Release: merge develop into master

.codefactorignore

@@ -0,0 +1,13 @@
+# CodeFactor exclude patterns configuration must be done online:
+# https://www.codefactor.io/repository/github/easyscience/diffraction-lib/ignore
+#
+# Last updated: 2026-01-05
+#
+# Exclude patterns:
+# deps/**
+# docs/**
+# src/easydiffraction/utils/_vendored/jupyter_dark_detect/**
+# tests/**
+# tmp/**
+# tools/**
+# tutorials/**

.github/workflows/coverage.yaml

@@ -34,7 +34,7 @@ jobs:
         uses: actions/checkout@v5
 
       - name: Set up pixi
-        uses: prefix-dev/[email protected].0
+        uses: prefix-dev/[email protected].3
         with:
           environments: default
           activate-environment: default
@@ -59,7 +59,7 @@ jobs:
         uses: actions/checkout@v5
 
       - name: Set up pixi
-        uses: prefix-dev/[email protected].0
+        uses: prefix-dev/[email protected].3
         with:
           environments: default
           activate-environment: default
@@ -95,7 +95,7 @@ jobs:
         uses: actions/checkout@v5
 
       - name: Set up pixi
-        uses: prefix-dev/[email protected].0
+        uses: prefix-dev/[email protected].3
         with:
           environments: default
           activate-environment: default

.github/workflows/dashboard.yaml

@@ -43,7 +43,7 @@ jobs:
           fetch-depth: 0
 
       - name: Set up pixi
-        uses: prefix-dev/[email protected].0
+        uses: prefix-dev/[email protected].3
         with:
           environments: default
           activate-environment: default

.github/workflows/docs.yaml

@@ -114,7 +114,7 @@ jobs:
       # Set up the pixi package manager and install dependencies from pixi.toml.
       # Uses frozen lockfile to ensure reproducible builds.
       - name: Set up pixi
-        uses: prefix-dev/[email protected].0
+        uses: prefix-dev/[email protected].3
         with:
           environments: default
           activate-environment: default

.github/workflows/pypi-publish.yaml

@@ -21,7 +21,7 @@ jobs:
           fetch-depth: '0' # full history with tags to get the version number by versioningit
 
       - name: Set up pixi
-        uses: prefix-dev/[email protected].0
+        uses: prefix-dev/[email protected].3
         with:
           environments: default
           activate-environment: default

.github/workflows/pypi-test.yaml

@@ -30,7 +30,7 @@ jobs:
 
     steps:
       - name: Set up pixi
-        uses: prefix-dev/[email protected].0
+        uses: prefix-dev/[email protected].3
         with:
           run-install: false
           cache: false

.github/workflows/quality.yaml

@@ -40,7 +40,7 @@ jobs:
         uses: actions/checkout@v5
 
       - name: Set up pixi
-        uses: prefix-dev/[email protected].0
+        uses: prefix-dev/[email protected].3
         with:
           environments: default
           activate-environment: default

.github/workflows/release-notes.yaml

@@ -25,7 +25,7 @@ jobs:
           fetch-depth: 0 # full history with tags to get the version number
 
       - name: Set up pixi
-        uses: prefix-dev/[email protected].0
+        uses: prefix-dev/[email protected].3
         with:
           environments: default
           activate-environment: default

.github/workflows/test.yaml

@@ -88,7 +88,7 @@ jobs:
           fetch-depth: '0' # full history with tags to get the version number by versioningit
 
       - name: Set up pixi
-        uses: prefix-dev/[email protected].0
+        uses: prefix-dev/[email protected].3
         with:
           environments: ${{ env.PIXI_ENVS }}
           run-install: true
@@ -190,7 +190,7 @@ jobs:
           path: . # directory to extract downloaded zipped artifacts
 
       - name: Set up pixi
-        uses: prefix-dev/[email protected].0
+        uses: prefix-dev/[email protected].3
         with:
           environments: ${{ env.PIXI_ENVS }}
           run-install: true

.github/workflows/tutorial-tests.yaml

@@ -41,7 +41,7 @@ jobs:
         uses: actions/checkout@v5
 
       - name: Set up pixi
-        uses: prefix-dev/[email protected].0
+        uses: prefix-dev/[email protected].3
         with:
           environments: default
           activate-environment: default

codecov.yml

@@ -0,0 +1,18 @@
+# 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%
+
+ignore:
+  # Vendored third-party code - not our code to test
+  - 'src/easydiffraction/utils/_vendored/**'
+  - 'src/easydiffraction/utils/_vendored/jupyter_dark_detect/**'

pixi.toml

@@ -52,10 +52,7 @@ jupyterlab = '*'                                      # Jupyter notebooks
 pixi-kernel = '*'                                     # Pixi Jupyter kernel
 easydiffraction = { version = '*', extras = ['all'] } # Main package
 
