pipeline — organize input and output files

This module defines the Workspace classes that are central to every script. The role of these classes is to provide paths to all the data files used in any part of the pipeline and to hide the organization of the directories containing those files. The base Workspace class deals with files in the root directory of a design. It’s subclasses deal with file in the different subdirectories of the design, each of which is related to a cluster job.

class pull_into_place.pipeline.BigJobWorkspace(root)

Provide paths needed to run big jobs on the cluster.

This is a base class for all the workspaces meant to store results from long simulations (which is presently all of them except for the root). This class provides paths to input directories, output directories, parameters files, and several other things like that.

class pull_into_place.pipeline.FixbbDesigns(root, round)

exception pull_into_place.pipeline.PathNotFound(path, *directories)

exception pull_into_place.pipeline.PipelineError(message)

class pull_into_place.pipeline.RestrainedModels(root)

exception pull_into_place.pipeline.RosettaNotFound(workspace)

exception pull_into_place.pipeline.UnspecifiedRemoteHost

class pull_into_place.pipeline.ValidatedDesigns(root, round)

class pull_into_place.pipeline.WithFragmentLibs

Provide paths needed to interact with fragment libraries.

This is a mixin class that provides a handful of paths and features useful for working with fragment libraries.

class pull_into_place.pipeline.Workspace(root)

Provide paths to every file used in the design pipeline.

Each workspace object is responsible for returning paths to files that are relevant to a particular stage of the design pipeline. These files are organized hierarchically: files that are relevant to many parts of the pipeline are stored in the root design directory while files that are relevant to specific stages are stored in subdirectories. You can think of each workspace class as representing a different directory.

The Workspace class itself represents the root directory, but it is also the superclass from which all of the other workspace derive. The reason for this is that the root workspace knows where all the shared parameter files are located, and this information is needed in every workspace.

When modifying or inheriting from this class, keep in mind two things. First, workspace objects should do little more than return paths to files. There are a few convenience functions that clear directories and things like that, but these are the exception rather than the rule. Second, use the @property decorator very liberally to keep the code that uses this API succinct and easy to read.

cd(*subpaths)

Change the current working directory and update all the paths in the workspace. This is useful for commands that have to be run from a certain directory.

find_path(basename)

Look in a few places for a file with the given name. If a custom version of the file is found in the directory being managed by this workspace, return it. Otherwise return the path to the default version of the file in the root directory.

This function makes it easy to provide custom parameters to any stage to the design pipeline. Just place the file with the custom parameters in the directory associated with that stage.

focus_dir

The particular directory managed by this class. This is meant to be overridden in subclasses.

exception pull_into_place.pipeline.WorkspaceNotFound(root)

pull_into_place.pipeline.load_loops(directory, loops_path=None)

Return a list of tuples indicating the start and end points of the loops that were sampled in the given directory.

pull_into_place.pipeline.load_resfile(directory, resfile_path=None)

Return a list of tuples indicating the start and end points of the loops that were sampled in the given directory.

pull_into_place.pipeline.workspace_from_dir(directory, recurse=True)

Construct a workspace object from a directory name. If recurse=True, this function will search down the directory tree and return the first workspace it finds. If recurse=False, an exception will be raised if the given directory is not a workspace. Workspace identification requires a file called ‘workspace.pkl’ to be present in each workspace directory, which can unfortunately be a little fragile.