How to use _setup method in molecule

Best Python code snippet using molecule_python

Setup.py

Source:Setup.py

1import warnings2import numpy as np3import json4import os5import datetime6import glob7import re8import ntpath9import shutil10from keras.models import load_model11class Setup(object):12    def __init__(self, name):13        self._name = name14        self._model = None15        self._emptyModel = None16        self._training_ids = None17        self._validation_ids = None18        self._testing_ids = None19        self._training_data = None20        self._validation_data = None21        self._testing_data = None22        self._training_targets = None23        self._validation_targets = None24        self._testing_targets = None25        self._training_ids_directory = None26        self._validation_ids_directory = None27        self._testing_ids_directory = None28        self._training_data_directory = None29        self._validation_data_directory = None30        self._testing_data_directory = None31        self._training_targets_directory = None32        self._validation_targets_directory = None33        self._testing_targets_directory = None34        self._training_accuracy = []35        self._training_auc = []36        self._training_loss = []37        self._validation_accuracy = []38        self._validation_auc = []39        self._validation_loss = []40        self._testing_accuracy = []41        self._testing_auc = []42        self._testing_loss = []43        self._batch_size = None44        self._epochs = 045        self._others = {}46        self._setup = {47            'name': self._name,48            'file': {49                'setup': '',50                'model': '',51                'model_arch_json': '',52                'model_arch_yaml': '',53                'model_weights': '',54                'training_ids': '',55                'validation_ids': '',56                'testing_ids': '',57                'training_data': '',58                'validation_data': '',59                'testing_data': '',60                'training_targets': '',61                'validation_targets': '',62                'testing_targets': '',63            },64            'directory': {65                'training_ids': '',66                'validation_ids': '',67                'testing_ids': '',68                'training_data': '',69                'validation_data': '',70                'testing_data': '',71                'training_targets': '',72                'validation_targets': '',73                'testing_targets': '',74            },75            'training_accuracy': self._training_accuracy,76            'training_accuracy': self._training_auc,77            'training_loss': self._training_loss,78            'validation_accuracy': self._validation_accuracy,79            'validation_accuracy': self._validation_auc,80            'validation_loss': self._validation_loss,81            'testing_accuracy': self._testing_accuracy,82            'testing_accuracy': self._testing_auc,83            'testing_loss': self._testing_loss,84            'epochs': self._epochs,85            'others': self._others,86        }87    def getName(self):88        return self._name89    def setName(self, name):90        self._name = name91    def getModel(self):92        return self._model93    def setModel(self, model):94        self._model = model95        # TODO: get the empty model and assign it to self._emptyModel96    def getData(self):97        return self._training_ids, self._training_data, self._training_targets, \98               self._validation_ids, self._validation_data, self._validation_targets, \99               self._testing_ids, self._testing_data, self._testing_targets100    def setData(self,101                training_ids=None, training_data=None, training_targets=None,102                validation_ids=None, validation_data=None, validation_targets=None,103                testing_ids=None, testing_data=None, testing_targets=None):104        self._training_ids = training_ids if training_ids is not None else self._training_ids105        self._validation_ids = validation_ids if validation_ids is not None else self._validation_ids106        self._testing_ids = testing_ids if testing_ids is not None else self._testing_ids107        self._training_data = training_data if training_data is not None else self._training_data108        self._validation_data = validation_data if validation_data is not None else self._validation_data109        self._testing_data = testing_data if testing_data is not None else self._testing_data110        self._training_targets = training_targets if training_targets is not None else self._training_targets111        self._validation_targets = validation_targets if validation_targets is not None else self._validation_targets112        self._testing_targets = testing_targets if testing_targets is not None else self._testing_targets113    def getDataDirectory(self):114        return self._training_data_directory, self._training_data_directory, self._training_targets_directory, \115               self._validation_data_directory, self._validation_data_directory, self._validation_targets_directory, \116               self._testing_data_directory, self._testing_data_directory, self._testing_targets_directory117    def setDataDirectory(self,118                         training_ids_directory=None, training_data_directory=None, training_targets_directory=None,119                         validation_ids_directory=None, validation_data_directory=None, validation_targets_directory=None,120                         testing_ids_directory=None, testing_data_directory=None, testing_targets_directory=None):121        self._training_ids_directory = training_ids_directory if training_ids_directory is not None else self._training_ids_directory122        self._validation_ids_directory = validation_ids_directory if validation_ids_directory is not None else self._validation_ids_directory123        self._testing_ids_directory = testing_ids_directory if testing_ids_directory is not None else self._testing_ids_directory124        self._training_data_directory = training_data_directory if training_data_directory is not None else self._training_data_directory125        self._validation_data_directory = validation_data_directory if validation_data_directory is not None else self._validation_data_directory126        self._testing_data_directory = testing_data_directory if testing_data_directory is not None else self._testing_data_directory127        self._training_targets_directory = training_targets_directory if training_targets_directory is not None else self._training_targets_directory128        self._validation_targets_directory = validation_targets_directory if validation_targets_directory is not None else self._validation_targets_directory129        self._testing_targets_directory = testing_targets_directory if testing_targets_directory is not None else self._testing_targets_directory130    def getEpoch(self):131        return self._epochs132    def updateEpochs(self, add_epochs,133                     training_acc, training_auc, training_loss,134                     validation_acc, validation_auc, validation_loss,135                     testing_acc, testing_auc, testing_loss,136                     allow_modify=True):137        # TODO: check138        def checkListLength(length, mList, listName, allowModify):139            modifiedList = mList140            if allow_modify:141                if len(modifiedList) < length:142                    modifiedList.extend([mList[-1] for i in range(length - len(modifiedList))])143                elif len(modifiedList) > length:144                    warnings.warn('%s list is longer than add_epochs. Trimmed list will be used.' % listName)145                    modifiedList = modifiedList[:length]146            else:147                if len(modifiedList) != length:148                    raise ValueError('%s list length is not equal to add_epochs' % listName)149            return modifiedList150        # Checking parameters151        # add_epochs152        if add_epochs is None or type(add_epochs) != int:153            raise TypeError('add_epochs should have type \'int\'')154        elif add_epochs < 0:155            raise ValueError('add_epochs should be > 0')156        if training_acc is None or type(training_acc) != list or \157                training_auc is None or type(training_auc) != list