From 3cf272f657cc3e0b329c6d159f5e476f06000f93 Mon Sep 17 00:00:00 2001 From: Marco Donadoni Date: Wed, 7 Feb 2024 16:24:30 +0100 Subject: [PATCH] refactor(docs): move from reST to Markdown (#263) Convert docs from reStructuredText to Markdown so that the changelog file is compatible with Release Please. --- AUTHORS.md | 19 ++ AUTHORS.rst | 20 -- CHANGELOG.md | 113 +++++++++++ CHANGES.rst | 139 -------------- CONTRIBUTING.rst => CONTRIBUTING.md | 12 +- MANIFEST.in | 3 +- README.md | 140 ++++++++++++++ README.rst | 284 ---------------------------- docs/conf.py | 8 +- docs/index.md | 30 +++ docs/index.rst | 27 --- setup.py | 7 +- 12 files changed, 318 insertions(+), 484 deletions(-) create mode 100644 AUTHORS.md delete mode 100644 AUTHORS.rst delete mode 100644 CHANGES.rst rename CONTRIBUTING.rst => CONTRIBUTING.md (73%) create mode 100644 README.md delete mode 100644 README.rst create mode 100644 docs/index.md delete mode 100644 docs/index.rst diff --git a/AUTHORS.md b/AUTHORS.md new file mode 100644 index 0000000..9993be5 --- /dev/null +++ b/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) +- [Anton Khodak](https://orcid.org/0000-0003-3263-4553) +- [Camila Diaz](https://orcid.org/0000-0001-5543-797X) +- [Dan Leehr](https://orcid.org/0000-0003-3221-9579) +- [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) +- [Marco Donadoni](https://orcid.org/0000-0003-2922-5505) +- [Marco Vidal](https://orcid.org/0000-0002-9363-4971) +- [Michael R. Crusoe](https://orcid.org/0000-0002-2961-9670) +- [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) diff --git a/AUTHORS.rst b/AUTHORS.rst deleted file mode 100644 index 12466fa..0000000 --- a/AUTHORS.rst +++ /dev/null @@ -1,20 +0,0 @@ -Authors -======= - -The list of contributors in alphabetical order: - -- `Adelina Lintuluoto `_ -- `Agisilaos Kounelis `_ -- `Audrius Mecionis `_ -- `Anton Khodak `_ -- `Camila Diaz `_ -- `Dan Leehr `_ -- `Daniel Prelipcean `_ -- `Diego Rodriguez `_ -- `Dinos Kousidis `_ -- `Marco Donadoni `_ -- `Marco Vidal `_ -- `Michael R. Crusoe `_ -- `Rokas Maciulaitis `_ -- `Sinclert Pérez `_ -- `Tibor Simko `_ diff --git a/CHANGELOG.md b/CHANGELOG.md index e69de29..6b09e28 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -0,0 +1,113 @@ +# 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. +- Fixes status reporting for failed jobs that were incorrectly considered successful. + +## 0.8.1 (2022-02-07) + +- Adds support for specifying `kubernetes_job_timeout` for Kubernetes compute backend jobs. + +## 0.8.0 (2021-11-22) + +- Adds support for custom workspace paths. +- Adds supoort for `cwltool` version `3.1.20210628163208` + +## 0.7.6 (2021-07-05) + +- Changes internal dependencies to remove click. + +## 0.7.5 (2021-04-28) + +- Adds support for specifying `kubernetes_memory_limit` for Kubernetes compute backend jobs. + +## 0.7.4 (2021-03-23) + +- Changes job command serialisation using central REANA-Commons job command serialiser. + +## 0.7.3 (2021-03-17) + +- Changes workflow engine instantiation to use central REANA-Commons factory. +- 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. +- Fixes restarting of CWL workflows. + +## 0.7.0 (2020-10-20) + +- Adds pinning of all Python dependencies allowing to easily rebuild component images at later times. +- Adds option to specify unpacked Docker images as workflow step requirement. +- Adds support for handling new workflow operational options. +- Adds support for VOMS proxy as a new authentication method. +- 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 CWL workflow jobs. +- Upgrades cwltool to 1.0.20191022103248. +- 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. +- Sets default file mode creation mask to 002 so that workflows are able to + write to shared directories for any user identity under which the workflow + processes may be running. +- Makes docker image slimmer by using `python:2.7-slim`. +- Centralises log level and log format configuration. +- Upgrades cwltool to 1.0.20181118133959. + +## 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) + +- Upgrades to latest `cwltool` (`1.0.20180912090223`). + +## 0.3.1 (2018-09-07) + +- Pins REANA-Commons dependency. + +## 0.3.0 (2018-08-10) + +- Tracks progress of workflow runs. + +## 0.2.0 (2018-04-19) + +- Initial public release. + diff --git a/CHANGES.rst b/CHANGES.rst deleted file mode 100644 index 9c46a4a..0000000 --- a/CHANGES.rst +++ /dev/null @@ -1,139 +0,0 @@ -Changes -======= - -Version 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. - -Version 0.9.1 (2023-09-27) --------------------------- - -- Fixes container image names to be Podman-compatible. - -Version 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. -- Fixes status reporting for failed jobs that were incorrectly considered successful. - -Version 0.8.1 (2022-02-07) --------------------------- - -- Adds support for specifying ``kubernetes_job_timeout`` for Kubernetes compute backend jobs. - -Version 0.8.0 (2021-11-22) --------------------------- - -- Adds support for custom workspace paths. -- Adds supoort for ``cwltool`` version ``3.1.20210628163208`` - -Version 0.7.6 (2021-07-05) --------------------------- - -- Changes internal dependencies to remove click. - -Version 0.7.5 (2021-04-28) --------------------------- - -- Adds support for specifying ``kubernetes_memory_limit`` for Kubernetes compute backend jobs. - -Version 0.7.4 (2021-03-23) --------------------------- - -- Changes job command serialisation using central REANA-Commons job command serialiser. - -Version 0.7.3 (2021-03-17) --------------------------- - -- Changes workflow engine instantiation to use central REANA-Commons factory. -- Changes status ``succeeded`` to ``finished`` to use central REANA nomenclature. - -Version 0.7.2 (2021-02-03) --------------------------- - -- Fixes minor code warnings. -- Changes CI system to include Python flake8 and Dockerfile hadolint checkers. - -Version 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 CWL workflows. - -Version 0.7.0 (2020-10-20) --------------------------- - -- Adds pinning of all Python dependencies allowing to easily rebuild component images at later times. -- Adds option to specify unpacked Docker images as workflow step requirement. -- Adds support for handling new workflow operational options. -- Adds support for VOMS proxy as a new authentication method. -- Changes base image to use Python 3.8. -- Changes code formatting to respect ``black`` coding style. -- Changes documentation to single-page layout. - -Version 0.6.1 (2020-05-25) --------------------------- - -- Upgrades REANA-Commons package using latest Kubernetes Python client version. - -Version 0.6.0 (2019-12-20) --------------------------- - -- Allows to specify compute backend (HTCondor, Kubernetes or Slurm) and - Kerberos authentication requirement for CWL workflow jobs. -- Upgrades cwltool to 1.0.20191022103248. -- Moves workflow engine to the same Kubernetes pod with the REANA-Job-Controller - (sidecar pattern). - -Version 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. -- Sets default file mode creation mask to 002 so that workflows are able to - write to shared directories for any user identity under which the workflow - processes may be running. -- Makes docker image slimmer by using ``python:2.7-slim``. -- Centralises log level and log format configuration. -- Upgrades cwltool to 1.0.20181118133959. - -Version 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. - -Version 0.3.2 (2018-09-25) --------------------------- - -- Upgrades to latest ``cwltool`` (``1.0.20180912090223``). - -Version 0.3.1 (2018-09-07) --------------------------- - -- Pins REANA-Commons dependency. - -Version 0.3.0 (2018-08-10) --------------------------- - -- Tracks progress of workflow runs. - -Version 0.2.0 (2018-04-19) --------------------------- - -- Initial public release. - -.. admonition:: Please beware - - Please note that REANA is in an early alpha stage of its development. The - developer preview releases are meant for early adopters and testers. Please - don't rely on released versions for any production purposes yet. diff --git a/CONTRIBUTING.rst b/CONTRIBUTING.md similarity index 73% rename from CONTRIBUTING.rst rename to CONTRIBUTING.md index 485b0f6..2f64450 100644 --- a/CONTRIBUTING.rst +++ b/CONTRIBUTING.md @@ -1,11 +1,9 @@ -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 - `_. +1. Search for [already reported problems](https://github.com/reanahub/reana-workflow-engine-cwl/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**. @@ -13,8 +11,8 @@ a demonstrable problem that is caused by the REANA code, please: 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. diff --git a/MANIFEST.in b/MANIFEST.in index 154f492..0515a3e 100644 --- a/MANIFEST.in +++ b/MANIFEST.in @@ -6,7 +6,6 @@ include *.json include *.md -include *.rst include *.sh include *.txt include *.yaml @@ -23,6 +22,6 @@ prune docs/_build recursive-include badges *.json recursive-include docs *.py recursive-include docs *.png -recursive-include docs *.rst +recursive-include docs *.md recursive-include tests *.py global-exclude *.py[co] .DS_Store diff --git a/README.md b/README.md new file mode 100644 index 0000000..aaafd65 --- /dev/null +++ b/README.md @@ -0,0 +1,140 @@ +# REANA-Workflow-Engine-CWL + +[![image](https://github.com/reanahub/reana-workflow-engine-cwl/workflows/CI/badge.svg)](https://github.com/reanahub/reana-workflow-engine-cwl/actions) +[![image](https://readthedocs.org/projects/reana-workflow-engine-cwl/badge/?version=latest)](https://reana-workflow-engine-cwl.readthedocs.io/en/latest/?badge=latest) +[![image](https://codecov.io/gh/reanahub/reana-workflow-engine-cwl/branch/master/graph/badge.svg)](https://codecov.io/gh/reanahub/reana-workflow-engine-cwl) +[![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-cwl.svg)](https://github.com/reanahub/reana-workflow-engine-cwl/blob/master/LICENSE) +[![image](https://img.shields.io/badge/code%20style-black-000000.svg)](https://github.com/psf/black) + +## About + +REANA-Workflow-Engine-CWL 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 [Common Workflow Language (CWL)](http://www.commonwl.org/) based +computational workflows. + +## Features + +- start Common Workflow Language (CWL) based 