Python shutil.copy() Examples

def _copy_file(filename, location, link):
    copy = True
    download_location = os.path.join(location, link.filename)
    if os.path.exists(download_location):
        response = ask_path_exists(
            'The file %s exists. (i)gnore, (w)ipe, (b)ackup, (a)abort' %
            display_path(download_location), ('i', 'w', 'b', 'a'))
        if response == 'i':
            copy = False
        elif response == 'w':
            logger.warning('Deleting %s', display_path(download_location))
            os.remove(download_location)
        elif response == 'b':
            dest_file = backup_dir(download_location)
            logger.warning(
                'Backing up %s to %s',
                display_path(download_location),
                display_path(dest_file),
            )
            shutil.move(download_location, dest_file)
        elif response == 'a':
            sys.exit(-1)
    if copy:
        shutil.copy(filename, download_location)
        logger.info('Saved %s', display_path(download_location)) 

def backup_propic(self):
        """Backups the profile picture for the given
           entity as the current peer profile picture, returning its path"""

        # Allow multiple versions of the profile picture
        # TODO Maybe this should be another method, because when downloading media... We also have multiple versions
        filename = self.media_handler.get_propic_path(self.entity, allow_multiple=True)
        generic_filename = self.media_handler.get_propic_path(self.entity)
        if filename:  # User may not have a profile picture
            if not isfile(filename):
                # Only download the file if it doesn't exist yet
                self.client.download_profile_photo(self.entity.photo,
                                                   file_path=filename,
                                                   add_extension=False)
                # If we downloaded a new version, copy it to the "default" generic file
                if isfile(generic_filename):
                    remove(generic_filename)
                shutil.copy(filename, generic_filename)

            # The user may not have a profile picture
            return generic_filename 

def _copy_file(filename, location, link):
    copy = True
    download_location = os.path.join(location, link.filename)
    if os.path.exists(download_location):
        response = ask_path_exists(
            'The file %s exists. (i)gnore, (w)ipe, (b)ackup, (a)abort' %
            display_path(download_location), ('i', 'w', 'b', 'a'))
        if response == 'i':
            copy = False
        elif response == 'w':
            logger.warning('Deleting %s', display_path(download_location))
            os.remove(download_location)
        elif response == 'b':
            dest_file = backup_dir(download_location)
            logger.warning(
                'Backing up %s to %s',
                display_path(download_location),
                display_path(dest_file),
            )
            shutil.move(download_location, dest_file)
        elif response == 'a':
            sys.exit(-1)
    if copy:
        shutil.copy(filename, download_location)
        logger.info('Saved %s', display_path(download_location)) 

def run(self):
        _install.run(self)
        print("Installing udev rules...")
        if not os.path.isdir("/etc/udev/rules.d"):
            print("WARNING: udev rules have not been installed (/etc/udev/rules.d is not a directory)")
            return
        try:
            shutil.copy("./rivalcfg/data/99-steelseries-rival.rules", "/etc/udev/rules.d/")
        except IOError:
            print("WARNING: udev rules have not been installed (permission denied)")
            return
        try:
            subprocess.call(["udevadm", "trigger"])
        except OSError:
            print("WARNING: unable to update udev rules, please run the 'udevadm trigger' command")
            return
        print("Done!") 

def concatenate(out_file_name, all_in_file_names):
    """ Concatenate a list of bam files into a final output file """

    # Filter out empty BAM files -- these cause samtools cat to generate
    # a BAM with a premature end block
    in_file_names = [f for f in all_in_file_names if not bam_is_empty(f)]

    if len(in_file_names) > 1:
        args = ['samtools', 'cat', '-o', out_file_name]
        args.extend(in_file_names)
        subprocess.check_call(args)
    elif len(in_file_names) == 0:
        # If all the BAMs are empty, just copy 1 over
        shutil.copy(all_in_file_names[0], out_file_name)
    else:
        shutil.copy(in_file_names[0], out_file_name) 

def post_action(self):
        mbed_tools_path = self.get_tools_dir()

        if not mbed_tools_path and (self.is_classic or os.path.exists(os.path.join(self.path, Cfg.file))):
            self.add_tools(os.path.join(self.path, '.temp'))
            mbed_tools_path = self.get_tools_dir()

        if not mbed_tools_path:
            warning("Cannot find the mbed tools directory in \"%s\"" % self.path)
            return False

        if (not os.path.isfile(os.path.join(self.path, 'mbed_settings.py')) and
                os.path.isfile(os.path.join(mbed_tools_path, 'default_settings.py'))):
            shutil.copy(os.path.join(mbed_tools_path, 'default_settings.py'), os.path.join(self.path, 'mbed_settings.py'))

        self.check_requirements(True) 

def copyFromReader(self, reader, sourcePath, destPath):
		"""
		Copy the sourcePath in the provided UFOReader to destPath
		in this writer. The paths must be relative. They may represent
		directories or paths. This uses the most memory efficient
		method possible for copying the data possible.
		"""
		if not isinstance(reader, UFOReader):
			raise UFOLibError("The reader must be an instance of UFOReader.")
		fullSourcePath = os.path.join(reader._path, sourcePath)
		if not reader._checkForFile(fullSourcePath):
			raise UFOLibError("No file named \"%s\" to copy from." % sourcePath)
		fullDestPath = os.path.join(self._path, destPath)
		if os.path.exists(fullDestPath):
			raise UFOLibError("A file named \"%s\" already exists." % sourcePath)
		self._buildDirectoryTree(destPath)
		if os.path.isdir(fullSourcePath):
			shutil.copytree(fullSourcePath, fullDestPath)
		else:
			shutil.copy(fullSourcePath, fullDestPath)

