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REANA-Commons.

Project description

REANA-Commons

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About

REANA-Commons is a component of the REANA reusable and reproducible research data analysis platform. It provides common utilities and schemas shared by the REANA cluster components.

Features

  • common API clients for internal communication
  • centralised OpenAPI specifications for REANA components
  • AMQP connection management and communication
  • utility functions for cluster components

Usage

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

Useful links

Changelog

0.9.7 (2024-02-20)

Build

Documentation

  • authors: complete list of contributors (#442) (4a74c10)

0.9.6 (2024-02-13)

Features

  • config: allow customisation of runtime group name (#440) (5cec305)
  • snakemake: upgrade to Snakemake 7.32.4 (#435) (20ae9ce)

Bug fixes

  • cache: handle deleted files when calculating access times (#437) (698900f)

Code refactoring

Continuous integration

  • commitlint: addition of commit message linter (#432) (a67906f)
  • commitlint: check for the presence of concrete PR number (#438) (d3035dc)
  • release-please: initial configuration (#432) (687f2f4)
  • shellcheck: check all shell scripts recursively (#436) (709a685)
  • shellcheck: fix exit code propagation (#438) (85d9a2a)

0.9.5 (2023-12-15)

  • Fixes installation by pinning bravado-core to versions lower than 6.1.1.

0.9.4 (2023-11-30)

  • Changes the REANA specification schema to use the draft-07 version of the JSON Schema specification.
  • Changes validation of REANA specification to expose functions for loading workflow input parameters and workflow specifications.
  • Changes validation of REANA specification to make the environment property mandatory for the steps of serial workflows.
  • Changes validation of REANA specification to raise a warning for unexpected properties for the steps of serial workflows.
  • Changes CVMFS support to allow users to automatically mount any available repository.
  • Fixes the mounting of CVMFS volumes for the REANA deployments that use non-default Kubernetes namespace.

0.9.3 (2023-09-26)

  • Adds support for Python 3.12.
  • Adds the OpenAPI specification support for prune_workspace endpoint that allows to delete files that are neither inputs nor outputs from the workspace.
  • Adds support for tests.files in reana.yaml allowing to specify Gherkin feature files for testing runnable examples.
  • Changes the OpenAPI specification to include the run_stopped_at property in the workflow progress information returned by the workflow list and workflow status endpoints.
  • Changes the OpenAPI specification to include the maximum_interactive_session_inactivity_period value to the info endpoint.
  • Changes the email sending utility to allow configuring authentication and encryption options.
  • Changes validation of REANA specification to emit warnings about unknown properties.
  • Fixes the verbs used to describe changes to the status of a workflow in order to avoid incorrect grammatical phrases such as workflow has been failed.
  • Fixes the loading of Snakemake and CWL workflow specifications when no parameters are specified.
  • Fixes the OpenAPI specification of GitLab OAuth endpoint return statuses.
  • Fixes container image names to be Podman-compatible.
  • Fixes the email sending utility to not send emails when notifications are disabled globally.

0.9.2.1 (2023-07-19)

  • Changes PyYAML dependency version bounds in order to fix installation on Python 3.10+.

0.9.2 (2023-02-10)

  • Fixes wcmatch dependency version specification.

0.9.1 (2023-01-18)

  • Changes Kerberos renew container's configuration to log each ticket renewal.

0.9.0 (2022-12-13)

  • Adds support for Python 3.11.
  • Adds support for Rucio.
  • Adds REANA specification validation and loading logic from reana-client.
  • Adds common utility functions for managing workspace files.
  • Adds OpenAPI specification support for launch endpoint that allows running workflows from remote sources.
  • Adds OpenAPI specification support for get_workflow_retention_rules endpoint that allows to retrieve the workspace file retention rules of a workflow.
  • Adds generation of Kerberos init and renew container's configuration.
  • Adds support for Unicode characters inside email body.
  • Changes OpenAPI specification to include missing response schema elements and some other small enhancements.
  • Changes the Kubernetes Python client to use the networking/v1 API.
  • Changes REANA specification loading functionality to allow specifying different working directories.
  • Changes REANA specification to allow enabling Kerberos for the whole workflow.
  • Changes REANA specification to allow specifying retention_days for the workflow.
  • Changes REANA specification to allow specifying slurm_partition and slurm_time for Slurm compute backend jobs.
  • Changes the loading of Snakemake specifications to preserve the current working directory.
  • Fixes the submission of jobs by stripping potential leading and trailing whitespaces in Docker image names.

0.8.5 (2022-02-23)

  • Adds retry_count parameter to WorkflowSubmissionPublisher.

0.8.4 (2022-02-08)

  • Adds new configuration variable to toggle Kubernetes security context. (K8S_USE_SECURITY_CONTEXT)
  • Changes installation to revert Yadage dependency versions.

0.8.3 (2022-02-04)

  • Changes installation to remove upper version pin on kombu.

0.8.2 (2022-02-01)

  • Adds support for Python 3.10.
  • Adds workflow name validation utility.
  • Changes Snakemake loaded specification to include compute backends.
  • Changes OpenAPI specification with respect to return supported compute backends in info endpoint.
  • Fixes file system usage calculation on CephFS shares in get_disk_usage utility function.

0.8.1 (2021-12-21)

  • Adds OpenAPI specification support for kubernetes_job_timeout handling.
  • Changes OpenAPI specification for cluster health status endpoint.
  • Changes Yadage dependencies to allow 0.21.x patchlevel-version updates.
  • Changes installation to require Python-3.6 or higher versions.

