REANA-Workflow-Engine-Serial

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REANA-Workflow-Engine-Serial is a component of the REANA reusable and reproducible research data analysis platform. It takes care of instantiating, executing and managing simple sequential computational workflows.

Features:

  • Run sequential workflows consisting of Bash commands.
  • Cache workflow steps by default to shorten computation time.

Usage

The detailed information on how to install and use REANA can be found in docs.reana.io.

Changes

Version 0.7.5 (2021-07-05)

  • Changes internal dependencies to remove click.

Version 0.7.4 (2021-04-28)

  • Adds support for specifying kubernetes_memory_limit for Kubernetes compute backend jobs.

Version 0.7.3 (2021-03-17)

  • Changes workflow engine instantiation to use central REANA-Commons factory.
  • Changes job command strings by removing interpreter and using central REANA-Commons job command serialisation.
  • Changes status succeeded to finished to use central REANA nomenclature.

Version 0.7.2 (2021-02-03)

  • Fixes minor code warnings.
  • Changes CI system to include Python flake8 and Dockerfile hadolint checkers.

Version 0.7.1 (2020-11-10)

  • Adds support for specifying htcondor_max_runtime and htcondor_accounting_group for HTCondor compute backend jobs.

Version 0.7.0 (2020-10-20)

  • Adds possibility to execute workflow from specified step.
  • Adds option to specify unpacked Docker images as workflow step requirement.
  • Adds option to specify Kubernetes UID for jobs.
  • Adds support for VOMS proxy as a new authentication method.
  • Adds pinning of all Python dependencies allowing to easily rebuild component images at later times.
  • Changes base image to use Python 3.8.
  • Changes code formatting to respect black coding style.
  • Changes documentation to single-page layout.

Version 0.6.1 (2020-05-25)

  • Upgrades REANA-Commons package using latest Kubernetes Python client version.

Version 0.6.0 (2019-12-20)

  • Allows to specify compute backend (HTCondor, Kubernetes or Slurm) and Kerberos authentication requirement for Serial workflow jobs.
  • Allows partial workflow execution until step specified by the user.
  • Moves workflow engine to the same Kubernetes pod with the REANA-Job-Controller (sidecar pattern).

Version 0.5.0 (2019-04-23)

  • Makes workflow engine independent of Celery so that independent workflow instances are created on demand for each user.
  • Replaces api_client module with centralised one from REANA-Commons.
  • Introduces CVMFS mounts in job specifications.
  • Makes docker image slimmer by using python:3.6-slim.
  • Centralises log level and log format configuration.

Version 0.4.0 (2018-11-06)

  • Improves AMQP re-connection handling. Switches from pika to kombu.
  • Utilises common openapi client for communication with REANA-Job-Controller.
  • Changes license to MIT.

Version 0.3.2 (2018-09-25)

  • Modifies OS related commands for CephFS compatibility.

Version 0.3.1 (2018-09-07)

  • Adds parameter passing to workflow steps.
  • Adds user guide and getting started sections to the documentation.

Version 0.3.0 (2018-08-10)

  • Initial public release.
  • Executes serial workflows.
  • Tracks progress of workflow runs.
  • Caches job results by default.

Contributing

Bug reports, issues, feature requests, and other contributions are welcome. If you find a demonstrable problem that is caused by the REANA code, please:

  1. Search for already reported problems.
  2. Check if the issue has been fixed or is still reproducible on the latest master branch.
  3. Create an issue, ideally with a test case.

If you create a pull request fixing a bug or implementing a feature, you can run the tests to ensure that everything is operating correctly:

$ ./run-tests.sh

Each pull request should preserve or increase code coverage.

License

MIT License

Copyright (C) 2018-2020 CERN.

Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the “Software”), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions:

The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software.

THE SOFTWARE IS PROVIDED “AS IS”, WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.

In applying this license, CERN does not waive the privileges and immunities granted to it by virtue of its status as an Intergovernmental Organization or submit itself to any jurisdiction.