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refactor(docs): move from reST to Markdown (#671)
Convert docs from reStructuredText to Markdown so that the changelog file is compatible with Release Please.
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| # Authors | ||
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| The list of contributors in alphabetical order: | ||
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| - [Adelina Lintuluoto](https://orcid.org/0000-0002-0726-1452) | ||
| - [Audrius Mecionis](https://orcid.org/0000-0002-3759-1663) | ||
| - [Anton Khodak](https://orcid.org/0000-0003-3263-4553) | ||
| - [Camila Diaz](https://orcid.org/0000-0001-5543-797X) | ||
| - [Daan Rosendal](https://github.com/DaanRosendal) | ||
| - [Diego Rodriguez](https://orcid.org/0000-0003-0649-2002) | ||
| - [Dinos Kousidis](https://orcid.org/0000-0002-4914-4289) | ||
| - [Domenic Gosein](https://orcid.org/0000-0002-1546-0435) | ||
| - [Giuseppe Steduto](https://orcid.org/0009-0002-1258-8553) | ||
| - [Harri Hirvonsalo](https://orcid.org/0000-0002-5503-510X) | ||
| - [Jan Okraska](https://orcid.org/0000-0002-1416-3244) | ||
| - [Leticia Wanderley](https://orcid.org/0000-0003-4649-6630) | ||
| - [Marco Donadoni](https://orcid.org/0000-0003-2922-5505) | ||
| - [Marco Vidal](https://orcid.org/0000-0002-9363-4971) | ||
| - [Michael R. Crusoe](https://orcid.org/0000-0002-2961-9670) | ||
| - [Rokas Maciulaitis](https://orcid.org/0000-0003-1064-6967) | ||
| - [Sinclert Perez](https://www.linkedin.com/in/sinclert) | ||
| - [Tibor Simko](https://orcid.org/0000-0001-7202-5803) | ||
| - [Vladyslav Moisieienkov](https://orcid.org/0000-0001-9717-0775) |
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| # Changelog | ||
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| ## 0.9.2 (2023-12-12) | ||
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| - Adds automated multi-platform container image building for amd64 and arm64 architectures. | ||
| - Adds metadata labels to Dockerfile. | ||
| - Changes workflow scheduler logging behaviour to also report the main reason behind scheduling errors to the users. | ||
| - Fixes runtime uWSGI warning by rebuilding uWSGI with the PCRE support. | ||
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| ## 0.9.1 (2023-09-27) | ||
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| - Adds new `prune_workspace` endpoint to allow users to delete all the files of a workflow, specifying whether to also delete the inputs and/or the outputs. | ||
| - Adds new `interactive-session-cleanup` command that can be used by REANA administrators to close interactive sessions that are inactive for more than the specified number of days. | ||
| - Adds logic to support SSO with third-party Keycloak authentication services. | ||
| - Adds the timestamp of when the workflow was stopped (`run_stopped_at`) to the workflow list and the workflow status endpoints. | ||
| - Adds the content of the `REANA_GITLAB_HOST` environment variable to the list of GitLab instances from which it is possible to launch a workflow. | ||
| - Adds progress meter to the logs of the periodic quota updater. | ||
| - Changes CPU and disk quota calculations to improve the performance of periodic quota updater. | ||
| - Changes the system status report to simplify and clarify the disk usage summary. | ||
| - Changes `check-workflows` command to also check the presence of workspaces on the shared volume. | ||
| - Changes `check-workflows` command to not show in-sync runs by default. If needed, they can be shown using the new `--show-all` option. | ||
| - Changes `launch` endpoint to also include the warnings of the validation of the workflow specification. | ||
| - Changes OpenAPI specification of the `info` endpoint to return the maximum inactivity time before automatic closure of interactive sessions. | ||
| - Changes `apispec` dependency version in order to be compatible with `PyYAML` v6. | ||
| - Changes `reana-admin` command options to require the passing of `--admin-access-token` argument more globally. | ||
| - Fixes the workflow priority calculation to avoid workflows stuck in the `queued` status when the number of allowed concurrent workflow is set to zero. | ||
| - Fixes GitLab integration to automatically redirect the user to the correct URL when the access request is accepted. | ||
| - Fixes `quota-set-default-limits` command to propagate default quota limits to all users without custom quota limit values. | ||
| - Fixes authentication flow to correctly deny access to past revoked tokens in case the same user has also other new active tokens. | ||
| - Fixes email templates to show the correct `kubectl` commands when REANA is deployed inside a non-default namespace or with a custom component name prefix. | ||
| - Fixes email sender for system emails to `notifications.email_config.sender` Helm value. | ||
| - Fixes email receiver for token request emails to use `notifications.email_config.receiver` Helm value. | ||
| - Fixes `start-scheduler` command to gracefully stop when being terminated. | ||
| - Fixes container image names to be Podman-compatible. | ||
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| ## 0.9.0 (2023-01-19) | ||
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| - Adds new `/api/launch` endpoint that allows running workflows from remote sources. | ||
| - Adds new `get_workflow_retention_rules` endpoint that allows to retrieve the workspace file retention rules of a workflow. | ||
| - Adds `queue-consume` command that can be used by REANA administrators to remove specific messages from the queue. | ||
| - Adds configuration environment variable to set an API rate limit for slow endpoints (`REANA_RATELIMIT_SLOW`). | ||
| - Adds REANA specification validation utilities. | ||
| - Adds `retention-rules-apply` command that can be used by REANA administrators to apply pending retention rules. | ||
