Merge pull request #163 from easyscience/develop

Release: merge develop into master

Author: henrikjacobsenfys

.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: v0.10.1-41-g508666e
 _src_path: gh:easyscience/templates
 app_docs_url: https://easyscience.github.io/dynamics-app
 app_doi: 10.5281/zenodo.18877180
@@ -12,8 +12,8 @@ home_repo_name: dynamics
 lib_docs_url: https://easyscience.github.io/dynamics-lib
 lib_doi: 10.5281/zenodo.18877180
 lib_package_name: easydynamics
-lib_python_max: '3.12'
-lib_python_min: '3.11'
+lib_python_max: '3.14'
+lib_python_min: '3.12'
 lib_repo_name: dynamics-lib
 project_contact_email: henrik.jacobsen@ess.eu
 project_copyright_years: 2025-2026

.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

.github/workflows/pypi-test.yml

@@ -45,30 +45,26 @@ jobs:
       - name: Init pixi project
         run: pixi init easydynamics
 
-      - name: Add Python 3.12 from Conda
+      - name: Set the minimum system requirements
         working-directory: easydynamics
-        run: pixi add "python=3.12"
+        run: pixi project system-requirements add macos 14.0
 
-      - name: Add other Conda dependencies
+      - name: Add Python 3.14 from Conda
         working-directory: easydynamics
-        run: pixi add gsl
+        run: pixi add "python=3.14"
 
-      - name: Add easydynamics from PyPI
+      - name: Add easydynamics (with dev dependencies) from PyPI
         working-directory: easydynamics
-        run: pixi add --pypi "easydynamics"
-
-      - name: Add dev dependencies from PyPI
-        working-directory: easydynamics
-        run: pixi add --pypi pytest pytest-xdist
-
-      - name: Add Pixi task as a shortcut
-        working-directory: easydynamics
-        run: pixi task add easydynamics "python -m easydynamics"
+        run: pixi add --pypi "easydynamics[dev]"
 
       - name: Run unit tests to verify the installation
         working-directory: easydynamics
         run: pixi run python -m pytest ../tests/unit/ --color=yes -v
 
+      - name: Run functional tests to verify the installation
+        working-directory: easydynamics
+        run: pixi run python -m pytest ../tests/functional/ --color=yes -v
+
       - name: Run integration tests to verify the installation
         working-directory: easydynamics
         run: pixi run python -m pytest ../tests/integration/ --color=yes -n auto

.github/workflows/test.yml

@@ -44,8 +44,8 @@ concurrency:
 # Set the environment variables to be used in all jobs defined in this workflow
 env:
   CI_BRANCH: ${{ github.head_ref || github.ref_name }}
-  PY_VERSIONS: '3.11 3.12'
-  PIXI_ENVS: 'py-311-env py-312-env'
+  PY_VERSIONS: '3.12 3.14'
+  PIXI_ENVS: 'py-312-env py-314-env'
 
 jobs:
   # Job 1: Set up environment variables
@@ -96,12 +96,27 @@ jobs:
             echo
             echo "🔹🔸🔹🔸🔹 Python: $py_ver 🔹🔸🔹🔸🔹"
 
-            env="py-$(echo $py_ver | tr -d .)-env" # Converts 3.11 -> py-311-env
+            env="py-$(echo $py_ver | tr -d .)-env" # Converts 3.XX -> py-3XX-env
 
             echo "Running tests in environment: $env"
             pixi run --environment $env unit-tests
           done
 
+      - name: Run functional tests
+        shell: bash
+        run: |
+          set -euo pipefail
+
+          for py_ver in $PY_VERSIONS; do
+            echo
+            echo "🔹🔸🔹🔸🔹 Python: $py_ver 🔹🔸🔹🔸🔹"
+
+            env="py-$(echo $py_ver | tr -d .)-env" # Converts 3.XX -> py-3XX-env
+
+            echo "Running tests in environment: $env"
+            pixi run --environment $env functional-tests
+          done
+
       - name: Run integration tests ${{ needs.env-prepare.outputs.pytest-marks }}
         shell: bash
         run: |
@@ -111,7 +126,7 @@ jobs:
             echo
             echo "🔹🔸🔹🔸🔹 Python: $py_ver 🔹🔸🔹🔸🔹"
 
-            env="py-$(echo $py_ver | tr -d .)-env" # Converts 3.11 -> py-311-env
+            env="py-$(echo $py_ver | tr -d .)-env" # Converts 3.XX -> py-3XX-env
 
             echo "Running tests in environment: $env"
             pixi run --environment $env integration-tests ${{ needs.env-prepare.outputs.pytest-marks }}
@@ -236,7 +251,26 @@ jobs:
             cd easydynamics_py$py_ver
 
             echo "Running tests"
-            pixi run python -m pytest ../tests/unit/ --color=yes --cov= --cov-report=
+            pixi run python -m pytest ../tests/unit/ --color=yes -v
+
+            echo "Exiting pixi project directory"
+            cd ..
+          done
+
+      - name: Run functional tests
+        shell: bash
+        run: |
+          set -euo pipefail
+
+          for py_ver in $PY_VERSIONS; do
+            echo
+            echo "🔹🔸🔹🔸🔹 Python: $py_ver 🔹🔸🔹🔸🔹"
+
+            echo "Entering pixi project directory easydynamics_py$py_ver"
+            cd easydynamics_py$py_ver
+
+            echo "Running tests"
+            pixi run python -m pytest ../tests/functional/ --color=yes -v
 
             echo "Exiting pixi project directory"
             cd ..

.github/workflows/tutorial-tests.yml

@@ -45,10 +45,6 @@ jobs:
       - name: Set up pixi
         uses: ./.github/actions/setup-pixi
 
-      - name: Test tutorials as python scripts
-        shell: bash
-        run: pixi run script-tests
-
       - name: Prepare notebooks
         shell: bash
         run: pixi run notebook-prepare

.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/