	# UFO mod time 

def summonMagic():
    import magic
    if hasattr(magic, 'from_file'):
        # https://pypi.python.org/pypi/python-magic
        return magic
    elif hasattr(magic, 'open'):
        # http://www.darwinsys.com/file/, in Debian as python3-magic
        class WrapMagic:
            def __init__(self):
                self.magic = magic.open(magic.NONE)
                self.magic.load()

            def from_file(self, name):
                return self.magic.file(name)
        return WrapMagic()
    else:
        raise NotImplementedError("I do not understand your magic")

### directory copy ### 

def load_layer_index(self):
        # Load Layer_Index

        # Check if we have a mirror-index, and load it if we do...
        mirror_index_path = self.load_mirror_index(self.base_url + '/mirror-index')

        # Mirror also has a copy of the associated XML bits
        if mirror_index_path:
            self.xml_dir = os.path.join(mirror_index_path, 'xml')

        # Setup replace strings as late as possible.  The various self.* values
        # may be modified prior to this place.
        replace = []
        replace = replace + settings.REPLACE
        replace = replace + [
                   ( '#INSTALL_DIR#', self.install_dir ),
                   ( '#BASE_URL#', self.base_url ),
                   ( '#BASE_BRANCH#', self.base_branch ),
                  ]

        self.index = Layer_Index(indexcfg=settings.INDEXES, base_branch=self.base_branch, replace=replace, mirror=mirror_index_path) 

def sourcecpy(src, des):
    src = os.path.normpath(src)
    des = os.path.normpath(des)
    if not os.path.exists(src) or not os.path.exists(src):
        print("folder is not exist")
        sys.exit(1)
    # ?????????????????????????
    os.chdir(src)
    src_file = [os.path.join(src, file) for file in os.listdir()]
    for source in src_file:
        # ????
        if os.path.isfile(source):
            shutil.copy(source, des)  # ????????????????
        # ????
        if os.path.isdir(source):
            p, src_name = os.path.split(source)
            des = os.path.join(des, src_name)
            shutil.copytree(source, des)  # ??????????????????

# ??CLI????? 

def __unitsNumChanged(self):
        if hasattr(self,"auto_result"):
            if self.autoSortThisCheck.isChecked():

                self.saveChannelCheck.setChecked(False)
                self.chnResultPool.pop(self.selectChan,None)

                self.units = self.auto_result.copy()
                self.units[self.units>int(self.unitsNumWgt.currentText())] = 0

                self.__draw_pk3()
                self.__update_pk3_roi()
                self.__draw_pk2()
                if self.pca_3d is True:
                    self.__draw_3D_PCA()

                
# The SpikeSorting class use this class to draw multiple lines quickly in a memory-efficient way. 

def __unitsNumChanged(self):
        if hasattr(self,"auto_result"):
            if self.autoSortThisCheck.isChecked():

                self.saveChannelCheck.setChecked(False)
                self.chnResultPool.pop(self.selectChan,None)

                self.units = self.auto_result.copy()
                self.units[self.units>int(self.unitsNumWgt.currentText())] = 0

                self.__draw_pk3()
                self.__update_pk3_roi()
                self.__draw_pk2()
                if self.pca_3d is True:
                    self.__draw_3D_PCA()

                
# The SpikeSorting class use this class to draw multiple lines quickly in a memory-efficient way. 

def _copy_file(filename, location, content_type, link):
    copy = True
    download_location = os.path.join(location, link.filename)
    if os.path.exists(download_location):
        response = ask_path_exists(
            'The file %s exists. (i)gnore, (w)ipe, (b)ackup ' %
            display_path(download_location), ('i', 'w', 'b'))
        if response == 'i':
            copy = False
        elif response == 'w':
            logger.warn('Deleting %s' % display_path(download_location))
            os.remove(download_location)
        elif response == 'b':
            dest_file = backup_dir(download_location)
            logger.warn('Backing up %s to %s'
                        % (display_path(download_location), display_path(dest_file)))
            shutil.move(download_location, dest_file)
    if copy:
        shutil.copy(filename, download_location)
        logger.notify('Saved %s' % display_path(download_location)) 

def test_updates_package(self):
        tempdir = tempfile.mkdtemp()
        requirements = os.path.join(tempdir, 'requirements.txt')
        shutil.copy('tests/samples/requirements.txt', requirements)
        args = ['-r', requirements]

        with utils.mock.patch('pip._internal.index.PackageFinder.find_all_candidates') as mock_find_all_candidates:
            project = 'flask'
            version = '0.10.1'
            link = Link('')
            candidate = InstallationCandidate(project, version, link)
            mock_find_all_candidates.return_value = [candidate]

            result = self.runner.invoke(pur, args)
            self.assertIsNone(result.exception)
            expected_output = "Updated flask: 0.9 -> 0.10.1\nAll requirements up-to-date.\n"
            self.assertEquals(u(result.output), u(expected_output))
            self.assertEquals(result.exit_code, 0)
            expected_requirements = open('tests/samples/results/test_updates_package').read()
            self.assertEquals(open(requirements).read(), expected_requirements) 

def test_updates_package_in_nested_requirements(self):
        tempdir = tempfile.mkdtemp()
        requirements = os.path.join(tempdir, 'requirements-with-nested-reqfile.txt')
        requirements_nested = os.path.join(tempdir, 'requirements-nested.txt')
        shutil.copy('tests/samples/requirements-with-nested-reqfile.txt', requirements)
        shutil.copy('tests/samples/requirements-nested.txt', requirements_nested)
        args = ['-r', requirements]

        with utils.mock.patch('pip._internal.index.PackageFinder.find_all_candidates') as mock_find_all_candidates:
            project = 'readtime'
            version = '0.10.1'
            link = Link('')
            candidate = InstallationCandidate(project, version, link)
            mock_find_all_candidates.return_value = [candidate]