-[target.osx.pypi-dependencies]
-h5py = "==3.14.0" # macOS only: avoid broken 3.15.0 wheel
-
-# Features for specific Python versions
+# Specific features
 
 # Each feature sets a specific Python version for the environment.
 
@@ -193,7 +190,7 @@ docs-setup = { depends-on = [
 dist-build = 'python -m build --wheel --outdir dist'
 spdx-update = 'python tools/update_spdx.py'
 #dev-install = 'uv pip install --requirements pyproject.toml --extra all'
-dev-install = "python -m uv pip install --editable '.[all]'"
+dev-install = "python -m uv pip install --force-reinstall --editable '.[all]'"
 npm-config = 'npm config set registry https://registry.npmjs.org/'
 prettier-install = 'npm install --no-save --no-audit --no-fund prettier prettier-plugin-toml'
 pre-commit-setup = 'pre-commit clean && pre-commit uninstall && pre-commit install --hook-type pre-commit --hook-type pre-push --overwrite'

pyproject.toml

@@ -22,7 +22,7 @@ classifiers = [
 ]
 requires-python = '>=3.11,<3.14'
 dependencies = [
-  'numpy<2.4',      # Numerical computing library; <2.4 required for cryspy 0.9.x compatibility
+  'numpy',          # Numerical computing library
   'colorama',       # Color terminal output
   'tabulate',       # Pretty-print tabular data for terminal output
   'asciichartpy',   # ASCII charts for terminal output
@@ -68,19 +68,18 @@ docs = [
   'mike',                            # MkDocs: Versioned documentation support
   'mkdocs',                          # Static site generator
   'mkdocs-material',                 # Documentation framework on top of MkDocs
-  'mkdocs-autorefs<1.3.0',           # MkDocs: Auto-references support. 1.3.0 => DeprecationWarning: Setting a fallback anchor function is deprecated and ...
-  'mkdocs-jupyter',                  # MkDocs: Jupyter notebook support.
+  'mkdocs-autorefs',                 # MkDocs: Auto-references support
+  'mkdocs-jupyter',                  # MkDocs: Jupyter notebook support
   'mkdocs-plugin-inline-svg',        # MkDocs: Inline SVG support
   'mkdocs-markdownextradata-plugin', # MkDocs: Markdown extra data support, such as global variables
   'mkdocstrings-python',             # MkDocs: Python docstring support
   'pyyaml',                          # YAML parser
 ]
 visualization = [
-  'darkdetect',          # Detecting dark mode
-  'jupyter_dark_detect', # Jupyter notebook dark mode support
-  'pandas',              # Displaying tables in juptyer notebooks
-  'plotly',              # Interactive plots
-  'py3Dmol',             # Visualisation of crystal structures
+  'darkdetect', # Detecting dark mode (system-level)
+  'pandas',     # Displaying tables in Jupyter notebooks
+  'plotly',     # Interactive plots
+  'py3Dmol',    # Visualisation of crystal structures
 ]
 all = [
   'easydiffraction[dev]',
@@ -266,6 +265,18 @@ force-single-line = true
 
 [tool.ruff.lint.per-file-ignores]
 '*test_*.py' = ['S101'] # allow asserts in test files
+# Vendored jupyter_dark_detect: keep as-is from upstream for easy updates
+# https://github.com/OpenMined/jupyter-dark-detect/tree/main/jupyter_dark_detect
+'src/easydiffraction/utils/_vendored/jupyter_dark_detect/*' = [
+  'S110',   # try-except-pass
+  'S112',   # try-except-continue
+  'S404',   # subprocess module
+  'S607',   # partial executable path
+  'TID252', # relative imports
+  'W291',   # trailing whitespace (in JS strings)
+  'W505',   # doc line too long
+  'E501',   # line too long (in JS strings)
+]
 
