Copier update with switch to ruff and automatic updates

.copier-answers.yml

@@ -1,5 +1,5 @@
 # Changes here will be overwritten by Copier; NEVER EDIT MANUALLY
-_commit: 8484c9e
+_commit: 7afbc9a
 _src_path: gh:scipp/copier_template
 description: Diffraction data reduction for the European Spallation Source
 max_python: '3.12'

.github/workflows/ci.yml

@@ -21,7 +21,7 @@ jobs:
         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
-      - uses: actions/setup-python@v4
+      - uses: actions/setup-python@v5
         with:
           python-version-file: '.github/workflows/python-version-ci'
       - uses: pre-commit/action@v3.0.1

.github/workflows/copier.yml

@@ -0,0 +1,25 @@
+name: Copier template sync
+
+on:
+  workflow_dispatch:
+  schedule:
+    - cron: '0 1 * * 1'
+
+jobs:
+  update:
+    name: Sync with copier template
+    runs-on: 'ubuntu-latest'
+    steps:
+      - uses: actions/checkout@v4
+      - uses: actions/setup-python@v5
+        with:
+          python-version: '3.X'
+      - run: pip install copier
+      - run: copier update --skip-answered --vcs-ref=HEAD --conflict=rej
+      - name: Create Pull Request
+        uses: peter-evans/create-pull-request@v6
+        with:
+          title: '[CRON] Sync with copier template'
+          body: |
+            This PR updates the project to the latest version of scipp's [copier-template](https://github.com/scipp/copier_template).
+            Remember to check for any conflicts and resolve them.

.github/workflows/docs.yml

@@ -47,8 +47,9 @@ jobs:
       - uses: actions/checkout@v4
         with:
           ref: ${{ inputs.branch == '' && github.ref_name || inputs.branch }}
+          repository: ${{ github.event.pull_request.head.repo.full_name }}
           fetch-depth: 0  # history required so cmake can determine version
-      - uses: actions/setup-python@v4
+      - uses: actions/setup-python@v5
         with:
           python-version-file: '.github/workflows/python-version-ci'
       - run: python -m pip install --upgrade pip
@@ -59,12 +60,12 @@ jobs:
         if: ${{ inputs.version == '' }}
       - run: tox -e linkcheck
         if: ${{ inputs.linkcheck }}
-      - uses: actions/upload-artifact@v3
+      - uses: actions/upload-artifact@v4
         with:
           name: docs_html
           path: html/
 
-      - uses: JamesIves/github-pages-deploy-action@v4.5.0
+      - uses: JamesIves/github-pages-deploy-action@v4.6.0
         if: ${{ inputs.publish }}
         with:
           branch: gh-pages

.github/workflows/release.yml

@@ -28,7 +28,7 @@ jobs:
             boa
       - run: conda mambabuild --channel conda-forge --channel scipp --no-anaconda-upload --override-channels --output-folder conda/package conda
 
-      - uses: actions/upload-artifact@v3
+      - uses: actions/upload-artifact@v4
         with:
           name: conda-package-noarch
           path: conda/package/noarch/*.tar.bz2
@@ -42,7 +42,7 @@ jobs:
         with:
           fetch-depth: 0  # history required so setuptools_scm can determine version
 
-      - uses: actions/setup-python@v4
+      - uses: actions/setup-python@v5
         with:
           python-version-file: '.github/workflows/python-version-ci'
 
@@ -53,7 +53,7 @@ jobs:
         run: python -m build
 
       - name: Upload wheels
-        uses: actions/upload-artifact@v3
+        uses: actions/upload-artifact@v4
         with:
           name: dist
           path: dist
@@ -67,7 +67,7 @@ jobs:
       id-token: write
     if: github.event_name == 'release' && github.event.action == 'published'
     steps:
-      - uses: actions/download-artifact@v3
+      - uses: actions/download-artifact@v4
       - uses: pypa/gh-action-pypi-publish@v1.8.14
 
   upload_conda:
@@ -77,7 +77,7 @@ jobs:
     if: github.event_name == 'release' && github.event.action == 'published'
 
     steps:
-      - uses: actions/download-artifact@v3
+      - uses: actions/download-artifact@v4
       - uses: mamba-org/setup-micromamba@v1
         with:
           environment-name: upload-env
@@ -101,7 +101,7 @@ jobs:
     permissions:
       contents: write  # This is needed so that the action can upload the asset
     steps:
-    - uses: actions/download-artifact@v3
+    - uses: actions/download-artifact@v4
     - name: Zip documentation
       run: |
         mv docs_html documentation-${{ github.ref_name }}

.github/workflows/test.yml

@@ -54,7 +54,7 @@ jobs:
       - run: python -m pip install --upgrade pip
       - run: python -m pip install -r ${{ inputs.pip-recipe }}
       - run: tox -e ${{ inputs.tox-env }}
-      - uses: actions/upload-artifact@v3
+      - uses: actions/upload-artifact@v4
         if: ${{ inputs.coverage-report }}
         with:
           name: CoverageReport

.pre-commit-config.yaml

@@ -13,34 +13,21 @@ repos:
       - id: trailing-whitespace
         args: [ --markdown-linebreak-ext=md ]
         exclude: '\.svg'
-  - repo: https://github.com/pycqa/isort
-    rev: 5.12.0
-    hooks:
-      - id: isort
-        name: isort (python)
-  - repo: https://github.com/psf/black-pre-commit-mirror
-    rev: 23.11.0
-    hooks:
-      - id: black
   - repo: https://github.com/kynan/nbstripout
     rev: 0.6.0
     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/pycqa/flake8
-    rev: 6.1.0
-    hooks:
-      - id: flake8
-        types: ["python"]
-        additional_dependencies: ["flake8-bugbear==23.9.16"]
-  - repo: https://github.com/pycqa/bandit
-    rev: 1.7.5
-    hooks:
-      - id: bandit
-        additional_dependencies: ["bandit[toml]"]
-        args: ["-c", "pyproject.toml"]
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: v0.4.1
+    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
     hooks:

conda/meta.yaml

@@ -6,6 +6,11 @@ package:
 source:
   path: ..
 
+
+{% set pyproject = load_file_data('pyproject.toml') %}
+{% set dependencies = pyproject.get('project', {}).get('dependencies', {}) %}
+
+
 requirements:
   build:
     - setuptools
@@ -23,6 +28,11 @@ requirements:
     - scippnexus>=23.12.0
     - python>=3.10
 
+  {% for package in dependencies %}
+    - {% if package == "graphviz" %}python-graphviz{% else %}{{ package }}{% endif %}
+  {% endfor %}
+
+
 test:
   imports:
     - ess.diffraction

docs/conf.py

@@ -3,15 +3,14 @@
 import doctest
 import os
 import sys
-
-from ess import diffraction
+from importlib.metadata import version as get_version
 
 sys.path.insert(0, os.path.abspath('.'))
 
 # General information about the project.
-project = u'ESSdiffraction'
-copyright = u'2024 Scipp contributors'
-author = u'Scipp contributors'
+project = 'ESSdiffraction'
+copyright = '2024 Scipp contributors'
+author = 'Scipp contributors'
 
 html_show_sourcelink = True
 
@@ -112,10 +111,8 @@
 # built documents.
 #
 
-# The short X.Y version.
-version = diffraction.__version__
-# The full version, including alpha/beta/rc tags.
-release = diffraction.__version__
+release = get_version("essdiffraction")
+version = ".".join(release.split('.')[:3])  # CalVer
 
 warning_is_error = True
 

docs/developer/coding-conventions.md

@@ -2,7 +2,7 @@
 
 ## Code formatting
 
-There are no explicit code formatting conventions since we use `black` to enforce a format.
+There are no explicit code formatting conventions since we use `ruff` to enforce a format.
 
 ## Docstring format
 

docs/user-guide/dream/dream-data-reduction.ipynb

@@ -15,8 +15,6 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "from pathlib import Path\n",
-    "\n",
     "import scipp as sc\n",
     "import scippneutron as scn\n",
     "import sciline\n",

docs/user-guide/sns-instruments/POWGEN_data_reduction.ipynb

@@ -26,7 +26,6 @@
     "import scippneutron as scn\n",
     "import sciline\n",
     "\n",
-    "import ess.diffraction\n",
     "from ess import powder\n",
     "from ess.powder.external import powgen\n",
     "from ess.powder.types import *"

pyproject.toml

@@ -67,17 +67,43 @@ filterwarnings = [
   'ignore:\s*Pyarrow will become a required dependency of pandas:DeprecationWarning',
 ]
 
