Configuration file handling and setup — bornprofiler.config

The user can set important paths in ~/.bornprofiler.cfg. The file is automatically created with default values if it does not exist.

Edit the file with a text editor.

In order to restore the default values, simply delete the config file.

Format

The configuration file is in “INI” format: Section titles and variable assignments:

[executables]
apbs = apbs
drawmembrane = /path/to/drawmembrane2a

[membrane]

Meaning of variables

executables

paths to binaries or just the name if they are found via PATH

membrane

configuration variables for apbs-mem-setup and friends

Accessing the configuration

Important variables are stored in the dict configuration. Any variable can be accessed via the getter method of the ConfigParser.SafeConfigParser instance, cfg:

from bornprofiler.config import cfg
varname = cfg.get(section, varname)

bornprofiler.config.CONFIGNAME = '/home/docs/.bornprofiler.cfg'

Default name for the configuration file.

bornprofiler.config.cfg = <bornprofiler.config.BPConfigParser instance>

cfg is the instance of BPConfigParser that makes all global configuration data accessible

bornprofiler.config.check_APBS(name=None)

Return ABPS version if apbs can be run and has the minimum required version.

Raises:error if it cannot be found (OSError ENOENT) or wrong version (EnvironmentError).

bornprofiler.config.check_drawmembrane(name=None)

Return drawmembrane version or raise EnvironmentError if incompatible version of drawmembrane

bornprofiler.config.check_setup()

Check if templates directories are setup and issue a warning and help.

bornprofiler.config.configuration = {'apbs': 'apbs', 'configfilename': '/home/docs/.bornprofiler.cfg', 'drawmembrane': 'draw_membrane2a'}

Dict containing important configuration variables, populated by get_configuration() (mainly a shortcut; use cfg in most cases)

bornprofiler.config.get_configuration(filename='/home/docs/.bornprofiler.cfg')

Reads and parses the configuration file.

Default values are loaded and then replaced with the values from ~/.bornprofiler.cfg if that file exists. The global configuration instance bornprofiler.config.cfg is updated.

Normally, the configuration is only loaded when the bornprofiler package is imported but a re-reading of the configuration can be forced anytime by calling get_configuration().

bornprofiler.config.get_template(t)

Find template file t and return its real path.

t can be a single string or a list of strings. A string should be one of

1. a relative or absolute path,
2. a file in one of the directories listed in bornprofiler.config.path,
3. a filename in the package template directory (defined in the template dictionary bornprofiler.config.templates) or
4. a key into templates.

The first match (in this order) is returned. If the argument is a single string then a single string is returned, otherwise a list of strings.

Arguments:t : template file or key (string or list of strings) Returns:os.path.realpath(t) (or a list thereof) Raises:ValueError if no file can be located.

bornprofiler.config.get_templates(t)

Find template file(s) t and return their real paths.

t can be a single string or a list of strings. A string should be one of

1. a relative or absolute path,
2. a file in one of the directories listed in bornprofiler.config.path,
3. a filename in the package template directory (defined in the template dictionary bornprofiler.config.templates) or
4. a key into templates.

The first match (in this order) is returned for each input argument.

Arguments:t : template file or key (string or list of strings) Returns:list of os.path.realpath(t) Raises:ValueError if no file can be located.

bornprofiler.config.path = ['.', '/home/docs/.bornprofiler/qscripts', '/home/docs/.bornprofiler/templates']

Search path for user queuing scripts and templates. The internal package-supplied templates are always searched last via bornprofiler.config.get_templates(). Modify bornprofiler.config.path directly in order to customize the template and qscript searching. By default it has the value ['.', qscriptdir, templatesdir]. (Note that it is not a good idea to have template files and qscripts with the same name as they are both searched on the same path.)

bornprofiler.config.resource_basename(resource)

Last component of a resource (which always uses ‘/’ as sep).

bornprofiler.config.setup(filename='/home/docs/.bornprofiler.cfg')

Prepare a default BornProfiler global environment.

1. Create the global config file.
2. Create the directories in which the user can store template and config files.

This function can be run repeatedly without harm.

bornprofiler.config.templates = {'array_ASU_workstations.ge': '/home/docs/checkouts/readthedocs.org/user_builds/bornprofiler/checkouts/latest/bornprofiler/templates/array_ASU_workstations.ge', 'array_SBCB_workstations.sge': '/home/docs/checkouts/readthedocs.org/user_builds/bornprofiler/checkouts/latest/bornprofiler/templates/array_SBCB_workstations.sge', 'bornions.dat': '/home/docs/checkouts/readthedocs.org/user_builds/bornprofiler/checkouts/latest/bornprofiler/templates/bornions.dat', 'drawmembrane2.bash': '/home/docs/checkouts/readthedocs.org/user_builds/bornprofiler/checkouts/latest/bornprofiler/templates/drawmembrane2.bash', 'dummy.in': '/home/docs/checkouts/readthedocs.org/user_builds/bornprofiler/checkouts/latest/bornprofiler/templates/dummy.in', 'mdummy.in': '/home/docs/checkouts/readthedocs.org/user_builds/bornprofiler/checkouts/latest/bornprofiler/templates/mdummy.in', 'mplaceion.in': '/home/docs/checkouts/readthedocs.org/user_builds/bornprofiler/checkouts/latest/bornprofiler/templates/mplaceion.in', 'mplaceion_memonly.in': '/home/docs/checkouts/readthedocs.org/user_builds/bornprofiler/checkouts/latest/bornprofiler/templates/mplaceion_memonly.in', 'placeion.in': '/home/docs/checkouts/readthedocs.org/user_builds/bornprofiler/checkouts/latest/bornprofiler/templates/placeion.in', 'q_ASU.sh': '/home/docs/checkouts/readthedocs.org/user_builds/bornprofiler/checkouts/latest/bornprofiler/templates/q_ASU.sh', 'q_SBCB.sh': '/home/docs/checkouts/readthedocs.org/user_builds/bornprofiler/checkouts/latest/bornprofiler/templates/q_SBCB.sh', 'q_array.sge': '/home/docs/checkouts/readthedocs.org/user_builds/bornprofiler/checkouts/latest/bornprofiler/templates/q_array.sge', 'q_local.sh': '/home/docs/checkouts/readthedocs.org/user_builds/bornprofiler/checkouts/latest/bornprofiler/templates/q_local.sh', 'solvation.in': '/home/docs/checkouts/readthedocs.org/user_builds/bornprofiler/checkouts/latest/bornprofiler/templates/solvation.in', 'solvation_no_membrane.in': '/home/docs/checkouts/readthedocs.org/user_builds/bornprofiler/checkouts/latest/bornprofiler/templates/solvation_no_membrane.in'}

Registry of all template files that come with the package.