 [tool.ruff.lint.pycodestyle]
 max-line-length = 100 #99# https://peps.python.org/pep-0008/#maximum-line-length

src/easydiffraction/__init__.py

@@ -1,4 +1,4 @@
-# SPDX-FileCopyrightText: 2021-2025 EasyDiffraction contributors <https://github.com/easyscience/diffraction>
+# SPDX-FileCopyrightText: 2021-2026 EasyDiffraction contributors <https://github.com/easyscience/diffraction>
 # SPDX-License-Identifier: BSD-3-Clause
 
 from easydiffraction.experiments.experiment.factory import ExperimentFactory

src/easydiffraction/__main__.py

@@ -1,4 +1,4 @@
-# SPDX-FileCopyrightText: 2021-2025 EasyDiffraction contributors <https://github.com/easyscience/diffraction>
+# SPDX-FileCopyrightText: 2021-2026 EasyDiffraction contributors <https://github.com/easyscience/diffraction>
 # SPDX-License-Identifier: BSD-3-Clause
 
 import sys

src/easydiffraction/analysis/__init__.py

@@ -1,2 +1,2 @@
-# SPDX-FileCopyrightText: 2021-2025 EasyDiffraction contributors <https://github.com/easyscience/diffraction>
+# SPDX-FileCopyrightText: 2021-2026 EasyDiffraction contributors <https://github.com/easyscience/diffraction>
 # SPDX-License-Identifier: BSD-3-Clause

src/easydiffraction/analysis/analysis.py

@@ -1,4 +1,4 @@
-# SPDX-FileCopyrightText: 2021-2025 EasyDiffraction contributors <https://github.com/easyscience/diffraction>
+# SPDX-FileCopyrightText: 2021-2026 EasyDiffraction contributors <https://github.com/easyscience/diffraction>
 # SPDX-License-Identifier: BSD-3-Clause
 
 from typing import List

src/easydiffraction/analysis/calculators/__init__.py

@@ -1,2 +1,2 @@
-# SPDX-FileCopyrightText: 2021-2025 EasyDiffraction contributors <https://github.com/easyscience/diffraction>
+# SPDX-FileCopyrightText: 2021-2026 EasyDiffraction contributors <https://github.com/easyscience/diffraction>
 # SPDX-License-Identifier: BSD-3-Clause

src/easydiffraction/analysis/calculators/base.py

@@ -1,4 +1,4 @@
-# SPDX-FileCopyrightText: 2021-2025 EasyDiffraction contributors <https://github.com/easyscience/diffraction>
+# SPDX-FileCopyrightText: 2021-2026 EasyDiffraction contributors <https://github.com/easyscience/diffraction>
 # SPDX-License-Identifier: BSD-3-Clause
 
 from abc import ABC

src/easydiffraction/analysis/calculators/crysfml.py

@@ -1,4 +1,4 @@
-# SPDX-FileCopyrightText: 2021-2025 EasyDiffraction contributors <https://github.com/easyscience/diffraction>
+# SPDX-FileCopyrightText: 2021-2026 EasyDiffraction contributors <https://github.com/easyscience/diffraction>
 # SPDX-License-Identifier: BSD-3-Clause
 
 from typing import Any

src/easydiffraction/analysis/calculators/cryspy.py

@@ -1,4 +1,4 @@
-# SPDX-FileCopyrightText: 2021-2025 EasyDiffraction contributors <https://github.com/easyscience/diffraction>
+# SPDX-FileCopyrightText: 2021-2026 EasyDiffraction contributors <https://github.com/easyscience/diffraction>
 # SPDX-License-Identifier: BSD-3-Clause
 
 import contextlib

src/easydiffraction/analysis/calculators/factory.py

@@ -1,4 +1,4 @@
-# SPDX-FileCopyrightText: 2021-2025 EasyDiffraction contributors <https://github.com/easyscience/diffraction>
+# SPDX-FileCopyrightText: 2021-2026 EasyDiffraction contributors <https://github.com/easyscience/diffraction>
 # SPDX-License-Identifier: BSD-3-Clause
 
 from typing import Dict

src/easydiffraction/analysis/calculators/pdffit.py

@@ -1,4 +1,4 @@
-# SPDX-FileCopyrightText: 2021-2025 EasyDiffraction contributors <https://github.com/easyscience/diffraction>
+# SPDX-FileCopyrightText: 2021-2026 EasyDiffraction contributors <https://github.com/easyscience/diffraction>
 # SPDX-License-Identifier: BSD-3-Clause
 """PDF calculation backend using diffpy.pdffit2 if available.
 

src/easydiffraction/analysis/categories/__init__.py

@@ -1,2 +1,2 @@
-# SPDX-FileCopyrightText: 2021-2025 EasyDiffraction contributors <https://github.com/easyscience/diffraction>
+# SPDX-FileCopyrightText: 2021-2026 EasyDiffraction contributors <https://github.com/easyscience/diffraction>
 # SPDX-License-Identifier: BSD-3-Clause

src/easydiffraction/analysis/categories/aliases.py

@@ -1,4 +1,4 @@
-# SPDX-FileCopyrightText: 2021-2025 EasyDiffraction contributors <https://github.com/easyscience/diffraction>
+# SPDX-FileCopyrightText: 2021-2026 EasyDiffraction contributors <https://github.com/easyscience/diffraction>
 # SPDX-License-Identifier: BSD-3-Clause
 """Alias category for mapping friendly names to parameter UIDs.
 

