README.md

Script of Scripts (SoS) consists of SoS Notebook, a Jupyter-based polyglot notebook that allows the use of multiple Jupyter kernels in one notebook, and SoS Workflow, a workflow system 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 bash, Python, R, and SAS. This repository contains the SoS Workflow workflow engine.

Please refer to relevant publications SoS Notebook: An Interactive Multi-Language Data Analysis Environment in Bioinformatics, Script of Scripts: a pragmatic workflow system for daily computational research in PLoS Computational Biology, and the SoS homepage for more information on SoS Notebook and SoS Workflow.

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. In addition, if you are interesting in extending SoS, for example adding a new target type or task engine, please have a look at our tutorial on extending SoS here.

Installing SoS Workflow and Notebook

• If you are using conda, you can install sos using command

  conda install sos -c conda-forge

  You can also install a majority of the SoS suite of tools using commands such as

  conda install sos sos-pbs sos-notebook jupyterlab-sos sos-bash sos-python sos-r -c conda-forge

  This will install SoS Workflow, SoS Notebook and its JupyterLab extension, language modules for Bash, Python2, Python3, R, R itself (r-base and r-irkernel etc) and needed libraries (e.g. feather) if needed.

• If you are not using conda, you will have to install all the pieces one by one, but you will also have the freedom to use non-conda installation of R, Julia etc. With a working Python 3.6 installation, you can install SoS Workflow with command

  pip install sos

  and also

  pip install sos-pbs

  if you would like to use SoS with a remote batch system such as LSF or Slurm.

  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 Workflow and SoS Notebook

SoS 0.25.1:

• sos#1542: Fix a compatibility issue with Python 3.12.

SoS 0.25.0:

• sos#1535: Remove 'R' formatter, remote target type, remote push and pull, named (#name) path because SoS now assumes that all input and output files are available on shared drives with identical path names.

SoS 0.24.5:

• sos#1530: Outputcontent of script to stderr when the script fails to execute.

SoS 0.22.5:

• sos#1420: Allow checking the status, killing, and purge of remote workflows.

SoS Notebook 0.22.3

• sos-notebook#303: Make task execution non-blocking in sos notebook, so that the buttons to check status and remove tasks actually operatable.

SoS Notebook 0.22.2

• sos-notebook#307: Use a new template organization method for nbconvert > 0.6.0.

SoS 0.21.12

• sos#1392: Allow the use of pem_file to authenticate to remote hosts.

SoS 0.20.9

• sos#1319: Extend option -r host to allow workflow to be executed with templates and on PBS
• sos#1322: Deprecate option -b BIN_DIR due to sos#1319

SoS 0.19.15

• sos#1273: Allow workflows to be executed on cluster systems.
• sos#1277: Allow master tasks to be executed on cluster systems with extended runtime option trunk_workers.
• sos#1279: Extend option -j of commands sos run and sos execute to use remote workers.
• sos#1288: Change the default value of option -q from localhost to None (no task).

SoS 0.19.0

• sos#1056, sos#1218: Use a new shared execution model to enforce optio -j.
• sos#1219: Make sure global sections are executed only once

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#786: Support singularity. See SoS Singularity Guide for details.

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

• jupyterlab-sos#11: Magic %cd now changes directory of all subkernels

SoS Notebook 0.9.12.12

• sos-notebook#52: All new syntax highlighter that highlights expanded expressions
• sos-notebook#58: Stop removing leading comments from cells.

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-notebook#44: Allow sending text in markdown cells to side panel for execution.
• sos-notebook#47: Allow clear any HTML element with magic %clear --class
• sos-notebook#50: Re-design logo for SoS Notebook.

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-notebook#41: Stop saving unused kernels in sos notebook.

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

• sos-notebook#32: Add magic %capture to capture output of cells