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How to use config_file method in molecule

Best Python code snippet using molecule_python

base_tests.py

Source:base_tests.py

1import os2import tempfile3import unittest4from tempfile import TemporaryDirectory5from mkdocs import exceptions6from mkdocs.config import base, defaults7from mkdocs.config.config_options import BaseConfigOption8class ConfigBaseTests(unittest.TestCase):9    def test_unrecognised_keys(self):10        c = base.Config(schema=defaults.DEFAULT_SCHEMA)11        c.load_dict({12            'not_a_valid_config_option': "test"13        })14        failed, warnings = c.validate()15        self.assertEqual(warnings, [16            ('not_a_valid_config_option',17                'Unrecognised configuration name: not_a_valid_config_option')18        ])19    def test_missing_required(self):20        c = base.Config(schema=defaults.DEFAULT_SCHEMA)21        errors, warnings = c.validate()22        self.assertEqual(len(errors), 1)23        self.assertEqual(errors[0][0], 'site_name')24        self.assertEqual(str(errors[0][1]), 'Required configuration not provided.')25        self.assertEqual(len(warnings), 0)26    def test_load_from_file(self):27        """28        Users can explicitly set the config file using the '--config' option.29        Allows users to specify a config other than the default `mkdocs.yml`.30        """31        temp_dir = TemporaryDirectory()32        config_file = open(os.path.join(temp_dir.name, 'mkdocs.yml'), 'w')33        os.mkdir(os.path.join(temp_dir.name, 'docs'))34        try:35            config_file.write("site_name: MkDocs Test\n")36            config_file.flush()37            config_file.close()38            cfg = base.load_config(config_file=config_file.name)39            self.assertTrue(isinstance(cfg, base.Config))40            self.assertEqual(cfg['site_name'], 'MkDocs Test')41        finally:42            os.remove(config_file.name)43            temp_dir.cleanup()44    def test_load_from_missing_file(self):45        self.assertRaises(exceptions.ConfigurationError,46                          base.load_config, config_file='missing_file.yml')47    def test_load_from_open_file(self):48        """49        `load_config` can accept an open file descriptor.50        """51        temp_dir = TemporaryDirectory()52        temp_path = temp_dir.name53        config_fname = os.path.join(temp_path, 'mkdocs.yml')54        config_file = open(config_fname, 'w+')55        os.mkdir(os.path.join(temp_path, 'docs'))56        try:57            config_file.write("site_name: MkDocs Test\n")58            config_file.flush()59            cfg = base.load_config(config_file=config_file)60            self.assertTrue(isinstance(cfg, base.Config))61            self.assertEqual(cfg['site_name'], 'MkDocs Test')62            # load_config will always close the file63            self.assertTrue(config_file.closed)64        finally:65            temp_dir.cleanup()66    def test_load_from_closed_file(self):67        """68        The `serve` command with auto-reload may pass in a closed file descriptor.69        Ensure `load_config` reloads the closed file.70        """71        temp_dir = TemporaryDirectory()72        config_file = open(os.path.join(temp_dir.name, 'mkdocs.yml'), 'w')73        os.mkdir(os.path.join(temp_dir.name, 'docs'))74        try:75            config_file.write("site_name: MkDocs Test\n")76            config_file.flush()77            config_file.close()78            cfg = base.load_config(config_file=config_file)79            self.assertTrue(isinstance(cfg, base.Config))80            self.assertEqual(cfg['site_name'], 'MkDocs Test')81        finally:82            temp_dir.cleanup()83    def test_load_from_deleted_file(self):84        """85        Deleting the config file could trigger a server reload.86        """87        config_file = tempfile.NamedTemporaryFile('w', delete=False)88        try:89            config_file.write("site_name: MkDocs Test\n")90            config_file.flush()91            config_file.close()92        finally:93            os.remove(config_file.name)94        self.assertRaises(exceptions.ConfigurationError,95                          base.load_config, config_file=config_file)96    def test_load_missing_required(self):97        """98        `site_name` is a required setting.99        """100        config_file = tempfile.NamedTemporaryFile('w', delete=False)101        try:102            config_file.write(103                "site_dir: output\nsite_uri: https://www.mkdocs.org\n")104            config_file.flush()105            config_file.close()106            self.assertRaises(exceptions.ConfigurationError,107                              base.load_config, config_file=config_file.name)108        finally:109            os.remove(config_file.name)110    def test_pre_validation_error(self):111        class InvalidConfigOption(BaseConfigOption):112            def pre_validation(self, config, key_name):113                raise base.ValidationError('pre_validation error')114        c = base.Config(schema=(('invalid_option', InvalidConfigOption()), ))115        errors, warnings = c.validate()116        self.assertEqual(len(errors), 1)117        self.assertEqual(errors[0][0], 