refactor(docs): move from reST to Markdown (#198)

AUTHORS.md

@@ -0,0 +1,17 @@
+# 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)
+- [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)

CHANGELOG.md

@@ -0,0 +1,104 @@
+# Changelog
+
+## 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.
+
+## 0.8.1 (2022-02-07)
+
+- Adds support for specifying `kubernetes_job_timeout` for Kubernetes compute backend jobs.
+- Fixes workflow stuck in pending status due to early engine fail.
+
+## 0.8.0 (2021-11-22)
+
+- Adds support for custom workspace paths.
+
+## 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 and using central REANA-Commons job command serialisation.
+- Changes status `succeeded` to `finished` to use central REANA nomenclature.
+
+## 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.
+
+## 0.7.0 (2020-10-20)
+
+- Adds possibility to execute workflow from specified step.
+- Adds option to specify unpacked Docker images as workflow step requirement.
+- Adds option to specify Kubernetes UID for jobs.
+- Adds support for VOMS proxy as a new authentication method.
+- Adds pinning of all Python dependencies allowing to easily rebuild component images at later times.
+- 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 Serial workflow jobs.
+- Allows partial workflow execution until step specified by the 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.
+- Replaces `api_client` module with centralised one from REANA-Commons.
+- Introduces CVMFS mounts in job specifications.
+- Makes docker image slimmer by using `python:3.6-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.
+
+## 0.3.2 (2018-09-25)
+
+- Modifies OS related commands for CephFS compatibility.
+
+## 0.3.1 (2018-09-07)
+
+- Adds parameter passing to workflow steps.
+- Adds user guide and getting started sections to the documentation.
+
+## 0.3.0 (2018-08-10)
+
+- Initial public release.
+- Executes serial workflows.
+- Tracks progress of workflow runs.
+- Caches job results by default.

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-serial/issues>`_.
+1. Search for [already reported problems](https://github.com/reanahub/reana-workflow-engine-serial/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 *.txt
 include *.yaml
@@ -21,6 +20,6 @@ recursive-include reana_workflow_engine_serial *.py
 recursive-include reana_workflow_engine_serial *.json
 recursive-include docs *.py
 recursive-include docs *.png
-recursive-include docs *.rst
+recursive-include docs *.md
 recursive-include docs *.txt
 recursive-include tests *.py

README.md

@@ -0,0 +1,35 @@
+# REANA-Workflow-Engine-Serial
+
+[![image](https://github.com/reanahub/reana-workflow-engine-serial/workflows/CI/badge.svg)](https://github.com/reanahub/reana-workflow-engine-serial/actions)
+[![image](https://readthedocs.org/projects/reana-workflow-engine-serial/badge/?version=latest)](https://reana-workflow-engine-serial.readthedocs.io/en/latest/?badge=latest)
+[![image](https://codecov.io/gh/reanahub/reana-workflow-engine-serial/branch/master/graph/badge.svg)](https://codecov.io/gh/reanahub/reana-workflow-engine-serial)
+[![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-serial.svg)](https://github.com/reanahub/reana-workflow-engine-serial/blob/master/LICENSE)
+[![image](https://img.shields.io/badge/code%20style-black-000000.svg)](https://github.com/psf/black)
+
+## About
+
+REANA-Workflow-Engine-Serial 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 simple sequential computational workflows.
+
+## Features
+
+- Run sequential workflows consisting of Bash commands.
+- Cache workflow steps by default to shorten computation time.
+
+## 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-Serial releases](https://reana-workflow-engine-serial.readthedocs.io/en/latest#changes)
+- [REANA-Workflow-Engine-Serial docker images](https://hub.docker.com/r/reanahub/reana-workflow-engine-serial)
+- [REANA-Workflow-Engine-Serial developer documentation](https://reana-workflow-engine-serial.readthedocs.io/)
+- [REANA-Workflow-Engine-Serial known issues](https://github.com/reanahub/reana-workflow-engine-serial/issues)
+- [REANA-Workflow-Engine-Serial source code](https://github.com/reanahub/reana-workflow-engine-serial)