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

@@ -5,10 +5,13 @@ name: Python application
 
 on:
   push:
+    branches: ["main"]
   pull_request:
     branches: ["main"]
   schedule:
     - cron: "0 2 * * 3"
+  release:
+    types: [published]
 
 permissions:
   contents: read
@@ -19,6 +22,7 @@ jobs:
     steps:
       - uses: actions/checkout@v4
       - uses: psf/black@stable
+      - uses: isort/isort-action@v1
   lint:
     name: Lint with ruff
     runs-on: ubuntu-latest
@@ -40,7 +44,7 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: ["3.11", "3.12"]
+        python-version: ["3.10", "3.11", "3.12", "3.13"]
     steps:
       - uses: actions/checkout@v4
       - name: Set up Python ${{ matrix.python-version }}
@@ -106,6 +110,8 @@ 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.