| - Adds `retention-rules-extend` command that can be used by REANA administrators to extend the duration of active retentions rules. | ||
| - Adds `check-workflows` command that can be used by REANA administrators to check for out-of-sync workflows and interactive sessions. | ||
| - Changes OpenAPI specification to include missing response schema elements and some other small enhancements. | ||
| - Changes `/api/info` endpoint to also include the kubernetes maximum memory limit, the kubernetes default memory limit and the maximum workspace retention period. | ||
| - Changes `start_workflow` endpoint to validate the REANA specification of the workflow. | ||
| - Changes `create_workflow` endpoint to populate workspace retention rules for the workflow. | ||
| - Changes `start_workflow` endpoint to disallow restarting a workflow when retention rules are pending. | ||
| - Changes API rate limiter error messages to be more verbose. | ||
| - Changes workflow scheduler to allow defining the checks needed to assess whether the cluster can start new workflows. | ||
| - Changes the Invenio dependencies to the latest versions. | ||
| - Changes OAuth configuration to enable the new CERN SSO. | ||
| - Changes to PostgreSQL 12.13. | ||
| - Changes GitLab integration to also retrieve user's projects that are in groups and subgroups. | ||
| - Changes the base image of the component to Ubuntu 20.04 LTS and reduces final Docker image size by removing build-time dependencies. | ||
| - Fixes issue when irregular number formats are passed to `REANA_SCHEDULER_REQUEUE_COUNT` configuration environment variable. | ||
| - Fixes GitLab integration error reporting in case user exceeds CPU or Disk quota usage limits. | ||
| - Fixes CERN OIDC authentication to possibly allow eduGAIN and social login users. | ||
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| ## 0.8.4 (2022-02-23) | ||
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| - Changes workflow scheduler to count number of workflow retries. | ||
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| ## 0.8.3 (2022-02-10) | ||
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| - Adds Kubernetes job memory limits validation before publishing workflow submission. | ||
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| ## 0.8.2 (2022-02-07) | ||
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| - Adds email validation to the `user-create` command used by the REANA administrators. | ||
| - Adds workflow name validation to the `create_workflow` endpoint. | ||
| - Changes `/api/info` endpoint to return a list of supported compute backends. | ||
| - Changes `/api/status` endpoint to calculate the cluster health status based on the availablity instead of the usage. | ||
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| ## 0.8.1 (2021-11-29) | ||
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| - Changes `quota-set` command used by the REANA administrators to use the resource type along with a resource name for specifying the resource. | ||
| - Changes email validation used in `create-admin-user` command by the REANA administrators to be more permissive. | ||
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| ## 0.8.0 (2021-11-22) | ||
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| - Adds users quota accounting. | ||
| - Adds support for Snakemake workflow engine. | ||
| - Adds `include_progress` and `include_workspace_size` query args to workflow list endpoint. | ||
| - Adds workflow prioritization in the queue by complexity. | ||
| - Adds `priority` and `min_job_memory` params to workflow submission publisher. | ||
| - Adds Yadage workflow specification loading to `start_workflow` endpoint. | ||
| - Adds a check in scheduler if at least one workflow job could be started in Kubernetes. | ||
| - Adds configuration environment variable to set workflow scheduling policy (`REANA_WORKFLOW_SCHEDULING_POLICY`). | ||
| - Adds configuration environment variable to set a timeout between consuming workflows (`REANA_SCHEDULER_REQUEUE_SLEEP`). | ||
| - Adds configuration environment variable to set an API rate limiter (`REANA_RATELIMIT_AUTHENTICATED_USER`, `REANA_RATELIMIT_GUEST_USER`). | ||
| - Adds new `info` endpoint allowing to retrieve information about cluster capabilities such as available workspaces. | ||
| - Changes workflow execution consumer to receive only one message at a time. | ||
| - Changes to PostgreSQL 12.8. | ||
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| ## 0.7.6 (2021-07-05) | ||
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| - Changes internal dependencies. | ||
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| ## 0.7.5 (2021-04-28) | ||
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| - Adds support for listing files using glob patterns. | ||
| - Adds support for glob patterns and directory downloads, packaging the content into a zip file. | ||
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| ## 0.7.4 (2021-03-17) | ||
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| - Adds configuration to set a timeout between `reana_ready` checks. (`REANA_SCHEDULER_SECONDS_TO_WAIT_FOR_REANA_READY`) | ||
| - Fixes start workflow endpoint to work with unspecified `operational_options` parameter | ||
| - Fixes workflow scheduling bug in which failed worfklows would count as running, reaching `REANA_MAX_CONCURRENT_BATCH_WORKFLOWS` and therefore, blocking the `job-submission` queue. | ||
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| ## 0.7.3 (2021-02-03) | ||
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| - Adds optional email confirmation step after users sign up. | ||
| - Changes email notifications with enriched instructions on how to grant user tokens. | ||
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| ## 0.7.2 (2020-11-24) | ||
