refactor(docs): move from reST to Markdown (#259)

AUTHORS.md

@@ -0,0 +1,19 @@
+# Authors
+
+The list of contributors in alphabetical order:
+
+- [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)
+- [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)
+- [Jan Okraska](https://orcid.org/0000-0002-1416-3244)
+- [Lukas Heinrich](https://orcid.org/0000-0002-4048-7584)
+- [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 Pérez](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 +1,123 @@
+# Changelog
+
+## 0.9.3 (2023-12-14)
+
+- Changes `jq` dependency version on amd64 architecture to older version, making certain Yadage workflows much faster.
+
+## 0.9.2 (2023-12-12)
+
+- Adds automated multi-platform container image building for amd64 and arm64 architectures.
+- Adds metadata labels to Dockerfile.
+- Fixes container image building on the arm64 architecture.
+
+## 0.9.1 (2023-09-27)
+
+- Fixes container image names to be Podman-compatible.
+
+## 0.9.0 (2023-01-19)
+
+- Adds support for specifying `slurm_partition` and `slurm_time` for Slurm compute backend jobs.
+- Adds support for Kerberos authentication for workflow orchestration.
+- Adds support for Rucio authentication for workflow jobs.
+- Changes the base image of the component to Ubuntu 20.04 LTS and reduces final Docker image size by removing build-time dependencies.
+
+## 0.8.2 (2022-02-08)
+
+- Changes dependencies to solve compatibility issues with `Yadage 0.20.2` version.
+
+## 0.8.1 (2022-02-07)
+
+- Adds support for specifying `kubernetes_job_timeout` for Kubernetes compute backend jobs.
+- Fixes workflow stuck in pending status due to early Yadage fail.
+
+## 0.8.0 (2021-11-22)
+
+- Adds users quota accounting.
+- Changes workflow specification loading to be done in `reana-commons`.
+- Changes workflow engine to reduce the number of API calls to REANA-Job-Controller.
+- Changes workflow engine to remove duplicated messages to the job status message queue.
+
+## 0.7.5 (2021-07-05)
+
+- Changes internal dependencies to remove click.
+
+## 0.7.4 (2021-04-28)
+
+- Adds support for specifying `kubernetes_memory_limit` for Kubernetes compute backend jobs.
+
+## 0.7.3 (2021-03-17)
+
+- Changes workflow engine instantiation to use central REANA-Commons factory.
+- Changes job command strings by removing interpreter when possible and using central REANA-Commons job command serialisation.
+
+## 0.7.2 (2021-02-03)
+
+- Fixes minor code warnings.
+- Changes CI system to include Python flake8 and Dockerfile hadolint checkers.
+
+## 0.7.1 (2020-11-10)
+
+- Adds support for specifying `htcondor_max_runtime` and `htcondor_accounting_group` for HTCondor compute backend jobs.
+- Fixes restarting of Yadage workflows.
+
+## 0.7.0 (2020-10-20)
+
+- Adds creation of workflow visualisation graph by default when a workflow runs.
+- Adds option to specify unpacked Docker images as workflow step requirement.
+- Adds handling of workflow specification load logic that was done before in `reana-client`.
+- Adds support for VOMS proxy as a new authentication method.
+- Adds support for `initfiles` operational option.
+- Adds pinning of all Python dependencies allowing to easily rebuild component images at later times.
+- Changes Yadage workflow engine to version 0.20.1.
+- 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.
+
+## 0.6.0 (2019-12-20)
+
+- Allows to specify compute backend (HTCondor, Kubernetes or Slurm) and
+  Kerberos authentication requirement for Yadage workflow jobs.
+- Upgrades Python to 3.6.
+- Upgrades Yadage to 0.20.0.
+- Upgrades Packtivity to 0.14.21.
+- Sets default umask 002 for jobs writing to the workflow workspace.
+- Allows setting UID for the job container runtime user.
+- Moves workflow engine to the same Kubernetes pod with the REANA-Job-Controller
+  (sidecar pattern).
+
+## 0.5.0 (2019-04-23)
+
+- Makes workflow engine independent of Celery so that independent workflow
+  instances are created on demand for each user.
+- Centralises the initialisation of `WorkflowStatusPublisher`.
+- Introduces CVMFS mounts in job specifications.
+- Makes docker image slimmer by using `python:2.7-slim`.
+- Centralises log level and log format configuration.
+
+## 0.4.0 (2018-11-06)
+
+- Improves AMQP re-connection handling. Switches from `pika` to `kombu`.
+- Utilises common openapi client for communication with REANA-Job-Controller.
+- Changes license to MIT.
+
+## 0.3.1 (2018-09-07)
+
+- Pins REANA-Commons and Celery dependencies.
+
+## 0.3.0 (2018-08-10)
+
+- Tracks workflow progress.
+
+## 0.2.0 (2018-04-19)
+
+- Upgrades Yadage workflow ecosystem versions (Yadage 0.13, Packtivity 0.10).
+- Adds logs to the workflow models in the database.
+
+## 0.1.0 (2018-01-30)
+
+- Initial public release.
+