or \158                training_loss is None or type(training_loss) != list or \159                validation_acc is None or type(validation_acc) != list or \160                validation_auc is None or type(validation_auc) != list or \161                validation_loss is None or type(validation_loss) != list or \162                testing_acc is None or type(testing_acc) != list or \163                testing_auc is None or type(testing_auc) != list or \164                testing_loss is None or type(testing_loss) != list:165            raise TypeError('training_acc, training_auc, training_loss, '166                            'validation_acc, validation_auc, validation_loss, '167                            'testing_acc, testing_auc, testing_loss should have type \'list\'')168        new_train_acc = checkListLength(add_epochs, training_acc, 'training_acc', allow_modify)169        new_train_auc = checkListLength(add_epochs, training_auc, 'training_auc', allow_modify)170        new_train_loss = checkListLength(add_epochs, training_loss, 'training_loss', allow_modify)171        new_val_acc = checkListLength(add_epochs, validation_acc, 'validation_acc', allow_modify)172        new_val_auc = checkListLength(add_epochs, validation_auc, 'validation_auc', allow_modify)173        new_val_loss = checkListLength(add_epochs, validation_loss, 'validation_loss', allow_modify)174        new_test_acc = checkListLength(add_epochs, testing_acc, 'testing_acc', allow_modify)175        new_test_auc = checkListLength(add_epochs, testing_auc, 'testing_auc', allow_modify)176        new_test_loss = checkListLength(add_epochs, testing_loss, 'testing_loss', allow_modify)177        self._epochs += add_epochs178        self._training_accuracy.extend(new_train_acc)179        self._training_auc.extend(new_train_auc)180        self._training_loss.extend(new_train_loss)181        self._validation_accuracy.extend(new_val_acc)182        self._validation_auc.extend(new_val_auc)183        self._validation_loss.extend(new_val_loss)184        self._testing_accuracy.extend(new_test_acc)185        self._testing_auc.extend(new_test_auc)186        self._testing_loss.extend(new_test_loss)187    def getOthers(self):188        return self._others189    def setOthers(self, others):190        for key in others:191            self._others[key] = others[key]192    def save(self, rel_path):193        # Save every information or object194        if rel_path is None:195            raise ValueError('rel_path should not be None')196        else:197            pass198        self._setup['name'] = self._name199        self._setup['time'] = str(datetime.datetime.now()),200        self._setup['file']['setup'] = os.path.join('setup.json')201        self._setup['file']['model'] = os.path.join('model.h5')202        self._setup['file']['model_arch_json'] = os.path.join('model_architecture.json')203        self._setup['file']['model_arch_yaml'] = os.path.join('model_architecture.yaml')204        self._setup['file']['model_weights'] = os.path.join('model_weights.h5')205        self._setup['file']['training_ids'] = os.path.join('training_ids.npy')206        self._setup['file']['validation_ids'] = os.path.join('validation_ids.npy')207        self._setup['file']['testing_ids'] = os.path.join('testing_ids.npy')208        self._setup['file']['training_data'] = os.path.join('training_data.npy')209        self._setup['file']['validation_data'] = os.path.join('validation_data.npy')210        self._setup['file']['testing_data'] = os.path.join('testing_data.npy')211        self._setup['file']['training_targets'] = os.path.join('training_targets.npy')212        self._setup['file']['validation_targets'] = os.path.join('validation_targets.npy')213        self._setup['file']['testing_targets'] = os.path.join('testing_targets.npy')214        self._setup['directory']['training_ids'] = self._training_ids_directory215        self._setup['directory']['validation_ids'] = self._validation_ids_directory216        self._setup['directory']['testing_ids'] = self._testing_ids_directory217        self._setup['directory']['training_data'] = self._training_data_directory218        self._setup['directory']['validation_data'] = self._validation_data_directory219        self._setup['directory']['testing_data'] = self._testing_data_directory220        self._setup['directory']['training_targets'] = self._training_targets_directory221        self._setup['directory']['validation_targets'] = self._validation_targets_directory222        self._setup['directory']['testing_targets'] = self._testing_targets_directory223        self._setup['training_accuracy'] = self._training_accuracy224        self._setup['training_auc'] = self._training_auc225        self._setup['training_loss'] = self._training_loss226        self._setup['validation_accuracy'] = self._validation_accuracy227        self._setup['validation_auc'] = self._validation_auc228        self._setup['validation_loss'] = self._validation_loss229        self._setup['testing_accuracy'] = self._testing_accuracy230        self._setup['testing_auc'] = self._testing_auc231        self._setup['testing_loss'] = self._testing_loss232        self._setup['epochs'] = self._epochs233        self._setup['others'] = self._others234        if not os.path.exists(os.path.join(os.getcwd(), rel_path)):235            os.mkdir(os.path.join(os.getcwd(), rel_path))236        if not os.path.exists(os.path.join(os.getcwd(), rel_path, self._name)):237            os.mkdir(os.path.join(os.getcwd(), rel_path, self._name))238        if len(glob.glob(os.path.join(os.getcwd(), rel_path, self._name, '*.*'))) > 0:239            versions = []240            pattern = r'^.*version(?P<versionnumber>\d*)$'241            for dir in glob.glob(os.path.join(os.getcwd(), rel_path, self._name, 'version*')):242                regex = re.search(pattern, dir)243                versions.append(int(regex.group('versionnumber')))244            if len(versions) == 0:245                maxVer = 0246            else:247                maxVer = np.max(versions)248            newVerDirName = 'version%s' % (maxVer + 1)249            os.mkdir(os.path.join(os.getcwd(), rel_path, self._name, newVerDirName))250            self._backup_version(os.path.join(os.getcwd(), rel_path, self._name),251                                 os.path.join(os.getcwd(), rel_path, self._name, newVerDirName))252            if (maxVer + 1 - 10) > 0 and (maxVer + 1 - 10) % 20 != 0:253                oldVerDirName = 'version%s' % (maxVer + 1 - 10)254                shutil.rmtree(os.path.join(os.getcwd(), rel_path, self._name, oldVerDirName))255        # ==========================================256        # Save whole model257        self._model.save(os.path.join(os.getcwd(), rel_path, self._name, self._setup['file']['model']))258        # ==========================================259        # Save model architecture260        json_model_arch = self._model.to_json()261        with open(os.path.join(os.getcwd(), rel_path, self._name, self._setup['file']['model_arch_json']), 'w') as jsonfile:262            jsonfile.write(json_model_arch)263        yaml_model_arch = self._model.to_yaml()264        with open(os.path.join(os.getcwd(), rel_path, self._name, self._setup['file']['model_arch_yaml']), 'w') as yamlfile:265            yamlfile.write(yaml_model_arch)266        # ==========================================267        # Save model weights268        self._model.save_weights(os.path.join(os.getcwd(), rel_path, self._name, self._setup['file']['model_weights']))269        # ==========================================270        # Save data271        if self._training_ids is not None and type(self._training_ids) == np.ndarray:272            try:273                np.save(os.path.join(os.getcwd(), rel_path, self._name, self._setup['file']['training_ids']), self._training_ids)274            except Exception as e:275                self._setup['file']['training_ids'] = None276        if self._validation_ids is not None and type(self._validation_ids) == np.ndarray:277            try:278                np.save(os.path.join(os.getcwd(), rel_path, self._name, self._setup['file']['validation_ids']), self._validation_ids)279            except Exception as e:280                self._setup['file']['validation_ids'] = None281        if self._testing_ids is not None and type(self._testing_ids) == np.ndarray:282            try:283                np.save(os.path.join(os.getcwd(), rel_path, self._name, self._setup['file']['testing_ids']), self._testing_ids)284            except Exception as e:285                self._setup['file']['testing_ids'] = None286        if self._training_data is not None and type(self._training_data) == np.ndarray:287            try:288                np.save(os.path.join(os.getcwd(), rel_path, self._name, self._setup['file']['training_data']), self._training_data)289            except Exception as e:290                self._setup['file']['training_data'] = None291        if self._validation_data is not None and type(self._validation_data) == np.ndarray:292            try:293                np.save(os.path.join(os.getcwd(), rel_path, self._name, self._setup['file']['validation_data']), self._validation_data)294            except Exception as e:295                self._setup['file']['validation_data'] = None296        if self._testing_data is not None and type(self._testing_data) == np.ndarray:297            try:298                np.save(os.path.join(os.getcwd(), rel_path, self._name, self._setup['file']['testing_data']), self._testing_data)299            except Exception as e:300                self._setup['file']['testing_data'] = None301        if self._training_targets is not None and type(self._training_targets) == np.ndarray:302            try:303                np.save(os.path.join(os.getcwd(), rel_path, self._name, self._setup['file']['training_targets']), self._training_targets)304            except Exception as e:305                self._setup['file']['training_targets'] = None306        if self._validation_targets is not None and type(self._validation_targets) == np.ndarray:307            try:308                np.save(os.path.join(os.getcwd(), rel_path, self._name, self._setup['file']['validation_targets']), self._validation_targets)309            except Exception as e:310                self._setup['file']['validation_targets'] = None311        if self._testing_targets is not None and type(self._testing_targets) == np.ndarray:312            try:313                np.save(os.path.join(os.getcwd(), rel_path, self._name, self._setup['file']['testing_targets']), self._testing_targets)314            except Exception as e:315                self._setup['file']['testing_targets'] = None316        # ==========================================317        # Save setup318        with open(os.path.join(os.getcwd(), rel_path, self._name, self._setup['file']['setup']), 'w') as setupfile:319            json.dump(self._setup, setupfile)320    def load(self, rel_filepath):321        cwd = os.getcwd()322        if rel_filepath is None:323            raise ValueError('rel_filepath should be None')324        else:325            pass326        # ==========================================327        # Load info328        with open(os.path.join(cwd, rel_filepath), 'r') as setupfile:329            self._setup = json.load(setupfile)330        rel_filepath = rel_filepath.replace('setup.json', '')331        # ==========================================332        # Load name333        self._name = self._setup['name']334        # ==========================================335        # Load whole model336        self._model = load_model(os.path.join(cwd, rel_filepath, self._setup['file']['model']))337        # TODO: if loading from model h5 file fails, then load from model arch file and load weights338        # # ==========================================339        # # Load model architecture340        # with open(os.path.join(directory, self.setup['model_arch_json']), 'r') as jsonfile:341        #     self.emptyModel = model_from_json(jsonfile.read())342        #343        # with open(os.path.join(directory, self.setup['model_arch_yaml']), 'r') as yamlfile:344        #     self.emptyModel = model_from_yaml(yamlfile.read())345        # # ==========================================346        # # Load model weights347        # self.model.load_weights(os.path.join(directory, self.setup['model_weights']))348        # ==========================================349        # Load data350        self._training_ids = np.load(os.path.join(cwd, rel_filepath, self._setup['file']['training_ids'])) \351            if os.path.exists(os.path.join(cwd, rel_filepath, self._setup['file']['training_ids'])) else self._training_ids352        self._validation_ids = np.load(os.path.join(cwd, rel_filepath, self._setup['file']['validation_ids'])) \353            if os.path.exists(os.path.join(cwd, rel_filepath, self._setup['file']['validation_ids'])) else self._validation_ids354        self._testing_ids = np.load(os.path.join(cwd, rel_filepath, self._setup['file']['testing_ids'])) \355            if os.path.exists(os.path.join(cwd, rel_filepath, self._setup['file']['testing_ids'])) else self._testing_ids356        self._training_data = np.load(os.path.join(cwd, rel_filepath, self._setup['file']['training_data'])) \357            if os.path.exists(os.path.join(cwd, rel_filepath, self._setup['file']['training_data'])) else self._training_data358        self._validation_data = np.load(os.path.join(cwd, rel_filepath, self._setup['file']['validation_data'])) \359            if os.path.exists(os.path.join(cwd, rel_filepath, self._setup['file']['validation_data'])) else self._validation_data360        self._testing_data = np.load(os.path.join(cwd, rel_filepath, self._setup['file']['testing_data'])) \361            if os.path.exists(os.path.join(cwd, rel_filepath, self._setup['file']['testing_data'])) else self._testing_data362        self._training_targets = np.load(os.path.join(cwd, rel_filepath, self._setup['file']['training_targets'])) \363            if os.path.exists(os.path.join(cwd, rel_filepath, self._setup['file']['training_targets'])) else self._training_targets364        self._validation_targets = np.load(os.path.join(cwd, rel_filepath, self._setup['file']['validation_targets'])) \365            if os.path.exists(os.path.join(cwd, rel_filepath, self._setup['file']['validation_targets'])) else self._validation_targets366        self._testing_targets = np.load(os.path.join(cwd, rel_filepath, self._setup['file']['testing_targets'])) \367            if os.path.exists(os.path.join(cwd, rel_filepath, self._setup['file']['testing_targets'])) else self._testing_targets368        # ==========================================369        # Load data directory370        self._training_data_directory = self._setup['directory']['training_data']371        self._validation_data_directory = self._setup['directory']['validation_data']372        self._testing_data_directory = self._setup['directory']['testing_data']373        self._training_targets_directory = self._setup['directory']['training_targets']374        self._validation_targets_directory = self._setup['directory']['validation_targets']375        self._testing_targets_directory = self._setup['directory']['testing_targets']376        # ==========================================377        # Load info378        self._training_accuracy = self._setup['training_accuracy']379        self._training_auc = self._setup['training_auc']380        self._training_loss = self._setup['training_loss']381        self._validation_accuracy = self._setup['validation_accuracy']382        self._validation_auc = self._setup['validation_auc']383        self._validation_loss = self._setup['validation_loss']384        self._testing_accuracy = self._setup['testing_accuracy']385        self._testing_auc = self._setup['testing_auc']386        self._testing_loss = self._setup['testing_loss']387        self._epochs = self._setup['epochs']388        self._others = self._setup['others']389    def save_setupfile(self, rel_path):390        with open(os.path.join(os.getcwd(), rel_path, self._name, self._setup['file']['setup']), 'w') as setupfile:391            json.dump(self._setup, setupfile)392    def _backup_version(self, source, destination):393        ignore_list = ['training_data',394                       'validation_data',395                       'testing_data',396                       'training_targets',397                       'validation_targets',398                       'testing_targets']399        for file in glob.glob(os.path.join(source, '*.*')):400            ignore = False401            for ignored_filename in ignore_list:402                if ignored_filename in file:403                    ignore = True404            if ignore:405                continue406            else:...

