Release: merge develop into master

.copier-answers.yml

@@ -1,19 +1,19 @@
 # WARNING: Do not edit this file manually.
 # Any changes will be overwritten by Copier.
-_commit: v0.10.1-33-g0f85abf
+_commit: v0.10.1-40-g29e2ccf
 _src_path: gh:easyscience/templates
 app_docs_url: https://easyscience.github.io/diffraction-app
 app_doi: 10.5281/zenodo.18163581
 app_package_name: easydiffraction_app
-app_python: '3.13'
+app_python: '3.14'
 app_repo_name: diffraction-app
 home_page_url: https://easyscience.github.io/diffraction
 home_repo_name: diffraction
 lib_docs_url: https://easyscience.github.io/diffraction-lib
 lib_doi: 10.5281/zenodo.18163581
 lib_package_name: easydiffraction
 lib_python_max: '3.14'
-lib_python_min: '3.11'
+lib_python_min: '3.12'
 lib_repo_name: diffraction-lib
 project_contact_email: support@easydiffraction.org
 project_copyright_years: 2021-2026

.github/copilot-instructions.md

@@ -42,7 +42,8 @@
   and UPPER_SNAKE_CASE for constants.
 - Use `from __future__ import annotations` in every module.
 - Type-annotate all public function signatures.
-- Docstrings on all public classes and methods (numpy style).
+- Docstrings on all public classes and methods (numpy style). These must
+  include sections Parameters, Returns and Raises, where applicable.
 - Prefer flat over nested, explicit over clever.
 - Write straightforward code; do not add defensive checks for unlikely
   edge cases.
@@ -59,6 +60,19 @@
   with both getter and setter) or **read-only** (property with getter
   only). If internal code needs to mutate a read-only property, add a
   private `_set_<name>` method instead of exposing a public setter.
+- Lint complexity thresholds (`max-args`, `max-branches`,
+  `max-statements`, `max-locals`, `max-nested-blocks`, etc. in
+  `pyproject.toml`) are intentional code-quality guardrails. They are
+  not arbitrary numbers — the project uses ruff's defaults (with
+  `max-args` and `max-positional-args` set to 6 instead of 5 to account
+  for ruff counting `self`/`cls`). When code violates a threshold, it is
+  a signal that the function or class needs refactoring — not that the
+  threshold needs raising. Do not raise thresholds, add `# noqa`
+  comments, or use any other mechanism to silence complexity violations.
+  Instead, refactor the code (extract helpers, introduce parameter
+  objects, flatten nesting, etc.). For complex refactors that touch many
+  lines or change public API, propose a refactoring plan and wait for
+  approval before proceeding.
 
 ## Architecture
 
@@ -107,6 +121,26 @@
   `*.py` script, then run `pixi run notebook-prepare` to regenerate the
   notebook.
 
+## Testing
+
+- Every new module, class, or bug fix must ship with tests. See
+  `docs/architecture/architecture.md` §10 for the full test strategy.
+- **Unit tests mirror the source tree:**
+  `src/easydiffraction/<pkg>/<mod>.py` →
+  `tests/unit/easydiffraction/<pkg>/test_<mod>.py`. Run
+  `pixi run test-structure-check` to verify.
+- Category packages with only `default.py`/`factory.py` may use a single
+  parent-level `test_<package>.py` instead of per-file tests.
+- Supplementary test files use the pattern `test_<mod>_coverage.py`.
+- Tests that expect `log.error()` to raise must `monkeypatch` Logger to
+  RAISE mode (another test may have leaked WARN mode).
+- `@typechecked` setters raise `typeguard.TypeCheckError`, not
+  `TypeError`.
+- No test-ordering dependence, no network, no sleeping, no real
+  calculation engines in unit tests.
+- After adding or modifying tests, run `pixi run unit-tests` and confirm
+  all tests pass.
+
 ## Changes
 
 - Before implementing any structural or design change (new categories,
@@ -147,6 +181,8 @@
   `docs/architecture/architecture.md`.
 - After changes, run linting and formatting fixes with `pixi run fix`.
   Do not check what was auto-fixed, just accept the fixes and move on.
+  Then, run linting and formatting checks with `pixi run check` and
+  address any remaining issues until the code is clean.
 - After changes, run unit tests with `pixi run unit-tests`.
 - After changes, run integration tests with
   `pixi run integration-tests`.