            result = self.runner.invoke(pur, args)
            self.assertIsNone(result.exception)
            expected_output = "Updated readtime: 0.9 -> 0.10.1\nAll requirements up-to-date.\n"
            self.assertEquals(u(result.output), u(expected_output))
            self.assertEquals(result.exit_code, 0)
            expected_requirements = open('tests/samples/results/test_updates_package_in_nested_requirements').read()
            self.assertEquals(open(requirements).read(), expected_requirements)
            expected_requirements = open('tests/samples/results/test_updates_package_in_nested_requirements_nested').read()
            self.assertEquals(open(requirements_nested).read(), expected_requirements) 

def test_requirements_long_option_accepted(self):
        tempdir = tempfile.mkdtemp()
        requirements = os.path.join(tempdir, 'requirements.txt')
        shutil.copy('tests/samples/requirements.txt', requirements)
        args = ['--requirement', requirements]

        with utils.mock.patch('pip._internal.index.PackageFinder.find_all_candidates') as mock_find_all_candidates:
            project = 'flask'
            version = '0.10.1'
            link = Link('')
            candidate = InstallationCandidate(project, version, link)
            mock_find_all_candidates.return_value = [candidate]

            result = self.runner.invoke(pur, args)
            self.assertIsNone(result.exception)
            expected_output = "Updated flask: 0.9 -> 0.10.1\nAll requirements up-to-date.\n"
            self.assertEquals(u(result.output), u(expected_output))
            self.assertEquals(result.exit_code, 0)
            expected_requirements = open('tests/samples/results/test_updates_package').read()
            self.assertEquals(open(requirements).read(), expected_requirements) 

def test_exit_code_from_no_updates(self):
        tempdir = tempfile.mkdtemp()
        requirements = os.path.join(tempdir, 'requirements.txt')
        shutil.copy('tests/samples/requirements-up-to-date.txt', requirements)
        args = ['-r', requirements, '--nonzero-exit-code']

        with utils.mock.patch('pip._internal.index.PackageFinder.find_all_candidates') as mock_find_all_candidates:
            project = 'flask'
            version = '0.10.1'
            link = Link('')
            candidate = InstallationCandidate(project, version, link)
            mock_find_all_candidates.return_value = [candidate]

            result = self.runner.invoke(pur, args)
            self.assertEqual(result.exception.code, 10)
            expected_output = "All requirements up-to-date.\n"
            self.assertEquals(u(result.output), u(expected_output))
            self.assertEquals(result.exit_code, 10)
            expected_requirements = open('tests/samples/results/test_updates_package').read()
            self.assertEquals(open(requirements).read(), expected_requirements) 

def test_exit_code_from_nested_requirements_file(self):
        tempdir = tempfile.mkdtemp()
        requirements = os.path.join(tempdir, 'requirements-with-nested-reqfile.txt')
        requirements_nested = os.path.join(tempdir, 'requirements-nested.txt')
        shutil.copy('tests/samples/requirements-with-nested-reqfile.txt', requirements)
        shutil.copy('tests/samples/requirements-nested.txt', requirements_nested)
        args = ['-r', requirements, '--nonzero-exit-code']

        with utils.mock.patch('pip._internal.index.PackageFinder.find_all_candidates') as mock_find_all_candidates:
            project = 'readtime'
            version = '0.10.1'
            link = Link('')
            candidate = InstallationCandidate(project, version, link)
            mock_find_all_candidates.return_value = [candidate]

            result = self.runner.invoke(pur, args)
            self.assertEqual(result.exception.code, 11)
            expected_output = "Updated readtime: 0.9 -> 0.10.1\nAll requirements up-to-date.\n"
            self.assertEquals(u(result.output), u(expected_output))
            self.assertEquals(result.exit_code, 11)
            expected_requirements = open('tests/samples/results/test_updates_package_in_nested_requirements').read()
            self.assertEquals(open(requirements).read(), expected_requirements)
            expected_requirements = open('tests/samples/results/test_updates_package_in_nested_requirements_nested').read()
            self.assertEquals(open(requirements_nested).read(), expected_requirements) 

def test_no_recursive_option(self):
        tempdir = tempfile.mkdtemp()
        requirements = os.path.join(tempdir, 'requirements-with-nested-reqfile.txt')
        requirements_nested = os.path.join(tempdir, 'requirements-nested.txt')
        shutil.copy('tests/samples/requirements-with-nested-reqfile.txt', requirements)
        shutil.copy('tests/samples/requirements-nested.txt', requirements_nested)
        args = ['-r', requirements, '-n']

        with utils.mock.patch('pip._internal.index.PackageFinder.find_all_candidates') as mock_find_all_candidates:
            project = 'readtime'
            version = '0.10.1'
            link = Link('')
            candidate = InstallationCandidate(project, version, link)
            mock_find_all_candidates.return_value = [candidate]

            result = self.runner.invoke(pur, args)
            self.assertIsNone(result.exception)
            expected_output = "All requirements up-to-date.\n"
            self.assertEquals(u(result.output), u(expected_output))
            self.assertEquals(result.exit_code, 0)

            expected_requirements = open('tests/samples/requirements-with-nested-reqfile.txt').read()
            self.assertEquals(open(requirements).read(), expected_requirements)
            expected_requirements = open('tests/samples/requirements-nested.txt').read()
            self.assertEquals(open(requirements_nested).read(), expected_requirements) 

def test_skip_package(self):
        tempdir = tempfile.mkdtemp()
        requirements = os.path.join(tempdir, 'requirements.txt')
        shutil.copy('tests/samples/requirements-multiple.txt', requirements)
        args = ['-r', requirements, '-s', 'flask']

        with utils.mock.patch('pip._internal.index.PackageFinder.find_all_candidates') as mock_find_all_candidates:
            project = 'flask'
            version = '0.10.1'
            link = Link('')
            candidate = InstallationCandidate(project, version, link)
            mock_find_all_candidates.return_value = [candidate]