test_scales.py

Source:test_scales.py

...25    @pytest.fixture26    def x(self):27        return pd.Series([1, 3, 9], name="x", dtype=float)28    def setup_ticks(self, x, *args, **kwargs):29        s = Continuous().tick(*args, **kwargs)._setup(x, Coordinate())30        a = PseudoAxis(s._matplotlib_scale)31        a.set_view_interval(0, 1)32        return a33    def setup_labels(self, x, *args, **kwargs):34        s = Continuous().label(*args, **kwargs)._setup(x, Coordinate())35        a = PseudoAxis(s._matplotlib_scale)36        a.set_view_interval(0, 1)37        locs = a.major.locator()38        return a, locs39    def test_coordinate_defaults(self, x):40        s = Continuous()._setup(x, Coordinate())41        assert_series_equal(s(x), x)42    def test_coordinate_transform(self, x):43        s = Continuous(trans="log")._setup(x, Coordinate())44        assert_series_equal(s(x), np.log10(x))45    def test_coordinate_transform_with_parameter(self, x):46        s = Continuous(trans="pow3")._setup(x, Coordinate())47        assert_series_equal(s(x), np.power(x, 3))48    def test_coordinate_transform_error(self, x):49        s = Continuous(trans="bad")50        with pytest.raises(ValueError, match="Unknown value provided"):51            s._setup(x, Coordinate())52    def test_interval_defaults(self, x):53        s = Continuous()._setup(x, IntervalProperty())54        assert_array_equal(s(x), [0, .25, 1])55    def test_interval_with_range(self, x):56        s = Continuous((1, 3))._setup(x, IntervalProperty())57        assert_array_equal(s(x), [1, 1.5, 3])58    def test_interval_with_norm(self, x):59        s = Continuous(norm=(3, 7))._setup(x, IntervalProperty())60        assert_array_equal(s(x), [-.5, 0, 1.5])61    def test_interval_with_range_norm_and_transform(self, x):62        x = pd.Series([1, 10, 100])63        # TODO param order?64        s = Continuous((2, 3), (10, 100), "log")._setup(x, IntervalProperty())65        assert_array_equal(s(x), [1, 2, 3])66    def test_color_defaults(self, x):67        cmap = color_palette("ch:", as_cmap=True)68        s = Continuous()._setup(x, Color())69        assert_array_equal(s(x), cmap([0, .25, 1])[:, :3])  # FIXME RGBA70    def test_color_named_values(self, x):71        cmap = color_palette("viridis", as_cmap=True)72        s = Continuous("viridis")._setup(x, Color())73        assert_array_equal(s(x), cmap([0, .25, 1])[:, :3])  # FIXME RGBA74    def test_color_tuple_values(self, x):75        cmap = color_palette("blend:b,g", as_cmap=True)76        s = Continuous(("b", "g"))._setup(x, Color())77        assert_array_equal(s(x), cmap([0, .25, 1])[:, :3])  # FIXME RGBA78    def test_color_callable_values(self, x):79        cmap = color_palette("light:r", as_cmap=True)80        s = Continuous(cmap)._setup(x, Color())81        assert_array_equal(s(x), cmap([0, .25, 1])[:, :3])  # FIXME RGBA82    def test_color_with_norm(self, x):83        cmap = color_palette("ch:", as_cmap=True)84        s = Continuous(norm=(3, 7))._setup(x, Color())85        assert_array_equal(s(x), cmap([-.5, 0, 1.5])[:, :3])  # FIXME RGBA86    def test_color_with_transform(self, x):87        x = pd.Series([1, 10, 100], name="x", dtype=float)88        cmap = color_palette("ch:", as_cmap=True)89        s = Continuous(trans="log")._setup(x, Color())90        assert_array_equal(s(x), cmap([0, .5, 1])[:, :3])  # FIXME RGBA91    def test_tick_locator(self, x):92        locs = [.2, .5, .8]93        locator = mpl.ticker.FixedLocator(locs)94        a = self.setup_ticks(x, locator)95        assert_array_equal(a.major.locator(), locs)96    def test_tick_locator_input_check(self, x):97        err = "Tick locator must be an instance of .*?, not <class 'tuple'>."98        with pytest.raises(TypeError, match=err):99            Continuous().tick((1, 2))100    def test_tick_upto(self, x):101        for n in [2, 5, 10]:102            a = self.setup_ticks(x, upto=n)103            assert len(a.major.locator()) <= (n + 1)104    def test_tick_every(self, x):105        for d in [.05, .2, .5]:106            a = self.setup_ticks(x, every=d)107            assert np.allclose(np.diff(a.major.locator()), d)108    def test_tick_every_between(self, x):109        lo, hi = .2, .8110        for d in [.05, .2, .5]:111            a = self.setup_ticks(x, every=d, between=(lo, hi))112            expected = np.arange(lo, hi + d, d)113            assert_array_equal(a.major.locator(), expected)114    def test_tick_at(self, x):115        locs = [.2, .5, .9]116        a = self.setup_ticks(x, at=locs)117        assert_array_equal(a.major.locator(), locs)118    def test_tick_count(self, x):119        n = 8120        a = self.setup_ticks(x, count=n)121        assert_array_equal(a.major.locator(), np.linspace(0, 1, n))122    def test_tick_count_between(self, x):123        n = 5124        lo, hi = .2, .7125        a = self.setup_ticks(x, count=n, between=(lo, hi))126        assert_array_equal(a.major.locator(), np.linspace(lo, hi, n))127    def test_tick_minor(self, x):128        n = 3129        a = self.setup_ticks(x, count=2, minor=n)130        # I am not sure why matplotlib's minor ticks include the131        # largest major location but exclude the smalllest one ...132        expected = np.linspace(0, 1, n + 2)[1:]133        assert_array_equal(a.minor.locator(), expected)134    def test_log_tick_default(self, x):135        s = Continuous(trans="log")._setup(x, Coordinate())136        a = PseudoAxis(s._matplotlib_scale)137        a.set_view_interval(.5, 1050)138        ticks = a.major.locator()139        assert np.allclose(np.diff(np.log10(ticks)), 1)140    def test_log_tick_upto(self, x):141        n = 3142        s = Continuous(trans="log").tick(upto=n)._setup(x, Coordinate())143        a = PseudoAxis(s._matplotlib_scale)144        assert a.major.locator.numticks == n145    def test_log_tick_count(self, x):146        with pytest.raises(RuntimeError, match="`count` requires"):147            Continuous(trans="log").tick(count=4)148        s = Continuous(trans="log").tick(count=4, between=(1, 1000))149        a = PseudoAxis(s._setup(x, Coordinate())._matplotlib_scale)150        a.set_view_interval(.5, 1050)151        assert_array_equal(a.major.locator(), [1, 10, 100, 1000])152    def test_log_tick_every(self, x):153        with pytest.raises(RuntimeError, match="`every` not supported"):154            Continuous(trans="log").tick(every=2)155    def test_symlog_tick_default(self, x):156        s = Continuous(trans="symlog")._setup(x, Coordinate())157        a = PseudoAxis(s._matplotlib_scale)158        a.set_view_interval(-1050, 1050)159        ticks = a.major.locator()160        assert ticks[0] == -ticks[-1]161        pos_ticks = np.sort(np.unique(np.abs(ticks)))162        assert np.allclose(np.diff(np.log10(pos_ticks[1:])), 1)163        assert pos_ticks[0] == 0164    def test_label_formatter(self, x):165        fmt = mpl.ticker.FormatStrFormatter("%.3f")166        a, locs = self.setup_labels(x, fmt)167        labels = a.major.formatter.format_ticks(locs)168        for text in labels:169            assert re.match(r"^\d\.