.github/workflows/backmerge.yml

@@ -20,6 +20,11 @@ concurrency:
   group: backmerge-master-into-develop
   cancel-in-progress: false
 
+# Opt into Node.js 24 for all JavaScript actions.
+# Remove once all referenced actions natively target Node 24.
+env:
+  FORCE_JAVASCRIPT_ACTIONS_TO_NODE24: true
+
 jobs:
   backmerge:
     runs-on: ubuntu-latest

.github/workflows/cleanup.yml

@@ -61,6 +61,11 @@ on:
           - 'false'
           - 'true'
 
+# Opt into Node.js 24 for all JavaScript actions.
+# Remove once all referenced actions natively target Node 24.
+env:
+  FORCE_JAVASCRIPT_ACTIONS_TO_NODE24: true
+
 jobs:
   del-runs:
     runs-on: ubuntu-latest

.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
@@ -15,15 +17,18 @@ 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:
   CI_BRANCH: ${{ github.head_ref || github.ref_name }}
+  # Opt into Node.js 24 for all JavaScript actions.
+  # Remove once all referenced actions natively target Node 24.
+  FORCE_JAVASCRIPT_ACTIONS_TO_NODE24: true
 
 jobs:
   # Job 1: Run docstring coverage

.github/workflows/dashboard.yml

@@ -14,6 +14,9 @@ env:
   DEVELOP_BRANCH: develop
   REPO_OWNER: ${{ github.repository_owner }}
   REPO_NAME: ${{ github.event.repository.name }}
+  # Opt into Node.js 24 for all JavaScript actions.
+  # Remove once all referenced actions natively target Node 24.
+  FORCE_JAVASCRIPT_ACTIONS_TO_NODE24: true
 
 jobs:
   dashboard:

.github/workflows/docs.yml

@@ -48,6 +48,9 @@ env:
   IS_RELEASE_TAG: ${{ startsWith(github.ref, 'refs/tags/v') }}
   GITHUB_REPOSITORY: ${{ github.repository }}
   NOTEBOOKS_DIR: tutorials
+  # Opt into Node.js 24 for all JavaScript actions.
+  # Remove once all referenced actions natively target Node 24.
+  FORCE_JAVASCRIPT_ACTIONS_TO_NODE24: true
 
 jobs:
   # Single job that builds and deploys documentation.

.github/workflows/issues-labels.yml

@@ -11,10 +11,21 @@ on:
 permissions:
   issues: write
 
+# Opt into Node.js 24 for all JavaScript actions.
+# Remove once all referenced actions natively target Node 24.
+env:
+  FORCE_JAVASCRIPT_ACTIONS_TO_NODE24: true
+
 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

.github/workflows/lint-format.yml

@@ -34,6 +34,9 @@ permissions:
 # Set the environment variables to be used in all jobs defined in this workflow
 env:
   CI_BRANCH: ${{ github.head_ref || github.ref_name }}
+  # Opt into Node.js 24 for all JavaScript actions.
+  # Remove once all referenced actions natively target Node 24.
+  FORCE_JAVASCRIPT_ACTIONS_TO_NODE24: true
 
 jobs:
   lint-format:

.github/workflows/pypi-publish.yml

@@ -10,6 +10,11 @@ on:
   # Allows you to run this workflow manually from the Actions tab
   workflow_dispatch:
 
