Fixes and cleanups after applying Copier templates

.badgery.yaml

@@ -5,19 +5,18 @@ cards:
   - group: Tests
     type: gh_action
     title: Code/package tests (GitHub)
-    file: test.yaml
+    file: test.yml
     enabled: true
-
   - group: Tests
     type: gh_action
     title: Tutorial tests (GitHub)
-    file: tutorial-tests.yaml
+    file: tutorial-tests.yml
     enabled: true
 
   - group: Tests
     type: gh_action
     title: Package tests (PyPI)
-    file: pypi-test.yaml
+    file: pypi-test.yml
     enabled: true
 
   - group: Code Quality
@@ -60,15 +59,14 @@ cards:
     title: Docstring coverage (interrogate)
     report: reports/{branch}/coverage-docstring.txt
     enabled: true
-
   - group: Build & Release
     type: gh_action
     title: Publishing (PyPI)
-    workflow: pypi-publish.yaml
+    workflow: pypi-publish.yml
     enabled: true
 
   - group: Build & Release
     type: gh_action
     title: Docs build/deployment
-    workflow: docs.yaml
+    workflow: docs.yml
     enabled: true

.copier-answers.yml

@@ -0,0 +1,25 @@
+# WARNING: Do not edit this file manually.
+# Any changes will be overwritten by Copier.
+_commit: v0.0.3
+_src_path: gh:easyscience/templates
+app_docs_url: https://easyscience.github.io/dynamics-app
+app_doi: 10.5281/zenodo.18163581
+app_package_name: easydynamics_app
+app_python: '3.12'
+app_repo_name: dynamics-app
+lib_docs_url: https://easyscience.github.io/dynamics-lib
+lib_doi: 10.5281/zenodo.18163581
+lib_package_name: easydynamics
+lib_python_max: '3.12'
+lib_python_min: '3.11'
+lib_repo_name: dynamics-lib
+project_contact_email: henrik.jacobsen@ess.eu
+project_copyright_years: 2025-2026
+project_extended_description: For plotting and fitting QENS and INS powder data
+project_homepage_url: https://easyscience.github.io/dynamics
+project_name: EasyDynamics
+project_repo_name: dynamics
+project_short_description: QENS data analysis
+project_shortcut: EQ
+project_type: both
+template_type: lib

.github/workflows/coverage.yaml → .github/workflows/coverage.yml

@@ -90,5 +90,5 @@ jobs:
   # Job 4: Build and publish dashboard (reusable workflow)
   run-reusable-workflows:
     needs: [docstring-coverage, unit-tests-coverage, integration-tests-coverage] # depend on the previous jobs
-    uses: ./.github/workflows/dashboard.yaml
+    uses: ./.github/workflows/dashboard.yml
     secrets: inherit

.github/workflows/dashboard.yaml → .github/workflows/dashboard.yml

@@ -29,9 +29,10 @@ jobs:
         shell: bash
         run: pixi add --pypi --git https://github.com/enhantica/badgery badgery
 
+      # Temporary: do not use $DEFAULT_BRANCH in $DEFAULT_BRANCH $DEVELOP_BRANCH $CI_BRANCH
       - name: Run docstring coverage and code complexity/maintainability checks
         run: |
-          for BRANCH in $DEFAULT_BRANCH $DEVELOP_BRANCH $CI_BRANCH; do
+          for BRANCH in $DEVELOP_BRANCH $CI_BRANCH; do
             echo
             echo "🔹🔸🔹🔸🔹 Processing branch $BRANCH 🔹🔸🔹🔸🔹"
             if [ -d "../$BRANCH" ]; then
@@ -41,20 +42,25 @@ jobs:
 
             git worktree add ../$BRANCH origin/$BRANCH
             mkdir -p reports/$BRANCH
+            CODE_PATH="../$BRANCH/src"
 
             echo "Docstring coverage for branch $BRANCH"
-            pixi run interrogate -c pyproject.toml --fail-under=0 ../$BRANCH/src > reports/$BRANCH/coverage-docstring.txt
+            pixi run interrogate -c pyproject.toml --fail-under=0 $CODE_PATH > reports/$BRANCH/coverage-docstring.txt
 
             echo "Cyclomatic complexity for branch $BRANCH"
-            pixi run radon cc -s -j ../$BRANCH/src > reports/$BRANCH/cyclomatic-complexity.json
+            pixi run radon cc -s -j $CODE_PATH > reports/$BRANCH/cyclomatic-complexity.json
 
             echo "Maintainability index for branch $BRANCH"
-            pixi run radon mi -j ../$BRANCH/src > reports/$BRANCH/maintainability-index.json
+            pixi run radon mi -j $CODE_PATH > reports/$BRANCH/maintainability-index.json
 
             echo "Raw metrics for branch $BRANCH"
-            pixi run radon raw -s -j ../$BRANCH/src > reports/$BRANCH/raw-metrics.json
+            pixi run radon raw -s -j $CODE_PATH > reports/$BRANCH/raw-metrics.json
           done
 