            result = self.runner.invoke(pur, args)
            self.assertIsNone(result.exception)
            expected_output = "Updated Alembic: 0.9 -> 0.10.1\nUpdated sqlalchemy: 0.9 -> 0.10.1\nAll requirements up-to-date.\n"
            self.assertEquals(u(result.output), u(expected_output))
            self.assertEquals(result.exit_code, 0)
            expected_requirements = open('tests/samples/results/test_skip_package').read()
            self.assertEquals(open(requirements).read(), expected_requirements) 

def test_skip_multiple_packages(self):
        requirements = 'tests/samples/requirements-multiple.txt'
        tempdir = tempfile.mkdtemp()
        tmpfile = os.path.join(tempdir, 'requirements.txt')
        shutil.copy(requirements, tmpfile)
        args = ['-r', tmpfile, '-s', 'flask, alembic , SQLAlchemy']

        with utils.mock.patch('pip._internal.index.PackageFinder.find_all_candidates') as mock_find_all_candidates:
            project = 'flask'
            version = '0.10.1'
            link = Link('')
            candidate = InstallationCandidate(project, version, link)
            mock_find_all_candidates.return_value = [candidate]

            result = self.runner.invoke(pur, args)
            self.assertIsNone(result.exception)
            expected_output = "All requirements up-to-date.\n"
            self.assertEquals(u(result.output), u(expected_output))
            self.assertEquals(result.exit_code, 0)
            expected_requirements = open(requirements).read()
            self.assertEquals(open(tmpfile).read(), expected_requirements) 

def test_only(self):
        tempdir = tempfile.mkdtemp()
        requirements = os.path.join(tempdir, 'requirements.txt')
        shutil.copy('tests/samples/requirements-multiple.txt', requirements)
        args = ['-r', requirements, '--only', 'flask']

        with utils.mock.patch('pip._internal.index.PackageFinder.find_all_candidates') as mock_find_all_candidates:
            project = 'flask'
            version = '0.10.1'
            link = Link('')
            candidate = InstallationCandidate(project, version, link)
            mock_find_all_candidates.return_value = [candidate]

            result = self.runner.invoke(pur, args)
            self.assertIsNone(result.exception)
            expected_output = "Updated flask: 0.9 -> 0.10.1\nAll requirements up-to-date.\n"
            self.assertEquals(u(result.output), u(expected_output))
            self.assertEquals(result.exit_code, 0)
            expected_requirements = open('tests/samples/results/test_only').read()
            self.assertEquals(open(requirements).read(), expected_requirements) 

def test_updates_package_with_no_version_specified(self):
        tempdir = tempfile.mkdtemp()
        requirements = os.path.join(tempdir, 'requirements.txt')
        shutil.copy('tests/samples/requirements.txt', requirements)
        args = ['-r', requirements, '-f']

        with utils.mock.patch('pip._internal.index.PackageFinder.find_all_candidates') as mock_find_all_candidates:
            project = 'flask'
            version = '0.10.1'
            link = Link('')
            candidate = InstallationCandidate(project, version, link)
            mock_find_all_candidates.return_value = [candidate]

            result = self.runner.invoke(pur, args)
            self.assertIsNone(result.exception)
            expected_output = "Updated flask: 0.9 -> 0.10.1\nUpdated flask: Unknown -> 0.10.1\nAll requirements up-to-date.\n"
            self.assertEquals(u(result.output), u(expected_output))
            self.assertEquals(result.exit_code, 0)
            expected_requirements = open('tests/samples/results/test_updates_package_with_no_version_specified').read()
            self.assertEquals(open(requirements).read(), expected_requirements) 

def test_invalid_package(self):
        requirements = 'tests/samples/requirements.txt'
        tempdir = tempfile.mkdtemp()
        tmpfile = os.path.join(tempdir, 'requirements.txt')
        shutil.copy(requirements, tmpfile)
        args = ['-r', tmpfile]

        with utils.mock.patch('pip._internal.index.PackageFinder.find_all_candidates') as mock_find_all_candidates:
            mock_find_all_candidates.return_value = []

            result = self.runner.invoke(pur, args)
            expected_output = "All requirements up-to-date.\n"
            self.assertEquals(u(result.output), u(expected_output))
            self.assertIsNone(result.exception)
            self.assertEquals(result.exit_code, 0)
            self.assertEquals(open(tmpfile).read(), open(requirements).read()) 

def test_no_arguments(self):
        tempdir = tempfile.mkdtemp()
        requirements = os.path.join(tempdir, 'requirements.txt')
        shutil.copy('tests/samples/requirements.txt', requirements)
        args = []

        with utils.mock.patch('pip._internal.index.PackageFinder.find_all_candidates') as mock_find_all_candidates:
            project = 'flask'
            version = '0.10.1'
            link = Link('')
            candidate = InstallationCandidate(project, version, link)
            mock_find_all_candidates.return_value = [candidate]

            with self.cd(tempdir):
                result = self.runner.invoke(pur, args)

            self.assertIsNone(result.exception)
            expected_output = "Updated flask: 0.9 -> 0.10.1\nAll requirements up-to-date.\n"
            self.assertEquals(u(result.output), u(expected_output))
            self.assertEquals(result.exit_code, 0)
            expected_requirements = open('tests/samples/results/test_updates_package').read()
            self.assertEquals(open(requirements).read(), expected_requirements) 

def test_updates_package_with_number_in_name(self):
        tempdir = tempfile.mkdtemp()
        requirements = os.path.join(tempdir, 'requirements.txt')
        shutil.copy('tests/samples/requirements-version-in-name.txt', requirements)
        args = ['-r', requirements]

        with utils.mock.patch('pip._internal.index.PackageFinder.find_all_candidates') as mock_find_all_candidates:
            project = 'package1'
            version = '2.0'
            link = Link('')
            candidate = InstallationCandidate(project, version, link)
            mock_find_all_candidates.return_value = [candidate]

