refactor(docs): move from reST to Markdown (#225)

Convert docs from reStructuredText to Markdown so that the changelog
file is compatible with Release Please.

AUTHORS.md

@@ -0,0 +1,17 @@
+# Authors
+
+The list of contributors in alphabetical order:
+
+- [Audrius Mecionis](https://orcid.org/0000-0002-3759-1663)
+- [Camila Diaz](https://orcid.org/0000-0001-5543-797X)
+- [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)
+- [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)
+- [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)

CHANGELOG.md

@@ -0,0 +1,128 @@
+# Changelog
+
+## 0.9.3 (2023-12-01)
+
+- Changes the `Workflow` table to replace the `run_number` column with two new columns `run_number_major` and `run_number_minor` in order to allow for more than nine restarts of user workflows.
+- Changes the names of database table, column, index and key constraints in order to follow the SQLAlchemy upstream naming conventions everywhere.
+- Changes several database index definitions in order to improve performance of most common database queries.
+
+## 0.9.2 (2023-09-26)
+
+- 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.
+- Fixes the workflow priority calculation to avoid workflows stuck in the `queued` status when the number of allowed concurrent workflow is set to zero.
+
+## 0.9.1 (2023-01-18)
+
+- Changes to PostgreSQL 12.13.
+- Fixes conversion of possibly-negative resource usage values to human-readable formats.
+- Fixes disk quota updater to prevent setting negative disk quota usage values.
+- Fixes quota updater to reduce memory usage.
+
+## 0.9.0 (2022-12-13)
+
+- Adds new `launcher_url` column to the `Workflow` table to store the remote origin of workflows submitted via the Launch-on-REANA functionality.
+- Adds the possibility to force resource quota updates irrespective of globally-configured quota update policy.
+- Adds new `WorkspaceRetentionRule` table to store workspace file retention rules.
+- Adds new `WorkspaceRetentionAuditLog` table to store the audit log of workspace file retention rule updates.
+- Changes percentage ranges used to calculate the health status of user resource quota usage.
+- Changes to PostgreSQL 12.10.
+- Fixes wrong numbering of restarted workflows by limiting the number of times a workflow can be restarted to nine.
+- Fixes `Workflow.get_workspace_disk_usage` to always calculate disk usage rather than relying on the quota usage values from the database, since these may not be up-to-date depending on the global quota update policy.
+- Fixes helper function that retrieves workflows by UUID to also additionally check that the provided user is the owner of the workflow.
+
+## 0.8.2 (2022-02-23)
+
+- Adds transition for workflow from queued to failed status.
+
+## 0.8.1 (2022-02-01)
+
+- Adds an option to periodically calculate CPU quota usage.
+- Changes CLI quota command from `disk-usage-update` to `resource-usage-update` since it can also perform CPU quota calculation.
+- Fixes quota update functions to handle exceptional situation as continuable errors.
+- Removes extra `QuotaResourceType` enum in favor of `ResourceType.name`.
+
+## 0.8.0 (2021-11-22)
+
+- Adds new disk usage retrieval methods using canonical (bytes) and human-readable (KiB) units. (`User`, `Workflow`)
+- Adds Quota models which calculates CPU and disk usage.
+- Adds `InteractiveSession` model.
+- Adds new properties `started_at` and `finished_at` to the `Job` model, updated on status change.
+- Adds `get_priority` workflow method, that combines both complexity and concurrency, to pass to the scheduler.
+- Adds a possibility to configure database connection pool parameters via environment variables.
+- Adds new `pending` state to `RunStatus` table.
+- Adds workflow complexity property in `Workflow` table.
+- Adds environment variable to configure which quotas to update.
+- Changes `WorkflowStatus` table to `RunStatus`.
+- Changes disk quota calculation functions to allow passing raw bytes to increase the used quota.
+- Changes to PostgreSQL 12.8.
+- Removes support for Python 2.
+
+## 0.7.3 (2021-03-17)
+
+- Fixes REANA installation by pinning SQLAlchemy version less than 1.4.0 due to <https://github.com/kvesteri/sqlalchemy-utils/issues/505>.
+
+## 0.7.2 (2021-02-22)
+
+- Adds utility to status enums to decide whether to clean workflows and jobs depending on their status.
+
+## 0.7.1 (2021-02-02)
+
+- Adds support for Python 3.9.
+- Fixes minor code warnings.
+- Changes CI system to include Python flake8 checker.
+
+## 0.7.0 (2020-10-20)
+
+- Adds initial central workflow status transition logic handler.
+- Adds new audit table and logic to register actions. (`AuditLog`, `AuditLogAction`)
+- Adds fixtures for better testing of database models.
+- Changes user token storage to move tokens from `User` table to `UserToken` table and to encrypt them.
+- Changes `Workflow` table to add a new `workspace_path` column.
+- Changes default database service to use centrally configured one from REANA-Commons. (`REANA_INFRASTRUCTURE_COMPONENTS_HOSTNAMES`)
+- Changes code formatting to respect `black` coding style.
+- Changes documentation to single-page layout.
+
+## 0.6.0 (2019-12-19)
+
+- Adds new method which returns full workflow name.
+- Adds more granular DB configuration.
+- Adds Git repository information to the workflow model.
+  (`Workflow.git_repo`, `Workflow.git_provider`)
+- Adds user name information to the user model.
+  (`User.full_name`, `User.username`)
+- Removes restart count information from the job model.
+  (`Job.restart_count`, `Job.max_restart_count`)
+- Adds support for Python 3.8.
+
+## 0.5.0 (2019-04-16)
+
+- Introduces new workflow statuses: `deleted`, `stopped`, `queued`.
+- Adds new field to store workflow stopping time. (`Workflow.run_stopped_at`)
+- Moves workflow input parameters to its own column to separate them from
+  operational options. Adapts getters accordingly.
+  (`Workflow.input_parameters`)
+- Adds new method to retrieve the workflow owner's token.
+  (`Workflow.get_owner_access_token`)
+- Introduces new utility function to retrieve workflows by `uuid` or name.
+  (`_get_workflow_with_uuid_or_name`)
+- Introduces new fields for interactive sessions: `interactive_session`,
+  `interactive_session_name` and `interactive_session_type`. Note that with
+  current design only one interactive session per workflow is supported.
+- Adds a new enumeration for possible job statuses. (`JobStatus`)
+- Adds new field to identify jobs in the underlying compute backend.
+  (`Job.backend_job_id`)
+
+## 0.4.0 (2018-11-06)
+
+- Stores `reana.yaml` in database models.
+- Adds Workflow specification and parameter getters.
+- Adds support for Python 3.7.
+- Changes license to MIT.
+
+## 0.3.0 (2018-08-10)
+
+- This package is a result of refactoring [reana-commons](https://reana-commons.readthedocs.io/).
+- Provides common REANA models.
+- Provides database connection logic.
+