0.8.0 (2021-11-22)

  • Adds get_disk_usage utility function to calculate disk usage for a directory.
  • Adds Yadage workflow specification loading utilities.
  • Adds workspace validation utilities.
  • Adds Snakemake workflow engine integration.
  • Adds custom objects API instance to k8s client.
  • Adds available worklow engines configuration.
  • Adds environment variable to define time between job controller connection checks.
  • Adds cluster health status endpoint.
  • Adds OpenAPI specifications with respect to user quotas.
  • Changes workflow-submission queue as a priority queue and allows to set the priority number on workflow submission.
  • Changes OpenAPI specifications with respect to turning workspaces endpoint into info.
  • Changes publisher logging level on error callback.
  • Removes support for Python 2.

0.7.5 (2021-07-02)

  • Adds support for glob patterns when listing workflow files.
  • Adds support for specifying kubernetes_memory_limit for Kubernetes compute backend jobs.

0.7.4 (2021-03-17)

  • Adds new functions to serialise/deserialise job commands between REANA components.
  • Changes reana_ready function location to REANA-Server.

0.7.3 (2021-02-22)

  • Adds new configuration variable to toggle runtime user jobs clean up depending on their statuses. (REANA_RUNTIME_KUBERNETES_KEEP_ALIVE_JOBS_WITH_STATUSES)
  • Adds central class to instantiate workflow engines with more resilience. (workflow_engine.create_workflow_engine_command)

0.7.2 (2021-02-02)

  • Adds support for Python 3.9.
  • Fixes minor code warnings.
  • Fixes a helper function that calculates directory hashes.
  • Changes OpenAPI specifications with respect to sign-up form.
  • Changes OpenAPI specifications with respect to email confirmation.
  • Changes CI system to include Python flake8 checker.

0.7.1 (2020-11-09)

  • Adds support for restarting yadage workflows (through accept_metadir operational option).
  • Allows htcondor_max_runtime and htcondor_accounting_group to be specified for HTC jobs.
  • Adds new field in REANA-Server OpenAPI spec to return server version.
  • Changes CI system from Travis to GitHub Actions.

0.7.0 (2020-10-20)

  • Adds new utility to send emails.
  • Adds centralised validation utility for workflow operational options.
  • Adds new configuration variable to set the maximum number of running workflows. (REANA_MAX_CONCURRENT_BATCH_WORKFLOWS)
  • Adds new configuration variable to set prefix of REANA cluster component names. (REANA_COMPONENT_PREFIX)
  • Adds new configuration variable for the runtime pod node selector label. (REANA_RUNTIME_KUBERNETES_NODE_LABEL)
  • Adds new configuration variable to define the Kubernetes namespace in which REANA infrastructure components run. (REANA_INFRASTRUCTURE_KUBERNETES_NAMESPACE)
  • Adds new configuration variable to define the Kubernetes namespace in which REANA runtime components components run. (REANA_RUNTIME_KUBERNETES_NAMESPACE)
  • Adds possibility to specify unpacked container images for running jobs.
  • Adds support for initfiles operational option for the Yadage workflow engine.
  • Fixes memory leak in Bravado client instantiation.
  • Changes CephFS Persistent Volume Claim name. (REANA_SHARED_PVC_NAME)
  • Changes default logging level to INFO.
  • Changes default CVMFS volume list to include LHCb Gaudi related workflows.
  • Changes code formatting to respect black coding style.
  • Changes underlying requirements to use Kubernetes Python library version 11.
  • Changes underlying requirements to use latest CVMFS CSI driver version.
  • Changes documentation to single-page layout.

0.6.1 (2020-05-25)

  • Upgrades Kubernetes Python client.

0.6.0 (2019-12-19)

  • Adds new API for Gitlab integration.
  • Adds new Kubernetes client API for ingresses.
  • Adds new APIs for management of user secrets.
  • Adds EOS storage Kubernetes configuration.
  • Adds HTCondor and Slurm compute backends.
  • Adds support for streaming file uploads.
  • Allows unpacked CVMFS and CMS open data volumes.
  • Adds Serial workflow step name and compute backend.
  • Adds support for Python 3.8.

0.5.0 (2019-04-16)

  • Centralises log level and log format configuration.
  • Adds new utility to inspect the disk usage on a given workspace. (get_workspace_disk_usage)
  • Introduces the module to share Celery tasks accross REANA components. (tasks.py)
  • Introduces common Celery task to determine whether REANA can execute new workflows depending on a set of conditions such as running job count. (reana_ready, check_predefined_conditions, check_running_job_count)
  • Allows the AMQP consumer to be configurable with multiple queues.
  • Introduces new queue for workflow submission. (workflow-submission)
  • Introduces new publisher for workflow submissions. (WorkflowSubmissionPublisher)
  • Centralises Kubernetes API client configuration and initialisation.
  • Adds Kubernetes specific configuration for CVMFS volumes as utils.
  • Introduces a new method, copy_openapi_specs, to automatically move validated OpenAPI specifications from components to REANA Commons openapi_specifications directory.
  • Centralises interactive session types.
  • Introduces central REANA errors through the errors.py module.
  • Skips SSL verification for all HTTPS requests performed with the BaseAPIClient.

0.4.0 (2018-11-06)

  • Aggregates OpenAPI specifications of REANA components.
  • Improves AMQP re-connection handling. Switches from pika to kombu.
  • Enhances test suite and increases code coverage.
  • Changes license to MIT.

0.3.1 (2018-09-04)

  • Adds parameter expansion and validation utilities for parametrised Serial workflows.

0.3.0 (2018-08-10)

  • Initial public release.
  • Provides basic AMQP pub/sub methods for REANA components.
  • Utilities for caching used in different REANA components.
  • Click formatting helpers.

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