'invalid_option')118        self.assertEqual(str(errors[0][1]), 'pre_validation error')119        self.assertTrue(isinstance(errors[0][1], base.ValidationError))120        self.assertEqual(len(warnings), 0)121    def test_run_validation_error(self):122        class InvalidConfigOption(BaseConfigOption):123            def run_validation(self, value):124                raise base.ValidationError('run_validation error')125        c = base.Config(schema=(('invalid_option', InvalidConfigOption()), ))126        errors, warnings = c.validate()127        self.assertEqual(len(errors), 1)128        self.assertEqual(errors[0][0], 'invalid_option')129        self.assertEqual(str(errors[0][1]), 'run_validation error')130        self.assertTrue(isinstance(errors[0][1], base.ValidationError))131        self.assertEqual(len(warnings), 0)132    def test_post_validation_error(self):133        class InvalidConfigOption(BaseConfigOption):134            def post_validation(self, config, key_name):135                raise base.ValidationError('post_validation error')136        c = base.Config(schema=(('invalid_option', InvalidConfigOption()), ))137        errors, warnings = c.validate()138        self.assertEqual(len(errors), 1)139        self.assertEqual(errors[0][0], 'invalid_option')140        self.assertEqual(str(errors[0][1]), 'post_validation error')141        self.assertTrue(isinstance(errors[0][1], base.ValidationError))142        self.assertEqual(len(warnings), 0)143    def test_pre_and_run_validation_errors(self):144        """ A pre_validation error does not stop run_validation from running. """145        class InvalidConfigOption(BaseConfigOption):146            def pre_validation(self, config, key_name):147                raise base.ValidationError('pre_validation error')148            def run_validation(self, value):149                raise base.ValidationError('run_validation error')150        c = base.Config(schema=(('invalid_option', InvalidConfigOption()), ))151        errors, warnings = c.validate()152        self.assertEqual(len(errors), 2)153        self.assertEqual(errors[0][0], 'invalid_option')154        self.assertEqual(str(errors[0][1]), 'pre_validation error')155        self.assertTrue(isinstance(errors[0][1], base.ValidationError))156        self.assertEqual(errors[1][0], 'invalid_option')157        self.assertEqual(str(errors[1][1]), 'run_validation error')158        self.assertTrue(isinstance(errors[1][1], base.ValidationError))159        self.assertEqual(len(warnings), 0)160    def test_run_and_post_validation_errors(self):161        """ A run_validation error stops post_validation from running. """162        class InvalidConfigOption(BaseConfigOption):163            def run_validation(self, value):164                raise base.ValidationError('run_validation error')165            def post_validation(self, config, key_name):166                raise base.ValidationError('post_validation error')167        c = base.Config(schema=(('invalid_option', InvalidConfigOption()), ))168        errors, warnings = c.validate()169        self.assertEqual(len(errors), 1)170        self.assertEqual(errors[0][0], 'invalid_option')171        self.assertEqual(str(errors[0][1]), 'run_validation error')172        self.assertTrue(isinstance(errors[0][1], base.ValidationError))173        self.assertEqual(len(warnings), 0)174    def test_validation_warnings(self):175        class InvalidConfigOption(BaseConfigOption):176            def pre_validation(self, config, key_name):177                self.warnings.append('pre_validation warning')178            def run_validation(self, value):179                self.warnings.append('run_validation warning')180            def post_validation(self, config, key_name):181                self.warnings.append('post_validation warning')182        c = base.Config(schema=(('invalid_option', InvalidConfigOption()), ))183        errors, warnings = c.validate()184        self.assertEqual(len(errors), 0)185        self.assertEqual(warnings, [186            ('invalid_option', 'pre_validation warning'),187            ('invalid_option', 'run_validation warning'),188            ('invalid_option', 'post_validation warning'),189        ])190    def test_load_from_file_with_relative_paths(self):191        """192        When explicitly setting a config file, paths should be relative to the193        config file, not the working directory.194        """195        config_dir = TemporaryDirectory()196        config_fname = os.path.join(config_dir.name, 'mkdocs.yml')197        docs_dir = os.path.join(config_dir.name, 'src')198        os.mkdir(docs_dir)199        config_file = open(config_fname, 'w')200        try:201            config_file.write("docs_dir: src\nsite_name: MkDocs Test\n")202            config_file.flush()203            config_file.close()204            cfg = base.load_config(config_file=config_file)205            self.assertTrue(isinstance(cfg, base.Config))206            self.assertEqual(cfg['site_name'], 'MkDocs Test')207            self.assertEqual(cfg['docs_dir'], docs_dir)208            self.assertEqual(cfg.config_file_path, config_fname)209            self.assertIsInstance(cfg.config_file_path, str)210        finally:...