            result = self.runner.invoke(pur, args)
            self.assertIsNone(result.exception)
            expected_output = "Updated package1: 1 -> 2.0\nAll requirements up-to-date.\n"
            self.assertEquals(u(result.output), u(expected_output))
            self.assertEquals(result.exit_code, 0)
            expected_requirements = open('tests/samples/results/test_updates_package_with_version_in_name').read()
            self.assertEquals(open(requirements).read(), expected_requirements) 

def test_updates_package_with_extras(self):
        tempdir = tempfile.mkdtemp()
        requirements = os.path.join(tempdir, 'requirements.txt')
        shutil.copy('tests/samples/requirements-with-extras.txt', requirements)
        args = ['-r', requirements]

        with utils.mock.patch('pip._internal.index.PackageFinder.find_all_candidates') as mock_find_all_candidates:
            project = 'firstpackage'
            version = '2.0'
            link = Link('')
            candidate = InstallationCandidate(project, version, link)
            mock_find_all_candidates.return_value = [candidate]

            result = self.runner.invoke(pur, args)
            expected_output = "Updated firstpackage1: 1 -> 2.0\nAll requirements up-to-date.\n"
            self.assertEquals(u(result.output), u(expected_output))
            self.assertIsNone(result.exception)
            self.assertEquals(result.exit_code, 0)
            expected_requirements = open('tests/samples/results/test_updates_package_with_extras').read()
            self.assertEquals(open(requirements).read(), expected_requirements) 

def test_max_version_spec_prevents_updating_package(self):
        requirements = 'tests/samples/requirements-with-max-version-spec.txt'
        tempdir = tempfile.mkdtemp()
        tmpfile = os.path.join(tempdir, 'requirements.txt')
        shutil.copy(requirements, tmpfile)
        args = ['-r', tmpfile]

        with utils.mock.patch('pip._internal.index.PackageFinder.find_all_candidates') as mock_find_all_candidates:
            project = 'afakepackage'
            version = '2.0'
            link = Link('')
            candidate = InstallationCandidate(project, version, link)
            mock_find_all_candidates.return_value = [candidate]

            result = self.runner.invoke(pur, args)
            self.assertIsNone(result.exception)
            expected_output = "All requirements up-to-date.\n"
            self.assertEquals(u(result.output), u(expected_output))
            self.assertEquals(result.exit_code, 0)
            expected_requirements = open(tmpfile).read()
            self.assertEquals(open(tmpfile).read(), expected_requirements) 

def test_notequal_version_spec_prevents_updating_package(self):
        requirements = 'tests/samples/requirements-multiline.txt'
        tempdir = tempfile.mkdtemp()
        tmpfile = os.path.join(tempdir, 'requirements.txt')
        shutil.copy(requirements, tmpfile)
        args = ['-r', tmpfile]

        with utils.mock.patch('pip._internal.index.PackageFinder.find_all_candidates') as mock_find_all_candidates:
            project = 'afakepackage'
            version = '0.9.1'
            link = Link('')
            candidate = InstallationCandidate(project, version, link)
            mock_find_all_candidates.return_value = [candidate]

            result = self.runner.invoke(pur, args)
            self.assertIsNone(result.exception)
            expected_output = "All requirements up-to-date.\n"
            self.assertEquals(u(result.output), u(expected_output))
            self.assertEquals(result.exit_code, 0)
            expected_requirements = open(tmpfile).read()
            self.assertEquals(open(tmpfile).read(), expected_requirements) 

def test_updates_package_with_multiline_spec(self):
        requirements = 'tests/samples/requirements-multiline.txt'
        tempdir = tempfile.mkdtemp()
        tmpfile = os.path.join(tempdir, 'requirements.txt')
        shutil.copy(requirements, tmpfile)
        args = ['-r', tmpfile]

        with utils.mock.patch('pip._internal.index.PackageFinder.find_all_candidates') as mock_find_all_candidates:
            project = 'afakepackage'
            version = '1.0'
            link = Link('')
            candidate = InstallationCandidate(project, version, link)
            mock_find_all_candidates.return_value = [candidate]

            result = self.runner.invoke(pur, args)
            self.assertIsNone(result.exception)
            expected_output = "Updated afakepackage: 0.9 -> 1.0\nUpdated afakepackage: 0.9 -> 1.0\nAll requirements up-to-date.\n"
            self.assertEquals(u(result.output), u(expected_output))
            self.assertEquals(result.exit_code, 0)
            expected_requirements = open('tests/samples/results/test_updates_package_with_multiline_spec').read()
            self.assertEquals(open(tmpfile).read(), expected_requirements) 

def test_does_not_update_package_with_multiline_spec(self):
        requirements = 'tests/samples/requirements-multiline.txt'
        tempdir = tempfile.mkdtemp()
        tmpfile = os.path.join(tempdir, 'requirements.txt')
        shutil.copy(requirements, tmpfile)
        args = ['-r', tmpfile]

        with utils.mock.patch('pip._internal.index.PackageFinder.find_all_candidates') as mock_find_all_candidates:
            project = 'afakepackage'
            version = '1.1'
            link = Link('')
            candidate = InstallationCandidate(project, version, link)
            mock_find_all_candidates.return_value = [candidate]

            result = self.runner.invoke(pur, args)
            self.assertIsNone(result.exception)
            expected_output = "All requirements up-to-date.\n"
            self.assertEquals(u(result.output), u(expected_output))
            self.assertEquals(result.exit_code, 0)
            expected_requirements = open(requirements).read()
            self.assertEquals(open(tmpfile).read(), expected_requirements) 

def test_updates_package_with_min_version_spec(self):
        requirements = 'tests/samples/requirements-with-min-version-spec.txt'
        tempdir = tempfile.mkdtemp()
        tmpfile = os.path.join(tempdir, 'requirements.txt')
        shutil.copy(requirements, tmpfile)
        args = ['-r', tmpfile]

        with utils.mock.patch('pip._internal.index.PackageFinder.find_all_candidates') as mock_find_all_candidates:
            project = 'django'
            version = '1.8.13'
            link = Link('')
            candidate = InstallationCandidate(project, version, link)
            mock_find_all_candidates.return_value = [candidate]

