From 720cc6f10c2e99d7790110549eaca56894ac5e92 Mon Sep 17 00:00:00 2001
From: Henry Webel <heweb@dtu.dk>
Date: Wed, 23 Jul 2025 13:03:41 +0200
Subject: [PATCH 1/2] :memo::wrench: start adressing recommendations from
 Sebastian, see #5

---
 Contributing.md         | 36 ++++++++++++++++++++++++++++++++++++
 docs/tutorial/.jupytext |  6 +++++-
 pyproject.toml          |  2 +-
 3 files changed, 42 insertions(+), 2 deletions(-)
 create mode 100644 Contributing.md

diff --git a/Contributing.md b/Contributing.md
new file mode 100644
index 0000000..94d1032
--- /dev/null
+++ b/Contributing.md
@@ -0,0 +1,36 @@
+# Contributing code
+
+Install the code with development dependencies:
+
+```bash
+pip install -e '.[dev]'
+```
+
+## Format code and sort imports
+
+```bash
+black .
+isort .
+```
+
+## lint code
+
+```bash
+ruff check .
+```
+
+## Run tests
+
+```bash
+pytest
+```
+
+## Sync notebooks with jupytext
+
+For easier diffs, you can use jupytext to sync notebooks in the `docs/tutorial` directory with the percent format.
+
+```bash
+jupytext --sync docs/tutorial/*.ipynb
+```
+
+This is configured in the [`.jupytext`](docs/tutorial/.jupytext) file in that directory.
diff --git a/docs/tutorial/.jupytext b/docs/tutorial/.jupytext
index 46e9467..c213311 100644
--- a/docs/tutorial/.jupytext
+++ b/docs/tutorial/.jupytext
@@ -1,2 +1,6 @@
-# all notebooks in this directory are in the percent format
+# all notebooks in this directory are synced percent format when typing
+# (jupytext is a dev dependency)
+# jupytext --sync *.ipynb
+# or from root directory
+# jupytext --sync docs/api_examples/*.ipynb
 formats = "ipynb,py:percent"
diff --git a/pyproject.toml b/pyproject.toml
index 8d614cd..1afdec2 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -43,7 +43,7 @@ docs = [
   "sphinx-copybutton",
 ]
 # local development options
-dev = ["black[jupyter]", "ruff", "pytest"]
+dev = ["black[jupyter]", "ruff", "pytest", "isort", "jupytext"]
 
 [tool.ruff]
 # https://docs.astral.sh/ruff/rules/#flake8-bandit-s

From 7535642e4f84554f73523d1785eabfb7a6c7bf99 Mon Sep 17 00:00:00 2001
From: Henry Webel <heweb@dtu.dk>
Date: Wed, 23 Jul 2025 13:10:12 +0200
Subject: [PATCH 2/2] :art: add default citation

---
 CITATION.cff | 12 ++++++++++++
 README.md    |  7 ++++---
 2 files changed, 16 insertions(+), 3 deletions(-)
 create mode 100644 CITATION.cff

diff --git a/CITATION.cff b/CITATION.cff
new file mode 100644
index 0000000..b78dd26
--- /dev/null
+++ b/CITATION.cff
@@ -0,0 +1,12 @@
+# https://docs.github.com/en/repositories/managing-your-repositorys-settings-and-features/customizing-your-repository/about-citation-files
+cff-version: 1.2.0
+message: "If you use this software, please cite it as below."
+authors:
+- family-names: "Last"
+  given-names: "First"
+  orcid: "https://orcid.org/0000-0000-0000-0000"
+title: "Python Package Template repository"
+version: 0.0.1
+doi: 10.5281/zenodo.1234
+date-released: 2025-07-23
+url: "https://github.com/biosustain/python_package"
diff --git a/README.md b/README.md
index a248d35..0b2d238 100644
--- a/README.md
+++ b/README.md
@@ -11,14 +11,15 @@ see [GitHub documentation](https://docs.github.com/en/repositories/creating-and-
 You will need to find and replace occurences of
 
 - `python_package` -> `your_package_name`
-    - also the folder `src/python_package` 
+  - also the folder `src/python_package`
 - `RasmussenLab` -> `GitHub_user_name` (or `organization`)
-with the name of your package and GitHub user name (or organization).
+  with the name of your package and GitHub user name (or organization).
 
 - look for `First Last` to see where to replace with your name
 - choose a license, see [GitHub documentation](https://docs.github.com/en/repositories/creating-and-managing-repositories/licensing-a-repository)
   and [Creative Commons](https://creativecommons.org/chooser/).
   Replace [`LICENSE`](LICENSE) file with the license you choose.
+- Update the `CITATION.cff` file with your information.
 
 ## Development environment
 
@@ -41,7 +42,7 @@ print(hello_world(4))
 ## Readthedocs
 
 The documentation can be build using readthedocs automatically. See
-[project on Readthedocs](https://readthedocs.org/projects/rasmussenlab-python-package/) 
+[project on Readthedocs](https://readthedocs.org/projects/rasmussenlab-python-package/)
 for the project based on this template. A new project needs
 to [be registered on ReadTheDocs](https://docs.readthedocs.com/platform/stable/intro/add-project.html).