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refactor(docs): move from reST to markdown (#441)
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) | ||
| - [Agisilaos Kounelis](https://orcid.org/0000-0001-9312-3189) | ||
| - [Audrius Mecionis](https://orcid.org/0000-0002-3759-1663) | ||
| - [Camila Diaz](https://orcid.org/0000-0001-5543-797X) | ||
| - [Burt Holzman](https://orcid.org/0000-0001-5235-6314) | ||
| - [Daniel Prelipcean](https://orcid.org/0000-0002-4855-194X) | ||
| - [Diego Rodriguez](https://orcid.org/0000-0003-0649-2002) | ||
| - [Dinos Kousidis](https://orcid.org/0000-0002-4914-4289) | ||
| - [Giuseppe Steduto](https://orcid.org/0009-0002-1258-8553) | ||
| - [Jan Okraska](https://orcid.org/0000-0002-1416-3244) | ||
| - [Kenyi Hurtado-Anampa](https://orcid.org/0000-0002-9779-3566) | ||
| - [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) | ||
| - [Matthew Feickert](https://orcid.org/0000-0003-4124-7862) | ||
| - [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) |
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| # Changelog | ||
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| ## 0.9.5 (2023-12-15) | ||
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| - Fixes installation by pinning `bravado-core` to versions lower than 6.1.1. | ||
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| ## 0.9.4 (2023-11-30) | ||
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| - 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. | ||
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| ## 0.9.3 (2023-09-26) | ||
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| - 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. | ||
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| ## 0.9.2.1 (2023-07-19) | ||
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| - Changes `PyYAML` dependency version bounds in order to fix installation on Python 3.10+. | ||
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| ## 0.9.2 (2023-02-10) | ||
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| - Fixes `wcmatch` dependency version specification. | ||
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| ## 0.9.1 (2023-01-18) | ||
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| - Changes Kerberos renew container's configuration to log each ticket renewal. | ||
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| ## 0.9.0 (2022-12-13) | ||
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| - 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. | ||
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| ## 0.8.5 (2022-02-23) | ||
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| - Adds `retry_count` parameter to WorkflowSubmissionPublisher. | ||
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| ## 0.8.4 (2022-02-08) | ||
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| - Adds new configuration variable to toggle Kubernetes security context. (`K8S_USE_SECURITY_CONTEXT`) | ||
| - Changes installation to revert `Yadage` dependency versions. | ||
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| ## 0.8.3 (2022-02-04) | ||
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| - Changes installation to remove upper version pin on `kombu`. | ||
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| ## 0.8.2 (2022-02-01) | ||
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| - 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. | ||
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| ## 0.8.1 (2021-12-21) | ||
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| - 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. | ||
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| ## 0.8.0 (2021-11-22) | ||
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| - 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. | ||
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| ## 0.7.5 (2021-07-02) | ||
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| - Adds support for glob patterns when listing workflow files. | ||
| - Adds support for specifying `kubernetes_memory_limit` for Kubernetes compute backend jobs. | ||
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| ## 0.7.4 (2021-03-17) | ||
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| - Adds new functions to serialise/deserialise job commands between REANA components. | ||
| - Changes `reana_ready` function location to REANA-Server. | ||
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| ## 0.7.3 (2021-02-22) | ||
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| - 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`) | ||
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| ## 0.7.2 (2021-02-02) | ||
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| - 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. | ||
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| ## 0.7.1 (2020-11-09) | ||
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| - 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. | ||
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| ## 0.7.0 (2020-10-20) | ||
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| - 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. | ||
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| ## 0.6.1 (2020-05-25) | ||
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| - Upgrades Kubernetes Python client. | ||
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| ## 0.6.0 (2019-12-19) | ||
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| - 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. | ||
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| ## 0.5.0 (2019-04-16) | ||
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| - 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`. | ||
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| ## 0.4.0 (2018-11-06) | ||
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| - 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. | ||
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| ## 0.3.1 (2018-09-04) | ||
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| - Adds parameter expansion and validation utilities for parametrised Serial | ||
| workflows. | ||
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| ## 0.3.0 (2018-08-10) | ||
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| - 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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