            result = self.runner.invoke(pur, args)
            expected_output = "Updated django: 1.8.6 -> 1.8.13\nNew version for django found (1.8.13), but current spec prohibits updating: django > 1.8.6, < 1.9\nAll requirements up-to-date.\n"
            self.assertEquals(u(result.output), u(expected_output))
            self.assertIsNone(result.exception)
            self.assertEquals(result.exit_code, 0)
            expected_requirements = open('tests/samples/results/test_updates_package_with_min_version_spec').read()
            self.assertEquals(open(tmpfile).read(), expected_requirements) 

def test_dry_run(self):
        requirements = 'tests/samples/requirements.txt'
        tempdir = tempfile.mkdtemp()
        tmpfile = os.path.join(tempdir, 'requirements.txt')
        shutil.copy(requirements, tmpfile)
        args = ['-r', tmpfile, '-d']

        with utils.mock.patch('pip._internal.index.PackageFinder.find_all_candidates') as mock_find_all_candidates:
            project = 'flask'
            version = '0.10.1'
            link = Link('')
            candidate = InstallationCandidate(project, version, link)
            mock_find_all_candidates.return_value = [candidate]

            result = self.runner.invoke(pur, args)
            self.assertIsNone(result.exception)
            expected_output = '==> ' + tmpfile + ' <==\n' + \
                open('tests/samples/results/test_updates_package').read() + "\n"
            self.assertEquals(u(result.output), u(expected_output))
            self.assertEquals(result.exit_code, 0)
            self.assertEquals(open(tmpfile).read(), open(requirements).read()) 

def test_interactive_choice_default(self):
        tempdir = tempfile.mkdtemp()
        requirements = os.path.join(tempdir, 'requirements.txt')
        shutil.copy('tests/samples/requirements.txt', requirements)
        args = ['-r', requirements, '-i']

        with utils.mock.patch('pip._internal.index.PackageFinder.find_all_candidates') as mock_find_all_candidates:
            project = 'flask'
            version = '0.10.1'
            link = Link('')
            candidate = InstallationCandidate(project, version, link)
            mock_find_all_candidates.return_value = [candidate]

            result = self.runner.invoke(pur, args)

            self.assertIsNone(result.exception)
            expected_output = "Update flask from 0.9 to 0.10.1? (y, n, q) [y]: \nUpdated flask: 0.9 -> 0.10.1\nAll requirements up-to-date.\n"
            self.assertEquals(u(result.output), u(expected_output))
            self.assertEquals(result.exit_code, 0)
            expected_requirements = open('tests/samples/results/test_updates_package').read()
            self.assertEquals(open(requirements).read(), expected_requirements) 

def test_interactive_choice_yes(self):
        tempdir = tempfile.mkdtemp()
        requirements = os.path.join(tempdir, 'requirements.txt')
        shutil.copy('tests/samples/requirements.txt', requirements)
        args = ['-r', requirements, '-i']

        with utils.mock.patch('pip._internal.index.PackageFinder.find_all_candidates') as mock_find_all_candidates:
            project = 'flask'
            version = '0.10.1'
            link = Link('')
            candidate = InstallationCandidate(project, version, link)
            mock_find_all_candidates.return_value = [candidate]

            result = self.runner.invoke(pur, args, input='y\n')

            self.assertIsNone(result.exception)
            expected_output = "Update flask from 0.9 to 0.10.1? (y, n, q) [y]: y\nUpdated flask: 0.9 -> 0.10.1\nAll requirements up-to-date.\n"
            self.assertEquals(u(result.output), u(expected_output))
            self.assertEquals(result.exit_code, 0)
            expected_requirements = open('tests/samples/results/test_updates_package').read()
            self.assertEquals(open(requirements).read(), expected_requirements) 

def test_interactive_choice_quit(self):
        tempdir = tempfile.mkdtemp()
        requirements = os.path.join(tempdir, 'requirements.txt')
        shutil.copy('tests/samples/requirements-multiple.txt', requirements)
        args = ['-r', requirements, '-i']

        with utils.mock.patch('pip._internal.index.PackageFinder.find_all_candidates') as mock_find_all_candidates:
            project = 'flask'
            version = '0.10.1'
            link = Link('')
            candidate = InstallationCandidate(project, version, link)
            mock_find_all_candidates.return_value = [candidate]

            result = self.runner.invoke(pur, args, input='y\nq\n')
            self.assertIsNone(result.exception)
            expected_output = "Update flask from 0.9 to 0.10.1? (y, n, q) [y]: y\nUpdated flask: 0.9 -> 0.10.1\nUpdate Alembic from 0.9 to 0.10.1? (y, n, q) [y]: q\nAll requirements up-to-date.\n"
            self.assertEquals(u(result.output), u(expected_output))
            self.assertEquals(result.exit_code, 0)
            expected_requirements = open('tests/samples/results/test_interactive_choice_quit').read()
            self.assertEquals(open(requirements).read(), expected_requirements) 

def test_interactive_choice_invalid(self):
        tempdir = tempfile.mkdtemp()
        requirements = os.path.join(tempdir, 'requirements.txt')
        shutil.copy('tests/samples/requirements-multiple.txt', requirements)
        args = ['-r', requirements, '-i']

        with utils.mock.patch('pip._internal.index.PackageFinder.find_all_candidates') as mock_find_all_candidates:
            project = 'flask'
            version = '0.10.1'
            link = Link('')
            candidate = InstallationCandidate(project, version, link)
            mock_find_all_candidates.return_value = [candidate]

