Document (#1) (#8)

* 🎨 add flake8 and ruff line length default (to 90 characters)

* 🎨 add formatting of jupyter notebooks per default

* 📝 highlight that also a folder has to be renamed

* 📝 document what extension are used for

* 📝 document debian (ubuntu) package adding which might be needed

* 🎨 use PyPI and GitHub integration instead of secret api token

* 🙈 hide folders creating when locally building the documentation website

* 📝 document desing choices and layout of Python package

* 🎨 add copy button for code blocks per default

* 🎨 small corrections after proof-reading

* 🎨 make name generic and document it. Choose a Licence hint

* 🎨 add design document to Sphinx documentation

* 🎨 add some more common error checking

- set line-length to black default of 88 characters

* Apply suggestions from code review



* 🐛 correct python pkg configuration file

* 🐛 add missing changes for requirments.txt

As noted by Angel using requirements.txt needed one additional change:
- add dependencies to the dynamic field

Add hint to section with dependencies

* 📝 Add hint to GitHub Releases and Source distribution testing

* 🎨 follow Pasquale's advices (.gitignore + unnecessary config)

- add more to .gitignore and link template
- remove line-length configuration as it is already on the default 88 of black formatter

* 📝 add sebastians hints on other ressources

* 🎨 add license key and remove from classifiers as suggested by Sebastian

* 📝 docstring and src layout hints (noted by sebastian)

* 🐛 add missing key to pyproject.toml

---------

Co-authored-by: Copilot <[email protected]>

Author: enryH

.github/workflows/cicd.yml

@@ -34,7 +34,7 @@ jobs:
       - name: Lint with ruff
         run: |
           # stop the build if there are Python syntax errors or undefined names
-          ruff check .
+          ruff check src
   test:
     name: Test
     runs-on: ubuntu-latest
@@ -119,10 +119,9 @@ jobs:
         with:
           name: artifact
           path: ./dist
-
+      # register PyPI integration:
+      # https://packaging.python.org/en/latest/guides/publishing-package-distribution-releases-using-github-actions-ci-cd-workflows/
       - uses: pypa/gh-action-pypi-publish@release/v1
         with:
           # remove repository key to set the default to pypi (not test.pypi.org)
           repository-url: https://test.pypi.org/legacy/
-          user: __token__
-          password: ${{ secrets.PYPI_API_TOKEN }}

.gitignore

@@ -1,3 +1,5 @@
+# find more examples here:
+# https://github.com/github/gitignore/blob/main/Python.gitignore
 # Binaries (object files) produced by a compiler
 *.so
 *.o
@@ -27,3 +29,28 @@ _templates
 
 # VSCode may create a config file with this name
 **.vscode
+
+# Ruff stuff:
+.ruff_cache/
+
+# Environments
+.env
+.envrc
+.venv
+env/
+venv/
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.nox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+*.py.cover
+.hypothesis/
+.pytest_cache/
+cover/

.readthedocs.yaml

@@ -14,6 +14,9 @@ build:
     # nodejs: "19"
     # rust: "1.64"
     # golang: "1.19"
+  # apt_packages:
+  #  - some_package
+
 
 # Build documentation in the "docs/" directory with Sphinx
 sphinx:

LICENSE

@@ -1,6 +1,6 @@
 MIT License
 
-Copyright (c) 2023: Jakob Nybo Nissen.
+Copyright (c) 2025: First Last.
 
 Permission is hereby granted, free of charge, to any person obtaining
 a copy of this software and associated documentation files (the

README.md

@@ -1,5 +1,8 @@
 # Example Python package
 
+All design principles are explained in the [developing.md](developing.md) file.
+The Python package template was created by Jakob Nybo Nissen and Henry Webel.
+
 ## How to use
 
 Can be used as GitHub template repository,
@@ -8,10 +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` 
 - `RasmussenLab` -> `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.
+
 ## Development environment
 
 Install package so that new code is picked up in a restared python interpreter:
@@ -22,6 +30,8 @@ pip install -e ".[dev]"
 
 ## Basic usage
 
+> works using this template
+
 ```python
 from python_package import hello_world
 print (python_package.__version__)
@@ -31,8 +41,9 @@ print(hello_world(4))
 ## Readthedocs
 
 The documentation can be build using readthedocs automatically. See
-[project on Readthedocs](https://readthedocs.org/projects/rasmussenlab-python-package/) for the project. A new project needs
-to be registered.
+[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).
 
 - make sure to enable build from PRs in the settings (advanded settings)
 - checkout configuration file: [`.readthedocs.yaml`](.readthedocs.yaml)