update upstream

.github/workflows/README.md

@@ -4,7 +4,7 @@
 
 Basic continuous integration and deployment (CI/CD) workflow for Python packages.
 
-- checks formatting (black)
+- checks formatting (black, isort)
 - checks linting (ruff)
 - run unit tests (pytest)
 - optional: add c extensions to a package

.github/workflows/cicd.yml

@@ -19,6 +19,7 @@ jobs:
     steps:
       - uses: actions/checkout@v4
       - uses: psf/black@stable
+      - uses: isort/isort-action@v1
   lint:
     name: Lint with ruff
     runs-on: ubuntu-latest
@@ -106,6 +107,8 @@ jobs:
   publish:
     name: Publish package
     if: startsWith(github.ref, 'refs/tags')
+    permissions:
+      id-token: write
     needs:
       - format
       - lint

.readthedocs.yaml

@@ -7,9 +7,9 @@ version: 2
 
 # Set the OS, Python version and other tools you might need
 build:
-  os: ubuntu-22.04
+  os: ubuntu-24.04
   tools:
-    python: "3.11"
+    python: "3.13"
     # You can also specify other tool versions:
     # nodejs: "19"
     # rust: "1.64"

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"

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.

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).
 

developing.md

@@ -142,6 +142,28 @@ Please also update the project URL to your project:
 "Homepage" = "https://github.com/RasmussenLab/python_package"
 ```
 
+The template also sets a command line script entry point, which allows to run
+the function `main` in the `mockup` module of the package as a command line script,
+wrapping the `hello_world` function from the `mockup` module.
+The template uses the standard library [argparse](https://docs.python.org/3/library/argparse.html)
+module to parse parameters from the command line and creates a basic interface.
+
+```toml
+# Script entry points, i.e. command line commands available after installing the package
+# e.g. implemented using argparse
+# Then you can type: `python-package-hello -h` in the terminal
+[project.scripts]
+python-package-hello = "python_package.cli:main"
+```
+
+You can therefore run the command line script using:
+
+```bash
+python-package-hello -h
+# print hello world 3 times
+python-package-hello -n 3
+```
+
 ## Source directory layout of the package
 
 The source code of the package is located in the `src` directory, to have a project 

docs/README.md

@@ -1,10 +1,10 @@
 # Docs creation
 
-In order to build the docs you need to 
+In order to build the docs you need to
 
-  1. install sphinx and additional support packages
-  2. build the package reference files
-  3. run sphinx to create a local html version
+1. install sphinx and additional support packages
+2. build the package reference files
+3. run sphinx to create a local html version
 
 The documentation is build using readthedocs automatically.
 
@@ -17,12 +17,13 @@ pip install ".[docs]"
 
 ## Build docs using Sphinx command line tools
 
-Command to be run from `path/to/docs`, i.e. from within the `docs` package folder: 
+Command to be run from `path/to/docs`, i.e. from within the `docs` package folder:
 
 Options:
-  - `--separate` to build separate pages for each (sub-)module
 
-```bash	
+- `--separate` to build separate pages for each (sub-)module
+
+```bash
 # pwd: docs
 # apidoc
 sphinx-apidoc --force --implicit-namespaces --module-first -o reference ../src/python_package

docs/conf.py

@@ -49,6 +49,7 @@
 html_js_files = [
     "https://cdnjs.cloudflare.com/ajax/libs/require.js/2.3.4/require.min.js"
 ]
+os.environ["PLOTLY_RENDERER"] = "notebook"  # compatibility with plotly6
 
 # https://myst-nb.readthedocs.io/en/latest/configuration.html
 # Execution

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"

pyproject.toml

@@ -1,14 +1,13 @@
 # ref: https://setuptools.pypa.io/en/stable/userguide/pyproject_config.html
 [project]
-authors = [