src/easydiffraction/analysis/categories/constraints.py

@@ -1,4 +1,4 @@
-# SPDX-FileCopyrightText: 2021-2025 EasyDiffraction contributors <https://github.com/easyscience/diffraction>
+# SPDX-FileCopyrightText: 2021-2026 EasyDiffraction contributors <https://github.com/easyscience/diffraction>
 # SPDX-License-Identifier: BSD-3-Clause
 """Simple symbolic constraint between parameters.
 

src/easydiffraction/analysis/categories/joint_fit_experiments.py

@@ -1,4 +1,4 @@
-# SPDX-FileCopyrightText: 2021-2025 EasyDiffraction contributors <https://github.com/easyscience/diffraction>
+# SPDX-FileCopyrightText: 2021-2026 EasyDiffraction contributors <https://github.com/easyscience/diffraction>
 # SPDX-License-Identifier: BSD-3-Clause
 """Joint-fit experiment weighting configuration.
 

src/easydiffraction/analysis/fit_helpers/__init__.py

@@ -1,2 +1,2 @@
-# SPDX-FileCopyrightText: 2021-2025 EasyDiffraction contributors <https://github.com/easyscience/diffraction>
+# SPDX-FileCopyrightText: 2021-2026 EasyDiffraction contributors <https://github.com/easyscience/diffraction>
 # SPDX-License-Identifier: BSD-3-Clause

src/easydiffraction/analysis/fit_helpers/metrics.py

@@ -1,4 +1,4 @@
-# SPDX-FileCopyrightText: 2021-2025 EasyDiffraction contributors <https://github.com/easyscience/diffraction>
+# SPDX-FileCopyrightText: 2021-2026 EasyDiffraction contributors <https://github.com/easyscience/diffraction>
 # SPDX-License-Identifier: BSD-3-Clause
 
 from typing import Optional

src/easydiffraction/analysis/fit_helpers/reporting.py

@@ -1,4 +1,4 @@
-# SPDX-FileCopyrightText: 2021-2025 EasyDiffraction contributors <https://github.com/easyscience/diffraction>
+# SPDX-FileCopyrightText: 2021-2026 EasyDiffraction contributors <https://github.com/easyscience/diffraction>
 # SPDX-License-Identifier: BSD-3-Clause
 
 from typing import Any

src/easydiffraction/analysis/fit_helpers/tracking.py

@@ -1,4 +1,4 @@
-# SPDX-FileCopyrightText: 2021-2025 EasyDiffraction contributors <https://github.com/easyscience/diffraction>
+# SPDX-FileCopyrightText: 2021-2026 EasyDiffraction contributors <https://github.com/easyscience/diffraction>
 # SPDX-License-Identifier: BSD-3-Clause
 
 import time

src/easydiffraction/analysis/fitting.py

@@ -1,4 +1,4 @@
-# SPDX-FileCopyrightText: 2021-2025 EasyDiffraction contributors <https://github.com/easyscience/diffraction>
+# SPDX-FileCopyrightText: 2021-2026 EasyDiffraction contributors <https://github.com/easyscience/diffraction>
 # SPDX-License-Identifier: BSD-3-Clause
 
 from typing import TYPE_CHECKING

src/easydiffraction/analysis/minimizers/__init__.py

@@ -1,2 +1,2 @@
-# SPDX-FileCopyrightText: 2021-2025 EasyDiffraction contributors <https://github.com/easyscience/diffraction>
+# SPDX-FileCopyrightText: 2021-2026 EasyDiffraction contributors <https://github.com/easyscience/diffraction>
 # SPDX-License-Identifier: BSD-3-Clause

src/easydiffraction/analysis/minimizers/base.py

@@ -1,4 +1,4 @@
-# SPDX-FileCopyrightText: 2021-2025 EasyDiffraction contributors <https://github.com/easyscience/diffraction>
+# SPDX-FileCopyrightText: 2021-2026 EasyDiffraction contributors <https://github.com/easyscience/diffraction>
 # SPDX-License-Identifier: BSD-3-Clause
 
 from abc import ABC

src/easydiffraction/analysis/minimizers/dfols.py

@@ -1,4 +1,4 @@
-# SPDX-FileCopyrightText: 2021-2025 EasyDiffraction contributors <https://github.com/easyscience/diffraction>
+# SPDX-FileCopyrightText: 2021-2026 EasyDiffraction contributors <https://github.com/easyscience/diffraction>
 # SPDX-License-Identifier: BSD-3-Clause
 