+      # Temporary: copy develop branch code metrics to default branch folder
+      - name: Copy develop branch reports to default branch folder
+        run: cp -r reports/$DEVELOP_BRANCH reports/$DEFAULT_BRANCH
+
       - name: Generate dashboard HTML
         run: >
           pixi run python -m badgery --config .badgery.yaml --repo ${{ github.repository

.github/workflows/docs.yaml → .github/workflows/docs.yml

@@ -100,7 +100,6 @@ jobs:
       # Uses frozen lockfile to ensure reproducible builds.
       - name: Set up pixi
         uses: ./.github/actions/setup-pixi
-
       # Pre-import the main package to exclude info messages from the docs
       # E.g., Matplotlib may print messages to stdout/stderr when first
       # imported. This step allows to avoid "Matplotlib is building the font

.github/workflows/pypi-test.yaml → .github/workflows/pypi-test.yml

@@ -42,9 +42,9 @@ jobs:
       - name: Init pixi project
         run: pixi init easydynamics
 
-      - name: Add Python 3.13 from Conda
+      - name: Add Python 3.12 from Conda
         working-directory: easydynamics
-        run: pixi add "python=3.13"
+        run: pixi add "python=3.12"
 
       - name: Add other Conda dependencies
         working-directory: easydynamics
@@ -73,5 +73,5 @@ jobs:
   # Job 2: Build and publish dashboard (reusable workflow)
   run-reusable-workflows:
     needs: pypi-package-tests # depend on previous job
-    uses: ./.github/workflows/dashboard.yaml
+    uses: ./.github/workflows/dashboard.yml
     secrets: inherit

.github/workflows/quality.yaml → .github/workflows/quality.yml

@@ -80,15 +80,6 @@ jobs:
         shell: bash
         run: pixi run nonpy-format-check
 
-      # Check formatting of Jupyter Notebooks in the tutorials folder
-      - name: Convert tutorial scripts to notebooks and check formatting
-        id: check_notebooks_formatting
-        continue-on-error: true
-        shell: bash
-        run: |
-          pixi run notebook-prepare
-          pixi run notebook-format-check
-
       # Add summary
       - name: Add quality checks summary
         if: always()
@@ -104,17 +95,15 @@ jobs:
             echo "| py format        | ${{ steps.check_code_formatting.outcome == 'success' && '✅' || '❌' }} |"
             echo "| docstring format | ${{ steps.check_docs_formatting.outcome == 'success' && '✅' || '❌' }} |"
             echo "| nonpy format     | ${{ steps.check_others_formatting.outcome == 'success' && '✅' || '❌' }} |"
-            echo "| notebooks format | ${{ steps.check_notebooks_formatting.outcome == 'success' && '✅' || '❌' }} |"
           } >> "$GITHUB_STEP_SUMMARY"
 
       # Fail job if any check failed
       - name: Fail job if any check failed
         if: |
-          steps.check_pyproject.outcome == 'failure' ||
-          steps.check_code_linting.outcome == 'failure' ||
-          steps.check_code_formatting.outcome == 'failure' ||
-          steps.check_docs_formatting.outcome == 'failure' ||
-          steps.check_others_formatting.outcome == 'failure' ||
-          steps.check_notebooks_formatting.outcome == 'failure'
+          steps.check_pyproject.outcome == 'failure'
+          || steps.check_code_linting.outcome == 'failure'
+          || steps.check_code_formatting.outcome == 'failure'
+          || steps.check_docs_formatting.outcome == 'failure'
+          || steps.check_others_formatting.outcome == 'failure'
         shell: bash
         run: exit 1

.github/workflows/test-trigger.yaml → .github/workflows/test-trigger.yml

@@ -32,6 +32,6 @@ jobs:
             await github.rest.actions.createWorkflowDispatch({
               owner: context.repo.owner,
               repo: context.repo.repo,
-              workflow_id: "test.yaml",
+              workflow_id: "test.yml",
               ref: "develop"
             });

.github/workflows/test.yaml → .github/workflows/test.yml

@@ -45,8 +45,8 @@ 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 3.13'
-  PIXI_ENVS: 'py-311-env py-313-env'
+  PY_VERSIONS: '3.11 3.12'
+  PIXI_ENVS: 'py-311-env py-312-env'
 
 jobs:
   # Job 1: Set up environment variables
@@ -240,7 +240,7 @@ jobs:
             cd easydynamics_py$py_ver
 
             echo "Running tests"
-            pixi run python -m pytest ../tests/unit/ --color=yes -v
+            pixi run python -m pytest ../tests/unit/ --color=yes --cov= --cov-report=
 
             echo "Exiting pixi project directory"
             cd ..
@@ -268,5 +268,5 @@ jobs:
   # Job 4: Build and publish dashboard (reusable workflow)
   run-reusable-workflows:
     needs: package-test # depend on previous job
-    uses: ./.github/workflows/dashboard.yaml
+    uses: ./.github/workflows/dashboard.yml
     secrets: inherit

