Add contributing guidelines and clean up makefile (#17)

* Add contributing guidelines and clean up makefile

* Add citation file and more docs

* Actually add file

* Remove citation.cff link in readme

Author: jorgensd

CITATION.cff

@@ -0,0 +1,9 @@
+cff-version: 1.2.0
+message: "If you use this software, please cite it as below."
+authors:
+- family-names: "Dokken"
+  given-names: "Jørgen S."
+  orcid: "https://orcid.org/0000-0001-6489-8858"
+title: "Template for reproducible research"
+version: 0.1.0
+date-released: 2022-09-13

CONTRIBUTING.md

@@ -0,0 +1,9 @@
+# Contributing
+
+To contribute to this repository: 
+1. Create a [fork](https://docs.github.com/en/get-started/quickstart/fork-a-repo) of the repository.
+2. [Clone](https://docs.github.com/en/get-started/quickstart/fork-a-repo#cloning-your-forked-repository) the forked repository.
+3. Checkout a new branch (using `git checkout -b name_of_branch`), where name of branch should be replaced by `your_github_username/description_of_feature`. For instance, `jorgensd/add_guidelines`.
+4. Add your contribution and push it to your fork.
+5. Make a [pull request from your fork](https://docs.github.com/en/pull-requests/collaborating-with-pull-requests/proposing-changes-to-your-work-with-pull-requests/creating-a-pull-request-from-a-fork).
+

Makefile

@@ -1,10 +1,19 @@
-doc: # Generate Sphinx HTML documentation, including API docs
-# We want to use the README.md file from the folder as the front page of the book.
-# It has been added to _toc.yml as root
-	cp README.md docs/README.md 
-# We want to use the demos in the book, we convert them with jupytext and copy them to the documentation
-	jupytext --to=ipynb demo/demo.py --output=docs/demo.ipynb
-	jupyter book build docs
+# We want to use the README.md and contributing.md file from this folder 
+# in the Jupter book. These files should be listed in `docs/_toc.yml`
+DOCS = README.md CONTRIBUTING.md
+
+# List of Python demos (without file extenion) from the repo `demo` to include in the jupyterbook. 
+# These files should be listed in `docs/_toc.yml`
+DEMOS = demo
+
+doc: # Generate Sphinx HTML documentation, including API docs 
+	@for file in ${DOCS}; do \
+		cp $$file docs/. ;\
+	done 
+	@for demo in ${DEMOS}; do \
+		jupytext --to=ipynb demo/$$demo.py --output=docs/$$demo.ipynb ;\
+		jupyter book build -W docs ;\
+	done
 
 clean-pytest: # Remove output from pytest
 	rm -rf .pytest_cache

README.md

@@ -1,8 +1,24 @@
 # Reproducible workflow for researchers
 [![Jupyter Book Badge](https://jupyterbook.org/badge.svg)](https://jorgensd.github.io/reproducibility)
+[![MIT License](https://img.shields.io/badge/License-MIT-green.svg)](https://choosealicense.com/licenses/mit/)
 
 This repository is a template for how to set up a reproducible python environment with GitHub.
 
 ## Python-packaging
 
 To be able to create a python package, we need a folder with the name of the package (in this repository `mypackage`), and a `pyproject.toml` file.
+
+
+## Make a repository citable
+The easiest way to make your repository citable is to add a `CITATION.cff` file to the repository, as it is supported by both 
+[Zenodo's](https://zenodo.org/) and it's [Github integration](https://docs.github.com/en/repositories/archiving-a-github-repository/referencing-and-citing-content) and [Github](https://docs.github.com/en/repositories/managing-your-repositorys-settings-and-features/customizing-your-repository/about-citation-files) itself.
+
+## Contributing
+
+Contributions are always welcome!
+
+See [CONTRIBUTING.md](CONTRIBUTING.md) for ways to get started.
+
+A good idea is to look at the [issue tracker](https://github.com/jorgensd/reproducibility/issues) and see if you can resolve any open issues.
+
+If you find a bug in the source code, please [open an issue](https://github.com/jorgensd/reproducibility/issues/new).

docs/_toc.yml

@@ -4,3 +4,4 @@ root: README
 chapters:
   - file: "demo"
   - file: "api"
+  - file: "CONTRIBUTING"