Merge pull request #52 from scipp/copier-update-2024-06

Copier update 2024 06

.copier-answers.yml

@@ -1,5 +1,5 @@
 # Changes here will be overwritten by Copier; NEVER EDIT MANUALLY
-_commit: '2955216'
+_commit: 91ffffb
 _src_path: gh:scipp/copier_template
 description: Reflectometry data reduction for the European Spallation Source
 max_python: '3.12'

.github/workflows/docs.yml

@@ -47,6 +47,7 @@ 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@v5
         with:
@@ -64,7 +65,7 @@ jobs:
           name: docs_html
           path: html/
 
-      - uses: JamesIves/github-pages-deploy-action@v4.5.0
+      - uses: JamesIves/github-pages-deploy-action@v4.6.1
         if: ${{ inputs.publish }}
         with:
           branch: gh-pages

.github/workflows/release.yml

@@ -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/[email protected]
 
   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 }}

.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: v0.4.3
+    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

@@ -6,23 +6,23 @@ package:
 source:
   path: ..
 
+
+{% set pyproject = load_file_data('pyproject.toml') %}
+{% set dependencies = pyproject.get('project', {}).get('dependencies', {}) %}
+
+
 requirements:
   build:
     - setuptools
     - setuptools_scm
   run:
-    - dask
-    - python-dateutil
-    - graphviz
-    - plopp
-    - pythreejs
-    - orsopy
-    - sciline>=23.9.1
-    - scipp>=23.8.0
-    - scippneutron>=23.9.0
-    - essreduce
     - python>=3.10
 
+  {% for package in dependencies %}
+    - {% if package == "graphviz" %}python-graphviz{% else %}{{ package }}{% endif %}
+  {% endfor %}
+
+
 test:
   imports:
     - ess.reflectometry

docs/_templates/doc_version.html

@@ -1,2 +1,2 @@
 <!-- This will display the version of the docs -->
-Current {{ project }} version: {{ version }} (<a href="https://github.com/{{orgname}}/{{ project|lower }}/releases">older versions</a>).
+Current ESSreflectometry version: {{ version }} (<a href="https://github.com/scipp/essreflectometry/releases">older versions</a>).

docs/conf.py

@@ -1,17 +1,19 @@
-# -*- coding: utf-8 -*-
-
 import doctest
 import os
 import sys
+from importlib.metadata import PackageNotFoundError
+from importlib.metadata import version as get_version
 
-from ess import reflectometry
+from sphinx.util import logging
 
 sys.path.insert(0, os.path.abspath('.'))
 
+logger = logging.getLogger(__name__)
+
 # General information about the project.
-project = u'ESSreflectometry'
-copyright = u'2024 Scipp contributors'
-author = u'Scipp contributors'
+project = 'ESSreflectometry'
+copyright = '2024 Scipp contributors'
+author = 'Scipp contributors'
 
 html_show_sourcelink = True
 
@@ -35,6 +37,8 @@
     import sciline.sphinxext.domain_types  # noqa: F401
 
     extensions.append('sciline.sphinxext.domain_types')
+    # See https://github.com/tox-dev/sphinx-autodoc-typehints/issues/457
+    suppress_warnings = ["config.cache"]
 except ModuleNotFoundError:
     pass
 
@@ -111,10 +115,15 @@
 # built documents.
 #
 
-# The short X.Y version.
-version = reflectometry.__version__
-# The full version, including alpha/beta/rc tags.
-release = reflectometry.__version__
+try:
+    release = get_version("essreflectometry")
+    version = ".".join(release.split('.')[:3])  # CalVer
+except PackageNotFoundError:
+    logger.info(
+        "Warning: determining version from package metadata failed, falling back to "
+        "a dummy version number."
+    )
+    release = version = "0.0.0-dev"
 
 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/amor/amor-reduction.ipynb

@@ -25,7 +25,6 @@
    "outputs": [],
    "source": [
     "import scipp as sc\n",
-    "import sciline\n",
     "from ess import amor\n",
     "from ess.reflectometry.types import *\n",
     "from ess.amor.types import *"
@@ -354,8 +353,7 @@
    "mimetype": "text/x-python",
    "name": "python",
    "nbconvert_exporter": "python",
-   "pygments_lexer": "ipython3",
-   "version": "3.10.13"
+   "pygments_lexer": "ipython3"
   }
  },
  "nbformat": 4,