+# Opt into Node.js 24 for all JavaScript actions.
+# Remove once all referenced actions natively target Node 24.
+env:
+  FORCE_JAVASCRIPT_ACTIONS_TO_NODE24: true
+
 jobs:
   pypi-publish:
     runs-on: ubuntu-latest

.github/workflows/pypi-test.yml

@@ -20,6 +20,9 @@ permissions:
 env:
   CI_BRANCH: ${{ github.head_ref || github.ref_name }}
   DEFAULT_BRANCH: ${{ github.event.repository.default_branch }}
+  # Opt into Node.js 24 for all JavaScript actions.
+  # Remove once all referenced actions natively target Node 24.
+  FORCE_JAVASCRIPT_ACTIONS_TO_NODE24: true
 
 jobs:
   # Job 1: Test installation from PyPI on multiple OS
@@ -45,30 +48,38 @@ jobs:
       - name: Init pixi project
         run: pixi init easydiffraction
 
+      - name: Set the minimum system requirements
+        run: pixi project system-requirements add macos 14.0
+
       - name: Add Python 3.14 from Conda
         working-directory: easydiffraction
         run: pixi add "python=3.14"
 
       - name: Add other Conda dependencies
         working-directory: easydiffraction
-        run: pixi add gsl
-
-      - name: Add easydiffraction from PyPI
-        working-directory: easydiffraction
-        run: pixi add --pypi "easydiffraction"
+        run: |
+          pixi add gsl
+          pixi add --platform osx-arm64 libcxx
 
-      - name: Add dev dependencies from PyPI
+      - name: Add pycrysfml calculator from custom PyPI index
         working-directory: easydiffraction
-        run: pixi add --pypi pytest pytest-xdist
+        run: |
+          echo '' >> pixi.toml
+          echo '[pypi-dependencies]' >> pixi.toml
+          echo 'pycrysfml = { version = ">=0.2.1", index = "https://easyscience.github.io/pypi/" }' >> pixi.toml
 
-      - name: Add Pixi task as a shortcut
+      - name: Add easydiffraction (with dev dependencies) from PyPI
         working-directory: easydiffraction
-        run: pixi task add easydiffraction "python -m easydiffraction"
+        run: pixi add --pypi "easydiffraction[dev]"
 
       - name: Run unit tests to verify the installation
         working-directory: easydiffraction
         run: pixi run python -m pytest ../tests/unit/ --color=yes -v
 
+      - name: Run functional tests to verify the installation
+        working-directory: easydiffraction
+        run: pixi run python -m pytest ../tests/functional/ --color=yes -v
+
       - name: Run integration tests to verify the installation
         working-directory: easydiffraction
         run: pixi run python -m pytest ../tests/integration/ --color=yes -n auto

.github/workflows/release-notes.yml

@@ -10,6 +10,11 @@ on:
   # Allows you to run this workflow manually from the Actions tab
   workflow_dispatch:
 
+# Opt into Node.js 24 for all JavaScript actions.
+# Remove once all referenced actions natively target Node 24.
+env:
+  FORCE_JAVASCRIPT_ACTIONS_TO_NODE24: true
+
 jobs:
   draft-release-notes:
     permissions:

.github/workflows/release-pr.yml

@@ -24,6 +24,9 @@ permissions:
 env:
   DEFAULT_BRANCH: ${{ github.event.repository.default_branch }}
   SOURCE_BRANCH: ${{ inputs.source_branch || 'develop' }}
+  # Opt into Node.js 24 for all JavaScript actions.
+  # Remove once all referenced actions natively target Node 24.
+  FORCE_JAVASCRIPT_ACTIONS_TO_NODE24: true
 
 jobs:
   create-pull-request:

.github/workflows/security.yml

@@ -44,6 +44,11 @@ permissions:
   contents: read
   security-events: write
 
+# Opt into Node.js 24 for all JavaScript actions.
+# Remove once all referenced actions natively target Node 24.
+env:
+  FORCE_JAVASCRIPT_ACTIONS_TO_NODE24: true
+
 jobs:
   codeql:
     name: Code scanning

