REANA-Workflow-Engine-CWL

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REANA-Workflow-Engine-CWL is a component of the REANA reusable and reproducible research data analysis platform. It takes care of instantiating, executing and managing Common Workflow Language (CWL) based computational workflows.

Features

  • start Common Workflow Language (CWL) based workflows

  • control workflow steps

Usage

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

Changelog

0.9.3 (2024-03-04)

Build

  • docker: install correct extras of reana-commons submodule (#261) (21957fe)

  • docker: non-editable submodules in “latest” mode (#255) (a6acc88)

  • python: bump all required packages as of 2024-03-04 (#267) (ed6a846)

  • python: bump shared REANA packages as of 2024-03-04 (#267) (47155ef)

Bug fixes

Code refactoring

Continuous integration

  • commitlint: addition of commit message linter (#256) (021854e)

  • commitlint: allow release commit style (#268) (ed7ad11)

  • commitlint: check for the presence of concrete PR number (#262) (9a45817)

  • release-please: initial configuration (#256) (bcd87d1)

  • release-please: update version in Dockerfile (#259) (0961257)

  • shellcheck: fix exit code propagation (#262) (6568b9b)

Documentation

  • authors: complete list of contributors (#266) (2960cd9)

  • conformance-tests: update CWL conformance test badges (#264) (45afa2e)

0.9.2 (2023-12-12)

  • Adds automated multi-platform container image building for amd64 and arm64 architectures.

  • Adds metadata labels to Dockerfile.

  • Fixes container image building on the arm64 architecture.

0.9.1 (2023-09-27)

  • Fixes container image names to be Podman-compatible.

0.9.0 (2023-01-19)

  • Adds support for specifying slurm_partition and slurm_time for Slurm compute backend jobs.

  • Adds support for Kerberos authentication for workflow orchestration.

  • Adds support for Rucio authentication for workflow jobs.

  • Changes the base image of the component to Ubuntu 20.04 LTS and reduces final Docker image size by removing build-time dependencies.

  • Fixes status reporting for failed jobs that were incorrectly considered successful.

0.8.1 (2022-02-07)

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

0.8.0 (2021-11-22)

  • Adds support for custom workspace paths.

  • Adds supoort for cwltool version 3.1.20210628163208

0.7.6 (2021-07-05)

  • Changes internal dependencies to remove click.

0.7.5 (2021-04-28)

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

0.7.4 (2021-03-23)

  • Changes job command serialisation using central REANA-Commons job command serialiser.

0.7.3 (2021-03-17)

  • Changes workflow engine instantiation to use central REANA-Commons factory.

  • Changes status succeeded to finished to use central REANA nomenclature.

0.7.2 (2021-02-03)

  • Fixes minor code warnings.

  • Changes CI system to include Python flake8 and Dockerfile hadolint checkers.

0.7.1 (2020-11-10)

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

  • Fixes restarting of CWL workflows.

0.7.0 (2020-10-20)

  • Adds pinning of all Python dependencies allowing to easily rebuild component images at later times.

  • Adds option to specify unpacked Docker images as workflow step requirement.

  • Adds support for handling new workflow operational options.

  • Adds support for VOMS proxy as a new authentication method.

  • Changes base image to use Python 3.8.

  • Changes code formatting to respect black coding style.

  • Changes documentation to single-page layout.

0.6.1 (2020-05-25)

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

0.6.0 (2019-12-20)

  • Allows to specify compute backend (HTCondor, Kubernetes or Slurm) and Kerberos authentication requirement for CWL workflow jobs.

  • Upgrades cwltool to 1.0.20191022103248.

  • Moves workflow engine to the same Kubernetes pod with the REANA-Job-Controller (sidecar pattern).

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.

  • Sets default file mode creation mask to 002 so that workflows are able to write to shared directories for any user identity under which the workflow processes may be running.

  • Makes docker image slimmer by using python:2.7-slim.

  • Centralises log level and log format configuration.

  • Upgrades cwltool to 1.0.20181118133959.

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.

0.3.2 (2018-09-25)

  • Upgrades to latest cwltool (1.0.20180912090223).

0.3.1 (2018-09-07)

  • Pins REANA-Commons dependency.

0.3.0 (2018-08-10)

  • Tracks progress of workflow runs.

0.2.0 (2018-04-19)

  • Initial public release.

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) 2017, 2018, 2019, 2020, 2021, 2022, 2023, 2024 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.

Authors

The list of contributors in alphabetical order: