copier update, py313, tox deps

.copier-answers.yml

@@ -1,8 +1,8 @@
 # Changes here will be overwritten by Copier; NEVER EDIT MANUALLY
-_commit: 101e594
+_commit: aa5dc5e
 _src_path: gh:scipp/copier_template
 description: Data reduction for NMX at the European Spallation Source.
-max_python: '3.12'
+max_python: '3.13'
 min_python: '3.10'
 namespace_package: ess
 nightly_deps: scipp,sciline,scippnexus,plopp

.github/workflows/ci.yml

@@ -10,7 +10,7 @@ on:
 jobs:
   formatting:
     name: Formatting and static analysis
-    runs-on: 'ubuntu-22.04'
+    runs-on: 'ubuntu-24.04'
     outputs:
       min_python: ${{ steps.vars.outputs.min_python }}
       min_tox_env: ${{ steps.vars.outputs.min_tox_env }}
@@ -19,15 +19,15 @@ jobs:
       - name: Get Python version for other CI jobs
         id: vars
         run: |
-          echo "min_python=$(cat .github/workflows/python-version-ci)" >> $GITHUB_OUTPUT
-          echo "min_tox_env=py$(cat .github/workflows/python-version-ci | sed 's/\.//g')" >> $GITHUB_OUTPUT
+          echo "min_python=$(< .github/workflows/python-version-ci)" >> "$GITHUB_OUTPUT"
+          echo "min_tox_env=py$(sed 's/\.//g' < .github/workflows/python-version-ci)" >> "$GITHUB_OUTPUT"
       - uses: actions/setup-python@v5
         with:
           python-version-file: '.github/workflows/python-version-ci'
       - uses: pre-commit/[email protected]
         with:
           extra_args: --all-files
-      - uses: pre-commit-ci/lite-action@v1.0.2
+      - uses: pre-commit-ci/lite-action@v1.1.0
         if: always()
         with:
           msg: Apply automatic formatting
@@ -37,7 +37,7 @@ jobs:
     needs: formatting
     strategy:
       matrix:
-        os: ['ubuntu-22.04']
+        os: ['ubuntu-24.04']
         python:
           - version: '${{needs.formatting.outputs.min_python}}'
             tox-env: '${{needs.formatting.outputs.min_tox_env}}'
@@ -53,6 +53,6 @@ jobs:
     uses: ./.github/workflows/docs.yml
     with:
       publish: false
-      linkcheck: ${{ contains(matrix.variant.os, 'ubuntu') && github.ref == 'refs/heads/main' }}
+      linkcheck: ${{ github.ref == 'refs/heads/main' }}
       branch: ${{ github.head_ref == '' && github.ref_name || github.head_ref }}
     secrets: inherit

.github/workflows/docs.yml

@@ -41,7 +41,7 @@ env:
 jobs:
   docs:
     name: Build documentation
-    runs-on: 'ubuntu-22.04'
+    runs-on: 'ubuntu-24.04'
     env:
         ESS_PROTECTED_FILESTORE_USERNAME: ${{ secrets.ESS_PROTECTED_FILESTORE_USERNAME }}
         ESS_PROTECTED_FILESTORE_PASSWORD: ${{ secrets.ESS_PROTECTED_FILESTORE_PASSWORD }}
@@ -58,7 +58,7 @@ jobs:
           python-version-file: '.github/workflows/python-version-ci'
       - run: python -m pip install --upgrade pip
       - run: python -m pip install -r requirements/ci.txt
-      - run: tox -e releasedocs -- ${VERSION}
+      - run: tox -e releasedocs -- "${VERSION}"
         if: ${{ inputs.version != '' }}
       - run: tox -e docs
         if: ${{ inputs.version == '' }}
@@ -69,7 +69,7 @@ jobs:
           name: docs_html
           path: html/
 
-      - uses: JamesIves/[email protected].3
+      - uses: JamesIves/[email protected].9
         if: ${{ inputs.publish }}
         with:
           branch: gh-pages

.github/workflows/nightly_at_main.yml

@@ -8,21 +8,21 @@ on:
 jobs:
   setup:
     name: Setup variables
-    runs-on: 'ubuntu-22.04'
+    runs-on: 'ubuntu-24.04'
     outputs:
       min_python: ${{ steps.vars.outputs.min_python }}
     steps:
       - uses: actions/checkout@v4
       - name: Get Python version for other CI jobs
         id: vars
-        run: echo "min_python=$(cat .github/workflows/python-version-ci)" >> $GITHUB_OUTPUT
+        run: echo "min_python=$(< .github/workflows/python-version-ci)" >> "$GITHUB_OUTPUT"
 
   tests:
     name: Tests
     needs: setup
     strategy:
       matrix:
-        os: ['ubuntu-22.04']
+        os: ['ubuntu-24.04']
         python:
           - version: '${{needs.setup.outputs.min_python}}'
             tox-env: 'nightly'

