refactor(docs): move from reST to Markdown (#82)

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

AUTHORS.md

@@ -0,0 +1,11 @@
+# Authors
+
+The list of contributors in alphabetical order:
+
+- [Agisilaos Kounelis](https://orcid.org/0000-0001-9312-3189)
+- [Camila Diaz](https://orcid.org/0000-0001-5543-797X)
+- [Marco Donadoni](https://orcid.org/0000-0003-2922-5505)
+- [Marco Vidal](https://orcid.org/0000-0002-9363-4971)
+- [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 +1,37 @@
+# Changelog
+
+## 0.9.2 (2023-12-12)
+
+- Adds automated container image building for amd64 architecture.
+- Adds metadata labels to Dockerfile.
+- Fixes creation of image thumbnails for output files in Snakemake HTML execution reports.
+- Fixes container image building on the arm64 architecture.
+
+## 0.9.1 (2023-09-27)
+
+- Changes remote storage file support to use XRootD 5.6.0.
+- Fixes the reported total number of jobs for restarted workflows by excluding cached jobs that were simply reused from previous runs in the workspace and not really executed by Snakemake.
+- Fixes an issue where workflows could get stuck waiting for already-finished jobs.
+- 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 XRootD remote file locations in workflow specification definitions.
+- Adds support for Kerberos authentication for workflow orchestration.
+- Adds support for Rucio authentication for workflow jobs.
+- Changes global setting of maximum number of parallel jobs to 300.
+- Changes the base image of the component to Ubuntu 20.04 LTS and reduces final Docker image size by removing build-time dependencies.
+- Fixes progress reporting for failed workflow jobs.
+
+## 0.8.1 (2022-02-07)
+
+- Adds support for specifying `kubernetes_job_timeout` for Kubernetes compute backend jobs.
+- Adds polling job-controller to determine job statuses instead of checking files.
+
+## 0.8.0 (2021-11-22)
+
+- Adds initial REANA Snakemake executor implementation.
+- Adds support for snakemake reports generation.
+- Adds support for REANA custom resources.
+- Adds support for parallel job execution.

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-snakemake/issues>`_.
+1. Search for [already reported problems](https://github.com/reanahub/reana-workflow-engine-snakemake/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
@@ -20,7 +19,7 @@ exclude .readthedocs.yaml
 prune docs/_build
 recursive-include docs *.py
 recursive-include docs *.png
-recursive-include docs *.rst
+recursive-include docs *.md
 recursive-include docs *.txt
 recursive-include reana_workflow_engine_snakemake *.json
 recursive-include scripts *.sh

README.md

@@ -0,0 +1,36 @@
+# REANA-Workflow-Engine-Snakemake
+
+[![image](https://github.com/reanahub/reana-workflow-engine-snakemake/workflows/CI/badge.svg)](https://github.com/reanahub/reana-workflow-engine-snakemake/actions)
+[![image](https://readthedocs.org/projects/reana-workflow-engine-snakemake/badge/?version=latest)](https://reana-workflow-engine-snakemake.readthedocs.io/en/latest/?badge=latest)
+[![image](https://codecov.io/gh/reanahub/reana-workflow-engine-snakemake/branch/master/graph/badge.svg)](https://codecov.io/gh/reanahub/reana-workflow-engine-snakemake)
+[![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-snakemake.svg)](https://github.com/reanahub/reana-workflow-engine-snakemake/blob/master/LICENSE)
+[![image](https://img.shields.io/badge/code%20style-black-000000.svg)](https://github.com/psf/black)
+
+## About
+
+REANA-Workflow-Engine-Snakemake 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 [Snakemake](https://snakemake.github.io/) based
+computational workflows.
+
+## Features
+
+- start Snakemake 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-Snakemake releases](https://reana-workflow-engine-snakemake.readthedocs.io/en/latest#changes)
+- [REANA-Workflow-Engine-Snakemake docker images](https://hub.docker.com/r/reanahub/reana-workflow-engine-snakemake)
+- [REANA-Workflow-Engine-Snakemake developer documentation](https://reana-workflow-engine-snakemake.readthedocs.io/)
+- [REANA-Workflow-Engine-Snakemake known issues](https://github.com/reanahub/reana-workflow-engine-snakemake/issues)
+- [REANA-Workflow-Engine-Snakemake source code](https://github.com/reanahub/reana-workflow-engine-snakemake)

docs/conf.py

@@ -34,6 +34,7 @@
 # extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
 # ones.
 extensions = [
+    "myst_parser",
     "sphinx.ext.autodoc",
     "sphinx.ext.coverage",
     "sphinx.ext.doctest",
@@ -52,14 +53,17 @@
 # You can specify multiple suffix as a list of string:
 #
 # source_suffix = ['.rst', '.md']
-source_suffix = ".rst"
+source_suffix = [".rst", ".md"]
+
+# Allow using ::: in Markdown files
+myst_enable_extensions = ["colon_fence"]
 
 # The master toctree document.
 master_doc = "index"
 
 # General information about the project.
 project = "reana"
-copyright = "2017-2023, info@reana.io"
+copyright = "2017-2024, info@reana.io"
 author = "info@reana.io"
 
 # The version info for the project you're documenting, acts as replacement for

docs/index.md

@@ -0,0 +1,30 @@
+```{include} ../README.md
+:end-before: "## About"
+```
+
+```{include} ../README.md
+:start-after: "## About"
+:end-before: "## Useful links"
+```
+
+```{include} ../CHANGELOG.md
+:heading-offset: 1
+```
+
+```{include} ../CONTRIBUTING.md
+:heading-offset: 1
+```
+
+## License
+
+```{eval-rst}
+.. include:: ../LICENSE
+```
+
+In applying this license, CERN does not waive the privileges and immunities
+granted to it by virtue of its status as an Intergovernmental Organization or
+submit itself to any jurisdiction.
+
+```{include} ../AUTHORS.md
+:heading-offset: 1
+```

setup.py

@@ -15,8 +15,8 @@
 
 from setuptools import find_packages, setup
 
-readme = open("README.rst").read()
-history = open("CHANGES.rst").read()
+readme = open("README.md").read()
+history = open("CHANGELOG.md").read()
 
 tests_require = [
     "pytest-reana>=0.9.2,<0.10.0",
@@ -29,6 +29,7 @@
         "Flask-DebugToolbar",
     ],
     "docs": [
+        "myst-parser",
         "Sphinx>=1.5.1",
         "sphinx-rtd-theme>=0.1.9",
     ],
@@ -67,6 +68,7 @@
     version=version,
     description=__doc__,
     long_description=readme + "\n\n" + history,
+    long_description_content_type="text/markdown",
     author="REANA",
     author_email="info@reana.io",
     url="https://github.com/reanahub/reana-workflow-engine-snakemake",