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Merge pull request #1 from ReactionMechanismGenerator/hwpang-patch-1
Add settings to __init__.py
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‎molecule/__init__.py‎

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#!/usr/bin/env python3
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###############################################################################
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# #
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# RMG - Reaction Mechanism Generator #
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# #
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# Copyright (c) 2002-2021 Prof. William H. Green (whgreen@mit.edu), #
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# Prof. Richard H. West (r.west@neu.edu) and the RMG Team (rmg_dev@mit.edu) #
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# #
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# Permission is hereby granted, free of charge, to any person obtaining a #
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# copy of this software and associated documentation files (the 'Software'), #
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# to deal in the Software without restriction, including without limitation #
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# the rights to use, copy, modify, merge, publish, distribute, sublicense, #
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# and/or sell copies of the Software, and to permit persons to whom the #
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# Software is furnished to do so, subject to the following conditions: #
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# #
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# The above copyright notice and this permission notice shall be included in #
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# all copies or substantial portions of the Software. #
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# #
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# THE SOFTWARE IS PROVIDED 'AS IS', WITHOUT WARRANTY OF ANY KIND, EXPRESS OR #
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# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, #
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# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE #
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# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER #
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# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING #
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# FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER #
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# DEALINGS IN THE SOFTWARE. #
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# #
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###############################################################################
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"""
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This is the rmg module.
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"""
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import os
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import os.path
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from rmgpy.version import __version__
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from rmgpy.exceptions import SettingsError
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################################################################################
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class Settings(dict):
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"""
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A dictionary-like object containing global settings for RMG jobs. These
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settings are generally loaded from a file named ``rmgrc`` located at one
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of several possible places on disk. The ``rmgrc`` file used is stored in
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the `filename` attribute. This class inherits from the built-in dict class
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and adds methods for loading and resetting the settings, as well as a
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custom :meth:`__setitem__` method for processing the setting values before
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adding them to the dictionary.
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In general you should be working with the module-level variable
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``settings`` in this module, which is an instance of this class.
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"""
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def __init__(self, path=None):
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super(Settings, self).__init__()
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self.filename = None
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self.sources = dict()
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self.load(path)
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def __setitem__(self, key, value):
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if key == 'database.directory':
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value = os.path.abspath(os.path.expandvars(value))
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elif key == 'test_data.directory':
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value = os.path.abspath(os.path.expandvars(value))
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else:
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raise SettingsError('Unexpecting setting "{0}" encountered.'.format(key))
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self.sources[key] = '-'
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super(Settings, self).__setitem__(key, value)
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def report(self):
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"""
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Returns a string saying what is set and where things came from, suitable for logging
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"""
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lines = ['Global RMG Settings:']
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for key in self.keys():
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lines.append(" {0:20s} = {1:20s} ({2})".format(key, self[key], self.sources[key]))
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return '\n'.join(lines)
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def load(self, path=None):
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"""
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Load settings from a file on disk. If an explicit file is not specified,
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the following locations will be searched for a settings file, and the
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first one found will be loaded:
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* An rmgrc file in the current working directory
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* An rmgrc file in the user's $HOME/.rmg directory
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* An rmgrc file in the same directory as this package
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If none of these can be found, a SettingsError is raised.
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"""
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# First set all settings to their default values
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self.reset()
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if path:
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# The user specified an explicit file to use for the settings
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# Make sure that it exists, fail if it does not
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if not os.path.exists(path):
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raise SettingsError('Specified RMG settings file "{0}" does not exist.'.format(path))
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else:
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self.filename = path
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else:
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# The user did not specify an explicit file to use for the settings
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# Load one of the default settings files instead
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working_dir = os.path.abspath(os.path.dirname(__file__))
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if os.path.exists('rmgrc'):
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self.filename = 'rmgrc'
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elif os.path.exists(os.path.expanduser('~/.rmg/rmgrc')):
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self.filename = os.path.expanduser('~/.rmg/rmgrc')
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elif os.path.exists(os.path.join(working_dir, 'rmgrc')):
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self.filename = os.path.join(working_dir, 'rmgrc')
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else:
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return # fail silently, instead of raising an error
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# From here on we assume that we have identified the appropriate
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# settings file to load
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with open(self.filename, 'r') as f:
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for line in f:
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# Remove any comments from the line
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index = line.find('#')
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if index != -1:
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line = line[:index]
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# Is there a key-value pair remaining?
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if line.find('database.directory') != -1:
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value = line.split()[-1] # Get the last token from this line
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value = value.strip()
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self['database.directory'] = value
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self.sources['database.directory'] = "from {0}".format(self.filename)
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elif line.find('test_data.directory') != -1:
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value = line.split()[-1] # Get the last token from this line
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value = value.strip()
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self['test_data.directory'] = value
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self.sources['test_data.directory'] = "from {0}".format(self.filename)
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def reset(self):
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"""
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Reset all settings to their default values.
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"""
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self.filename = None
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rmgpy_module_dir = os.path.abspath(os.path.dirname(__file__))
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self['database.directory'] = os.path.realpath(
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os.path.join(rmgpy_module_dir, '..', '..', 'RMG-database', 'input'))
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self.sources['database.directory'] = 'Default, relative to RMG-Py source code'
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self['test_data.directory'] = os.path.realpath(os.path.join(rmgpy_module_dir, 'test_data'))
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self.sources['test_data.directory'] = 'Default, relative to RMG-Py source code'
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# The global settings object
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settings = Settings(path=None)
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################################################################################
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def get_path():
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"""
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Return the directory that this file is found in on disk.
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"""
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return os.path.abspath(os.path.dirname(__file__))

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