Migrate docstrings to NumPy style

.copier-answers.yml

@@ -1,6 +1,6 @@
 # WARNING: Do not edit this file manually.
 # Any changes will be overwritten by Copier.
-_commit: v0.10.1-25-ga5301e9
+_commit: v0.10.1-38-g85fbe04
 _src_path: gh:easyscience/templates
 app_docs_url: https://easyscience.github.io/dynamics-app
 app_doi: 10.5281/zenodo.18877180

.github/workflows/coverage.yml

@@ -1,8 +1,10 @@
 name: Coverage checks
 
 on:
-  # Trigger the workflow on push
+  # Trigger the workflow on push to develop
   push:
+    branches:
+      - develop
     # Do not run on version tags (those are handled by other workflows)
     tags-ignore: ['v*']
   # Trigger the workflow on pull request
@@ -15,11 +17,11 @@ permissions:
   actions: write
   contents: read
 
-# Allow only one concurrent workflow, skipping runs queued between the run
-# in-progress and latest queued. And cancel in-progress runs.
+# Allow only one concurrent workflow per PR or branch ref.
+# Cancel in-progress runs only for pull requests, but let branch push runs finish.
 concurrency:
   group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}
-  cancel-in-progress: true
+  cancel-in-progress: ${{ github.event_name == 'pull_request' }}
 
 # Set the environment variables to be used in all jobs defined in this workflow
 env:

.github/workflows/issues-labels.yml

@@ -13,9 +13,18 @@ permissions:
 
 jobs:
   check-labels:
+    if: github.actor != 'easyscience[bot]'
+
     runs-on: ubuntu-latest
 
+    concurrency:
+      group: issue-labels-${{ github.event.issue.number }}
+      cancel-in-progress: true
+
     steps:
+      - name: Checkout repository
+        uses: actions/checkout@v5
+
       - name: Setup easyscience[bot]
         id: bot
         uses: ./.github/actions/setup-easyscience-bot

.github/workflows/lint-format.yml

@@ -79,12 +79,6 @@ jobs:
         shell: bash
         run: pixi run docstring-lint-check
 
-      - name: Check formatting of docstrings in Python code
-        id: docstring_format
-        continue-on-error: true
-        shell: bash
-        run: pixi run docstring-format-check
-
       - name: Check formatting of non-Python files (md, toml, etc.)
         id: nonpy_format
         continue-on-error: true
@@ -112,7 +106,6 @@ jobs:
             echo "| py lint          | ${{ steps.py_lint.outcome == 'success' && '✅' || '❌' }} |"
             echo "| py format        | ${{ steps.py_format.outcome == 'success' && '✅' || '❌' }} |"
             echo "| docstring lint   | ${{ steps.docstring_lint.outcome == 'success' && '✅' || '❌' }} |"
-            echo "| docstring format | ${{ steps.docstring_format.outcome == 'success' && '✅' || '❌' }} |"
             echo "| nonpy format     | ${{ steps.nonpy_format.outcome == 'success' && '✅' || '❌' }} |"
             echo "| notebooks lint   | ${{ steps.notebook_lint.outcome == 'success' && '✅' || '❌' }} |"
           } >> "$GITHUB_STEP_SUMMARY"
@@ -125,7 +118,6 @@ jobs:
           || steps.py_lint.outcome == 'failure'
           || steps.py_format.outcome == 'failure'
           || steps.docstring_lint.outcome == 'failure'
-          || steps.docstring_format.outcome == 'failure'
           || steps.nonpy_format.outcome == 'failure'
           || steps.notebook_lint.outcome == 'failure'
         shell: bash

.gitignore

@@ -41,5 +41,6 @@ CMakeLists.txt.user*
 *.dmg
 
 # Misc
+.cache/
 *.log
 *.zip

.pre-commit-config.yaml

@@ -39,13 +39,6 @@ repos:
         pass_filenames: false
         stages: [manual]
 
-      - id: pixi-docstring-format-check
-        name: pixi run docstring-format-check
-        entry: pixi run docstring-format-check
-        language: system
-        pass_filenames: false
-        stages: [manual]
-
       - id: pixi-nonpy-format-check
         name: pixi run nonpy-format-check
         entry: pixi run nonpy-format-check

.prettierignore

@@ -1,3 +1,6 @@
+# Git
+.git/
+
 # Copier
 .copier-answers*.yml
 
@@ -14,4 +17,16 @@ docs/docs/assets/
 .pytest_cache/
 
 # MyPy
-.mypy_cache
+.mypy_cache/
+
+# Ruff
+.ruff_cache/
+
+# Node
+node_modules
+
+# Misc
+.benchmarks
+.cache
+deps/
+tmp/

CONTRIBUTING.md

@@ -230,7 +230,6 @@ pixi run license-check.........................Passed
 pixi run py-lint-check.........................Passed
 pixi run py-format-check.......................Passed
 pixi run docstring-lint-check..................Passed
-pixi run docstring-format-check................Passed
 pixi run nonpy-format-check....................Passed
 pixi run notebook-lint-check...................Passed
 pixi run unit-tests............................Passed

docs/mkdocs.yml

@@ -148,8 +148,7 @@ plugins:
         python:
           paths: ['src'] # Change 'src' to your actual sources directory
           options:
-            docstring_style: google
-            render_markdown: true
+            docstring_style: numpy
             group_by_category: false
             heading_level: 1
             show_root_heading: true
@@ -183,6 +182,7 @@ nav:
       - Tutorials: tutorials/index.md
       - Getting Started:
           - Tutorial 1. Brownian Diffusion: tutorials/tutorial1_brownian.ipynb
+          - Tutorial 2. Magnetic nanoparticles: tutorials/tutorial2_nanoparticles.ipynb
       - Classes and Methods:
           - Components: tutorials/components.ipynb
           - Component collection: tutorials/component_collection.ipynb