\d{3}$", text)170    def test_label_like_pattern(self, x):171        a, locs = self.setup_labels(x, like=".4f")172        labels = a.major.formatter.format_ticks(locs)173        for text in labels:174            assert re.match(r"^\d\.\d{4}$", text)175    def test_label_like_string(self, x):176        a, locs = self.setup_labels(x, like="x = {x:.1f}")177        labels = a.major.formatter.format_ticks(locs)178        for text in labels:179            assert re.match(r"^x = \d\.\d$", text)180    def test_label_like_function(self, x):181        a, locs = self.setup_labels(x, like="{:^5.1f}".format)182        labels = a.major.formatter.format_ticks(locs)183        for text in labels:184            assert re.match(r"^ \d\.\d $", text)185    def test_label_base(self, x):186        a, locs = self.setup_labels(100 * x, base=2)187        labels = a.major.formatter.format_ticks(locs)188        for text in labels[1:]:189            assert not text or "2^" in text190    def test_label_unit(self, x):191        a, locs = self.setup_labels(1000 * x, unit="g")192        labels = a.major.formatter.format_ticks(locs)193        for text in labels[1:-1]:194            assert re.match(r"^\d+ mg$", text)195    def test_label_unit_with_sep(self, x):196        a, locs = self.setup_labels(1000 * x, unit=("", "g"))197        labels = a.major.formatter.format_ticks(locs)198        for text in labels[1:-1]:199            assert re.match(r"^\d+mg$", text)200    def test_label_empty_unit(self, x):201        a, locs = self.setup_labels(1000 * x, unit="")202        labels = a.major.formatter.format_ticks(locs)203        for text in labels[1:-1]:204            assert re.match(r"^\d+m$", text)205    def test_label_base_from_transform(self, x):206        s = Continuous(trans="log")207        a = PseudoAxis(s._setup(x, Coordinate())._matplotlib_scale)208        a.set_view_interval(10, 1000)209        label, = a.major.formatter.format_ticks([100])210        assert r"10^{2}" in label211    def test_label_type_checks(self):212        s = Continuous()213        with pytest.raises(TypeError, match="Label formatter must be"):214            s.label("{x}")215        with pytest.raises(TypeError, match="`like` must be"):216            s.label(like=2)217class TestNominal:218    @pytest.fixture219    def x(self):220        return pd.Series(["a", "c", "b", "c"], name="x")221    @pytest.fixture222    def y(self):223        return pd.Series([1, -1.5, 3, -1.5], name="y")224    def test_coordinate_defaults(self, x):225        s = Nominal()._setup(x, Coordinate())226        assert_array_equal(s(x), np.array([0, 1, 2, 1], float))227    def test_coordinate_with_order(self, x):228        s = Nominal(order=["a", "b", "c"])._setup(x, Coordinate())229        assert_array_equal(s(x), np.array([0, 2, 1, 2], float))230    def test_coordinate_with_subset_order(self, x):231        s = Nominal(order=["c", "a"])._setup(x, Coordinate())232        assert_array_equal(s(x), np.array([1, 0, np.nan, 0], float))233    def test_coordinate_axis(self, x):234        ax = mpl.figure.Figure().subplots()235        s = Nominal()._setup(x, Coordinate(), ax.xaxis)236        assert_array_equal(s(x), np.array([0, 1, 2, 1], float))237        f = ax.xaxis.get_major_formatter()238        assert f.format_ticks([0, 1, 2]) == ["a", "c", "b"]239    def test_coordinate_axis_with_order(self, x):240        order = ["a", "b", "c"]241        ax = mpl.figure.Figure().subplots()242        s = Nominal(order=order)._setup(x, Coordinate(), ax.xaxis)243        assert_array_equal(s(x), np.array([0, 2, 1, 2], float))244        f = ax.xaxis.get_major_formatter()245        assert f.format_ticks([0, 1, 2]) == order246    def test_coordinate_axis_with_subset_order(self, x):247        order = ["c", "a"]248        ax = mpl.figure.Figure().subplots()249        s = Nominal(order=order)._setup(x, Coordinate(), ax.xaxis)250        assert_array_equal(s(x), np.array([1, 0, np.nan, 0], float))251        f = ax.xaxis.get_major_formatter()252        assert f.format_ticks([0, 1, 2]) == [*order, ""]253    def test_coordinate_axis_with_category_dtype(self, x):254        order = ["b", "a", "d", "c"]255        x = x.astype(pd.CategoricalDtype(order))256        ax = mpl.figure.Figure().subplots()257        s = Nominal()._setup(x, Coordinate(), ax.xaxis)258        assert_array_equal(s(x), np.array([1, 3, 0, 3], float))259        f = ax.xaxis.get_major_formatter()260        assert f.format_ticks([0, 1, 2, 3]) == order261    def test_coordinate_numeric_data(self, y):262        ax = mpl.figure.Figure().subplots()263        s = Nominal()._setup(y, Coordinate(), ax.yaxis)264        assert_array_equal(s(y), np.array([1, 0, 2, 0], float))265        f = ax.yaxis.get_major_formatter()266        assert f.format_ticks([0, 1, 2]) == ["-1.5", "1.0", "3.0"]267    def test_coordinate_numeric_data_with_order(self, y):268        order = [1, 4, -1.5]269        ax = mpl.figure.Figure().subplots()270        s = Nominal(order=order)._setup(y, Coordinate(), ax.yaxis)271        assert_array_equal(s(y), np.array([0, 2, np.nan, 2], float))272        f = ax.yaxis.get_major_formatter()273        assert f.format_ticks([0, 1, 2]) == ["1.0", "4.0", "-1.5"]274    def test_color_defaults(self, x):275        s = Nominal()._setup(x, Color())276        cs = color_palette()277        assert_array_equal(s(x), [cs[0], cs[1], cs[2], cs[1]])278    def test_color_named_palette(self, x):279        pal = "flare"280        s = Nominal(pal)._setup(x, Color())281        cs = color_palette(pal, 3)282        assert_array_equal(s(x), [cs[0], cs[1], cs[2], cs[1]])283    def test_color_list_palette(self, x):284        cs = color_palette("crest", 3)285        s = Nominal(cs)._setup(x, Color())286        assert_array_equal(s(x), [cs[0], cs[1], cs[2], cs[1]])287    def test_color_dict_palette(self, x):288        cs = color_palette("crest", 3)289        pal = dict(zip("bac", cs))290        s = Nominal(pal)._setup(x, Color())291        assert_array_equal(s(x), [cs[1], cs[2], cs[0], cs[2]])292    def test_color_numeric_data(self, y):293        s = Nominal()._setup(y, Color())294        cs = color_palette()295        assert_array_equal(s(y), [cs[1], cs[0], cs[2], cs[0]])296    def test_color_numeric_with_order_subset(self, y):297        s = Nominal(order=[-1.5, 1])._setup(y, Color())298        c1, c2 = color_palette(n_colors=2)299        null = (np.nan, np.nan, np.nan)300        assert_array_equal(s(y), [c2, c1, null, c1])301    @pytest.mark.xfail(reason="Need to sort out float/int order")302    def test_color_numeric_int_float_mix(self):303        z = pd.Series([1, 2], name="z")304        s = Nominal(order=[1.0, 2])._setup(z, Color())305        c1, c2 = color_palette(n_colors=2)306        null = (np.nan, np.nan, np.nan)307        assert_array_equal(s(z), [c1, null, c2])308    def test_color_alpha_in_palette(self, x):309        cs = [(.2, .2, .3, .5), (.1, .2, .3, 1), (.5, .6, .2, 0)]310        s = Nominal(cs)._setup(x, Color())311        assert_array_equal(s(x), [cs[0], cs[1], cs[2], cs[1]])312    