Merge pull request #147 from easyscience/develop

Release: merge develop into master

Author: AndrewSazonov

.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