Switch to markdown

.gitignore

@@ -20,3 +20,9 @@ docs/apidocs
 
 # Mac
 .DS_Store
+
+# virtual environments
+env
+env3
+venv
+venv3

CODE_OF_CONDUCT.md

@@ -55,7 +55,7 @@ further defined and clarified by project maintainers.
 ## Enforcement
 
 Instances of abusive, harassing, or otherwise unacceptable behavior may be
-reported by contacting the project team at j.vanderzwaan@esciencecenter.nl. All
+reported by contacting the project team at XXX@esciencecenter.nl. All
 complaints will be reviewed and investigated and will result in a response that
 is deemed necessary and appropriate to the circumstances. The project team is
 obligated to maintain confidentiality with regard to the reporter of an incident.

{{cookiecutter.project_name}}/CHANGELOG.md

@@ -0,0 +1,18 @@
+# Changelog
+All notable changes to this project will be documented in this file.
+
+The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
+and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
+
+## [Unreleased]
+
+## [0.0.1] - 2021-12-31
+
+### Added
+
+### Removed
+
+### Changed
+
+[Unreleased]: https://github.com/olivierlacan/keep-a-changelog/compare/v1.0.0...HEAD
+[0.0.1]: https://github.com/olivierlacan/keep-a-changelog/releases/tag/v0.0.1

{{cookiecutter.project_name}}/CODE_OF_CONDUCT.rst → {{cookiecutter.project_name}}/CODE_OF_CONDUCT.md

@@ -1,9 +1,6 @@
-###############################################################################
-Contributor Covenant Code of Conduct
-###############################################################################
+# Contributor Covenant Code of Conduct
 
-Our Pledge
-**********
+## Our Pledge
 
 In the interest of fostering an open and welcoming environment, we as
 contributors and maintainers pledge to making participation in our project and
@@ -12,8 +9,7 @@ size, disability, ethnicity, gender identity and expression, level of experience
 education, socio-economic status, nationality, personal appearance, race,
 religion, or sexual identity and orientation.
 
-Our Standards
-*************
+## Our Standards
 
 Examples of behavior that contributes to creating a positive environment
 include:
@@ -35,8 +31,7 @@ Examples of unacceptable behavior by participants include:
 * Other conduct which could reasonably be considered inappropriate in a
   professional setting
 
-Our Responsibilities
-********************
+## Our Responsibilities
 
 Project maintainers are responsible for clarifying the standards of acceptable
 behavior and are expected to take appropriate and fair corrective action in
@@ -48,8 +43,7 @@ that are not aligned to this Code of Conduct, or to ban temporarily or
 permanently any contributor for other behaviors that they deem inappropriate,
 threatening, offensive, or harmful.
 
-Scope
-*****
+## Scope
 
 This Code of Conduct applies both within project spaces and in public spaces
 when an individual is representing the project or its community. Examples of
@@ -58,8 +52,7 @@ address, posting via an official social media account, or acting as an appointed
 representative at an online or offline event. Representation of a project may be
 further defined and clarified by project maintainers.
 
-Enforcement
-***********
+## Enforcement
 
 Instances of abusive, harassing, or otherwise unacceptable behavior may be
 reported by contacting the project team at {{ cookiecutter.code_of_conduct_email }}. All
@@ -72,8 +65,9 @@ Project maintainers who do not follow or enforce the Code of Conduct in good
 faith may face temporary or permanent repercussions as determined by other
 members of the project's leadership.
 
-Attribution
-***********
+## Attribution
 
-This Code of Conduct is adapted from the `Contributor Covenant <https://www.contributor-covenant.org>`_, version 1.4,
+This Code of Conduct is adapted from the [Contributor Covenant][homepage], version 1.4,
 available at https://www.contributor-covenant.org/version/1/4/code-of-conduct.html
+
+[homepage]: https://www.contributor-covenant.org

{{cookiecutter.project_name}}/CONTRIBUTING.md

@@ -0,0 +1,41 @@
+# Contributing guidelines
+
+We welcome any kind of contribution to our software, from simple comment or question to a full fledged [pull request](https://help.github.com/articles/about-pull-requests/). Please read and follow our [Code of Conduct](CODE_OF_CONDUCT.md).
+
+A contribution can be one of the following cases:
+
+1. you have a question;
+1. you think you may have found a bug (including unexpected behavior);
+1. you want to make some kind of change to the code base (e.g. to fix a bug, to add a new feature, to update documentation);
+1. you want to make a new release of the code base.
+
+The sections below outline the steps in each case.
+
+## You have a question
+
+1. use the search functionality [here]({{cookiecutter.repository}}/issues) to see if someone already filed the same issue;
+2. if your issue search did not yield any relevant results, make a new issue;
+3. apply the "Question" label; apply other labels when relevant.
+
+## You think you may have found a bug
+
+1. use the search functionality [here]({{cookiecutter.repository}}/issues) to see if someone already filed the same issue;
+1. if your issue search did not yield any relevant results, make a new issue, making sure to provide enough information to the rest of the community to understand the cause and context of the problem. Depending on the issue, you may want to include:
+    - the [SHA hashcode](https://help.github.com/articles/autolinked-references-and-urls/#commit-shas) of the commit that is causing your problem;
+    - some identifying information (name and version number) for dependencies you're using;
+    - information about the operating system;
+1. apply relevant labels to the newly created issue.
+
+## You want to make some kind of change to the code base
+
+1. (**important**) announce your plan to the rest of the community *before you start working*. This announcement should be in the form of a (new) issue;
+1. (**important**) wait until some kind of consensus is reached about your idea being a good idea;
+1. if needed, fork the repository to your own Github profile and create your own feature branch off of the latest master commit. While working on your feature branch, make sure to stay up to date with the master branch by pulling in changes, possibly from the 'upstream' repository (follow the instructions [here](https://help.github.com/articles/configuring-a-remote-for-a-fork/) and [here](https://help.github.com/articles/syncing-a-fork/));
+1. make sure the existing tests still work by running ``pytest``;
+1. add your own tests (if necessary);
+1. update or expand the documentation;
+1. update the `CHANGELOG.md` file with change;
+1. [push](http://rogerdudler.github.io/git-guide/>) your feature branch to (your fork of) the {{ cookiecutter.package_name }} repository on GitHub;
+1. create the pull request, e.g. following the instructions [here](https://help.github.com/articles/creating-a-pull-request/).
+
+In case you feel like you've made a valuable contribution, but you don't know how to write or run tests for it, or how to generate the documentation: don't let this discourage you from making the pull request; we can help you! Just go ahead and submit the pull request, but keep in mind that you might be asked to append additional commits to your pull request.