            result = self.runner.invoke(pur, args, input='z\nn\ny\nq\n')
            self.assertIsNone(result.exception)
            expected_output = "Update flask from 0.9 to 0.10.1? (y, n, q) [y]: z\nPlease enter either y, n, q.\nUpdate flask from 0.9 to 0.10.1? (y, n, q) [y]: n\nUpdate Alembic from 0.9 to 0.10.1? (y, n, q) [y]: y\nUpdated Alembic: 0.9 -> 0.10.1\nUpdate sqlalchemy from 0.9 to 0.10.1? (y, n, q) [y]: q\nAll requirements up-to-date.\n"
            self.assertEquals(u(result.output), u(expected_output))
            self.assertEquals(result.exit_code, 0)
            expected_requirements = open('tests/samples/results/test_interactive_choice_invalid').read()
            self.assertEquals(open(requirements).read(), expected_requirements) 

def _copy_file(filename, location, link):
    copy = True
    download_location = os.path.join(location, link.filename)
    if os.path.exists(download_location):
        response = ask_path_exists(
            'The file %s exists. (i)gnore, (w)ipe, (b)ackup, (a)abort' %
            display_path(download_location), ('i', 'w', 'b', 'a'))
        if response == 'i':
            copy = False
        elif response == 'w':
            logger.warning('Deleting %s', display_path(download_location))
            os.remove(download_location)
        elif response == 'b':
            dest_file = backup_dir(download_location)
            logger.warning(
                'Backing up %s to %s',
                display_path(download_location),
                display_path(dest_file),
            )
            shutil.move(download_location, dest_file)
        elif response == 'a':
            sys.exit(-1)
    if copy:
        shutil.copy(filename, download_location)
        logger.info('Saved %s', display_path(download_location)) 

def setup():                                                                    #Asks new user for information
    print('Enter the directory for your iTunes library')
    spacer_small()
    print('This is typically stored in your \'user/Music/iTunes\' folder')
    print('You can also make a copy wherever you want in iTunes')
    print('Just go File>Library>Export Library...')
    tunes_library_path = input()                                                #Where is my itunes library?
    spacer()
    print('Now you gotta give me the root directory for your media player')
    print('This is typically /Volumes/YOUR DEVICE NAME')
    fiio_dir = input()                                                          #Device directory
    if fiio_dir[len(fiio_dir) - 1] == '/':
        fiio_dir = fiio_dir[0: len(fiio_dir) - 1]                               #User may add an extra slash, get rid of it
    spacer()
    print('Ima save those settings')
    settings_body = 'iTunes Library Path:\n' + tunes_library_path + '\n' + 'Device Root Directory\n' + fiio_dir
    newsettings = open(fiio_dir + '/X1_sync_settings.txt', 'w')                 #Write a settings file into the root directory of device
    newsettings.write(settings_body)
    newsettings.close()
    return [tunes_library_path, fiio_dir] 

def Dumpfile(): 
    fv.write('##########')
    fv.write('\n')
    fv.write("local Administrators on machine ")
    fv.write(host)
    fv.write(" are : ....\n\n")
    result,t,r= NetLocalGroupGetMembers(None,"Administrators",1)
    for item in result:
        fv.write(str(item))
        fv.write('\n')
    fv.write('\n\n')
    fv.write ("##########\n")
    fv.write('the following software is installed on ')
    fv.write(host)
    fv.write(': .... \n\n')
    listofsoft=readSubKeys("HKLM", "SOFTWARE\Microsoft\Windows\CurrentVersion\Uninstall")
    listofsoft.sort()
    for software in listofsoft:
        fv.write(str(software))
        fv.write('\n')
    fv.close()
    shutil.copy(srcfile,r"\\10.1.1.12\gms")
    win32api.DeleteFile(srcfile) 

def cat_contig_files_from_subprocs( tup ):
	contig    = tup[0]
	tmp       = tup[1]
	j         = tup[2]
	N_contigs = tup[3]
	logging.info("...contig %s (%s/%s)" % (contig, j, N_contigs))
	contig_fns = glob.glob( os.path.join(tmp, "chunk_*", "%s_*.tmp" % contig) )
	ftypes = set( map(lambda x: os.path.basename(x).split("_")[-1], contig_fns) )
	for ftype in ftypes:
		if ftype in ["compkmers.tmp", "ipdskmers.tmp"]:
			first_fn = glob.glob( os.path.join(tmp, "chunk_*", "%s_%s" % (contig, ftype)) )[0]
			shutil.copy( first_fn, os.path.join(tmp, "%s_%s" % (contig,ftype)))
		else:
			to_cat  = glob.glob( os.path.join(tmp, "chunk_*", "%s_%s" % (contig, ftype)) )
			to_cat.sort()
			outname = os.path.join(tmp, "%s_%s" % (contig,ftype) )
			cat_list_of_files(to_cat, outname, del_ins=False) 

def minimize(self):
        self.tpr = "%s.tpr" % (self.basename)
        self.mdout = "%s.out.mdp" % (self.basename)
        self.pplog = "%s.pp.log" % (self.basename)
        self.deffnm = "%s.md" % (self.basename)
        self.mdgro = "%s.gro" % (self.deffnm)
        self.mdtrr = "%s.trr" % (self.deffnm)
        self.mdlog = "%s.log" % (self.deffnm)
        self.mdedr = "%s.edr" % (self.deffnm)

        ppargs = self.grompp + ["-f",self.mdp, "-p",self.top, "-c",self.gro, "-maxwarn","3", "-po",self.mdout, "-o",self.tpr]
        mdargs = self.mdrun + ["-s",self.tpr, "-nt","1", "-deffnm",self.deffnm, "-cpt","0"]

        with open(self.pplog, "w") as pplog:
            md_env = os.environ.copy()
            md_env["GMX_SUPPRESS_DUMP"] = '1'
            md_env["GMX_MAXBACKUP"] = '-1'
            pp = subprocess.call(ppargs, stdout=pplog, stderr=pplog, env=md_env)
        if pp:
            sys.stderr.write("grompp error: check %s\n" % (self.pplog))
            sys.exit()
        md = subprocess.call(mdargs, stdout=subprocess.PIPE, stderr=subprocess.PIPE, env=md_env)
        if md:
            sys.stderr.write("mdrun error: check %s\n" % (self.mdlog))
            sys.exit() 

def assess_status_func(configs):
    """Helper function to create the function that will assess_status() for
    the unit.
    Uses charmhelpers.contrib.openstack.utils.make_assess_status_func() to
    create the appropriate status function and then returns it.
    Used directly by assess_status() and also for pausing and resuming
    the unit.