docs/user-guide/amor/compare-to-eos.ipynb

@@ -23,7 +23,6 @@
     "\n",
     "import scipp as sc\n",
     "import plopp as pp\n",
-    "import sciline\n",
     "from ess import amor\n",
     "from ess.reflectometry.types import *\n",
     "from ess.amor.types import ChopperPhase"
@@ -137,7 +136,7 @@
    "outputs": [],
    "source": [
     "# PSI results\n",
-    "for key, angle in mu.items():\n",
+    "for key in mu:\n",
     "    d = orsopy.fileio.load_orso(amor.data.amor_psi_software_result(key))[0].data\n",
     "    y = sc.array(dims=['Q'], values=d[:, 1], variances=d[:, 2] ** 2)\n",
     "    results['psi'][key] = sc.DataArray(\n",
@@ -162,7 +161,7 @@
    "source": [
     "fig, axs = plt.subplots(3, 2, figsize=(12, 12))\n",
     "\n",
-    "for ax, (key, angle) in zip(axs.ravel(), mu.items()):\n",
+    "for ax, (key, angle) in zip(axs.ravel(), mu.items(), strict=True):\n",
     "    pp.plot(\n",
     "        {\n",
     "            facility: results[facility][key][results[facility][key].data > 0.0]\n",
@@ -196,9 +195,9 @@
    "source": [
     "fig, axs = plt.subplots(1, 2, figsize=(12, 4))\n",
     "\n",
-    "for ax, (facility, res) in zip(axs.ravel(), results.items()):\n",
+    "for ax, (facility, res) in zip(axs.ravel(), results.items(), strict=True):\n",
     "    pp.plot(\n",
-    "        {k: v for k, v in list(res.items())[:4]},  # First 4 curves\n",
+    "        dict(list(res.items())[:4]),  # First 4 curves\n",
     "        ax=ax,\n",
     "        norm='log',\n",
     "        ls='solid',\n",

pyproject.toml

@@ -67,17 +67,43 @@ filterwarnings = [
   "ignore:.*metadata to be logged in the data array, it is necessary to install the orsopy package.:UserWarning",
 ]
 
-[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", "UP", "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 = ["essreflectometry"]
+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 = ["essreflectometry"]
+[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

requirements/dev.in

@@ -9,6 +9,3 @@ copier
 jupyterlab
 pip-compile-multi
 pre-commit
-
-# See https://github.com/copier-org/copier/issues/1568
-pyyaml-include<2

requirements/make_base.py

@@ -1,7 +1,6 @@
 import sys
 from argparse import ArgumentParser
 from pathlib import Path
-from typing import List
 
 import tomli
 
@@ -20,7 +19,7 @@
 """
 
 
-def write_dependencies(dependency_name: str, dependencies: List[str]) -> None:
+def write_dependencies(dependency_name: str, dependencies: list[str]) -> None:
     path = Path(f"{dependency_name}.in")
     if path.exists():
         sections = path.read_text().split(CUSTOM_AUTO_SEPARATOR)

src/ess/amor/geometry.py

@@ -1,7 +1,5 @@
 # SPDX-License-Identifier: BSD-3-Clause
 # Copyright (c) 2024 Scipp contributors (https://github.com/scipp)
-from typing import Tuple
-
 import scipp as sc
 
 
@@ -30,7 +28,7 @@ class Detector:
 
 def _pixel_coordinate_in_detector_system(
     pixelID: sc.Variable,
-) -> Tuple[sc.Variable, sc.Variable]:
+) -> tuple[sc.Variable, sc.Variable]:
     """Determines beam travel distance inside the detector
     and the beam divergence angle from the detector number."""
     (bladeNr, bPixel) = (
@@ -55,7 +53,7 @@ def _pixel_coordinate_in_detector_system(
 
 def pixel_coordinate_in_lab_frame(
     pixelID: sc.Variable, nu: sc.Variable
-) -> Tuple[sc.Variable, sc.Variable]:
+) -> tuple[sc.Variable, sc.Variable]:
     """Computes spatial coordinates (lab reference frame), and the beam divergence
     angle for the detector pixel associated with `pixelID`"""
     distance_in_detector, divergence_angle = _pixel_coordinate_in_detector_system(

src/ess/amor/orso.py

@@ -2,8 +2,6 @@
 # Copyright (c) 2024 Scipp contributors (https://github.com/scipp)
 """ORSO utilities for Amor."""
 
-from typing import Optional
-
 import numpy as np
 import scipp as sc
 from orsopy.fileio import base as orso_base
@@ -81,9 +79,7 @@ def _extract_values_array(var: sc.Variable) -> np.ndarray:
     return var.values
 
 
-def _limits_of_coord(
-    data: sc.DataArray, name: str
-) -> Optional[tuple[float, float, str]]:
+def _limits_of_coord(data: sc.DataArray, name: str) -> tuple[float, float, str] | None:
     if (coord := _get_coord(data, name)) is None:
         return None
     min_ = coord.min().value
@@ -92,7 +88,7 @@ def _limits_of_coord(
     return float(min_), float(max_), _ascii_unit(coord.unit)
 
 
-def _get_coord(data: sc.DataArray, name: str) -> Optional[sc.Variable]:
+def _get_coord(data: sc.DataArray, name: str) -> sc.Variable | None:
     if name in data.coords:
         return sc.DataArray(data=data.coords[name], masks=data.masks)
     if (data.bins is not None) and (name in data.bins.coords):