def test_color_unknown_palette(self, x):313        pal = "not_a_palette"314        err = f"{pal} is not a valid palette name"315        with pytest.raises(ValueError, match=err):316            Nominal(pal)._setup(x, Color())317    def test_object_defaults(self, x):318        class MockProperty(ObjectProperty):319            def _default_values(self, n):320                return list("xyz"[:n])321        s = Nominal()._setup(x, MockProperty())322        assert s(x) == ["x", "y", "z", "y"]323    def test_object_list(self, x):324        vs = ["x", "y", "z"]325        s = Nominal(vs)._setup(x, ObjectProperty())326        assert s(x) == ["x", "y", "z", "y"]327    def test_object_dict(self, x):328        vs = {"a": "x", "b": "y", "c": "z"}329        s = Nominal(vs)._setup(x, ObjectProperty())330        assert s(x) == ["x", "z", "y", "z"]331    def test_object_order(self, x):332        vs = ["x", "y", "z"]333        s = Nominal(vs, order=["c", "a", "b"])._setup(x, ObjectProperty())334        assert s(x) == ["y", "x", "z", "x"]335    def test_object_order_subset(self, x):336        vs = ["x", "y"]337        s = Nominal(vs, order=["a", "c"])._setup(x, ObjectProperty())338        assert s(x) == ["x", "y", None, "y"]339    def test_objects_that_are_weird(self, x):340        vs = [("x", 1), (None, None, 0), {}]341        s = Nominal(vs)._setup(x, ObjectProperty())342        assert s(x) == [vs[0], vs[1], vs[2], vs[1]]343    def test_alpha_default(self, x):344        s = Nominal()._setup(x, Alpha())345        assert_array_equal(s(x), [.95, .625, .3, .625])346    def test_fill(self):347        x = pd.Series(["a", "a", "b", "a"], name="x")348        s = Nominal()._setup(x, Fill())349        assert_array_equal(s(x), [True, True, False, True])350    def test_fill_dict(self):351        x = pd.Series(["a", "a", "b", "a"], name="x")352        vs = {"a": False, "b": True}353        s = Nominal(vs)._setup(x, Fill())354        assert_array_equal(s(x), [False, False, True, False])355    def test_fill_nunique_warning(self):356        x = pd.Series(["a", "b", "c", "a", "b"], name="x")357        with pytest.warns(UserWarning, match="The variable assigned to fill"):358            s = Nominal()._setup(x, Fill())359        assert_array_equal(s(x), [True, False, True, True, False])360    def test_interval_defaults(self, x):361        class MockProperty(IntervalProperty):362            _default_range = (1, 2)363        s = Nominal()._setup(x, MockProperty())364        assert_array_equal(s(x), [2, 1.5, 1, 1.5])365    def test_interval_tuple(self, x):366        s = Nominal((1, 2))._setup(x, IntervalProperty())367        assert_array_equal(s(x), [2, 1.5, 1, 1.5])368    def test_interval_tuple_numeric(self, y):369        s = Nominal((1, 2))._setup(y, IntervalProperty())370        assert_array_equal(s(y), [1.5, 2, 1, 2])371    def test_interval_list(self, x):372        vs = [2, 5, 4]373        s = Nominal(vs)._setup(x, IntervalProperty())374        assert_array_equal(s(x), [2, 5, 4, 5])375    def test_interval_dict(self, x):376        vs = {"a": 3, "b": 4, "c": 6}377        s = Nominal(vs)._setup(x, IntervalProperty())378        assert_array_equal(s(x), [3, 6, 4, 6])379    def test_interval_with_transform(self, x):380        class MockProperty(IntervalProperty):381            _forward = np.square382            _inverse = np.sqrt383        s = Nominal((2, 4))._setup(x, MockProperty())384        assert_array_equal(s(x), [4, np.sqrt(10), 2, np.sqrt(10)])385class TestTemporal:386    @pytest.fixture387    def t(self):388        dates = pd.to_datetime(["1972-09-27", "1975-06-24", "1980-12-14"])389        return pd.Series(dates, name="x")390    @pytest.fixture391    def x(self, t):392        return pd.Series(mpl.dates.date2num(t), name=t.name)393    def test_coordinate_defaults(self, t, x):394        s = Temporal()._setup(t, Coordinate())395        assert_array_equal(s(t), x)396    def test_interval_defaults(self, t, x):397        s = Temporal()._setup(t, IntervalProperty())398        normed = (x - x.min()) / (x.max() - x.min())399        assert_array_equal(s(t), normed)400    def test_interval_with_range(self, t, x):401        values = (1, 3)402        s = Temporal((1, 3))._setup(t, IntervalProperty())403        normed = (x - x.min()) / (x.max() - x.min())404        expected = normed * (values[1] - values[0]) + values[0]405        assert_array_equal(s(t), expected)406    def test_interval_with_norm(self, t, x):407        norm = t[1], t[2]408        s = Temporal(norm=norm)._setup(t, IntervalProperty())409        n = mpl.dates.date2num(norm)410        normed = (x - n[0]) / (n[1] - n[0])411        assert_array_equal(s(t), normed)412    def test_color_defaults(self, t, x):413        cmap = color_palette("ch:", as_cmap=True)414        s = Temporal()._setup(t, Color())415        normed = (x - x.min()) / (x.max() - x.min())416        assert_array_equal(s(t), cmap(normed)[:, :3])  # FIXME RGBA417    def test_color_named_values(self, t, x):418        name = "viridis"419        cmap = color_palette(name, as_cmap=True)420        s = Temporal(name)._setup(t, Color())421        normed = (x - x.min()) / (x.max() - x.min())422        assert_array_equal(s(t), cmap(normed)[:, :3])  # FIXME RGBA423    def test_coordinate_axis(self, t, x):424        ax = mpl.figure.Figure().subplots()425        s = Temporal()._setup(t, Coordinate(), ax.xaxis)426        assert_array_equal(s(t), x)427        locator = ax.xaxis.get_major_locator()428        formatter = ax.xaxis.get_major_formatter()429        assert isinstance(locator, mpl.dates.AutoDateLocator)430        assert isinstance(formatter, mpl.dates.AutoDateFormatter)431    @pytest.mark.skipif(432        Version(mpl.__version__) < Version("3.3.0"),433        reason="Test requires new matplotlib date epoch."434    )435    def test_tick_locator(self, t):436        locator = mpl.dates.YearLocator(month=3, day=15)437        s = Temporal().tick(locator)438        a = PseudoAxis(s._setup(t, Coordinate())._matplotlib_scale)439        a.set_view_interval(0, 365)440        assert 73 in a.major.locator()441    def test_tick_upto(self, t, x):442        n = 8443        ax = mpl.figure.Figure().subplots()444        Temporal().tick(upto=n)._setup(t, Coordinate(), ax.xaxis)445        locator = ax.xaxis.get_major_locator()446        assert set(locator.maxticks.values()) == {n}447    @pytest.mark.skipif(448        Version(mpl.__version__) < Version("3.3.0"),449        reason="Test requires new matplotlib date epoch."450    )451    def test_label_formatter(self, t):452        formatter = mpl.dates.DateFormatter("%Y")453        s = Temporal().label(formatter)454        a = PseudoAxis(s._setup(t, Coordinate())._matplotlib_scale)455        a.set_view_interval(10, 1000)456        label, = a.major.formatter.format_ticks([100])457        assert label == "1970"458    def test_label_concise(self, t, x):459        ax = mpl.figure.Figure().subplots()460        Temporal().label(concise=True)._setup(t, Coordinate(), ax.xaxis)461        formatter = ax.xaxis.get_major_formatter()...