CONTRIBUTING.rst → CONTRIBUTING.md

@@ -1,20 +1,18 @@
-Contributing
-============
+# Contributing
 
 Bug reports, issues, feature requests, and other contributions are welcome. If you find
 a demonstrable problem that is caused by the REANA code, please:
 
-1. Search for `already reported problems
-   <https://github.com/reanahub/reana-db/issues>`_.
+1. Search for [already reported problems](https://github.com/reanahub/reana-db/issues).
 2. Check if the issue has been fixed or is still reproducible on the
    latest `master` branch.
 3. Create an issue, ideally with **a test case**.
 
 If you create a pull request fixing a bug or implementing a feature, you can run
 the tests to ensure that everything is operating correctly:
 
-.. code-block:: console
-
-    $ ./run-tests.sh
+```console
+$ ./run-tests.sh
+```
 
 Each pull request should preserve or increase code coverage.

MANIFEST.in

@@ -6,7 +6,6 @@
 
 include *.json
 include *.md
-include *.rst
 include *.sh
 include *.yaml
 include .dockerignore
@@ -20,7 +19,7 @@ recursive-include reana_db .gitkeep
 recursive-include reana_db *.ini
 recursive-include docs *.py
 recursive-include docs *.png
-recursive-include docs *.rst
+recursive-include docs *.md
 recursive-include docs *.txt
 recursive-include tests *.py
 prune docs/_build

README.md

@@ -0,0 +1,35 @@
+# REANA DB
+
+[![image](https://img.shields.io/pypi/pyversions/reana-db.svg)](https://pypi.org/pypi/reana-db)
+[![image](https://github.com/reanahub/reana-db/workflows/CI/badge.svg)](https://github.com/reanahub/reana-db/actions)
+[![image](https://readthedocs.org/projects/reana-db/badge/?version=latest)](https://reana-db.readthedocs.io/en/latest/?badge=latest)
+[![image](https://codecov.io/gh/reanahub/reana-db/branch/master/graph/badge.svg)](https://codecov.io/gh/reanahub/reana-db)
+[![image](https://img.shields.io/badge/discourse-forum-blue.svg)](https://forum.reana.io)
+[![image](https://img.shields.io/github/license/reanahub/reana-db.svg)](https://github.com/reanahub/reana-db/blob/master/LICENSE)
+[![image](https://img.shields.io/badge/code%20style-black-000000.svg)](https://github.com/psf/black)
+
+## About
+
+REANA-DB is a component of the [REANA](http://www.reana.io/) reusable analysis platform.
+It contains REANA database models and utilities.
+
+## Features
+
+- database persistence for REANA system
+- database models and utilities
+- database upgrades and migrations
+
+## Usage
+
+The detailed information on how to install and use REANA can be found in
+[docs.reana.io](https://docs.reana.io).
+
+## Useful links
+
+- [REANA project home page](http://www.reana.io/)
+- [REANA user documentation](https://docs.reana.io)
+- [REANA user support forum](https://forum.reana.io)
+- [REANA-DB releases](https://reana-db.readthedocs.io/en/latest#changes)
+- [REANA-DB developer documentation](https://reana-db.readthedocs.io/)
+- [REANA-DB known issues](https://github.com/reanahub/reana-db/issues)
+- [REANA-DB source code](https://github.com/reanahub/reana-db)