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Changelog

0.9.3 (2024-03-04)

Build

  • docker: non-editable submodules in "latest" mode (#551) (af74d0b)
  • python: bump all required packages as of 2024-03-04 (#574) (1373f4c)
  • python: bump shared REANA packages as of 2024-03-04 (#574) (e31d903)

Features

  • manager: call shutdown endpoint before workflow stop (#559) (719fa37)
  • manager: increase termination period of run-batch pods (#572) (f05096a)
  • manager: pass custom env variables to job controller (#571) (646f071)
  • manager: pass custom env variables to workflow engines (#571) (cb9369b)

Bug fixes

  • manager: graceful shutdown of job-controller (#559) (817b019)
  • manager: use valid group name when calling groupadd (#566) (73a9929), closes #561
  • stop: store engine logs of stopped workflow (#563) (199c163), closes #560

Code refactoring

Code style

Continuous integration

  • commitlint: addition of commit message linter (#555) (b9df20a)
  • commitlint: allow release commit style (#575) (b013d49)
  • commitlint: check for the presence of concrete PR number (#562) (4b8f539)
  • pytest: move to PostgreSQL 14.10 (#568) (9b6bfa0)
  • release-please: initial configuration (#555) (672083d)
  • release-please: update version in Dockerfile/OpenAPI specs (#558) (4be8086)
  • shellcheck: fix exit code propagation (#562) (c5d4982)

Documentation

  • authors: complete list of contributors (#570) (08ab9a3)

0.9.2 (2023-12-12)

  • Adds automated multi-platform container image building for amd64 and arm64 architectures.
  • Adds metadata labels to Dockerfile.
  • Changes CVMFS support to allow users to automatically mount any available repository.
  • Changes how pagination is performed in order to avoid counting twice the total number of records.
  • Changes the workflow deletion endpoint to return a different and more appropriate message when deleting all the runs of a workflow.
  • Fixes job status consumer exception while attempting to fetch workflow engine logs for workflows that were not successfully scheduled.
  • Fixes runtime uWSGI warning by rebuilding uWSGI with the PCRE support.

0.9.1 (2023-09-27)

  • Adds the timestamp of when the workflow was stopped (run_stopped_at) to the workflow list and the workflow status endpoints.
  • Adds PDF files to the list of file types that can be previewed from the web interface.
  • Changes the deletion of a workflow to automatically delete an open interactive session attached to its workspace.
  • Changes the k8s specification for interactive session pods to include labels for improved subset selection of objects.
  • Changes the k8s specification for interactive session ingress resource to include annotations.
  • Changes uWSGI configuration to increase buffer size, add vacuum option, etc.
  • Fixes job status inconsistency when stopping a workflow by setting the job statuses to stopped for any running jobs.
  • Fixes job status consumer to correctly rollback the database transaction when an error occurs.
  • Fixes uWSGI memory consumption on systems with very high allowed number of open files.
  • Fixes uWSGI and consume-job-queue command to gracefully stop when being terminated.
  • Fixes container image names to be Podman-compatible.

0.9.0 (2023-01-19)

  • Adds the remote origin of workflows submitted via Launch-on-REANA (launcher_url) to the workflow list endpoint.
  • Adds support for Kerberos authentication for workflow orchestration.
  • Adds the REANA_WORKSPACE environment variable to jupyter notebooks and terminals.
  • Adds option to sort workflows by most disk and cpu quota usage to the workflow list endpoint.
  • Adds support for specifying and listing workspace file retention rules.
  • Changes workflow list endpoint to add the possibility to filter by workflow ID.
  • Changes the deployment of interactive sessions to use networking/v1 Kubernetes API.
  • Changes default consumer prefetch count to handle 10 messages instead of 200 in order to reduce the probability of 406 PRECONDITION errors on message acknowledgement.
  • Changes to Flask v2.
  • Changes job status consumer to improve logging for not-alive workflows.
  • Changes the deletion of a workflow to also update the user disk quota usage if the workspace is deleted.
  • Changes the CWD of jupyter's terminals to the directory of the workflow's workspace.
  • Changes the k8s specification of interactive sessions' pods to remove the environment variables used for service discovery.
  • Changes GitLab integration to use reana as pipeline name instead of default when setting status of a commit.
  • Changes the deletion of a workflow to always remove the workflow's workspace and to fail if the request is asking not to delete the workspace.
  • Changes the move_files endpoint to allow moving files while a workflow is running.
  • Changes the deployment of interactive sessions to improve security by not automounting the Kubernetes service account token.
  • Changes workspace file management commands to use common utility functions present in reana-commons.
  • Changes to PostgreSQL 12.13.
  • Changes the deployment of job-controller to avoid unnecessarily mounting the database's directory.
  • Changes the base image of the component to Ubuntu 20.04 LTS and reduces final Docker image size by removing build-time dependencies.
  • Fixes the download of files by changing the default MIME type to application/octet-stream.
  • Fixes the workflow list endpoint to correctly parse the boolean parameters include_progress, include_workspace_size and include_retention_rules.
  • Fixes Kerberos authentication for long-running workflows by renewing the Kerberos ticket periodically.
  • Fixes job status consumer by discarding invalid job IDs.