    NOTE: REQUIRED_INTERFACES is augmented with the optional interfaces
    depending on the current config before being passed to the
    make_assess_status_func() function.

    @param configs: a templating.OSConfigRenderer() object
    @return f() -> None : a function that assesses the unit's workload status
    """
    required_interfaces = REQUIRED_INTERFACES.copy()
    required_interfaces.update(get_optional_interfaces())
    return make_assess_status_func(
        configs, required_interfaces,
        charm_func=check_optional_relations,
        services=services(),
        ports=determine_ports()) 

def assess_status_func(configs):
    """Helper function to create the function that will assess_status() for
    the unit.
    Uses charmhelpers.contrib.openstack.utils.make_assess_status_func() to
    create the appropriate status function and then returns it.
    Used directly by assess_status() and also for pausing and resuming
    the unit.

    NOTE: REQUIRED_INTERFACES is augmented with the optional interfaces
    depending on the current config before being passed to the
    make_assess_status_func() function.

    @param configs: a templating.OSConfigRenderer() object
    @return f() -> None : a function that assesses the unit's workload status
    """
    required_interfaces = REQUIRED_INTERFACES.copy()
    required_interfaces.update(get_optional_interfaces())
    return make_assess_status_func(
        configs, required_interfaces,
        charm_func=check_optional_relations,
        services=services(),
        ports=determine_ports()) 

def exit_cleanup():
	try:
		fileobj = sys.stdout.fileobj
	except AttributeError:
		pass
	else:
		sys.stdout.is_valid = False
		sys.stderr.is_valid = False
		fileobj.close()
		filename = sys.stdout.filename

		Logs.info('Output logged to %r' % filename)

		# then copy the log file to "latest.log" if possible
		up = os.path.dirname(os.path.abspath(filename))
		try:
			shutil.copy(filename, os.path.join(up, 'latest.log'))
		except OSError:
			# this may fail on windows due to processes spawned
			# 
			pass 

def exit_cleanup():
	try:
		fileobj = sys.stdout.fileobj
	except AttributeError:
		pass
	else:
		sys.stdout.is_valid = False
		sys.stderr.is_valid = False
		fileobj.close()
		filename = sys.stdout.filename

		Logs.info('Output logged to %r' % filename)

		# then copy the log file to "latest.log" if possible
		up = os.path.dirname(os.path.abspath(filename))
		try:
			shutil.copy(filename, os.path.join(up, 'latest.log'))
		except OSError:
			# this may fail on windows due to processes spawned
			# 
			pass 

def exit_cleanup():
	try:
		fileobj = sys.stdout.fileobj
	except AttributeError:
		pass
	else:
		sys.stdout.is_valid = False
		sys.stderr.is_valid = False
		fileobj.close()
		filename = sys.stdout.filename

		Logs.info('Output logged to %r' % filename)

		# then copy the log file to "latest.log" if possible
		up = os.path.dirname(os.path.abspath(filename))
		try:
			shutil.copy(filename, os.path.join(up, 'latest.log'))
		except OSError:
			# this may fail on windows due to processes spawned
			# 
			pass 

def _test_checkin_with_handoff(my):

        search_type = "unittest/person"
        code = "joe"
        search_key = my.server.build_search_key(search_type, code)

        # copy file to handoff dir
        path = "%s/test/miso_ramen.jpg" % my.client_lib_dir
        handoff_dir = my.server.get_handoff_dir()
        shutil.copy(path, handoff_dir)

        # check the file in
        snapshot = my.server.simple_checkin(search_key, "publish", path, use_handoff_dir=True)
        snapshot_code = snapshot.get("code")

        # get the filename
        file_type = "main"
        path = my.server.get_path_from_snapshot(snapshot_code, file_type)
        exists = os.path.exists(path)
        my.assertEquals(True, exists)

        # check that the file name is correct
        filename = os.path.basename(path)
        # changed naming.. adds "publish"
        my.assertEquals("miso_ramen_publish_v001.jpg", filename) 

def mean_variance_normalisation(h5f, mvn_h5f, vad=None):
    """Do mean variance normlization. Optionnaly use a vad.

    Parameters:
    ----------
    h5f: str. h5features file name
    mvn_h5f: str, h5features output name
    """
    dset = h5py.File(h5f).keys()[0]
    if vad is not None:
        raise NotImplementedError
    else:
        data = h5py.File(h5f)[dset]['features'][:]
        features = data
    epsilon = np.finfo(data.dtype).eps
    mean = np.mean(data)
    std = np.std(data)
    mvn_features = (features - mean) / (std + epsilon)
    shutil.copy(h5f, mvn_h5f)
    h5py.File(mvn_h5f)[dset]['features'][:] = mvn_features 

def _copy_file(filename, location, link):
    copy = True
    download_location = os.path.join(location, link.filename)
    if os.path.exists(download_location):
        response = ask_path_exists(
            'The file %s exists. (i)gnore, (w)ipe, (b)ackup ' %
            display_path(download_location), ('i', 'w', 'b'))
        if response == 'i':
            copy = False
        elif response == 'w':
            logger.warning('Deleting %s', display_path(download_location))
            os.remove(download_location)
        elif response == 'b':
            dest_file = backup_dir(download_location)
            logger.warning(
                'Backing up %s to %s',
                display_path(download_location),
                display_path(dest_file),
            )
            shutil.move(download_location, dest_file)
    if copy:
        shutil.copy(filename, download_location)
        logger.info('Saved %s', display_path(download_location))