-[tool.bandit]
-# Excluding tests because bandit doesn't like `assert`.
-exclude_dirs = ["docs/conf.py", "tests"]
+[tool.ruff]
+line-length = 88
+extend-include = ["*.ipynb"]
+extend-exclude = [
+    ".*", "__pycache__", "build", "dist", "install",
+]
+
+[tool.ruff.lint]
+# See https://docs.astral.sh/ruff/rules/
+select = ["B", "C4", "DTZ", "E", "F", "G", "I", "PERF", "PGH", "PT", "PYI", "RUF", "S", "T20", "W"]
+ignore = [
+    # Conflict with ruff format, see
+    # 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 = ["essdiffraction"]
+pydocstyle.convention = "numpy"
 
-[tool.black]
-skip-string-normalization = true
+[tool.ruff.lint.per-file-ignores]
+# those files have an increased risk of relying on import order
+"__init__.py" = ["I"]
+"tests/*" = [
+    "S101",  # asserts are fine in tests
+    "B018",  # 'useless expressions' are ok because some tests just check for exceptions
+]
+"*.ipynb" = [
+    "E501",  # longer lines are sometimes more readable
+    "F403",  # *-imports used with domain types
+    "F405",  # linter may fail to find names because of *-imports
+    "I",  # we don't collect imports at the top
+    "S101",  # asserts are used for demonstration and are safe in notebooks
+    "T201",  # printing is ok for demonstration purposes
+]
 
-[tool.isort]
-skip_gitignore = true
-profile = "black"
-known_first_party = ["essdiffraction"]
+[tool.ruff.format]
+quote-style = "preserve"
 
 [tool.mypy]
 strict = true
@@ -87,5 +113,4 @@ enable_error_code = [
     "redundant-expr",
     "truthy-bool",
 ]
-show_error_codes = true
 warn_unreachable = true

src/ess/diffraction/__init__.py

@@ -1,5 +1,6 @@
 # SPDX-License-Identifier: BSD-3-Clause
 # Copyright (c) 2024 Scipp contributors (https://github.com/scipp)
+# ruff: noqa: E402, F401
 
 """
 Components for diffraction experiments (powder and single crystal).

src/ess/dream/__init__.py

@@ -4,6 +4,7 @@
 """
 Components for DREAM
 """
+
 import importlib.metadata
 
 from . import beamline, data

src/ess/dream/instrument_view.py

@@ -116,9 +116,9 @@ def _add_module_control(self):
 
         self.fig = self.scatter[0]
         self.cutting_tool = self.scatter[1]
-        self.artist_mapping = {
-            name: key for name, key in zip(self.data.keys(), self.fig.artists.keys())
-        }
+        self.artist_mapping = dict(
+            zip(self.data.keys(), self.fig.artists.keys(), strict=True)
+        )
         self.checkboxes = {
             key: ipw.Checkbox(
                 value=True,
@@ -130,8 +130,10 @@ def _add_module_control(self):
         }
 
         self.modules_widget = ipw.HBox(
-            [ipw.HTML(value="Modules:     ")]
-            + list(self.checkboxes.values())
+            [
+                ipw.HTML(value="Modules:     "),
+                *self.checkboxes.values(),
+            ]
         )
         for key, ch in self.checkboxes.items():
             ch.key = key

src/ess/dream/io/geant4.py

@@ -8,15 +8,14 @@
 import numpy as np
 import sciline
 import scipp as sc
-from ess.reduce.nexus import extract_detector_data
-
 from ess.powder.types import (
     DetectorName,
     FilePath,
     RawDetector,
     RawDetectorData,
     RunType,
 )
+from ess.reduce.nexus import extract_detector_data
 
 MANTLE_DETECTOR_ID = sc.index(7)
 HIGH_RES_DETECTOR_ID = sc.index(8)
@@ -28,7 +27,7 @@ class AllRawDetectors(sciline.Scope[RunType, sc.DataGroup], sc.DataGroup):
 
 
 def load_geant4_csv(
-    file_path: Union[FilePath[RunType], str, StringIO, BytesIO]
+    file_path: Union[FilePath[RunType], str, StringIO, BytesIO],
 ) -> AllRawDetectors[RunType]:
     """Load a GEANT4 CSV file for DREAM.
 
@@ -73,7 +72,7 @@ def extract_geant4_detector_data(
 
 
 def _load_raw_events(
-    file_path: Union[str, os.PathLike, StringIO, BytesIO]
+    file_path: Union[str, os.PathLike, StringIO, BytesIO],
 ) -> sc.DataArray:
     table = sc.io.load_csv(
         file_path, sep='\t', header_parser='bracket', data_columns=[]