Workflow system designed for daily data analysis
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Bo Peng
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README.md

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Script of Scripts (SoS) is a Jupyter-based polyglot notebook that allows the use of multiple Jupyter kernels in one notebook, and a workflow engine for the execution of workflows in both process- and outcome-oriented styles. It is designed for data scientists and bioinformatics who routinely work with scripts in different languages such as R, Python, Perl, and bash.

Please refer to the SoS homepage for more information.

We welcome and value community contributions: please post issues to provide us feedback or get our support; please send pull requests if you have helped fixing bugs or making improvements to the source code.

Installing SoS

With Python 3.6 and above installed (anaconda python is recommended), you can install the SoS Workflow System and its extensions with command

% pip install sos

You can install the latest git version of SoS with commands

% git clone https://github.com/vatlab/SoS.git
% cd SoS
% pip install . -U

although the development version can be less stable than the released version.

You can install SoS Notebook, and register the sos kernel with Jupyter using the following commands

% pip install sos-notebook
% python -m sos_notebook.install

To exchange data between live kernels in SoS Notebook, you will need to install individual kernels (e.g. irkernel for R), make sure they work under Jupyter, and install SoS language modules using commands such as

% pip install sos-r sos-matlab sos-python sos-bash

Different modules might be needed to assist data exchange among kernels. Please refer to the installation page of sos website for details.

Change Log of SoS and SoS Notebook

SoS Notebook 0.18.5

  • sos-notebook#192: Allow language modules to support pattern matched kernel names such as julia-?.?

SoS 0.18.6

  • sos#1206: Allow output_from(step) to obtain output from a workflow.

SoS 0.18.5

  • sos#1186: Add command line option -T to enfore dependency tracing.
  • sos#1197: Introduce function traced to make dependencies that will always be traced
  • sos#1201: Introduce dependencies between compounded workflows

SoS 0.18.4

  • sos#1185: Disallow the use of parameters in tasks.
  • sos#1186: (reverted) Enforcing the concept that targets in depends statement always try to build dependency.

SoS Notebook 0.18.1

  • sos-notebook#178: Allow adding & to the end of magics %run, %sosrun, and %runfile to execute workflow in background.
  • sos-notebook#179: Remove magic %rerun and add magic %runfile
  • sos-notebook#180: Add option -r to %save to execute the cell after saving it.

SoS 0.18.0

  • sos#1115: Function output_from and named_output to support named inputs and outputs, among other new features summarized in this ticket.
  • sos#1120: Allow paremeters group_by, paired_with etc for functions output_from and named_output.
  • sos#1125: Set concurrent=True as default for substep execution.
  • sos#1132: Deprecate action stop_if and replace it with done_if and skip_if
  • sos#1175: Enforce the use of sos_variable to import shared variable in a step

SoS Notebook 0.18.0

  • sos-notebook#150: A new side panel that works in the same fashion as JupyterLab's console window.
  • sos-notebook#154: New task status table that allows reporting status, killing, and purging multiple tasks with the same tags.

SoS 0.9.16.10

SoS 0.9.16.0, SoS Notebook 0.9.16.0

  • sos#991: Use a new task file format to replace multiple files for each task. This change is not backward compatible so please upgrade only after you completed and removed all existing tasks.

SoS 0.9.15.1

  • sos-notebook#89: Added templates to highlight source code using codemirror, with optional auto-generated table of contents.

SoS 0.9.14.10

  • sos#983: Allow depending on an entire process-oriented workflow using a sos_step() target that matches multiple steps.

SoS 0.9.14.3:

  • sos#975: Add option -p to generate a summary report after the completion of workflow.
  • sos#976: Much improved workflow help message (sos run script -h).

SoS Notebook 0.9.14.4:

  • sos-notebook#79: Allow auto-completion and inspection in subkernel cells.

SoS Notebook 0.9.14.1

  • sos-notebook#74: Add a %revisions magic to display revision history of the current document.

SoS 0.9.14.1

  • sos#925: Output summary of executed and ignored step, substeps, and tasks after the execution of workflows.

SoS Notebook 0.9.13.4

SoS Notebook 0.9.12.12

SoS 0.9.12.11

  • sos#922: Use user-id for docker execution (-u)
  • sos#926: Add function zap() to SoS path classes path, paths, file_target, and sos_targets

SoS Notebook 0.9.12.11

SoS 0.9.12.9

  • sos#914: Allow option active of actions and tasks to accept conditions.
  • sos#915: Automatically expand user (~) for SoS path types path, paths and file_targets.
  • sos#916: Use hashlib instead of faster xxhash under windows

SoS Notebook 0.9.12.9

SoS 0.9.12.3

  • sos#859: Introduce automatic auxiliary steps to simplify the use of makefile steps.

SoS 0.9.11.3

  • sos#879: Add action options stdout and stderr to redict output from script-executing actions.
  • sos-notebook#42: Add option --append to magic %capture .

SoS 0.9.11.2

  • sos-notebook#39: Separation installation and deployment and use command python -m sos_notebook.install to install sos kernel to Jupyter.

SoS 0.9.10.19

  • sos#874: Add input option concurrent=True to allow parallel execution of input groups.
  • sos#874: Optimize task submission of task engines to reduce status checking

SoS Notebook 0.9.10.17