datalad.api.run(cmd=None, dataset=None, inputs=None, outputs=None, expand=None, explicit=False, message=None, sidecar=None, rerun=False)

Run an arbitrary shell command and record its impact on a dataset.

It is recommended to craft the command such that it can run in the root directory of the dataset that the command will be recorded in. However, as long as the command is executed somewhere underneath the dataset root, the exact location will be recorded relative to the dataset root.

If the executed command did not alter the dataset in any way, no record of the command execution is made.

If the given command errors, a CommandError exception with the same exit code will be raised, and no modifications will be saved.

Command format

A few placeholders are supported in the command via Python format specification. “{pwd}” will be replaced with the full path of the current working directory. “{dspath}” will be replaced with the full path of the dataset that run is invoked on. “{inputs}” and “{outputs}” represent the values specified by inputs and outputs. If multiple values are specified, the values will be joined by a space. The order of the values will match that order from the command line, with any globs expanded in alphabetical order (like bash). Individual values can be accessed with an integer index (e.g., “{inputs[0]}”).

Note that the representation of the inputs or outputs in the formatted command string depends on whether the command is given as a list of arguments or as a string. The concatenated list of inputs or outputs will be surrounded by quotes when the command is given as a list but not when it is given as a string. This means that the string form is required if you need to pass each input as a separate argument to a preceding script (i.e., write the command as “./script {inputs}”, quotes included). The string form should also be used if the input or output paths contain spaces or other characters that need to be escaped.

To escape a brace character, double it (i.e., “{{” or “}}”).

Custom placeholders can be added as configuration variables under “datalad.run.substitutions”. As an example:

Add a placeholder “name” with the value “joe”:

% git config --file=.datalad/config datalad.run.substitutions.name joe

% datalad run "echo my name is {name} >me"