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refactor(docs): move from reST to Markdown (#671) #671

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Feb 9, 2024
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refactor(docs): move from reST to Markdown (#671) #671

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23 changes: 23 additions & 0 deletions AUTHORS.md
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# Authors

The list of contributors in alphabetical order:

- [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)
24 changes: 0 additions & 24 deletions AUTHORS.rst
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213 changes: 213 additions & 0 deletions CHANGELOG.md
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# Changelog

## 0.9.2 (2023-12-12)

- 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.

## 0.9.1 (2023-09-27)

- 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.

## 0.9.0 (2023-01-19)

- 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.

## 0.8.4 (2022-02-23)

- Changes workflow scheduler to count number of workflow retries.

## 0.8.3 (2022-02-10)

- Adds Kubernetes job memory limits validation before publishing workflow submission.

## 0.8.2 (2022-02-07)

- 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.

## 0.8.1 (2021-11-29)

- 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.

## 0.8.0 (2021-11-22)

- 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.

## 0.7.6 (2021-07-05)

- Changes internal dependencies.

## 0.7.5 (2021-04-28)

- Adds support for listing files using glob patterns.
- Adds support for glob patterns and directory downloads, packaging the content into a zip file.

## 0.7.4 (2021-03-17)

- 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.

## 0.7.3 (2021-02-03)

- Adds optional email confirmation step after users sign up.
- Changes email notifications with enriched instructions on how to grant user tokens.

## 0.7.2 (2020-11-24)

- Changes rate limiting defaults to allow up to 20 connections per second.
- Fixes minor code warnings.

## 0.7.1 (2020-11-10)

- 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.

## 0.7.0 (2020-10-20)

- 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.

## 0.6.1 (2020-05-25)

- Upgrades REANA-Commons package using latest Kubernetes Python client version.
- Pins Flask and Invenio dependencies to fix REANA 0.6 installation troubles.

## 0.6.0 (2019-12-20)

- 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`.

## 0.5.0 (2019-04-23)

- 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.

## 0.4.0 (2018-11-06)

- Improves REST API documentation rendering.
- Enhances test suite and increases code coverage.
- Changes license to MIT.

## 0.3.1 (2018-09-07)

- Harmonises date and time outputs amongst various REST API endpoints.
- Pins REANA-Commons, REANA-DB and Bravado dependencies.

## 0.3.0 (2018-08-10)

- Adds support of Serial workflows.
- Adds API protection with API tokens.

## 0.2.0 (2018-04-19)

- Adds support of Common Workflow Language workflows.
- Adds support of specifying workflow names in REST API requests.
- Improves error messages and information.

## 0.1.0 (2018-01-30)

- Initial public release.

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