ConfigFileHandler.py

Source:ConfigFileHandler.py

1# -*- coding: UTF-8 -*-2import os3import arrow4from flask import request, current_app5from flask_restful import Resource6from werkzeug.exceptions import BadRequest7from SysManager.configs import SSHConfig8from SysManager.executor import Executor9from app import db10from app.models import ConfigFile, ConfigType, TradeSystem11from restful.errors import (DataNotJsonError,12                            DataNotNullError,13                            DataEnumValueError,14                            ApiError)15from restful.protocol import RestProtocol16class ConfigFileListApi(Resource):17    def __init__(self):18        super(ConfigFileListApi, self).__init__()19        self.not_null_list = ['name', 'dir', 'file', 'config_type', 'sys_id']20        self.system_list = []21    def gather_systems(self, parent_sys):22        self.system_list.append(parent_sys)23        for child_sys in parent_sys.child_systems:24            if child_sys.disabled is False:25                self.gather_systems(child_sys)26    def get(self, **kwargs):27        system = TradeSystem.find(**kwargs)28        if system:29            self.gather_systems(system)30            ''' for sys in self.system_list:31                # config_files = ConfigFile.query.filter_by(sys_id=sys.id).all()32                self.config_file_list.extend(sys.config_files) '''33            conf_file_list = ConfigFile.query.filter(34                ConfigFile.sys_id.in_([sys.id for sys in self.system_list])35            ).all()36            return RestProtocol(conf_file_list)37        else:38            return RestProtocol(message='System not found', error_code=-1), 40439    def post(self):40        try:41            data = request.get_json(force=True)42            for param in self.not_null_list:43                if not data.get(param):44                    raise DataNotNullError('Please input {}'.format(param))45            ConfigType[data.get('config_type')]46        except BadRequest:47            return RestProtocol(DataNotJsonError())48        except ApiError as e:49            return RestProtocol(e)50        except KeyError:51            return RestProtocol(DataEnumValueError())52        else:53            config_file = ConfigFile()54            config_file.name = data.get('name')55            config_file.sys_id = data.get('sys_id')56            config_file.config_type = ConfigType[data.get('config_type')]57            config_file.dir = data.get('dir')58            config_file.file = data.get('file')59            system = TradeSystem.find(id=data.get('sys_id'))60            if system:61                mod = {62                    'name': 'md5',63                    'args': {64                        'dir': data.get('dir'),65                        'file': data.get('file')66                    }67                }68                conf = SSHConfig(system.ip,69                                 system.user,70                                 system.password)71                executor = Executor.Create(conf)72                result = executor.run(mod)73                if result.return_code == 0:74                    config_file.hash_code = result.lines[0]75                    config_file.timestamp = arrow.utcnow()76                # Make directory for config file77                if not os.path.exists(current_app.config['CONFIG_FILES']):78                    os.mkdir(current_app.config['CONFIG_FILES'])79                os.chdir(os.path.join(current_app.config['CONFIG_FILES']))80                dir_name = system.name + '_' + system.ip81                if not os.path.exists(dir_name):82                    os.mkdir(dir_name)83                config_file.storage = current_app.config['CONFIG_FILES'] + '/' + os.path.join(dir_name)84                os.chdir('../')85            db.session.add(config_file)86            db.session.commit()87            return RestProtocol(config_file)88class ConfigFileApi(Resource):89    def __init__(self):90        super(ConfigFileApi, self).