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#########################################################################
# MacSyLib - Python library to detect macromolecular systems #
# in prokaryotes protein dataset using systems modelling #
# and similarity search. #
# #
# Authors: Sophie Abby, Bertrand Neron #
# Copyright (c) 2014-2025 Institut Pasteur (Paris) and CNRS. #
# See the COPYRIGHT file for details #
# #
# This file is part of MacSyLib package. #
# #
# MacSyLib is free software: you can redistribute it and/or modify #
# it under the terms of the GNU General Public License as published by #
# the Free Software Foundation, either version 3 of the License, or #
# (at your option) any later version. #
# #
# MacSyLib is distributed in the hope that it will be useful, #
# but WITHOUT ANY WARRANTY; without even the implied warranty of #
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the #
# GNU General Public License for more details . #
# #
# You should have received a copy of the GNU General Public License #
# along with MacSyLib (COPYING). #
# If not, see <https://www.gnu.org/licenses/>. #
#########################################################################
import os
import logging
import shutil
import tempfile
from macsylib.config import MacsyDefaults
from tests import MacsyTest
class TestMacsyDefaults(MacsyTest):
def setUp(self):
self.defaults = {'cfg_file': None,
'coverage_profile': 0.5,
'e_value_search': 0.1,
'cut_ga': True,
'db_type': None,
'hmmer': shutil.which('hmmsearch'),
'i_evalue_sel': 0.001,
'idx': False,
'index_dir': None,
'inter_gene_max_space': None,
'log_file': 'macsylib.log',
'log_level': logging.INFO,
'max_nb_genes': None,
'min_genes_required': None,
'min_mandatory_genes_required': None,
'models': [],
'models_dir': None,
'multi_loci': set(),
'mute': False,
'out_dir': None,
'previous_run': None,
'profile_suffix': '.hmm',
'pack_name': 'macsylib',
'tool_name': 'macsylib',
'quiet': 0,
'relative_path': False,
'replicon_topology': 'circular',
'res_extract_suffix': '.res_hmm_extract',
'res_search_dir': ".",
'res_search_suffix': '.search_hmm.out',
'sequence_db': None,
'topology_file': None,
'verbosity': 0,
'worker': 1,
'timeout': 0,
'force_run': False,
'mandatory_weight': 1.0,
'accessory_weight': .5,
'neutral_weight': 0.0,
'exchangeable_weight': .8,
'itself_weight': 1.0,
'redundancy_penalty': 1.5,
'out_of_cluster_weight': 0.7
}
def test_MacsyDefaults_virtual_env(self):
virtual_env = os.environ.get('VIRTUAL_ENV')
with tempfile.TemporaryDirectory() as fake_virtual_env:
os.environ['VIRTUAL_ENV'] = fake_virtual_env
system_models_dir = os.path.join(fake_virtual_env, 'share', 'macsylib', 'models')
os.makedirs(system_models_dir)
self.defaults['system_models_dir'] = [path for path in (system_models_dir,
os.path.join(os.path.expanduser('~'),
'.macsylib', 'models'))
if os.path.exists(path)]
try:
defaults = MacsyDefaults()
self.maxDiff = None
self.assertDictEqual(defaults, self.defaults)
new_defaults = {k: v for k, v in self.defaults.items()}
new_defaults['previous_run'] = True
new_defaults['worker'] = 5
defaults = MacsyDefaults(previous_run=True, worker=5)
self.assertDictEqual(defaults, new_defaults)
finally:
if virtual_env:
os.environ['VIRTUAL_ENV'] = virtual_env
def test_MacsyDefaults_no_virtual_env(self):
virtual_env = os.environ.get('VIRTUAL_ENV')
common_path = os.path.join('share', 'macsylib', 'models')
prefixes = ('/', os.path.join('/', 'usr', 'local'))
system_models_dir = [os.path.join(root, common_path) for root in prefixes]
system_models_dir.append(os.path.join(os.path.expanduser('~'), '.macsylib', 'models'))
self.defaults['system_models_dir'] = [path for path in system_models_dir if os.path.exists(path)]
if virtual_env:
del os.environ['VIRTUAL_ENV']
try:
defaults = MacsyDefaults()
self.maxDiff = None
self.assertDictEqual(defaults, self.defaults)
new_defaults = {k: v for k, v in self.defaults.items()}
new_defaults['previous_run'] = True
new_defaults['worker'] = 5
defaults = MacsyDefaults(previous_run=True, worker=5)
self.assertDictEqual(defaults, new_defaults)
finally:
if virtual_env:
os.environ['VIRTUAL_ENV'] = virtual_env
def test_MacsyDefaults_other_prog(self):
tool_name = 'NIMPORTNAOIK'
pack_name = 'MY_LIB'
common_path = os.path.join('share', pack_name, 'models')
prefixes = ('/', os.path.join('/', 'usr', 'local'))
system_models_dir = [os.path.join(root, common_path) for root in prefixes]
system_models_dir.append(os.path.join(os.path.expanduser('~'), f'.{pack_name}', 'models'))
self.defaults['system_models_dir'] = [path for path in system_models_dir if os.path.exists(path)]
self.defaults['tool_name'] = tool_name
self.defaults['pack_name'] = pack_name
self.defaults['log_file'] = f"{pack_name}.log"
try:
defaults = MacsyDefaults(package_name=pack_name, tool_name=tool_name)
self.maxDiff = None
self.assertDictEqual(defaults, self.defaults)
finally:
self.defaults['prog_name'] = 'macsylib'
self.defaults['log_file'] = 'macsylib.log'
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