sciunit2 0.1.post19.dev44275229

Sciunit command line

.. -*- mode: rst ; ispell-local-dictionary: "american" -*-

==========================
sciunit
==========================
-------------------------------------------------------------
deliver reproducibility in your research
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:Author: Zhihao Yuan <[e-mail]>
:Version: sciunit2 0.2
:Manual section: 1
:Copyright: Copyright 2017, DePaul University
:Licence: FreeBSD License (BSD-2-Clause)

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SYNOPSIS
==========

``sciunit`` [--version] [--help]

``sciunit`` <command> [<args...>]

DESCRIPTION
============

A command line utility to create, manage, and share *sciunits*.
A *sciunit* is a lightweight and portable unit that contains captured,
repeatable program executions.

OPTIONS
========

General Options
--------------------

``--version`` show program's version number and exit

``-h, --help`` show help message and exit


Commands
-----------------

``sciunit create`` <name>
Create a new sciunit under *~/sciunit/<name>* and open it.
If the directory already exists, exit with an error.

``sciunit open`` <name>|<token#>|<path to sciunit.zip>
Open the sciunit under *~/sciunit/<name>* or designated by
a *token#* obtained from ``sciunit copy``, or one in a
zipped sciunit package by extracting it to a temporary
directory.

``sciunit open -m`` <name>
Rename the currently-opened sciunit to *<name>* and open it.

``sciunit exec`` <executable> [<args...>]
Capture the execution of the given *executable* with
the command line arguments *args*. The newly-created
execution is added to the
currently-opened sciunit and assigned execution id "*eN*",
where *N* is a monotonically-increasing decimal.
The first execution created in a sciunit has execution id
"*e1*".

Note that the command line is launched using `execvp(3)`
rather than interpreted by a shell.

``sciunit exec -i``
Launch the current user's shell and capture the user's
interactions with the shell. This may involve executing
multiple commands. A new execution is created on exiting
the shell.

``sciunit repeat`` <execution id> [<args...>]
Repeat the execution of *execution id* from the
currently-opened sciunit. If *args* present, use them in
place of the command line arguments that were present when the
command was captured with the ``sciunit exec`` command.

``sciunit list``
List the existing executions in the currently-opened sciunit.

``sciunit show`` [<execution id>]
Show detailed information about a specific execution (or the
most recent execution, if no argument present) in the
currently-opened sciunit.

``sciunit rm`` <execution id>
Remove an existing execution from the currently-opened
sciunit. A malformed execution id causes an error.
Removing a nonexistent execution has no effect.

Note: the execution is removed from the records, but its
data remains and may be shared with other executions.

``sciunit push`` <codename> --setup <service>
Create an article on a research object sharing *service*
and attach the currently opened sciunit to the article.
Assign different *codenames* to track multiple articles or
multiple versions of an article created from a sciunit.
The supported services include
figshare_ (`fs`) and HydroShare_ (`hs`).

``sciunit push`` [<codename>]
Update the last pushed article with the latest sciunit data
if no argument present. Otherwise, update the article
referred to by *codename*.

``sciunit copy``
Copy the currently-opened sciunit to
`file.io <https://file.io/>`_ and obtain a token for
remotely opening it. The token is invalidated after being
accessed or after one day, whichever happens first.

``sciunit copy`` <remote>|<name>
Copy a sciunit to a *remote* server or *~/sciunit/<name>*.
The supported remote protocols include Globus_.

``sciunit copy -n``
Archive the currently-opened sciunit to
*~/sciunit/<name>.zip*.

``sciunit gc``
Reduce the currently-opened sciunit's disk usage by
garbage-collecting the unreferenced execution data.

``sciunit alias`` <newcmd> <sub...>
Add a new entry under the ``[alias]`` section in the
user-wide config file *~/sciunit/config*. The setting
enables ``sciunit`` *<newcmd> [<args...>]* to be
reinterpreted as ``sciunit`` *<sub...> [<args...>]*.

``sciunit ignore`` <path>
Add a new entry under the ``[ignore]`` section in the
unit-specific config file *~/sciunit/<name>/config*.
If the *path* ends with ``/``, exclude any paths prefixed
with *path* when capturing; otherwise, exclude just *path*.

SEE ALSO
=============

.. _HydroShare:

HydroShare: https://www.hydroshare.org/

.. _figshare:

figshare: https://figshare.com/

.. _Globus:

Globus: https://www.globus.org/