.github/workflows/tutorial-tests-trigger.yaml → .github/workflows/tutorial-tests-trigger.yml

@@ -32,6 +32,6 @@ jobs:
             await github.rest.actions.createWorkflowDispatch({
               owner: context.repo.owner,
               repo: context.repo.repo,
-              workflow_id: "tutorial-tests.yaml",
+              workflow_id: "tutorial-tests.yml",
               ref: "develop"
             });

.github/workflows/tutorial-tests.yaml → .github/workflows/tutorial-tests.yml

@@ -57,5 +57,5 @@ jobs:
   # Job 2: Build and publish dashboard (reusable workflow)
   run-reusable-workflows:
     needs: tutorial-tests # depend on previous job
-    uses: ./.github/workflows/dashboard.yaml
+    uses: ./.github/workflows/dashboard.yml
     secrets: inherit

.prettierignore

@@ -10,6 +10,8 @@ docs/overrides/
 docs/site/
 docs/docs/assets/
 
+# Python
+.pytest_cache/
 
 # MyPy
 .mypy_cache

README.md

@@ -13,9 +13,10 @@
 and ins powder data.
 
 **EasyDynamics** is available both as a Python library and as a
-cross-platform desktop application. Here, we focus on the Python
-library. For the graphical user interface (GUI), please see the
-corresponding
+cross-platform desktop application.
+
+Here, we focus on the Python library. For the graphical user interface
+(GUI), please see the corresponding
 [GUI resources](https://github.com/easyscience/dynamics-app).
 
 ## Useful Links

codecov.yml

@@ -0,0 +1,13 @@
+# Codecov configuration
+# https://docs.codecov.com/docs/codecovyml-reference
+
+coverage:
+  status:
+    project:
+      default:
+        # Make project coverage informational (won't block PR)
+        informational: true
+    patch:
+      default:
+        # Require patch coverage but with threshold
+        threshold: 1%

docs/docs/api-reference/convolution.md

@@ -0,0 +1 @@
+::: easydynamics.convolution

docs/docs/api-reference/index.md

@@ -6,3 +6,7 @@ icon: material/code-braces-box
 
 This section contains the reference detailing the functions and modules
 available in EasyDynamics.
+
+- [convolution](convolution.md) – Contains ...
+- [sample_model](sample_model.md) – Handles ...
+- [utils](utils.md) – Miscellaneous utility functions for ...

docs/docs/api-reference/sample_model.md

@@ -0,0 +1 @@
+::: easydynamics.sample_model

docs/docs/api-reference/utils.md

@@ -0,0 +1 @@
+::: easydynamics.utils

docs/docs/installation-and-setup/index.md

@@ -5,7 +5,7 @@ icon: material/cog-box
 # :material-cog-box: Installation & Setup
 
 **EasyDynamics** is a cross-platform Python library compatible with
-**Python 3.11** through **3.13**.
+**Python 3.11** through **3.12**.
 
 To install and set up EasyDynamics, we recommend using
 [**Pixi**](https://prefix.dev), a modern package manager for Windows,
@@ -42,9 +42,9 @@ This section describes the simplest way to set up EasyDynamics using
   pixi init easydynamics
   cd easydynamics
   ```
-- Set the Python version for the Pixi environment (e.g., 3.13):
+- Set the Python version for the Pixi environment (e.g., 3.12):
   ```txt
-  pixi add python=3.13
+  pixi add python=3.12
   ```
 - Add the GNU Scientific Library (GSL) dependency:
   ```txt

docs/docs/introduction/index.md

@@ -10,22 +10,23 @@ icon: material/information-slab-circle
 and ins powder data.
 
 **EasyDynamics** is available both as a Python library and as a
-cross-platform desktop application. Here, we focus on the Python
-library. For the graphical user interface (GUI), please see the
-corresponding
-[GUI resources](https://github.com/easyscience/dynamics-app).
+cross-platform desktop application.
+
+Here, we focus on the Python library. For the graphical user interface
+(GUI), please see the corresponding
+[GUI resources](https://easyscience.github.io/dynamics-app).
 
 **EasyDynamics** is developed using the
 [EasyScience framework](https://easyscience.org).
 
 ## License
 
-**EasyDynamics** is released under the
+**EasyDynamics** library is released under the
 [BSD 3-Clause License](https://raw.githubusercontent.com/easyscience/dynamics-lib/master/LICENSE).
 
 ## Releases
 
-The latest version of the **EasyDynamics** Python library is
+The latest version of the **EasyDynamics** library is
 [{{ vars.release_version }}](https://github.com/easyscience/dynamics-lib/releases/latest).
 
 For a complete list of new features, bug fixes, and improvements, see
@@ -34,8 +35,8 @@ the
 
 ## Citation
 
-If you use **EasyDynamics** in your work, please cite the specific
-version you used.
+If you use **EasyDynamics** library in your work, please cite the
+specific version you used.
 
 All official releases of the **EasyDynamics** library are archived on
 Zenodo, each with a version-specific Digital Object Identifier (DOI).