__init__()91    def get(self, **kwargs):92        config_file = ConfigFile.find(**kwargs)93        if config_file:94            return RestProtocol(config_file)95        else:96            return RestProtocol(message='Config file not found', error_code=-1), 40497    def post(self, **kwargs):98        config_file = ConfigFile.find(**kwargs)99        if config_file:100            remote_config = SSHConfig(101                config_file.process.server.ip,102                config_file.process.system.user,103                config_file.process.system.password104            )105            exe = Executor.Create(remote_config)106            mod = {107                'name': 'md5',108                'args': {109                    'dir': config_file.dir,110                    'file': config_file.file111                }112            }113            result = exe.run(mod)114            if result.return_code == 0:115                config_file.pre_hash_code = config_file.hash_code116                config_file.pre_timestamp = config_file.timestamp117                config_file.hash_code = result.lines[0]118                config_file.timestamp = arrow.utcnow()119            return RestProtocol({120                'id': config_file.id,121                'uuid': config_file.uuid,122                'name': config_file.name,123                'type': config_file.config_type.name,124                'dir': config_file.dir,125                'file': config_file.file,126                'hash': config_file.hash_code,127                'timestamp': config_file.timestamp and \128                    config_file.timestamp.to(current_app.config['TIME_ZONE']).format('YYYY-MM-DD HH:mm:ss'),129                'hash_changed': False130            })131        else:132            return RestProtocol(message='Config file not found', error_code=-1), 404133class ConfigFileCheckApi(Resource):134    def __init__(self):135        super(ConfigFileCheckApi, self).__init__()136        self.system_list = []137        self.config_file_list = []138        self.executor_dict = {}139        self.check_result = {}140    def gather_systems(self, parent_sys):141        self.system_list.append(parent_sys)142        for child_sys in parent_sys.child_systems:143            if child_sys.disabled is False:144                self.gather_systems(child_sys)145    def get(self, **kwargs):146        system = TradeSystem.find(**kwargs)147        if system:148            self.gather_systems(system)149            for sys in self.system_list:150                self.config_file_list.extend(sys.config_files)151                conf = SSHConfig(sys.ip,152                                 sys.user,153                                 sys.password)154                executor = Executor.Create(conf)155                self.executor_dict[sys.id] = executor156            for config_file in self.config_file_list:157                mod = {158                    'name': 'md5',159                    'args': {160                        'dir': config_file.dir,161                        'file': config_file.file162                    }163                }164                conf_sys = TradeSystem.find(id=config_file.sys_id)165                if conf_sys:166                    result = self.executor_dict[conf_sys.id].run(mod)167                    if result.return_code == 0:168                        # 'True' means not change, 'False' means change169                        if result.lines[0] == config_file.hash_code:170                            self.check_result[config_file.name] = True, config_file.dir171                        if result.lines[0] != config_file.hash_code:172                            self.check_result[config_file.name] = False, config_file.dir173            return RestProtocol(self.check_result)174        else:...

