Apply newest templates

.copier-answers.yml

@@ -1,6 +1,6 @@
 # WARNING: Do not edit this file manually.
 # Any changes will be overwritten by Copier.
-_commit: v0.12.0
+_commit: v0.13.1-3-g44c0369
 _src_path: gh:easyscience/templates
 app_docs_url: https://easyscience.github.io/dynamics-app
 app_doi: 10.5281/zenodo.18877180

.github/workflows/docs.yml

@@ -123,11 +123,14 @@ jobs:
 
       # Build the static files for the documentation site for local inspection
       # Input: docs/ directory containing the Markdown files
-      # Output: site/ directory containing the generated HTML files
+      # Output: docs/site/ directory containing the generated HTML files
+      # Also verifies that mkdocstrings generated docs/site/objects.inv.
       - name: Build site for local check
-        run: pixi run docs-build-local
+        run: |
+          pixi run docs-build-local
+          pixi run docs-inventory-check
 
-      # Upload the static files from the site/ directory to be used for
+      # Upload the static files from the docs/site/ directory to be used for
       # local check
       - name: Upload built site as artifact
         uses: ./.github/actions/upload-artifact

.github/workflows/pypi-test.yml

@@ -43,11 +43,15 @@ jobs:
           frozen: false
 
       - name: Init pixi project
-        run: pixi init easydynamics
+        run:
+          pixi init --platform linux-64 --platform osx-arm64 --platform win-64
+          easydynamics
 
-      - name: Set the minimum system requirements
+      - name: Configure pixi platforms
         working-directory: easydynamics
-        run: pixi project system-requirements add macos 14.0
+        run: |
+          pixi workspace platform edit linux-64 --glibc 2.35 --no-install
+          pixi workspace platform edit osx-arm64 --macos 14.0 --no-install
 
       - name: Add Python 3.14 from Conda
         working-directory: easydynamics

.github/workflows/test.yml

@@ -211,15 +211,16 @@ jobs:
             echo "🔹🔸🔹🔸🔹 Python: $py_ver 🔹🔸🔹🔸🔹"
 
             echo "Initializing pixi project"
-            pixi init easydynamics_py$py_ver
+            pixi init --platform linux-64 --platform osx-arm64 --platform win-64 easydynamics_py$py_ver
             cd easydynamics_py$py_ver
 
+            echo "Configure pixi platforms"
+            pixi workspace platform edit linux-64 --glibc 2.35 --no-install
+            pixi workspace platform edit osx-arm64 --macos 14.0 --no-install
+
             echo "Adding Python $py_ver"
             pixi add "python=$py_ver"
 
-            echo "Setting macOS 14.0 as minimum required"
-            pixi project system-requirements add macos 14.0
-
             echo "Looking for wheel in ../dist/py$py_ver/"
             ls -l "../dist/py$py_ver/"
 

CONTRIBUTING.md

@@ -42,8 +42,7 @@ Please make sure you follow the EasyScience organization-wide
 If you are not planning to contribute code, you may want to:
 
 - 🐞 Report a bug — see [Reporting Issues](#11-reporting-issues)
-- 🛡 Report a security issue — see
-  [Security Issues](#12-security-issues)
+- 🛡 Report a security issue — see [Security Issues](#12-security-issues)
 - 💬 Ask a question or start a discussion at
   [Project Discussions](https://github.com/easyscience/dynamics-lib/discussions)
 

docs/mkdocs.yml

@@ -168,6 +168,13 @@ plugins:
             docstring_options:
               ignore_init_summary: true
             summary: true
+            relative_crossrefs: true
+            scoped_crossrefs: true
+            filters: ['!^_[^_]', '!__repr__', '!__dir__'] # This is the default filter minus __repr__ and __dir__
+          inventories:
+            - url: https://scipp.github.io/objects.inv
+            - url: https://numpy.org/doc/stable/objects.inv
+            - url: https://easyscience.github.io/core/latest/objects.inv
   - search
 
 # Determines additional directories to watch when running mkdocs serve

pixi.toml

@@ -5,7 +5,19 @@
 [workspace]
 
 # Supported platforms for the lock file (pixi.lock)
-platforms = ['win-64', 'linux-64', 'osx-arm64']
+platforms = [
+  'win-64',
+  # Set minimum supported version for glibc to be 2.35 to ensure packages
+  # like `crysfml` that only have wheels for glibc 2.35+
+  # (manylinux_2_35_x86_64) are used.
+  #libc = { family = 'glibc', version = '2.35' }
+  { platform = 'linux-64', glibc = '2.35' },
+  # Set minimum supported version for macOS to be 14.0 to ensure packages
+  # like `scipp` that only have wheels for macOS 14.0+ (macosx_14_0_arm64)
+  # are used instead of building from source. This is a workaround for
+  # Pixi, see https://github.com/prefix-dev/pixi/issues/5667
+  { platform = 'osx-arm64', macos = '14.0' },
+]
 
 # Channels for fetching packages
 channels = ['nodefaults', 'conda-forge']
@@ -19,13 +31,6 @@ channels = ['nodefaults', 'conda-forge']
 [activation.env]
 PYTHONIOENCODING = 'utf-8'
 
-[system-requirements]
-# Set minimum supported version for macOS to be 14.0 to ensure packages
-# like `scipp` that only have wheels for macOS 14.0+ (macosx_14_0_arm64)
-# are used instead of building from source. This is a workaround for
-# Pixi, see https://github.com/prefix-dev/pixi/issues/5667
-macos = '14.0'
-
 # Non-default features:
 
 # Set specific Python versions to be used in CI testing.
@@ -187,8 +192,9 @@ docs-serve = 'pixi run docs-pre serve -f docs/mkdocs.yml'
 docs-serve-dirty = 'pixi run docs-serve --dirty'
 docs-build = 'pixi run docs-pre build -f docs/mkdocs.yml'
 docs-build-local = 'pixi run docs-build --no-directory-urls'
+docs-inventory-check = 'python -c "from pathlib import Path; p = Path(\"docs/site/objects.inv\"); raise SystemExit(0 if p.is_file() and p.stat().st_size > 0 else \"missing or empty docs/site/objects.inv\")"'
 
-docs-deploy-pre = 'mike deploy -F docs/mkdocs.yml --push --branch gh-pages --update-aliases --alias-type redirect'
+docs-deploy-pre = 'mike deploy -F docs/mkdocs.yml --push --branch gh-pages --update-aliases --alias-type copy'
 docs-set-default-pre = 'mike set-default -F docs/mkdocs.yml --push --branch gh-pages'
 
 docs-update-assets = 'python tools/update_docs_assets.py'

pyproject.toml

@@ -55,6 +55,7 @@ dev = [
   'jupytext',                        # Jupyter notebook text format support
   'jupyterquiz',                     # Quizzes in Jupyter notebooks
   'pydoclint',                       # Docstring linter
+  'docstring-parser-fork!=0.0.15',   # Parser used by pydoclint. 0.0.15 splits NumPy-style defaults -> DOC105 failures
   'format-docstring',                # Docstring formatter
   'docstripy',                       # Convert docstrings to other formats
   'interrogate',                     # Docstring coverage checker