.github/workflows/nightly_at_release.yml

@@ -8,7 +8,7 @@ on:
 jobs:
   setup:
     name: Setup variables
-    runs-on: 'ubuntu-22.04'
+    runs-on: 'ubuntu-24.04'
     outputs:
       min_python: ${{ steps.vars.outputs.min_python }}
       release_tag: ${{ steps.release.outputs.release_tag }}
@@ -18,17 +18,17 @@ jobs:
           fetch-depth: 0  # history required so we can determine latest release tag
       - name: Get last release tag from git
         id: release
-        run: echo "release_tag=$(git describe --tags --abbrev=0 --match '[0-9]*.[0-9]*.[0-9]*')" >> $GITHUB_OUTPUT
+        run: echo "release_tag=$(git describe --tags --abbrev=0 --match '[0-9]*.[0-9]*.[0-9]*')" >> "$GITHUB_OUTPUT"
       - name: Get Python version for other CI jobs
         id: vars
-        run: echo "min_python=$(cat .github/workflows/python-version-ci)" >> $GITHUB_OUTPUT
+        run: echo "min_python=$(cat .github/workflows/python-version-ci)" >> "$GITHUB_OUTPUT"
 
   tests:
     name: Tests
     needs: setup
     strategy:
       matrix:
-        os: ['ubuntu-22.04']
+        os: ['ubuntu-24.04']
         python:
           - version: '${{needs.setup.outputs.min_python}}'
             tox-env: 'nightly'

.github/workflows/release.yml

@@ -12,7 +12,7 @@ defaults:
 jobs:
   build_conda:
     name: Conda build
-    runs-on: 'ubuntu-22.04'
+    runs-on: 'ubuntu-24.04'
 
     steps:
       - uses: actions/checkout@v4
@@ -35,7 +35,7 @@ jobs:
 
   build_wheels:
     name: Wheels
-    runs-on: 'ubuntu-22.04'
+    runs-on: 'ubuntu-24.04'
 
     steps:
       - uses: actions/checkout@v4
@@ -61,7 +61,7 @@ jobs:
   upload_pypi:
     name: Deploy PyPI
     needs: [build_wheels, build_conda]
-    runs-on: 'ubuntu-22.04'
+    runs-on: 'ubuntu-24.04'
     environment: release
     permissions:
       id-token: write
@@ -73,7 +73,7 @@ jobs:
   upload_conda:
     name: Deploy Conda
     needs: [build_wheels, build_conda]
-    runs-on: 'ubuntu-22.04'
+    runs-on: 'ubuntu-24.04'
     if: github.event_name == 'release' && github.event.action == 'published'
 
     steps:
@@ -97,7 +97,7 @@ jobs:
   assets:
     name: Upload docs
     needs: docs
-    runs-on: 'ubuntu-22.04'
+    runs-on: 'ubuntu-24.04'
     permissions:
       contents: write  # This is needed so that the action can upload the asset
     steps:

.github/workflows/test.yml

@@ -4,7 +4,7 @@ on:
   workflow_dispatch:
     inputs:
       os-variant:
-        default: 'ubuntu-22.04'
+        default: 'ubuntu-24.04'
         type: string
       python-version:
         type: string
@@ -23,7 +23,7 @@ on:
   workflow_call:
     inputs:
       os-variant:
-        default: 'ubuntu-22.04'
+        default: 'ubuntu-24.04'
         type: string
       python-version:
         type: string
@@ -41,6 +41,21 @@ on:
         type: string
 
 jobs:
+  package-test:
+    runs-on: ${{ inputs.os-variant }}
+
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          ref: ${{ inputs.checkout_ref }}
+      - uses: actions/setup-python@v5
+        with:
+          python-version: ${{ inputs.python-version }}
+      - run: python -m pip install --upgrade pip
+      - run: python -m pip install .
+      - run: python tests/package_test.py
+        name: Run package tests
+
   test:
     runs-on: ${{ inputs.os-variant }}
     env:

.github/workflows/unpinned.yml

@@ -8,7 +8,7 @@ on:
 jobs:
   setup:
     name: Setup variables
-    runs-on: 'ubuntu-22.04'
+    runs-on: 'ubuntu-24.04'
     outputs:
       min_python: ${{ steps.vars.outputs.min_python }}
       release_tag: ${{ steps.release.outputs.release_tag }}
@@ -18,17 +18,17 @@ jobs:
           fetch-depth: 0  # history required so we can determine latest release tag
       - name: Get last release tag from git
         id: release
-        run: echo "release_tag=$(git describe --tags --abbrev=0 --match '[0-9]*.[0-9]*.[0-9]*')" >> $GITHUB_OUTPUT
+        run: echo "release_tag=$(git describe --tags --abbrev=0 --match '[0-9]*.[0-9]*.[0-9]*')" >> "$GITHUB_OUTPUT"
       - name: Get Python version for other CI jobs
         id: vars
-        run: echo "min_python=$(cat .github/workflows/python-version-ci)" >> $GITHUB_OUTPUT
+        run: echo "min_python=$(cat .github/workflows/python-version-ci)" >> "$GITHUB_OUTPUT"
 
   tests:
     name: Tests
     needs: setup
     strategy:
       matrix:
-        os: ['ubuntu-22.04']
+        os: ['ubuntu-24.04']
         python:
           - version: '${{needs.setup.outputs.min_python}}'
             tox-env: 'unpinned'

.gitignore

@@ -4,11 +4,13 @@ dist
 html
 .tox
 *.egg-info
+uv.lock  # we lock dependencies with pip-compile, not uv
 
 *.sw?
 