confmodif.py

Source:confmodif.py

1import os2def conf_file_modify(pop):3    config_file = open(os.path.join("utils", "config-feedforward.txt"), "w")4    config_file.write("[NEAT]\n")5    config_file.write("fitness_criterion     = max\n")6    config_file.write("fitness_threshold     = 10000\n")7    config_file.write("pop_size              = " + str(pop) + "\n")8    config_file.write("reset_on_extinction   = False\n\n")9    config_file.write("[DefaultGenome]\n")10    config_file.write("# node activation options\n")11    config_file.write("activation_default      = softplus\n")12    config_file.write("activation_mutate_rate  = 0.2\n")13    config_file.write("activation_options      = tanh sigmoid square\n\n")14    config_file.write("# node aggregation options\n")15    config_file.write("aggregation_default     = sum\n")16    config_file.write("aggregation_mutate_rate = 0.0\n")17    config_file.write("aggregation_options     = sum\n\n")18    config_file.write("# node bias options\n")19    config_file.write("bias_init_mean          = 0.0\n")20    config_file.write("bias_init_stdev         = 1.0\n")21    config_file.write("bias_max_value          = 30.0\n")22    config_file.write("bias_min_value          = -30.0\n")23    config_file.write("bias_mutate_power       = 0.5\n")24    config_file.write("bias_mutate_rate        = 0.7\n")25    config_file.write("bias_replace_rate       = 0.1\n\n")26    config_file.write("# genome compatibility options\n")27    config_file.write("compatibility_disjoint_coefficient = 1.0\n")28    config_file.write("compatibility_weight_coefficient   = 0.5\n\n")29    config_file.write("# connection add/remove rates\n")30    config_file.write("conn_add_prob           = 0.5\n")31    config_file.write("conn_delete_prob        = 0.5\n\n")32    config_file.write("# connection enable options\n")33    config_file.write("enabled_default         = True\n")34    config_file.write("enabled_mutate_rate     = 0.01\n\n")35    config_file.write("feed_forward            = True\n")36    config_file.write("initial_connection      = full\n\n")37    config_file.write("# node add/remove rates\n")38    config_file.write("node_add_prob           = 0.2\n")39    config_file.write("node_delete_prob        = 0.2\n\n")40    config_file.write("# network parameters\n")41    config_file.write("num_hidden              = 0\n")42    config_file.write("num_inputs              = 8\n")43    config_file.write("num_outputs             = 4\n\n")44    config_file.write("# node response options\n")45    config_file.write("response_init_mean      = 1.0\n")46    config_file.write("response_init_stdev     = 0.0\n")47    config_file.write("response_max_value      = 30.0\n")48    config_file.write("response_min_value      = -30.0\n")49    config_file.write("response_mutate_power   = 0.0\n")50    config_file.write("response_mutate_rate    = 0.0\n")51    config_file.write("response_replace_rate   = 0.0\n\n")52    config_file.write("# connection weight options\n")53    config_file.write("weight_init_mean        = 0.0\n")54    config_file.write("weight_init_stdev       = 1.0\n")55    config_file.write("weight_max_value        = 30\n")56    config_file.write("weight_min_value        = -30\n")57    config_file.write("weight_mutate_power     = 0.5\n")58    config_file.write("weight_mutate_rate      = 0.8\n")59    config_file.write("weight_replace_rate     = 0.1\n\n")60    config_file.write("[DefaultSpeciesSet]\n")61    config_file.write("compatibility_threshold = 3.0\n\n")62    config_file.write("[DefaultStagnation]\n")63    config_file.write("species_fitness_func = max\n")64    config_file.write("max_stagnation       = 10\n")65    config_file.write("species_elitism      = 2\n\n")66    config_file.write("[DefaultReproduction]\n")67    config_file.write("elitism            = 2\n")...

PreprocessingConfig.py

Source:PreprocessingConfig.py

1import yaml2from os.path import join3CONFIG_FILE = yaml.load(open("config_preprocessing.yml"))4def set_config_file(path_to_config):5    global CONFIG_FILE6    CONFIG_FILE = yaml.load(open("config_preprocessing.yml"))7# SOURCE DIR8def get_source_dir(dataset_name: str):9    return join(CONFIG_FILE["source_dir"],10                CONFIG_FILE["trimmomatic"]["dataset"][dataset_name]["name"])11# DATASET NAMES12def get_dataset_names():13    dataset_names = CONFIG_FILE["trimmomatic"]["dataset"]14    return [k for k in dataset_names.keys() if k != "default"]15# QC REPORT16def get_qcreport_fastq_thread_count():17    return CONFIG_FILE["qc_report"]["threads"]18def get_qcreport_source_path(dataset_name: str, trimmed: bool = False):...

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