-  { name = "First Last", email = "first.last@gmail.com" },
-]
+authors = [{ name = "First Last", email = "first.last@gmail.com" }]
 description = "A small example package"
 name = "python_package"
 # This means: Load the version from the package itself.
 # See the section below: [tools.setuptools.dynamic]
-dynamic = ["version", # version is loaded from the package
-#"dependencies", # add if using requirements.txt
+dynamic = [
+  "version", # version is loaded from the package
+  #"dependencies", # add if using requirements.txt
 ]
 readme = "README.md"
 requires-python = ">=3.9" # test all higher Python versions
@@ -17,7 +16,8 @@ classifiers = [
   "Programming Language :: Python :: 3",
   "Operating System :: OS Independent",
 ]
-license = "MIT" # https://choosealicense.com/
+# Also update LICENSE file if you pick another one
+license = "GPL-3.0-or-later" # https://choosealicense.com/licenses/gpl-3.0/
 # # add dependencies here: (use one of the two)
 # dependencies = ["numpy", "pandas", "scipy", "matplotlib", "seaborn"]
 # use requirements.txt instead of pyproject.toml for dependencies
@@ -44,20 +44,19 @@ docs = [
   "sphinx-copybutton",
 ]
 # local development options
-dev = ["black[jupyter]", "ruff", "pytest"]
+dev = ["black[jupyter]", "ruff", "pytest", "isort", "jupytext"]
 
-# Configure the Ruff linter: Ignore error number 501
 [tool.ruff]
 # https://docs.astral.sh/ruff/rules/#flake8-bandit-s
-# lint.ignore = ["E501"] # Ignore line length errors
-# Allow lines to be as long as (default is 88 in black)
 
 [tool.ruff.lint]
 # https://docs.astral.sh/ruff/tutorial/#rule-selection
 # 1. Enable flake8-bugbear (`B`) rules
 # 2. Enable pycodestyle (`E`) errors and (`W`) warnings
 # 3. Pyflakes (`F`) errors
 extend-select = ["E", "W", "F", "B"]
+# Ignore line length errors:
+# ignore = ["E501"]
 
 [build-system]
 build-backend = "setuptools.build_meta"
@@ -69,3 +68,9 @@ requires = ["setuptools>=64", "setuptools_scm>=8"]
 
 [tool.isort]
 profile = "black"
+
+# Script entry points, i.e. command line commands available after installing the package
+# e.g. implemented using argparse
+# Then you can type: `python-package-hello -h` in the terminal
+[project.scripts]
+python-package-hello = "python_package.cli:main"

src/python_package/__init__.py

@@ -4,8 +4,8 @@
 
 __version__ = metadata.version("python_package")
 
-from .mockup import hello_world
+from .mockup import hello_world, saved_world
 
 # The __all__ variable is a list of variables which are imported
 # when a user does "from example import *"
-__all__ = ["hello_world"]
+__all__ = ["hello_world", "saved_world"]

src/python_package/cli.py

@@ -0,0 +1,17 @@
+import argparse
+
+from .mockup import hello_world
+
+
+def main():
+    parser = argparse.ArgumentParser(description="Python Package CLI")
+    parser.add_argument(
+        "-n",
+        "--repeat",
+        type=int,
+        default=1,
+        help="Number of times to repeat the greeting hello world",
+    )
+    args = parser.parse_args()
+    msg = hello_world(args.repeat)
+    print(msg)

src/python_package/mockup.py

@@ -13,5 +13,33 @@ def hello_world(n: int) -> str:
     -------
     str
         str of 'hello world' n-times
+
+    Examples
+    --------
+    >>> hello_world(3)
+    'hello world hello world hello world'
     """
     return " ".join(repeat("hello world", n))
+
+
+def saved_world(filename: str) -> int:
+    """
+    Count how many times 'hello world' is in a file.
+
+    Parameters
+    ----------
+    filename : str
+        The file to read
+
+    Returns
+    -------
+    int
+        How many times 'hello world' is in the file
+
+    Examples
+    --------
+    >>> saved_world("not-real.txt") # doctest: +SKIP
+    """
+    with open(filename, "r") as f:
+        content = f.read()
+    return content.count("hello world")