 from typing import Any

src/easydiffraction/analysis/minimizers/factory.py

@@ -1,4 +1,4 @@
-# SPDX-FileCopyrightText: 2021-2025 EasyDiffraction contributors <https://github.com/easyscience/diffraction>
+# SPDX-FileCopyrightText: 2021-2026 EasyDiffraction contributors <https://github.com/easyscience/diffraction>
 # SPDX-License-Identifier: BSD-3-Clause
 
 from typing import Any

src/easydiffraction/analysis/minimizers/lmfit.py

@@ -1,4 +1,4 @@
-# SPDX-FileCopyrightText: 2021-2025 EasyDiffraction contributors <https://github.com/easyscience/diffraction>
+# SPDX-FileCopyrightText: 2021-2026 EasyDiffraction contributors <https://github.com/easyscience/diffraction>
 # SPDX-License-Identifier: BSD-3-Clause
 
 from typing import Any

src/easydiffraction/core/__init__.py

@@ -1,2 +1,2 @@
-# SPDX-FileCopyrightText: 2021-2025 EasyDiffraction contributors <https://github.com/easyscience/diffraction>
+# SPDX-FileCopyrightText: 2021-2026 EasyDiffraction contributors <https://github.com/easyscience/diffraction>
 # SPDX-License-Identifier: BSD-3-Clause

src/easydiffraction/core/category.py

@@ -1,4 +1,4 @@
-# SPDX-FileCopyrightText: 2021-2025 EasyDiffraction contributors <https://github.com/easyscience/diffraction>
+# SPDX-FileCopyrightText: 2021-2026 EasyDiffraction contributors <https://github.com/easyscience/diffraction>
 # SPDX-License-Identifier: BSD-3-Clause
 
 from __future__ import annotations

src/easydiffraction/core/collection.py

@@ -1,4 +1,4 @@
-# SPDX-FileCopyrightText: 2021-2025 EasyDiffraction contributors <https://github.com/easyscience/diffraction>
+# SPDX-FileCopyrightText: 2021-2026 EasyDiffraction contributors <https://github.com/easyscience/diffraction>
 # SPDX-License-Identifier: BSD-3-Clause
 """Lightweight container for guarded items with name-based indexing.
 

src/easydiffraction/core/datablock.py

@@ -1,4 +1,4 @@
-# SPDX-FileCopyrightText: 2021-2025 EasyDiffraction contributors <https://github.com/easyscience/diffraction>
+# SPDX-FileCopyrightText: 2021-2026 EasyDiffraction contributors <https://github.com/easyscience/diffraction>
 # SPDX-License-Identifier: BSD-3-Clause
 
 from __future__ import annotations

src/easydiffraction/core/diagnostic.py

@@ -1,4 +1,4 @@
-# SPDX-FileCopyrightText: 2021-2025 EasyDiffraction contributors <https://github.com/easyscience/diffraction>
+# SPDX-FileCopyrightText: 2021-2026 EasyDiffraction contributors <https://github.com/easyscience/diffraction>
 # SPDX-License-Identifier: BSD-3-Clause
 """Diagnostics helpers for logging validation messages.
 

src/easydiffraction/core/factory.py

@@ -1,4 +1,4 @@
-# SPDX-FileCopyrightText: 2021-2025 EasyDiffraction contributors <https://github.com/easyscience/diffraction>
+# SPDX-FileCopyrightText: 2021-2026 EasyDiffraction contributors <https://github.com/easyscience/diffraction>
 # SPDX-License-Identifier: BSD-3-Clause
 
 from typing import Iterable

src/easydiffraction/core/guard.py

@@ -1,4 +1,4 @@
-# SPDX-FileCopyrightText: 2021-2025 EasyDiffraction contributors <https://github.com/easyscience/diffraction>
+# SPDX-FileCopyrightText: 2021-2026 EasyDiffraction contributors <https://github.com/easyscience/diffraction>
 # SPDX-License-Identifier: BSD-3-Clause
 
 from abc import ABC

src/easydiffraction/core/identity.py

@@ -1,4 +1,4 @@
-# SPDX-FileCopyrightText: 2021-2025 EasyDiffraction contributors <https://github.com/easyscience/diffraction>
+# SPDX-FileCopyrightText: 2021-2026 EasyDiffraction contributors <https://github.com/easyscience/diffraction>
 # SPDX-License-Identifier: BSD-3-Clause
 """Identity helpers to build CIF-like hierarchical names.