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-workflow-engine-yadage/issues>`_.
+1. Search for [already reported problems](https://github.com/reanahub/reana-workflow-engine-yadage/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

@@ -7,7 +7,6 @@
 include *.in
 include *.json
 include *.md
-include *.rst
 include *.sh
 include *.txt
 include *.yaml
@@ -19,7 +18,7 @@ include pytest.ini
 exclude .readthedocs.yaml
 recursive-include docs *.py
 recursive-include docs *.png
-recursive-include docs *.rst
+recursive-include docs *.md
 recursive-include docs *.txt
 recursive-include tests *.py
 recursive-include reana_workflow_engine_yadage *.json

README.md

@@ -0,0 +1,36 @@
+# REANA-Workflow-Engine-Yadage
+
+[![image](https://github.com/reanahub/reana-workflow-engine-yadage/workflows/CI/badge.svg)](https://github.com/reanahub/reana-workflow-engine-yadage/actions)
+[![image](https://readthedocs.org/projects/reana-workflow-engine-yadage/badge/?version=latest)](https://reana-workflow-engine-yadage.readthedocs.io/en/latest/?badge=latest)
+[![image](https://codecov.io/gh/reanahub/reana-workflow-engine-yadage/branch/master/graph/badge.svg)](https://codecov.io/gh/reanahub/reana-workflow-engine-yadage)
+[![image](https://img.shields.io/badge/discourse-forum-blue.svg)](https://forum.reana.io)
+[![image](https://img.shields.io/github/license/reanahub/reana-workflow-engine-yadage.svg)](https://github.com/reanahub/reana-workflow-engine-yadage/blob/master/LICENSE)
+[![image](https://img.shields.io/badge/code%20style-black-000000.svg)](https://github.com/psf/black)
+
+## About
+
+REANA-Workflow-Engine-Yadage is a component of the [REANA](http://www.reana.io/) reusable
+and reproducible research data analysis platform. It takes care of instantiating,
+executing and managing [Yadage](https://github.com/diana-hep/yadage) based computational
+workflows.
+
+## Features
+
+- start Yadage workflows
+- control workflow steps
+
+## 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-Workflow-Engine-Yadage releases](https://reana-workflow-engine-yadage.readthedocs.io/en/latest#changes)
+- [REANA-Workflow-Engine-Yadage docker images](https://hub.docker.com/r/reanahub/reana-workflow-engine-yadage)
+- [REANA-Workflow-Engine-Yadage developer documentation](https://reana-workflow-engine-yadage.readthedocs.io/)
+- [REANA-Workflow-Engine-Yadage known issues](https://github.com/reanahub/reana-workflow-engine-yadage/issues)
+- [REANA-Workflow-Engine-Yadage source code](https://github.com/reanahub/reana-workflow-engine-yadage)