClass(cls):
-        pwtests.setupTestOutput(cls)
-    
-    def test_StepExecutor(self):
-        """Test the list with several Complex"""
-        fn = self.getOutputPath("protocol.sqlite")
-        print("Writing to db: %s" % fn)
-
-        # Discover objects and protocols
-        mapperDict = Domain.getMapperDict()
-
-        # Associate the project
-        proj = Project(Domain, path=self.getOutputPath(''))
-
-        # Check that the protocol has associated package
-        mapper = pwmapper.SqliteMapper(fn, mapperDict)
-        prot = SleepingProtocol(mapper=mapper, n=2, project= proj,
-                                workingDir=self.getOutputPath(''))
-        domain = prot.getClassDomain()
-        domain.printInfo()
-
-        prot.setStepsExecutor(pwprot.StepExecutor(hostConfig=None))
-        prot.makeWorkingDir()
-        prot.run()
-        mapper.commit()
-        mapper.close()
-
-        self.assertEqual(prot._steps[0].getStatus(), pwprot.STATUS_FINISHED)
-        
-        mapper2 = pwmapper.SqliteMapper(fn, mapperDict)
-        prot2 = mapper2.selectById(prot.getObjId())
-        
-        self.assertEqual(prot.endTime.get(), prot2.endTime.get())
-
-    def test_gpu_anonimization(self):
-
-        self.assertEqual(pwprot.anonimizeGPUs([0, 1, 2]),[0, 1, 2], "Anonimization of GPUs does not work")
-        self.assertEqual(pwprot.anonimizeGPUs([2, 1, 0]), [0, 1, 2], "Anonimization of GPUs does not work")
-        self.assertEqual(pwprot.anonimizeGPUs([2, 1, 2]), [0, 1, 0], "Anonimization of GPUs does not work")
-        self.assertEqual(pwprot.anonimizeGPUs([2, 1, 2, 4]), [0, 1, 0, 2], "Anonimization of GPUs does not work")
-
-    def test_gpuSlots(self):
-        """ Test gpu slots are properly composed in combination of threads"""
-
-        # Test basic GPU setu methods
-        stepExecutor = pwprot.ThreadStepExecutor(None, 1, gpuList=None)
-
-
-        self.assertEqual(stepExecutor.cleanVoidGPUs([0,1]), [0,1],
-                         "CleanVoidGpus does not work in absence of void GPUS")
-
-        self.assertEqual(stepExecutor.cleanVoidGPUs([0, VOID_GPU]), [0],
-                         "CleanVoidGpus does not work with a void GPU")
-
-        self.assertEqual(stepExecutor.cleanVoidGPUs([VOID_GPU, VOID_GPU]), [],
-                         "CleanVoidGpus does not work with all void GPU")
-
-
-        currThread = threading.currentThread()
-        currThread.thId = 1
-        self.assertEqual(stepExecutor.getGpuList(),[], "Gpu list should be empty")
-
-        # 2 threads 1 GPU
-        stepExecutor = pwprot.ThreadStepExecutor(None, 2, gpuList=[1])
-        self.assertEqual(stepExecutor.getGpuList(),[1], "Gpu list should be [1]")
-
-        currThread.thId = 2
-        self.assertEqual(stepExecutor.getGpuList(),[], "Gpu list should be empty after a second request")
-
-
-        # 2 threads 3 GPUs
-        stepExecutor = pwprot.ThreadStepExecutor(None, 2, gpuList=[0,1,2])
-        self.assertEqual(stepExecutor.getGpuList(),[0,1], "Gpu list should be [0,1]")
-
-        currThread.thId = 1
-        self.assertEqual(stepExecutor.getGpuList(),[2], "Gpu list should be [2] after a second request")
-
-
-        # 2 threads 4 GPUs with void gpus
-        stepExecutor = pwprot.ThreadStepExecutor(None, 2, gpuList=[0,1,2, VOID_GPU])
-        self.assertEqual(stepExecutor.getGpuList(),[0,1], "Gpu list should be [0,1]")
-
-        currThread.thId = 2
-        self.assertEqual(stepExecutor.getGpuList(),[2], "Gpu list should be [2] after a second request without the void gpu")
-
-        # less GPUs than threads. No extension should happen
-        stepExecutor = pwprot.ThreadStepExecutor(None, 4, gpuList=[0, VOID_GPU, 2])
-        self.assertEqual(stepExecutor.getGpuList(), [0], "Gpu list should not be extended")
-
-        currThread.thId = 1
-        self.assertEqual(stepExecutor.getGpuList(), [2],
-                         "Gpu list should be [2] after a second request, skipping the VOID gpu")
-
-        currThread.thId = 3
-        self.assertEqual(stepExecutor.getGpuList(), [], "Gpu list should be empty ather all GPU slots are busy")
-
-
-
-
-
-