trace_setup.py

Source:trace_setup.py

1from enum import Enum2from pathlib import Path3from subprocess import CalledProcessError, check_output4import yaml5import re6import cxxfilt7class BinaryAlreadyAddedError(Exception):8    def __init__(self, message=''):9        super().__init__(message)10class BinaryNotExistsError(Exception):11    def __init__(self, message=''):12        super().__init__(message)13class ConfigFileError(Exception):14    def __init__(self, message=''):15        super().__init__(message)16class FunctionNotInBinaryError(Exception):17    def __init__(self, message=''):18        super().__init__(message)19class BuiltInNotExistsError(Exception):20    def __init__(self, message=''):21        super().__init__(message)22class Setup:23    def __init__(self):24        self._setup = {}25    # initialize app and its functions for tracing26    def initialize_binary(self, path):27        if path in self._setup:28            raise BinaryAlreadyAddedError('Binary at {} already added'.format(path))29        try:30            symbols = check_output(['nm', path]).decode().rstrip().split('\n')31        except CalledProcessError:32            raise BinaryNotExistsError33        functions = [symbol.split()[-1] for symbol in symbols]34        init_state = {}35        for function in functions:36            try:37                name = cxxfilt.demangle(function)38            except cxxfilt.InvalidName:39                name = function40            init_state[name] = {41                'mangled': function,42                'traced': False,43                'parameters': {},44                'offset': 045            }46        self._setup[path] = init_state47    # search offset after setting stack pointer for built-in function48    def get_offset_for_built_in(self, func_name):49        offset = 050        try:51            # search address of function in symbol map52            sym_address = check_output(53                            ['sudo',54                             'grep',55                             '-A1',56                             '-w',57                             func_name,58                             '/proc/kallsyms']59                          ).decode().rstrip().split('\n')60            if len(sym_address) == 2:61                # address of given function62                start_address = -163                start_address_match = re.search(r'^([a-f0-9]+)', sym_address[0])64                if start_address_match:65                    start_address = int(start_address_match.group(1), base=16)66                # address of following symbol67                stop_address = -168                stop_address_match = re.search(r'^([a-f0-9]+)', sym_address[1])69                if stop_address_match:70                    stop_address = int(stop_address_match.group(1), base=16)71                if start_address >= 0 and stop_address >= 0:72                    # get instructions of function73                    objdump_out = check_output(74                                ['sudo',75                                    'objdump',76                                    '--prefix-addresses',77                                    '-d',78                                    '--start-address=0x{:X}'.format(start_address),79                                    '--stop-address=0x{:X}'.format(stop_address),80                                    '/proc/kcore']81                                ).decode().rstrip().split('\n')82                    # search first instruction after function prologue83                    first = False84                    second = False85                    for line in objdump_out:86                        if first and second:87                            func_offset = re.search(r'(0x[a-f0-9]+)', line)88                            if func_offset:89                                # needed offset is difference between function's base address and90                                # address of first instruction after function prologue91                                offset = int(func_offset.group(1), base=16) - start_address92                                break93                        # second instruction of function prologue94                        if first and re.search(r'mov\s+%rsp,%rbp', line):95                            second = True96                        # first instruction of function prologue97                        if not(first) and re.search(r'push\s+%rbp', line):98                            first = True99        except CalledProcessError:100            raise BuiltInNotExistsError101        return offset102    # initialize built-in function to be traced103    def initialize_built_in(self, func_name):104        if 'built-ins' not in self._setup:105            self._setup['built-ins'] = {}106        try:107            offset = self.get_offset_for_built_in(func_name)108            self._setup['built-ins'][func_name] = {109                'traced': True,110                'parameters': {},111                'offset': offset112            }113        except BuiltInNotExistsError:114            raise115    # Remove application from getting traced116    def remove_app(self, app):117        del self._setup[app]118    # Returns apps currently saved119    def get_apps(self):120        return list(self._setup.keys())121    # Return functions and their state of a given application122    def get_setup_of_app(self, app):123        return self._setup[app]124    # search offset after setting stack pointer for user function125    def get_offset_for_function(self, app_name, func_name):126        offset = 0127        # get instructions of function128        try:129            objdump_out = check_output(['objdump', "--disassemble="+func_name, "--prefix-addresses", app_name]).decode().rstrip().split('\n')130        except CalledProcessError:131            raise FunctionNotInBinaryError132        first = False133        second = False134        for line in objdump_out:135            if first and second:136                # first instruction after function prologue with offset137                func_offset = re.search(r'<'+func_name+r'\+(0x[a-f0-9]+)>', line)138                if func_offset:139                    offset = int(func_offset.group(1), base=16)140                    break141            # second instruction of function prologue142            if first and re.search(r'mov\s+%rsp,%rbp', line):143                second = True144            # first instruction of function prologue145            if not(first) and re.search(r'push\s+%rbp', line):146                first = True147        return offset148    # Sets up a function to be traced149    def setup_function_to_trace(self, app, function):150        try:151            self._setup[app][function]['traced'] = True152            offset = self.get_offset_for_function(app, function)153            self._setup[app][function]['offset'] = offset154        except KeyError:155            for func_name in self._setup[app]:156                if self._setup[app][func_name]['mangled'] == function:157                    self._setup[app][func_name]['traced'] = True158                    offset = self.get_offset_for_function(app, function)159                    self._setup[app][func_name]['offset'] = offset160                    return161            raise FunctionNotInBinaryError(162                'No function named {} was found in {}'.format(function, app)163            )164    # Removes a function from traced ones165    def remove_function_from_trace(self, app, function):166        try:167            self._setup[app][function]['traced'] = False168        except KeyError:169            for func_name in self._setup[app]:170                if self._setup[app][func_name]['mangled'] == function:171                    self._setup[app][func_name]['traced'] = False172                    return173            raise FunctionNotInBinaryError(174                'No function named {} was found in {}'.format(function, app)175            )176    # Returns the indexes where a parameter is set for tracing177    def get_parameters(self, app, function):178        return self._setup[app][function]['parameters']179    # Sets up a parameter to be traced180    def add_parameter(self, app, function, index, format):181        self._setup[app][function]['parameters'][index] = format182    # Removes a parameter from traced ones183    def remove_parameter(self, app, function, index):184        del self._setup[app][function]['parameters'][index]185    # Convert dictionary of functions to trace into properly186    # structured list of args to be used by the trace tool187    def generate_bcc_args(self):188        arguments = []189        for app in self._setup:190            for function in self._setup[app]:191                if self._setup[app][function]['traced']:192                    if app == 'built-ins':193                        argument = '{}+0x{:X}'.format(function, self._setup[app][function]['offset'])194                    else:195                        argument = '{}:{}+0x{:X}'.format(app, self._setup[app][function]['mangled'], self._setup[app][function]['offset'])196                    params = self._setup[app][function]['parameters']197                    if params:198                        argument = '{} "{}", {}'.format(199                            argument,200                            ' '.join([params[index] for index in params]),201                            ', '.join(['arg{}'.format(index) for index in params]))202                    arguments.append(argument)203        return arguments204    def load_from_file(self, path):205        try:206            content = Path(path).read_text()207        except FileNotFoundError:208            raise ConfigFileError('Could not find config file at {}'.format(path))209        except IsADirectoryError:210            raise ConfigFileError('{} is a directory, not a file'.format(path))211        try:212            config = yaml.safe_load(content)213        except (yaml.parser.ParserError, yaml.scanner.ScannerError):214            raise ConfigFileError('File needs to be yaml format')215        err_message = ''216        for app in config:217            try:218                self.initialize_binary(app)219                for function in config[app]:220                    self.setup_function_to_trace(app, function)221                    for index in config[app][function]:222                        self.add_parameter(app, function, index, config[app][function][index])223            except BinaryNotExistsError:224                try:225                    self.initialize_built_in(app)226                    for index in config[app]:227                        self.add_parameter('built-ins', app, index, config[app][index])228                    err_message = 'Some binaries were not found so they were assumed to be built-in functions'229                except BuiltInNotExistsError:230                    err_message = 'Some binaries were not found, and neither as built-in functions'231            except TypeError:232                raise ConfigFileError('File format is incorrect')...

