sane-workflows 1.0.0rc2

Simple Action 'n Environment Workflows

SANE Workflows

Simple Action 'n Environment Workflow

SANE is a DAG-based action workflow runner augmented with environments provided by hosts.

It provides:

• DAG-based action mapping, with statefulness to preserve runs
• both python and JSON config based workflow management
• sourcing workflows from multiple directories
• resource management between host and actions
• HPC-resource enabled hosts (PBS base fully implemented)
• environment variable manipulation via shell scripts, lmod, and explicit setting
• extensible Host, Environment, and Action classes that can be derived from
  • derived classes allowed within user workflow directories
  • derived classes accessible within user JSON configs
• a priority-based python registration decorator
• a priority-based JSON patching feature

Overview

Below is a high level overview of how running a workflow works. Many of the complex nuances, such as type finding, HPC submission, resource management, etc., are left out.

The focus should instead be:

• a single orchestrator manages the workflow
• a node in the DAG-workflow is an action
• a host provides environments for an action
• actions are run independently in an order informed by DAG dependencies
• an action itself is run() in a totally separate subprocess (not python subprocess!)
• instance information is transferred via python pickling

Install

This package is designed to work both as an installed python package or from source code with no modifications necessary. To install the package use:

python3 -m pip install sane-workflows

To utilize from source, clone this repository. You may add the path to your PYTHONPATH if you want to use it outside of the provided runner script, but this is not necessary.

Usage when installed:

sane_runner -h

Usage when from source:

<path to source>/bin/sane_runner.py -h

Python Usage

To utilize sane in a python setting, create a python file (module) and import the sane package. Assuming you are running via the provided entry point sane_runner[.py], you do not need to ensure sane is within your PYTHONPATH. Afterwards, to add, remove, or modify the orchestrator use the @sane.register(priority=0) decorator. Providing a priority is optional, and if no priority is given, no () call is necessary, as seen below. The orchestrator is provided as the single argument to the decorated function.

import sane

@sane.register
def my_workflow( orch ):
  my_action = sane.Action( "id" )
  orch.add_action( my_action )

If a priority is given, functions will be evaluated in descending order (highest priority first)

import sane

@sane.register
def last( orch ):
  # defaul priority is 0
  pass

@sane.register( priority=5 )
def second( orch ):
  pass

@sane.register( 99 )
def first( orch ):
  pass

JSON Usage

To utilize sane in a JSON config file setting, create a JSON file (config) that contains at least one of the keys : "hosts", "actions", or "patches". Refer to the docs/template.jsonc on what default fields are appropriate. Note that if you define your own type (and thus add your own load_extra_config()), additional fields may be provided in the config.

{
  "hosts" :
  {
    "dummy" : { "environment" : "generic" }
  },
  "actions" :
  {
    "my_action" :
    {
      "config" : { "command" : "echo", "arguments" : [ 1 ] },
      "environment" : "generic"
    }
  }
}

By default, you may utilize action attributes inside of the generic "config" : {} dictionary field. The attributes are automatically scoped to the current action and are accessed via YAML-like dereferencing (${{}}):

// ... previous config
  "actions" :
  {
    "my_action" :
    {
      "config" : { "command" : "echo", "arguments" : [ "${{ id }}" ] }
    }
  }
// ... rest of config

Running a workflow

To run a workflow, place all your .py and .json[c] files into any directory layout you want, but try to isolate your workflow files from other non-workflow .py and .json[c] files as all matching files under listed directories are loaded. Supplementary files, like shell scripts (.sh), will not be loaded.