0.8.2 (2022-10-06)

  • Fixes delete --include-all-runs functionality to delete only workflow owner's past runs.

0.8.1 (2022-02-07)

  • Adds configuration environment variable to set default timeout for user's jobs for the Kubernetes compute backend (REANA_KUBERNETES_JOBS_TIMEOUT_LIMIT).
  • Adds configuration environment variable to set maximum custom timeout limit that users can assign to their jobs for the Kubernetes compute backend (REANA_KUBERNETES_JOBS_MAX_USER_TIMEOUT_LIMIT).

0.8.0 (2021-11-22)

  • Adds users quota accounting.
  • Adds new job properties started_at and finished_at to the /logs endpoint.
  • Adds configuration environment variable to limit the number of messages received in the job status consumer (prefetch_count).
  • Adds file search capabilities to the workflow workspace endpoint.
  • Adds Snakemake workflow engine support.
  • Adds support for custom workflow workspace path.
  • Changes to PostgreSQL 12.8.
  • Changes workflow run manager to query the specific workflow engine during pod deletion.
  • Fixes workflow list endpoint query logic to improve optimization.

0.7.4 (2021-07-05)

  • Changes internal dependencies.

0.7.3 (2021-04-28)

  • Adds configuration environment variable to set job memory limits for the Kubernetes compute backend (REANA_KUBERNETES_JOBS_MEMORY_LIMIT).
  • Adds configuration environment variable to set maximum custom memory limits that users can assign to their job containers for the Kubernetes compute backend (REANA_KUBERNETES_JOBS_MAX_USER_MEMORY_LIMIT).
  • Adds support for listing files using glob patterns.
  • Adds support for glob patterns and directory downloads, packaging files into a zip.

0.7.2 (2021-03-17)

  • Adds new configuration to toggle Kubernetes user jobs clean up.
  • Fixes job-status-consumer exception detection for better resilience.

0.7.1 (2021-02-03)

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

0.7.0 (2020-10-20)

  • Adds possibility to restart workflows.
  • Adds exposure of workflow engines logs.
  • Adds possibility to pass workflow operational options.
  • Adds progress report information on workflow list response.
  • Adds code mount on dev mode in workflow engines and job controller.
  • Adds preview flag to file download endpoint.
  • Fixes deletion of workflows in queued state.
  • Fixes CVMFS availability for interactive sessions.
  • Fixes jobs status update.
  • Fixes response on close interactive session action.
  • Changes runtime component creation to use centrally configured namespace from REANA-Commons.
  • Changes workflow engine pod labelling for better traceability.
  • Changes logs endpoint to provide richer information.
  • Changes git clone depth when retrieving GitLab projects.
  • Changes REANA submodule installation in editable mode for live code updates for developers.
  • 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 client version.

0.6.0 (2019-12-20)

  • Modifies the batch workflow run creation, including an instance of REANA-Job-Controller running alongside with the workflow engine (sidecar pattern). Only DB and workflow worksapce are mounted.
  • Refactors volume mounts using reana-commons base.
  • Provides user secrets to the job controller.
  • Extends workflow APIs for GitLab integration.
  • Allows stream file uploads.

0.5.0 (2019-04-23)

  • Adds support to create interactive sessions so the workspace can be explored and modified through a Jupyter notebook.
  • Creates workflow engine instances on demand for each user and makes CVMFS available inside of them.
  • Adds new endpoint to compare two workflows. The output is a git like diff which can be configured to show differences at metadata level, workspace level or both.
  • Adds new endpoint to delete workflows including the stopped ones.
  • Adds new endpoints to delete and move files whithin the workspace. The deletion can be also done recursively with a wildcard.
  • Adds new endpoint which returns workflow parameters.
  • Adds new endpoint to query the disk usage of a given workspace.
  • Makes docker image slimmer by using python:3.6-slim.
  • Centralises log level and log format configuration.

0.4.0 (2018-11-06)

  • Improves AMQP re-connection handling. Switches from pika to kombu.
  • Improves REST API documentation rendering.
  • Changes license to MIT.

0.3.2 (2018-09-25)

  • Modifies job input identification process for caching purposes, adding compatibility with CephFS storage volumes.

0.3.1 (2018-09-07)

  • Harmonises date and time outputs amongst various REST API endpoints.
  • Separates workflow parameters and engine parameters when running Serial workflows.
  • Pins REANA-Commons and REANA-DB dependencies.

0.3.0 (2018-08-10)

  • Adds support for Serial workflows.
  • Tracks progress of workflow runs.
  • Adds uwsgi for production deployments.
  • Allows downloading of any file from a workflow workspace.

0.2.0 (2018-04-19)

  • Adds support for Common Workflow Language workflows.
  • Adds support for specifying workflow names in REST API requests.
  • Adds sequential incrementing of workflow run numbers.
  • Adds support for nested inputs and runtime code directory uploads.
  • Improves error messages and information.
  • Prevents multiple starts of the same workflow.

0.1.0 (2018-01-30)

  • Initial public release.