.github/workflows/test-trigger.yml

@@ -10,6 +10,11 @@ on:
 permissions:
   contents: read
 
+# Opt into Node.js 24 for all JavaScript actions.
+# Remove once all referenced actions natively target Node 24.
+env:
+  FORCE_JAVASCRIPT_ACTIONS_TO_NODE24: true
+
 jobs:
   code-tests-trigger:
     runs-on: ubuntu-latest

.github/workflows/test.yml

@@ -44,8 +44,11 @@ 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 3.14'
-  PIXI_ENVS: 'py-311-env py-314-env'
+  PY_VERSIONS: '3.12 3.14'
+  PIXI_ENVS: 'py-312-env py-314-env'
+  # Opt into Node.js 24 for all JavaScript actions.
+  # Remove once all referenced actions natively target Node 24.
+  FORCE_JAVASCRIPT_ACTIONS_TO_NODE24: true
 
 jobs:
   # Job 1: Set up environment variables
@@ -214,7 +217,14 @@ jobs:
             # platform-specific deps so this is a no-op on Linux/Windows.
             echo "Adding libc++ for macOS (required by diffpy.pdffit2)"
             pixi add --platform osx-arm64 libcxx
-            pixi add --platform osx-64 libcxx
+
+            # Doing this in a hacky way, as pixi does not support adding 
+            # dependencies from a custom PyPI index with a CLI command without
+            # specifying full wheel name.
+            echo "Adding pycrysfml from custom PyPI index"
+            echo '' >> pixi.toml
+            echo '[pypi-dependencies]' >> pixi.toml
+            echo 'pycrysfml = { version = ">=0.2.1", index = "https://easyscience.github.io/pypi/" }' >> pixi.toml
 
             echo "Looking for wheel in ../dist/py$py_ver/"
             ls -l "../dist/py$py_ver/"

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

@@ -10,6 +10,11 @@ on:
 permissions:
   contents: read
 
+# Opt into Node.js 24 for all JavaScript actions.
+# Remove once all referenced actions natively target Node 24.
+env:
+  FORCE_JAVASCRIPT_ACTIONS_TO_NODE24: true
+
 jobs:
   tutorial-tests-trigger:
     runs-on: ubuntu-latest

.github/workflows/tutorial-tests.yml

@@ -27,6 +27,9 @@ concurrency:
 # Set the environment variables to be used in all jobs defined in this workflow
 env:
   CI_BRANCH: ${{ github.head_ref || github.ref_name }}
+  # Opt into Node.js 24 for all JavaScript actions.
+  # Remove once all referenced actions natively target Node 24.
+  FORCE_JAVASCRIPT_ACTIONS_TO_NODE24: true
 
 jobs:
   # Job 1: Test tutorials as scripts and notebooks on multiple OS

.gitignore

@@ -44,3 +44,8 @@ CMakeLists.txt.user*
 .cache/
 *.log
 *.zip
+
+# ED
+# Used to fetch tutorials data during their runtime. Need to have '/' at
+# the beginning to avoid ignoring 'data' module in the src/.
+/data/

.pre-commit-config.yaml

@@ -53,9 +53,23 @@ repos:
         pass_filenames: false
         stages: [manual]
 
+      - id: pixi-test-structure-check
+        name: pixi run test-structure-check
+        entry: pixi run test-structure-check
+        language: system
+        pass_filenames: false
+        stages: [manual]
+
       - id: pixi-unit-tests
         name: pixi run unit-tests
         entry: pixi run unit-tests
         language: system
         pass_filenames: false
         stages: [manual]
+
+      - id: pixi-functional-tests
+        name: pixi run functional-tests
+        entry: pixi run functional-tests
+        language: system
+        pass_filenames: false
+        stages: [manual]