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-CWL releases](https://reana-workflow-engine-cwl.readthedocs.io/en/latest#changes) +- [REANA-Workflow-Engine-CWL docker images](https://hub.docker.com/r/reanahub/reana-workflow-engine-cwl) +- [REANA-Workflow-Engine-CWL developer documentation](https://reana-workflow-engine-cwl.readthedocs.io/) +- [REANA-Workflow-Engine-CWL known issues](https://github.com/reanahub/reana-workflow-engine-cwl/issues) +- [REANA-Workflow-Engine-CWL source code](https://github.com/reanahub/reana-workflow-engine-cwl) + +## CWL conformance tests + +REANA 0.8.0 tested on 2022-01-11 + +### CWL v1.0 + +[List of failed tests](https://docs.reana.io/running-workflows/supported-systems/cwl/#cwl-v10-specification-conformance-results) + +#### Classes + +[![image](https://badgen.net/https/raw.githubusercontent.com/reanahub/reana-workflow-engine-cwl/master/badges/v1.0/command_line_tool.json?icon=commonwl)](https://github.com/reanahub/reana-workflow-engine-cwl) +[![image](https://badgen.net/https/raw.githubusercontent.com/reanahub/reana-workflow-engine-cwl/master/badges/v1.0/expression_tool.json?icon=commonwl)](https://github.com/reanahub/reana-workflow-engine-cwl) +[![image](https://badgen.net/https/raw.githubusercontent.com/reanahub/reana-workflow-engine-cwl/master/badges/v1.0/workflow.json?icon=commonwl)](https://github.com/reanahub/reana-workflow-engine-cwl) + +#### Required features + +[![image](https://badgen.net/https/raw.githubusercontent.com/reanahub/reana-workflow-engine-cwl/master/badges/v1.0/required.json?icon=commonwl)](https://github.com/reanahub/reana-workflow-engine-cwl) + +#### Optional features + +[![image](https://badgen.net/https/raw.githubusercontent.com/reanahub/reana-workflow-engine-cwl/master/badges/v1.0/docker.json?icon=commonwl)](https://github.com/reanahub/reana-workflow-engine-cwl) +[![image](https://badgen.net/https/raw.githubusercontent.com/reanahub/reana-workflow-engine-cwl/master/badges/v1.0/env_var.json?icon=commonwl)](https://github.com/reanahub/reana-workflow-engine-cwl) +[![image](https://badgen.net/https/raw.githubusercontent.com/reanahub/reana-workflow-engine-cwl/master/badges/v1.0/initial_work_dir.json?icon=commonwl)](https://github.com/reanahub/reana-workflow-engine-cwl) +[![image](https://badgen.net/https/raw.githubusercontent.com/reanahub/reana-workflow-engine-cwl/master/badges/v1.0/inline_javascript.json?icon=commonwl)](https://github.com/reanahub/reana-workflow-engine-cwl) +[![image](https://badgen.net/https/raw.githubusercontent.com/reanahub/reana-workflow-engine-cwl/master/badges/v1.0/multiple_input.json?icon=commonwl)](https://github.com/reanahub/reana-workflow-engine-cwl) +[![image](https://badgen.net/https/raw.githubusercontent.com/reanahub/reana-workflow-engine-cwl/master/badges/v1.0/resource.json?icon=commonwl)](https://github.com/reanahub/reana-workflow-engine-cwl) +[![image](https://badgen.net/https/raw.githubusercontent.com/reanahub/reana-workflow-engine-cwl/master/badges/v1.0/scatter.json?icon=commonwl)](https://github.com/reanahub/reana-workflow-engine-cwl) +[![image](https://badgen.net/https/raw.githubusercontent.com/reanahub/reana-workflow-engine-cwl/master/badges/v1.0/schema_def.json?icon=commonwl)](https://github.com/reanahub/reana-workflow-engine-cwl) +[![image](https://badgen.net/https/raw.githubusercontent.com/reanahub/reana-workflow-engine-cwl/master/badges/v1.0/shell_command.json?icon=commonwl)](https://github.com/reanahub/reana-workflow-engine-cwl) +[![image](https://badgen.net/https/raw.githubusercontent.com/reanahub/reana-workflow-engine-cwl/master/badges/v1.0/step_input_expression.json?icon=commonwl)](https://github.com/reanahub/reana-workflow-engine-cwl) +[![image](https://badgen.net/https/raw.githubusercontent.com/reanahub/reana-workflow-engine-cwl/master/badges/v1.0/step_input.json?icon=commonwl)](https://github.com/reanahub/reana-workflow-engine-cwl) +[![image](https://badgen.net/https/raw.githubusercontent.com/reanahub/reana-workflow-engine-cwl/master/badges/v1.0/subworkflow.json?icon=commonwl)](https://github.com/reanahub/reana-workflow-engine-cwl) + +### CWL v1.1 + +[List of failed tests](https://docs.reana.io/running-workflows/supported-systems/cwl/#cwl-v11-specification-conformance-results) + +#### Classes + +[![image](https://badgen.net/https/raw.githubusercontent.com/reanahub/reana-workflow-engine-cwl/master/badges/v1.1/command_line_tool.json?icon=commonwl)](https://github.com/reanahub/reana-workflow-engine-cwl) +[![image](https://badgen.net/https/raw.githubusercontent.com/reanahub/reana-workflow-engine-cwl/master/badges/v1.1/expression_tool.json?icon=commonwl)](https://github.com/reanahub/reana-workflow-engine-cwl) +[![image](https://badgen.net/https/raw.githubusercontent.com/reanahub/reana-workflow-engine-cwl/master/badges/v1.1/workflow.json?icon=commonwl)](https://github.com/reanahub/reana-workflow-engine-cwl) + +#### Required features + +[![image](https://badgen.net/https/raw.githubusercontent.com/reanahub/reana-workflow-engine-cwl/master/badges/v1.1/required.json?icon=commonwl)](https://github.com/reanahub/reana-workflow-engine-cwl) + +#### Optional features + +[![image](https://badgen.net/https/raw.githubusercontent.com/reanahub/reana-workflow-engine-cwl/master/badges/v1.1/docker.json?icon=commonwl)](https://github.com/reanahub/reana-workflow-engine-cwl) +[![image](https://badgen.net/https/raw.githubusercontent.com/reanahub/reana-workflow-engine-cwl/master/badges/v1.1/env_var.json?icon=commonwl)](https://github.com/reanahub/reana-workflow-engine-cwl) +[![image](https://badgen.net/https/raw.githubusercontent.com/reanahub/reana-workflow-engine-cwl/master/badges/v1.1/format_checking.json?icon=commonwl)](https://github.com/reanahub/reana-workflow-engine-cwl) +[![image](https://badgen.net/https/raw.githubusercontent.com/reanahub/reana-workflow-engine-cwl/master/badges/v1.1/initial_work_dir.json?icon=commonwl)](https://github.com/reanahub/reana-workflow-engine-cwl) +[![image](https://badgen.net/https/raw.githubusercontent.com/reanahub/reana-workflow-engine-cwl/master/badges/v1.1/inline_javascript.json?icon=commonwl)](https://github.com/reanahub/reana-workflow-engine-cwl) +[![image](https://badgen.net/https/raw.githubusercontent.com/reanahub/reana-workflow-engine-cwl/master/badges/v1.1/inplace_update.json?icon=commonwl)](https://github.com/reanahub/reana-workflow-engine-cwl) +[![image](https://badgen.net/https/raw.githubusercontent.com/reanahub/reana-workflow-engine-cwl/master/badges/v1.1/input_object_requirements.json?icon=commonwl)](https://github.com/reanahub/reana-workflow-engine-cwl) +[![image](https://badgen.net/https/raw.githubusercontent.com/reanahub/reana-workflow-engine-cwl/master/badges/v1.1/multiple_input.json?icon=commonwl)](https://github.com/reanahub/reana-workflow-engine-cwl) +[![image](https://badgen.net/https/raw.githubusercontent.com/reanahub/reana-workflow-engine-cwl/master/badges/v1.1/networkaccess.json?icon=commonwl)](https://github.com/reanahub/reana-workflow-engine-cwl) +[![image](https://badgen.net/https/raw.githubusercontent.com/reanahub/reana-workflow-engine-cwl/master/badges/v1.1/resource.json?icon=commonwl)](https://github.com/reanahub/reana-workflow-engine-cwl) +[![image](https://badgen.net/https/raw.githubusercontent.com/reanahub/reana-workflow-engine-cwl/master/badges/v1.1/scatter.json?icon=commonwl)](https://github.com/reanahub/reana-workflow-engine-cwl) +[![image](https://badgen.net/https/raw.githubusercontent.com/reanahub/reana-workflow-engine-cwl/master/badges/v1.1/schema_def.json?icon=commonwl)](https://github.com/reanahub/reana-workflow-engine-cwl) +[![image](https://badgen.net/https/raw.githubusercontent.com/reanahub/reana-workflow-engine-cwl/master/badges/v1.1/shell_command.json?icon=commonwl)](https://github.com/reanahub/reana-workflow-engine-cwl) +[![image](https://badgen.net/https/raw.githubusercontent.com/reanahub/reana-workflow-engine-cwl/master/badges/v1.1/step_input_expression.json?icon=commonwl)](https://github.com/reanahub/reana-workflow-engine-cwl) +[![image](https://badgen.net/https/raw.githubusercontent.com/reanahub/reana-workflow-engine-cwl/master/badges/v1.1/step_input.json?icon=commonwl)](https://github.com/reanahub/reana-workflow-engine-cwl) +[![image](https://badgen.net/https/raw.githubusercontent.com/reanahub/reana-workflow-engine-cwl/master/badges/v1.1/subworkflow.json?icon=commonwl)](https://github.com/reanahub/reana-workflow-engine-cwl) +[![image](https://badgen.net/https/raw.githubusercontent.com/reanahub/reana-workflow-engine-cwl/master/badges/v1.1/timelimit.json?icon=commonwl)](https://github.com/reanahub/reana-workflow-engine-cwl) + +### CWL v1.2 + +[List of failed tests](https://docs.reana.io/running-workflows/supported-systems/cwl/#cwl-v12-specification-conformance-results) + +#### Classes + +[![image](https://badgen.net/https/raw.githubusercontent.com/reanahub/reana-workflow-engine-cwl/master/badges/v1.2/command_line_tool.json?icon=commonwl)](https://github.com/reanahub/reana-workflow-engine-cwl) +[![image](https://badgen.net/https/raw.githubusercontent.com/reanahub/reana-workflow-engine-cwl/master/badges/v1.2/expression_tool.json?icon=commonwl)](https://github.com/reanahub/reana-workflow-engine-cwl) +[![image](https://badgen.net/https/raw.githubusercontent.com/reanahub/reana-workflow-engine-cwl/master/badges/v1.2/workflow.json?icon=commonwl)](https://github.com/reanahub/reana-workflow-engine-cwl) + +#### Required features + +[![image](https://badgen.net/https/raw.githubusercontent.com/reanahub/reana-workflow-engine-cwl/master/badges/v1.2/required.json?icon=commonwl)](https://github.com/reanahub/reana-workflow-engine-cwl) + +#### Optional features + +[![image](https://badgen.net/https/raw.githubusercontent.com/reanahub/reana-workflow-engine-cwl/master/badges/v1.2/conditional.json?icon=commonwl)](https://github.com/reanahub/reana-workflow-engine-cwl) +[![image](https://badgen.net/https/raw.githubusercontent.com/reanahub/reana-workflow-engine-cwl/master/badges/v1.2/docker.json?icon=commonwl)](https://github.com/reanahub/reana-workflow-engine-cwl) +[![image](https://badgen.net/https/raw.githubusercontent.com/reanahub/reana-workflow-engine-cwl/master/badges/v1.2/env_var.json?icon=commonwl)](https://github.com/reanahub/reana-workflow-engine-cwl) +[![image](https://badgen.net/https/raw.githubusercontent.com/reanahub/reana-workflow-engine-cwl/master/badges/v1.2/format_checking.json?icon=commonwl)](https://github.com/reanahub/reana-workflow-engine-cwl) +[![image](https://badgen.net/https/raw.githubusercontent.com/reanahub/reana-workflow-engine-cwl/master/badges/v1.2/initial_work_dir.json?icon=commonwl)](https://github.com/reanahub/reana-workflow-engine-cwl) +[![image](https://badgen.net/https/raw.githubusercontent.com/reanahub/reana-workflow-engine-cwl/master/badges/v1.2/inline_javascript.json?icon=commonwl)](https://github.com/reanahub/reana-workflow-engine-cwl) +[![image](https://badgen.net/https/raw.githubusercontent.com/reanahub/reana-workflow-engine-cwl/master/badges/v1.2/inplace_update.json?icon=commonwl)](https://github.com/reanahub/reana-workflow-engine-cwl) +[![image](https://badgen.net/https/raw.githubusercontent.com/reanahub/reana-workflow-engine-cwl/master/badges/v1.2/input_object_requirements.json?icon=commonwl)](https://github.com/reanahub/reana-workflow-engine-cwl) +[![image](https://badgen.net/https/raw.githubusercontent.com/reanahub/reana-workflow-engine-cwl/master/badges/v1.2/multiple_input.json?icon=commonwl)](https://github.com/reanahub/reana-workflow-engine-cwl) +[![image](https://badgen.net/https/raw.githubusercontent.com/reanahub/reana-workflow-engine-cwl/master/badges/v1.2/multiple.json?icon=commonwl)](https://github.com/reanahub/reana-workflow-engine-cwl) +[![image](https://badgen.net/https/raw.githubusercontent.com/reanahub/reana-workflow-engine-cwl/master/badges/v1.2/networkaccess.json?icon=commonwl)](https://github.com/reanahub/reana-workflow-engine-cwl) +[![image](https://badgen.net/https/raw.githubusercontent.com/reanahub/reana-workflow-engine-cwl/master/badges/v1.2/resource.json?icon=commonwl)](https://github.com/reanahub/reana-workflow-engine-cwl) +[![image](https://badgen.net/https/raw.githubusercontent.com/reanahub/reana-workflow-engine-cwl/master/badges/v1.2/scatter.json?icon=commonwl)](https://github.com/reanahub/reana-workflow-engine-cwl) +[![image](https://badgen.net/https/raw.githubusercontent.com/reanahub/reana-workflow-engine-cwl/master/badges/v1.2/schema_def.json?icon=commonwl)](https://github.com/reanahub/reana-workflow-engine-cwl) +[![image](https://badgen.net/https/raw.githubusercontent.com/reanahub/reana-workflow-engine-cwl/master/badges/v1.2/secondary_files.json?icon=commonwl)](https://github.com/reanahub/reana-workflow-engine-cwl) +[![image](https://badgen.net/https/raw.githubusercontent.com/reanahub/reana-workflow-engine-cwl/master/badges/v1.2/shell_command.json?icon=commonwl)](https://github.com/reanahub/reana-workflow-engine-cwl) +[![image](https://badgen.net/https/raw.githubusercontent.com/reanahub/reana-workflow-engine-cwl/master/badges/v1.2/step_input_expression.json?icon=commonwl)](https://github.com/reanahub/reana-workflow-engine-cwl) +[![image](https://badgen.net/https/raw.githubusercontent.com/reanahub/reana-workflow-engine-cwl/master/badges/v1.2/step_input.json?icon=commonwl)](https://github.com/reanahub/reana-workflow-engine-cwl) +[![image](https://badgen.net/https/raw.githubusercontent.com/reanahub/reana-workflow-engine-cwl/master/badges/v1.2/subworkflow.json?icon=commonwl)](https://github.com/reanahub/reana-workflow-engine-cwl) +[![image](https://badgen.net/https/raw.githubusercontent.com/reanahub/reana-workflow-engine-cwl/master/badges/v1.2/timelimit.json?icon=commonwl)](https://github.com/reanahub/reana-workflow-engine-cwl) diff --git a/README.rst b/README.rst deleted file mode 100644 index 6a541a1..0000000 --- a/README.rst +++ /dev/null @@ -1,284 +0,0 @@ -######################### -REANA-Workflow-Engine-CWL -######################### - -.. image:: https://github.com/reanahub/reana-workflow-engine-cwl/workflows/CI/badge.svg - :target: https://github.com/reanahub/reana-workflow-engine-cwl/actions - -.. image:: https://readthedocs.org/projects/reana-workflow-engine-cwl/badge/?version=latest - :target: https://reana-workflow-engine-cwl.readthedocs.io/en/latest/?badge=latest - -.. image:: https://codecov.io/gh/reanahub/reana-workflow-engine-cwl/branch/master/graph/badge.svg - :target: https://codecov.io/gh/reanahub/reana-workflow-engine-cwl - -.. image:: https://badges.gitter.im/Join%20Chat.svg - :target: https://gitter.im/reanahub/reana?utm_source=badge&utm_medium=badge&utm_campaign=pr-badge - -.. image:: https://img.shields.io/github/license/reanahub/reana-workflow-engine-cwl.svg - :target: https://github.com/reanahub/reana-workflow-engine-cwl/blob/master/LICENSE - -.. image:: https://img.shields.io/badge/code%20style-black-000000.svg - :target: https://github.com/psf/black - -About -===== - -REANA-Workflow-Engine-CWL is a component of the `REANA `_ -reusable and reproducible research data analysis platform. It takes care of -instantiating, executing and managing `Common Workflow Language (CWL) -`_ based computational workflows. - -Features -======== - -- start Common Workflow Language (CWL) based workflows -- control workflow steps - -Usage -===== - -The detailed information on how to install and use REANA can be found in -`docs.reana.io `_. - -Useful links -============ - -- `REANA project home page `_ -- `REANA user documentation `_ -- `REANA user support forum `_ - -- `REANA-Workflow-Engine-CWL releases `_ -- `REANA-Workflow-Engine-CWL docker images `_ -- `REANA-Workflow-Engine-CWL developer documentation `_ -- `REANA-Workflow-Engine-CWL known issues `_ -- `REANA-Workflow-Engine-CWL source code `_ - -CWL conformance tests -============== - -REANA 0.8.0 tested on 2022-01-11 - -CWL v1.0 -######## - -`List of failed tests `_ - -Classes -******* - -.. image:: https://badgen.net/https/raw.githubusercontent.com/reanahub/reana-workflow-engine-cwl/master/badges/v1.0/command_line_tool.json?icon=commonwl - :target: https://github.com/reanahub/reana-workflow-engine-cwl - -.. image:: https://badgen.net/https/raw.githubusercontent.com/reanahub/reana-workflow-engine-cwl/master/badges/v1.0/expression_tool.json?icon=commonwl - :target: https://github.com/reanahub/reana-workflow-engine-cwl - -.. image:: https://badgen.net/https/raw.githubusercontent.com/reanahub/reana-workflow-engine-cwl/master/badges/v1.0/workflow.json?icon=commonwl - :target: https://github.com/reanahub/reana-workflow-engine-cwl - -Required features -***************** - -.. image:: https://badgen.net/https/raw.githubusercontent.com/reanahub/reana-workflow-engine-cwl/master/badges/v1.0/required.json?icon=commonwl - :target: https://github.com/reanahub/reana-workflow-engine-cwl - -Optional features -***************** - -.. image:: https://badgen.net/https/raw.githubusercontent.com/reanahub/reana-workflow-engine-cwl/master/badges/v1.0/docker.json?icon=commonwl - :target: https://github.com/reanahub/reana-workflow-engine-cwl - -.. image:: https://badgen.net/https/raw.githubusercontent.com/reanahub/reana-workflow-engine-cwl/master/badges/v1.0/env_var.json?icon=commonwl - :target: https://github.com/reanahub/reana-workflow-engine-cwl - -.. image:: https://badgen.net/https/raw.githubusercontent.com/reanahub/reana-workflow-engine-cwl/master/badges/v1.0/initial_work_dir.json?icon=commonwl - :target: https://github.com/reanahub/reana-workflow-engine-cwl - -.. image:: https://badgen.net/https/raw.githubusercontent.com/reanahub/reana-workflow-engine-cwl/master/badges/v1.0/inline_javascript.json?icon=commonwl - :target: https://github.com/reanahub/reana-workflow-engine-cwl - -.. image:: https://badgen.net/https/raw.githubusercontent.com/reanahub/reana-workflow-engine-cwl/master/badges/v1.0/multiple_input.json?icon=commonwl - :target: https://github.com/reanahub/reana-workflow-engine-cwl - -.. image:: https://badgen.net/https/raw.githubusercontent.com/reanahub/reana-workflow-engine-cwl/master/badges/v1.0/resource.json?icon=commonwl - :target: https://github.com/reanahub/reana-workflow-engine-cwl - -.. image:: https://badgen.net/https/raw.githubusercontent.com/reanahub/reana-workflow-engine-cwl/master/badges/v1.0/scatter.json?icon=commonwl - :target: https://github.com/reanahub/reana-workflow-engine-cwl - -.. image:: https://badgen.net/https/raw.githubusercontent.com/reanahub/reana-workflow-engine-cwl/master/badges/v1.0/schema_def.json?icon=commonwl - :target: https://github.com/reanahub/reana-workflow-engine-cwl - -.. image:: https://badgen.net/https/raw.githubusercontent.com/reanahub/reana-workflow-engine-cwl/master/badges/v1.0/shell_command.json?icon=commonwl - :target: https://github.com/reanahub/reana-workflow-engine-cwl - -.. image:: https://badgen.net/https/raw.githubusercontent.com/reanahub/reana-workflow-engine-cwl/master/badges/v1.0/step_input_expression.json?icon=commonwl - :target: https://github.com/reanahub/reana-workflow-engine-cwl - -.. image:: https://badgen.net/https/raw.githubusercontent.com/reanahub/reana-workflow-engine-cwl/master/badges/v1.0/step_input.json?icon=commonwl - :target: https://github.com/reanahub/reana-workflow-engine-cwl - -.. image:: https://badgen.net/https/raw.githubusercontent.com/reanahub/reana-workflow-engine-cwl/master/badges/v1.0/subworkflow.json?icon=commonwl - :target: https://github.com/reanahub/reana-workflow-engine-cwl - -CWL v1.1 -######## - -`List of failed tests `_ - -Classes -******* - -.. image:: https://badgen.net/https/raw.githubusercontent.com/reanahub/reana-workflow-engine-cwl/master/badges/v1.1/command_line_tool.json?icon=commonwl - :target: https://github.com/reanahub/reana-workflow-engine-cwl - -.. image:: https://badgen.net/https/raw.githubusercontent.com/reanahub/reana-workflow-engine-cwl/master/badges/v1.1/expression_tool.json?icon=commonwl - :target: https://github.com/reanahub/reana-workflow-engine-cwl - -.. image:: https://badgen.net/https/raw.githubusercontent.com/reanahub/reana-workflow-engine-cwl/master/badges/v1.1/workflow.json?icon=commonwl - :target: https://github.com/reanahub/reana-workflow-engine-cwl - -Required features -***************** - -.. image:: https://badgen.net/https/raw.githubusercontent.com/reanahub/reana-workflow-engine-cwl/master/badges/v1.1/required.json?icon=commonwl - :target: https://github.com/reanahub/reana-workflow-engine-cwl - -Optional features -***************** - -.. image:: https://badgen.net/https/raw.githubusercontent.com/reanahub/reana-workflow-engine-cwl/master/badges/v1.1/docker.json?icon=commonwl - :target: https://github.com/reanahub/reana-workflow-engine-cwl - -.. image:: https://badgen.net/https/raw.githubusercontent.com/reanahub/reana-workflow-engine-cwl/master/badges/v1.1/env_var.json?icon=commonwl - :target: https://github.com/reanahub/reana-workflow-engine-cwl - -.. image:: https://badgen.net/https/raw.githubusercontent.com/reanahub/reana-workflow-engine-cwl/master/badges/v1.1/format_checking.json?icon=commonwl - :target: https://github.com/reanahub/reana-workflow-engine-cwl - -.. image:: https://badgen.net/https/raw.githubusercontent.com/reanahub/reana-workflow-engine-cwl/master/badges/v1.1/initial_work_dir.json?icon=commonwl - :target: https://github.com/reanahub/reana-workflow-engine-cwl - -.. image:: https://badgen.net/https/raw.githubusercontent.com/reanahub/reana-workflow-engine-cwl/master/badges/v1.1/inline_javascript.json?icon=commonwl - :target: https://github.com/reanahub/reana-workflow-engine-cwl - -.. image:: https://badgen.net/https/raw.githubusercontent.com/reanahub/reana-workflow-engine-cwl/master/badges/v1.1/inplace_update.json?icon=commonwl - :target: https://github.com/reanahub/reana-workflow-engine-cwl - -.. image:: https://badgen.net/https/raw.githubusercontent.com/reanahub/reana-workflow-engine-cwl/master/badges/v1.1/input_object_requirements.json?icon=commonwl - :target: https://github.com/reanahub/reana-workflow-engine-cwl - -.. image:: https://badgen.net/https/raw.githubusercontent.com/reanahub/reana-workflow-engine-cwl/master/badges/v1.1/multiple_input.json?icon=commonwl - :target: https://github.com/reanahub/reana-workflow-engine-cwl - -.. image:: https://badgen.net/https/raw.githubusercontent.com/reanahub/reana-workflow-engine-cwl/master/badges/v1.1/networkaccess.json?icon=commonwl - :target: https://github.com/reanahub/reana-workflow-engine-cwl - -.. image:: https://badgen.net/https/raw.githubusercontent.com/reanahub/reana-workflow-engine-cwl/master/badges/v1.1/resource.json?icon=commonwl - :target: https://github.com/reanahub/reana-workflow-engine-cwl - -.. image:: https://badgen.net/https/raw.githubusercontent.com/reanahub/reana-workflow-engine-cwl/master/badges/v1.1/scatter.json?icon=commonwl - :target: https://github.com/reanahub/reana-workflow-engine-cwl - -.. image:: https://badgen.net/https/raw.githubusercontent.com/reanahub/reana-workflow-engine-cwl/master/badges/v1.1/schema_def.json?icon=commonwl - :target: https://github.com/reanahub/reana-workflow-engine-cwl - -.. image:: https://badgen.net/https/raw.githubusercontent.com/reanahub/reana-workflow-engine-cwl/master/badges/v1.1/shell_command.json?icon=commonwl - :target: https://github.com/reanahub/reana-workflow-engine-cwl - -.. image:: https://badgen.net/https/raw.githubusercontent.com/reanahub/reana-workflow-engine-cwl/master/badges/v1.1/step_input_expression.json?icon=commonwl - :target: https://github.com/reanahub/reana-workflow-engine-cwl - -.. image:: https://badgen.net/https/raw.githubusercontent.com/reanahub/reana-workflow-engine-cwl/master/badges/v1.1/step_input.json?icon=commonwl - :target: https://github.com/reanahub/reana-workflow-engine-cwl - -.. image:: https://badgen.net/https/raw.githubusercontent.com/reanahub/reana-workflow-engine-cwl/master/badges/v1.1/subworkflow.json?icon=commonwl - :target: https://github.com/reanahub/reana-workflow-engine-cwl - -.. image:: https://badgen.net/https/raw.githubusercontent.com/reanahub/reana-workflow-engine-cwl/master/badges/v1.1/timelimit.json?icon=commonwl - :target: https://github.com/reanahub/reana-workflow-engine-cwl - -CWL v1.2 -######## - -`List of failed tests `_ - -Classes -******* - -.. image:: https://badgen.net/https/raw.githubusercontent.com/reanahub/reana-workflow-engine-cwl/master/badges/v1.2/command_line_tool.json?icon=commonwl - :target: https://github.com/reanahub/reana-workflow-engine-cwl - -.. image:: https://badgen.net/https/raw.githubusercontent.com/reanahub/reana-workflow-engine-cwl/master/badges/v1.2/expression_tool.json?icon=commonwl - :target: https://github.com/reanahub/reana-workflow-engine-cwl - -.. image:: https://badgen.net/https/raw.githubusercontent.com/reanahub/reana-workflow-engine-cwl/master/badges/v1.2/workflow.json?icon=commonwl - :target: https://github.com/reanahub/reana-workflow-engine-cwl - -Required features -***************** - -.. image:: https://badgen.net/https/raw.githubusercontent.com/reanahub/reana-workflow-engine-cwl/master/badges/v1.2/required.json?icon=commonwl - :target: https://github.com/reanahub/reana-workflow-engine-cwl - -Optional features -***************** - -.. image:: https://badgen.net/https/raw.githubusercontent.com/reanahub/reana-workflow-engine-cwl/master/badges/v1.2/conditional.json?icon=commonwl - :target: https://github.com/reanahub/reana-workflow-engine-cwl - -.. image:: https://badgen.net/https/raw.githubusercontent.com/reanahub/reana-workflow-engine-cwl/master/badges/v1.2/docker.json?icon=commonwl - :target: https://github.com/reanahub/reana-workflow-engine-cwl - -.. image:: https://badgen.net/https/raw.githubusercontent.com/reanahub/reana-workflow-engine-cwl/master/badges/v1.2/env_var.json?icon=commonwl - :target: https://github.com/reanahub/reana-workflow-engine-cwl - -.. image:: https://badgen.net/https/raw.githubusercontent.com/reanahub/reana-workflow-engine-cwl/master/badges/v1.2/format_checking.json?icon=commonwl - :target: https://github.com/reanahub/reana-workflow-engine-cwl - -.. image:: https://badgen.net/https/raw.githubusercontent.com/reanahub/reana-workflow-engine-cwl/master/badges/v1.2/initial_work_dir.json?icon=commonwl - :target: https://github.com/reanahub/reana-workflow-engine-cwl - -.. image:: https://badgen.net/https/raw.githubusercontent.com/reanahub/reana-workflow-engine-cwl/master/badges/v1.2/inline_javascript.json?icon=commonwl - :target: https://github.com/reanahub/reana-workflow-engine-cwl - -.. image:: https://badgen.net/https/raw.githubusercontent.com/reanahub/reana-workflow-engine-cwl/master/badges/v1.2/inplace_update.json?icon=commonwl - :target: https://github.com/reanahub/reana-workflow-engine-cwl - -.. image:: https://badgen.net/https/raw.githubusercontent.com/reanahub/reana-workflow-engine-cwl/master/badges/v1.2/input_object_requirements.json?icon=commonwl - :target: https://github.com/reanahub/reana-workflow-engine-cwl - -.. image:: https://badgen.net/https/raw.githubusercontent.com/reanahub/reana-workflow-engine-cwl/master/badges/v1.2/multiple_input.json?icon=commonwl - :target: https://github.com/reanahub/reana-workflow-engine-cwl - -.. image:: https://badgen.net/https/raw.githubusercontent.com/reanahub/reana-workflow-engine-cwl/master/badges/v1.2/multiple.json?icon=commonwl - :target: https://github.com/reanahub/reana-workflow-engine-cwl - -.. image:: https://badgen.net/https/raw.githubusercontent.com/reanahub/reana-workflow-engine-cwl/master/badges/v1.2/networkaccess.json?icon=commonwl - :target: https://github.com/reanahub/reana-workflow-engine-cwl - -.. image:: https://badgen.net/https/raw.githubusercontent.com/reanahub/reana-workflow-engine-cwl/master/badges/v1.2/resource.json?icon=commonwl - :target: https://github.com/reanahub/reana-workflow-engine-cwl - -.. image:: https://badgen.net/https/raw.githubusercontent.com/reanahub/reana-workflow-engine-cwl/master/badges/v1.2/scatter.json?icon=commonwl - :target: https://github.com/reanahub/reana-workflow-engine-cwl - -.. image:: https://badgen.net/https/raw.githubusercontent.com/reanahub/reana-workflow-engine-cwl/master/badges/v1.2/schema_def.json?icon=commonwl - :target: https://github.com/reanahub/reana-workflow-engine-cwl - -.. image:: https://badgen.net/https/raw.githubusercontent.com/reanahub/reana-workflow-engine-cwl/master/badges/v1.2/secondary_files.json?icon=commonwl - :target: https://github.com/reanahub/reana-workflow-engine-cwl - -.. image:: https://badgen.net/https/raw.githubusercontent.com/reanahub/reana-workflow-engine-cwl/master/badges/v1.2/shell_command.json?icon=commonwl - :target: https://github.com/reanahub/reana-workflow-engine-cwl - -.. image:: https://badgen.net/https/raw.githubusercontent.com/reanahub/reana-workflow-engine-cwl/master/badges/v1.2/step_input_expression.json?icon=commonwl - :target: https://github.com/reanahub/reana-workflow-engine-cwl - -.. image:: https://badgen.net/https/raw.githubusercontent.com/reanahub/reana-workflow-engine-cwl/master/badges/v1.2/step_input.json?icon=commonwl - :target: https://github.com/reanahub/reana-workflow-engine-cwl - -.. image:: https://badgen.net/https/raw.githubusercontent.com/reanahub/reana-workflow-engine-cwl/master/badges/v1.2/subworkflow.json?icon=commonwl - :target: https://github.com/reanahub/reana-workflow-engine-cwl - -.. image:: https://badgen.net/https/raw.githubusercontent.com/reanahub/reana-workflow-engine-cwl/master/badges/v1.2/timelimit.json?icon=commonwl - :target: https://github.com/reanahub/reana-workflow-engine-cwl diff --git a/docs/conf.py b/docs/conf.py index dff665a..0f715e6 100644 --- a/docs/conf.py +++ b/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", @@ -49,14 +50,17 @@ # 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 diff --git a/docs/index.md b/docs/index.md new file mode 100644 index 0000000..9835327 --- /dev/null +++ b/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 +``` diff --git a/docs/index.rst b/docs/index.rst deleted file mode 100644 index 28a52c4..0000000 --- a/docs/index.rst +++ /dev/null @@ -1,27 +0,0 @@ -.. include:: ../README.rst - :end-before: About - -.. include:: ../README.rst - :start-after: ===== - :end-before: Features - -Features - -.. include:: ../README.rst - :start-line: 33 - :end-before: Useful links - -.. include:: ../CHANGES.rst - -.. include:: ../CONTRIBUTING.rst - -License -======= - -.. 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.rst \ No newline at end of file diff --git a/setup.py b/setup.py index 71b600f..e20536d 100644 --- a/setup.py +++ b/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", @@ -28,7 +28,7 @@ "ipdb", "Flask-DebugToolbar", ], - "docs": ["Sphinx>=1.4.4", "sphinx-rtd-theme>=0.1.9", "Jinja2<3.1"], + "docs": ["myst-parser", "Sphinx>=1.4.4", "sphinx-rtd-theme>=0.1.9", "Jinja2<3.1"], "tests": tests_require, } @@ -60,6 +60,7 @@ 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-cwl",