Provide the paths of your workflow with -p/--path, then list or filter for whichever actions you want to operate with, along with the -r flag to run these actions:

<path to sane_workflows>/bin/sane_runner.py -p <workflow path> [-p <other path>] -a my_action -r

[!NOTE] All paths provided are added to sys.path for importing of modules. Thus, when using custom classes within your workflow, import their module as if from the workflow path, e.g. -p .workflow for .workflow/custom_actions/my_action_def.py as import custom_actions.my_action_def

You will get output that looks like so:

./bin/sane_runner.py -p demo/ -a action_000 -r
2025-10-08 18:22:56 INFO     [sane_runner]        Logging output to /home/aislas/sane_workflows/log/runner.log
2025-10-08 18:22:56 INFO     [orchestrator]       Searching for workflow files...
2025-10-08 18:22:56 INFO     [orchestrator]         Searching demo/ for *.json
2025-10-08 18:22:56 INFO     [orchestrator]           Found demo/custom_def_usage.json
2025-10-08 18:22:56 INFO     [orchestrator]           Found demo/simple_action.json
2025-10-08 18:22:56 INFO     [orchestrator]           Found demo/resource_action.json
2025-10-08 18:22:56 INFO     [orchestrator]           Found demo/hpc_host.json
2025-10-08 18:22:56 INFO     [orchestrator]           Found demo/patches.json
2025-10-08 18:22:56 INFO     [orchestrator]         Searching demo/ for *.jsonc
2025-10-08 18:22:56 INFO     [orchestrator]           Found demo/simple_host.jsonc
2025-10-08 18:22:56 INFO     [orchestrator]         Searching demo/ for *.py
2025-10-08 18:22:56 INFO     [orchestrator]           Found demo/my_workflow.py
2025-10-08 18:22:56 INFO     [orchestrator]           Found demo/simple_host.py
2025-10-08 18:22:56 INFO     [orchestrator]           Found demo/actual_workflow.py
2025-10-08 18:22:56 INFO     [orchestrator]           Found demo/custom_defs.py
2025-10-08 18:22:56 INFO     [orchestrator]       Loading python file demo/my_workflow.py as 'my_workflow'
2025-10-08 18:22:56 INFO     [orchestrator]       Loading python file demo/simple_host.py as 'simple_host'
2025-10-08 18:22:56 INFO     [orchestrator]       Loading python file demo/actual_workflow.py as 'actual_workflow'
2025-10-08 18:22:56 INFO     [orchestrator]       Loading python file demo/custom_defs.py as 'custom_defs'
2025-10-08 18:22:56 INFO     [orchestrator::register] Creation of universe
2025-10-08 18:22:56 INFO     [orchestrator::register] Creation of world
2025-10-08 18:22:56 INFO     [orchestrator::register] Hello world from my_workflow
2025-10-08 18:22:56 INFO     [orchestrator::register] <class 'custom_defs.MyAction'>
2025-10-08 18:22:56 INFO     [orchestrator]       Loading config file demo/custom_def_usage.json
2025-10-08 18:22:56 WARNING  [fib_seq_fixed]        Unused keys in config : ['unused_action_param']
2025-10-08 18:22:56 WARNING  [orchestrator]         Unused keys in config : ['unused_orch_param']
2025-10-08 18:22:56 INFO     [orchestrator]       Loading config file demo/simple_action.json
2025-10-08 18:22:56 INFO     [orchestrator]       Loading config file demo/resource_action.json
2025-10-08 18:22:56 INFO     [orchestrator]       Loading config file demo/hpc_host.json
2025-10-08 18:22:56 INFO     [example_pbs]          Adding homogeneous node resources for 'cpu'
2025-10-08 18:22:56 INFO     [orchestrator]       Loading config file demo/patches.json
2025-10-08 18:22:56 INFO     [orchestrator]       Loading config file demo/simple_host.jsonc
2025-10-08 18:22:56 INFO     [orchestrator::patch] Applying patch to Host 'unique_host_config'
2025-10-08 18:22:56 INFO     [orchestrator::patch] Applying patch to Action 'fib_seq_fixed'
2025-10-08 18:22:56 INFO     [orchestrator::patch] Applying patch to Action 'fib_seq_calc_mult'