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| - Changes rate limiting defaults to allow up to 20 connections per second. | ||
| - Fixes minor code warnings. | ||
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| ## 0.7.1 (2020-11-10) | ||
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| - Fixes REANA \<-> GitLab synchronisation for projects having additional external webhooks. | ||
| - Fixes restarting of Yadage and CWL workflows. | ||
| - Fixes conflicting `kombu` installation requirements by requiring Celery version 4. | ||
| - Changes `/api/you` endpoint to include REANA server version information. | ||
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| ## 0.7.0 (2020-10-20) | ||
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| - Adds new endpoint to request user tokens. | ||
| - Adds email notifications on relevant events such as user token granted/revoked. | ||
| - Adds new templating system for notification email bodies. | ||
| - Adds possibility to query logs for a single workflow step. | ||
| - Adds endpoint to retrieve the workflow specification used for the workflow run. | ||
| - Adds preview flag to download file endpoint. | ||
| - Adds validation of submitted operational options before starting a workflow. | ||
| - Adds possibility to upload empty files. | ||
| - Adds new block size option to specify the type of units to use for disk size. | ||
| - Adds a possibility to upload new workflow definitions before restarting a workflow. | ||
| - Adds new command to generate status report for the REANA administrators; useful as a cronjob. | ||
| - Adds user token management commands to grant and revoke user tokens. | ||
| - Adds support for local user management. | ||
| - Adds pinning of all Python dependencies allowing to easily rebuild component images at later times. | ||
| - Fixes bug related to rescheduling deleted workflows. | ||
| - Changes `REANA_URL` configuration variable to more precise `REANA_HOSTNAME`. | ||
| - Changes workflow list endpoint response payload to include workflow progress information. | ||
| - Changes import/export commands with respect to new user model fields. | ||
| - Changes submodule installation in editable mode for live code updates for developers. | ||
| - Changes pre-requisites to Invenio-Accounts 1.3.0 to support REST API. | ||
| - Changes `/api/me` to `/api/you` endpoint due to conflict with Invenio-Accounts. | ||
| - Changes base image to use Python 3.8. | ||
| - Changes code formatting to respect `black` coding style. | ||
| - Changes documentation to single-page layout. | ||
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| ## 0.6.1 (2020-05-25) | ||
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| - Upgrades REANA-Commons package using latest Kubernetes Python client version. | ||
| - Pins Flask and Invenio dependencies to fix REANA 0.6 installation troubles. | ||
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| ## 0.6.0 (2019-12-20) | ||
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| - Fixes bug with big file uploads by using data streaming. | ||
| - Adds user login endpoints using OAuth, currently configured to work with CERN | ||
| SSO but extensible to use other OAuth providers such as GitHub, more in [Invenio-OAuthClient](https://invenio-oauthclient.readthedocs.io/en/latest/). | ||
| - Adds endpoints to integrate with GitLab (for retrieving user projects and creating/deleting webhooks). | ||
| - Adds new endpoint `/me` to retrieve user information. | ||
| - Improves security by allowing requests only with `REANA_URL` in the host header, avoiding host header injection attacks. | ||
| - Initialisation logs moved from `stdout` to `/var/log/reana-server-init-output.log`. | ||
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| ## 0.5.0 (2019-04-23) | ||
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| - 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 retrieve workflow parameters. | ||
| - Adds new endpoint to query the disk usage of a given workspace. | ||
| - Adds new endpoints to delete and move files whithin the workspace. | ||
| - Adds new endpoints to open and close interactive sessions inside the | ||
| workspace. | ||
| - Workflow start does not send start requests to REANA Workflow Controller | ||
| straight away, instead it will decide whether REANA can execute it or queue | ||
| it depending on a set of conditions, currently it depends on the number of | ||
| running jobs in the cluster. | ||
| - Adds new administrator command to export and import all REANA users. | ||
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| ## 0.4.0 (2018-11-06) | ||
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| - Improves REST API documentation rendering. | ||
| - Enhances test suite and increases code coverage. | ||
| - Changes license to MIT. | ||
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| ## 0.3.1 (2018-09-07) | ||
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| - Harmonises date and time outputs amongst various REST API endpoints. | ||
| - Pins REANA-Commons, REANA-DB and Bravado dependencies. | ||
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| ## 0.3.0 (2018-08-10) | ||
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| - Adds support of Serial workflows. | ||
| - Adds API protection with API tokens. | ||
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| ## 0.2.0 (2018-04-19) | ||
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| - Adds support of Common Workflow Language workflows. | ||
| - Adds support of specifying workflow names in REST API requests. | ||
| - Improves error messages and information. | ||
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| ## 0.1.0 (2018-01-30) | ||
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| - Initial public release. | ||
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