Demux16Way.py

Source:Demux16Way.py

...36        self.gate5 = Demux.Demux()37        self.gate6 = Demux.Demux()38        self.gate7 = Demux.Demux()39        self.gate8 = Demux.Demux()40    def _setup(self):41        self.gate0.a = self.a42        self.gate0.select = self.select[0:3]43        self.b = self.gate0.outaf()44        self.c = self.gate0.outbf()45        self.d = self.gate0.outcf()46        self.e = self.gate0.outdf()47        self.f = self.gate0.outef()48        self.g = self.gate0.outff()49        self.h = self.gate0.outgf()50        self.i = self.gate0.outhf()51        self.gate1.a = self.b52        self.gate1.select = self.select[3:4]53        self.outa = self.gate1.outaf()54        self.outb = self.gate1.outbf()55        self.gate2.a = self.c56        self.gate2.select = self.select[3:4]57        self.outc = self.gate2.outaf()58        self.outd = self.gate2.outbf()59        self.gate3.a = self.d60        self.gate3.select = self.select[3:4]61        self.oute = self.gate3.outaf()62        self.outf = self.gate3.outbf()63        self.gate4.a = self.e64        self.gate4.select = self.select[3:4]65        self.outg = self.gate4.outaf()66        self.outh = self.gate4.outbf()67        self.gate5.a = self.f68        self.gate5.select = self.select[3:4]69        self.outi = self.gate5.outaf()70        self.outj = self.gate5.outbf()71        self.gate6.a = self.g72        self.gate6.select = self.select[3:4]73        self.outk = self.gate6.outaf()74        self.outl = self.gate6.outbf()75        self.gate7.a = self.h76        self.gate7.select = self.select[3:4]77        self.outm = self.gate7.outaf()78        self.outn = self.gate7.outbf()79        self.gate8.a = self.i80        self.gate8.select = self.select[3:4]81        self.outo = self.gate8.outaf()82        self.outp = self.gate8.outbf()83    def outaf(self):84        self._setup()85        return self.outa86    def outbf(self):87        self._setup()88        return self.outb89    def outcf(self):90        self._setup()91        return self.outc92    def outdf(self):93        self._setup()94        return self.outd95    def outef(self):96        self._setup()97        return self.oute98    def outff(self):99        self._setup()100        return self.outf101    def outgf(self):102        self._setup()103        return self.outg104    def outhf(self):105        self._setup()106        return self.outh107    def outif(self):108        self._setup()109        return self.outi110    def outjf(self):111        self._setup()112        return self.outj113    def outkf(self):114        self._setup()115        return self.outk116    def outlf(self):117        self._setup()118        return self.outl119    def outmf(self):120        self._setup()121        return self.outm122    def outnf(self):123        self._setup()124        return self.outn125    def outof(self):126        self._setup()127        return self.outo128    def outpf(self):129        self._setup()...

Automation Testing Tutorials

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