2025-10-08 18:22:56 INFO     [orchestrator::patch] Applying patch filter to Action 'action_090'
2025-10-08 18:22:56 INFO     [orchestrator::patch] Applying patch filter to Action 'action_091'
2025-10-08 18:22:56 INFO     [orchestrator::patch] Applying patch filter to Action 'action_092'
2025-10-08 18:22:56 INFO     [orchestrator::patch] Applying patch filter to Action 'action_093'
2025-10-08 18:22:56 INFO     [orchestrator::patch] Applying patch filter to Action 'action_094'
2025-10-08 18:22:56 INFO     [orchestrator::patch] Applying patch filter to Action 'action_095'
2025-10-08 18:22:56 WARNING  [orchestrator::patch] Unused keys in patch : ['unused_patch_param']
2025-10-08 18:22:56 INFO     [orchestrator]       No previous save file to load
2025-10-08 18:22:56 INFO     [orchestrator]       Running actions:
2025-10-08 18:22:56 INFO     [orchestrator]         action_000  
2025-10-08 18:22:56 INFO     [orchestrator]       and any necessary dependencies
2025-10-08 18:22:56 INFO     [orchestrator]       Full action set:
2025-10-08 18:22:56 INFO     [orchestrator]         action_000  
2025-10-08 18:22:56 INFO     [orchestrator]       Checking host "generic"
2025-10-08 18:22:56 INFO     [orchestrator]       Running as 'generic'
2025-10-08 18:22:56 INFO     [orchestrator]       Checking ability to run all actions on 'generic'...
2025-10-08 18:22:56 INFO     [orchestrator]         Checking environments...
2025-10-08 18:22:56 INFO     [orchestrator]         Checking resource availability...
2025-10-08 18:22:56 INFO     [orchestrator]       * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * 
2025-10-08 18:22:56 INFO     [orchestrator]       * * * * * * * * * *            All prerun checks for 'generic' passed           * * * * * * * * * * 
2025-10-08 18:22:56 INFO     [orchestrator]       * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * 
2025-10-08 18:22:56 INFO     [orchestrator]       Saving host information...
2025-10-08 18:22:56 INFO     [orchestrator]       Setting state of all inactive actions to pending
2025-10-08 18:22:56 INFO     [orchestrator]       No previous save file to load
2025-10-08 18:22:56 INFO     [orchestrator]       Using working directory : '/home/aislas/sane_workflows'
2025-10-08 18:22:56 INFO     [orchestrator]       Running actions...
2025-10-08 18:22:56 INFO     [orchestrator]       Running 'action_000' on 'generic'
2025-10-08 18:22:56 INFO     [action_000[thread_0]] Saving action information for launch...
2025-10-08 18:22:56 INFO     [action_000[thread_0]] Using working directory : '/home/aislas/sane_workflows'
2025-10-08 18:22:56 INFO     [action_000[thread_0]] Running command:
2025-10-08 18:22:56 INFO     [action_000[thread_0]]   /home/aislas/sane_workflows/sane/action_launcher.py /home/aislas/sane_workflows /home/aislas/sane_workflows/tmp/action_action_000.json
2025-10-08 18:22:56 INFO     [action_000[thread_0]] Command output will be captured to logfile /home/aislas/sane_workflows/log/action_000.log
2025-10-08 18:22:56 INFO     [orchestrator]       FINISHED Action 'action_000'             completed with 'success'
2025-10-08 18:22:56 INFO     [orchestrator]       Finished running queued actions
2025-10-08 18:22:56 INFO     [orchestrator]         action_000: success  
2025-10-08 18:22:56 INFO     [orchestrator]       All actions finished with success
2025-10-08 18:22:56 INFO     [orchestrator]       Save file at /home/aislas/sane_workflows/tmp/orchestrator.json
2025-10-08 18:22:56 INFO     [orchestrator]       JUnit file at /home/aislas/sane_workflows/log/results.xml
2025-10-08 18:22:56 INFO     [sane_runner]        Finished

[!TIP] The above is generated from the demo/ folder in the repository. It should provide a decent starting example of what a workflow may look like.