 # Environments
 venv
+.venv
 
 # Caches
 .clangd/
@@ -39,3 +41,6 @@ docs/generated/
 *.cif
 *.rcif
 *.ort
+*.zip
+*.sqw
+*.nxspe

.pre-commit-config.yaml

@@ -1,8 +1,10 @@
 repos:
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.5.0
+    rev: v5.0.0
     hooks:
       - id: check-added-large-files
+      - id: check-case-conflict
+      - id: check-illegal-windows-names
       - id: check-json
         exclude: asv.conf.json
       - id: check-merge-conflict
@@ -14,22 +16,22 @@ repos:
         args: [ --markdown-linebreak-ext=md ]
         exclude: '\.svg'
   - repo: https://github.com/kynan/nbstripout
-    rev: 0.6.0
+    rev: 0.7.1
     hooks:
       - id: nbstripout
         types: [ "jupyter" ]
         args: [ "--drop-empty-cells",
                 "--extra-keys 'metadata.language_info.version cell.metadata.jp-MarkdownHeadingCollapsed cell.metadata.pycharm'" ]
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.4.3
+    rev: v0.6.9
     hooks:
       - id: ruff
         args: [ --fix ]
         types_or: [ python, pyi, jupyter ]
       - id: ruff-format
         types_or: [ python, pyi ]
   - repo: https://github.com/codespell-project/codespell
-    rev: v2.2.6
+    rev: v2.3.0
     hooks:
       - id: codespell
         additional_dependencies:
@@ -44,3 +46,9 @@ repos:
       - id: rst-directive-colons
       - id: rst-inline-touching-normal
       - id: text-unicode-replacement-char
+  - repo: https://github.com/rhysd/actionlint
+    rev: v1.7.3
+    hooks:
+      - id: actionlint
+        # Disable because of false-positive SC2046
+        args: ["-shellcheck="]

.python-version

@@ -0,0 +1 @@
+3.10

conda/meta.yaml

@@ -9,6 +9,7 @@ source:
 
 {% set pyproject = load_file_data('pyproject.toml') %}
 {% set dependencies = pyproject.get('project', {}).get('dependencies', {}) %}
+{% set test_dependencies = pyproject.get('project', {}).get('optional-dependencies', {}).get('test', {}) %}
 
 
 requirements:
@@ -38,7 +39,13 @@ test:
   imports:
     - ess.nmx
   requires:
-    - pytest
+
+  {# Conda does not allow spaces between package name and version, so remove them #}
+  {% for package in test_dependencies %}
+    - {% if package == "graphviz" %}python-graphviz{% else %}{{ package|replace(" ", "") }}{% endif %}
+  {% endfor %}
+
+
   source_files:
     - pyproject.toml
     - tests/

docs/conf.py

@@ -1,3 +1,6 @@
+# SPDX-License-Identifier: BSD-3-Clause
+# Copyright (c) 2024 Scipp contributors (https://github.com/scipp)
+
 import doctest
 import os
 import sys

pyproject.toml

@@ -21,6 +21,7 @@ classifiers = [
     "Programming Language :: Python :: 3.10",
     "Programming Language :: Python :: 3.11",
     "Programming Language :: Python :: 3.12",
+    "Programming Language :: Python :: 3.13",
     "Topic :: Scientific/Engineering",
     "Typing :: Typed",
 ]
@@ -44,6 +45,11 @@ dependencies = [
 
 dynamic = ["version"]
 
+[project.optional-dependencies]
+test = [
+    "pytest",
+]
+
 [project.urls]
 "Bug Tracker" = "https://github.com/scipp/essnmx/issues"
 "Documentation" = "https://scipp.github.io/essnmx"
@@ -80,8 +86,8 @@ ignore = [
     # https://docs.astral.sh/ruff/formatter/#conflicting-lint-rules
     "COM812", "COM819", "D206", "D300", "E111", "E114", "E117", "ISC001", "ISC002", "Q000", "Q001", "Q002", "Q003", "W191",
 ]
-fixable = ["I001", "B010"]
-isort.known-first-party = ["essnmx"]
+fixable = ["B010", "I001", "PT001"]
+isort.known-first-party = ["ess.nmx"]
 pydocstyle.convention = "numpy"
 
 [tool.ruff.lint.per-file-ignores]
@@ -112,3 +118,11 @@ enable_error_code = [
     "truthy-bool",
 ]
 warn_unreachable = true
+
+[tool.codespell]
+ignore-words-list = [
+    # Codespell wants "socioeconomic" which seems to be the standard spelling.
+    # But we use the word in our code of conduct which is the contributor covenant.
+    # Let's not modify it if we don't have to.
+    "socio-economic",
+]