{{cookiecutter.project_name}}/README.md

@@ -0,0 +1,55 @@
+## Badges
+
+(Customize these badges with your own links, and check https://shields.io/ or https://badgen.net/ to see which other badges are available.)
+
+| fair-software.nl recommendations | |
+| :-- | :--  |
+| (1/5) code repository              | [![github repo badge](https://img.shields.io/badge/github-repo-000.svg?logo=github&labelColor=gray&color=blue)]({{cookiecutter.repository}}) |
+| (2/5) license                      | [![github license badge](https://img.shields.io/github/license/{{cookiecutter.github_organization}}/{{cookiecutter.project_name}})]({{cookiecutter.repository}}) |
+| (3/5) community registry           | [![RSD](https://img.shields.io/badge/rsd-{{cookiecutter.project_name}}-00a3e3.svg)](https://www.research-software.nl/software/{{cookiecutter.project_name}}) |
+| PyPI Badge             | [![workflow pypi badge](https://img.shields.io/pypi/v/{{cookiecutter.project_name}}.svg?colorB=blue)](https://pypi.python.org/project/{{cookiecutter.project_name}}/) |
+| (4/5) citation                     | [![DOI](https://zenodo.org/badge/DOI/<replace-with-created-DOI>.svg)](https://doi.org/<replace-with-created-DOI>) |
+| (5/5) checklist                    | &nbsp; |
+| overall                            | [![fair-software badge](https://img.shields.io/badge/fair--software.eu-%E2%97%8F%20%20%E2%97%8F%20%20%E2%97%8F%20%20%E2%97%8F%20%20%E2%97%8B-yellow)](https://fair-software.eu) |
+| CII Best Practices Badge              | [![workflow cii badge](https://bestpractices.coreinfrastructure.org/projects/<replace-with-created-project-identifier>/badge)](https://bestpractices.coreinfrastructure.org/projects/<replace-with-created-project-identifier>) |
+| **Other best practices**           | &nbsp; |
+| Sonarcloud quality badge              | [![workflow scq badge](https://sonarcloud.io/api/project_badges/measure?project={{cookiecutter.github_organization}}_{{cookiecutter.project_name}}&metric=alert_status)](https://sonarcloud.io/dashboard?id={{cookiecutter.github_organization}}_{{cookiecutter.project_name}}) |
+| Sonarcloud coverage badge              | [![workflow scc badge](https://sonarcloud.io/api/project_badges/measure?project={{cookiecutter.github_organization}}_{{cookiecutter.project_name}}&metric=coverage)](https://sonarcloud.io/dashboard?id={{cookiecutter.github_organization}}_{{cookiecutter.project_name}}) |
+| **GitHub Actions**                 | &nbsp; |
+| Python Build              | [![workflow python badge]({{cookiecutter.repository}}/workflows/Python/badge.svg)]({{cookiecutter.repository}}/actions?query=workflow%3A%22Python%22) |
+| PyPI Publish      | [![workflow pypi badge]({{cookiecutter.repository}}/workflows/PyPI/badge.svg)]({{cookiecutter.repository}}/actions?query=workflow%3A%22PyPI%22) |
+| Metadata consistency                         | [![workflow tests badge]({{cookiecutter.repository}}/workflows/cffconvert/badge.svg)]({{cookiecutter.repository}}/actions?query=workflow%3A%22cffconvert%22) |
+
+## How to use {{ cookiecutter.package_name }}
+
+{{ cookiecutter.package_short_description }}
+
+
+The project setup is documented in [project_setup.md](project_setup.md). Feel free to remove this document (and/or the link to this document) if you don't need it.
+
+## Installation
+
+To install {{ cookiecutter.package_name }} from GitHub repository, do:
+
+```console
+git clone {{ cookiecutter.repository }}.git
+cd {{ cookiecutter.project_name }}
+python3 -m pip install .
+```
+
+## Documentation
+
+.. _README:
+
+Include a link to your project's full documentation here.
+
+## Contributing
+
+If you want to contribute to the development of {{ cookiecutter.project_name }},
+have a look at the [contribution guidelines](CONTRIBUTING.md).
+
+
+Credits
+*******
+
+This package was created with `Cookiecutter <https://github.com/audreyr/cookiecutter>`_ and the `NLeSC/python-template <https://github.com/NLeSC/python-template>`_.