lower bound scippnexus + copier update + tox -e deps

.copier-answers.yml

@@ -1,5 +1,5 @@
 # Changes here will be overwritten by Copier; NEVER EDIT MANUALLY
-_commit: 101e594
+_commit: a052529
 _src_path: gh:scipp/copier_template
 description: Reflectometry data reduction for the European Spallation Source
 max_python: '3.12'

.github/workflows/ci.yml

@@ -27,7 +27,7 @@ jobs:
       - uses: pre-commit/action@v3.0.1
         with:
           extra_args: --all-files
-      - uses: pre-commit-ci/lite-action@v1.0.2
+      - uses: pre-commit-ci/lite-action@v1.0.3
         if: always()
         with:
           msg: Apply automatic formatting

.github/workflows/docs.yml

@@ -69,7 +69,7 @@ jobs:
           name: docs_html
           path: html/
 
-      - uses: JamesIves/github-pages-deploy-action@v4.6.3
+      - uses: JamesIves/github-pages-deploy-action@v4.6.4
         if: ${{ inputs.publish }}
         with:
           branch: gh-pages

.github/workflows/test.yml

@@ -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:

.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 +41,4 @@ docs/generated/
 *.cif
 *.rcif
 *.ort
+*.zip

.pre-commit-config.yaml

@@ -1,6 +1,6 @@
 repos:
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.5.0
+    rev: v4.6.0
     hooks:
       - id: check-added-large-files
       - id: check-json
@@ -14,22 +14,22 @@ 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: v0.6.2
     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:

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:
@@ -29,8 +30,12 @@ test:
     - ess.reflectometry
     - ess.amor
   requires:
-    - pytest
-    - pooch
+
+  {# 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

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

@@ -2,7 +2,7 @@
  "cells": [
   {
    "cell_type": "markdown",
-   "id": "b97647a4-29ab-45a3-870e-aa49fbddb0c5",
+   "id": "0",
    "metadata": {},
    "source": [
     "# Comparison with PSI reduction software\n",
@@ -14,7 +14,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "9aaa5e0c-def6-4da5-9f63-b4c72a0de8f1",
+   "id": "1",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -31,7 +31,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "f9f28ab3-b9fd-4cfd-88bd-d290ea5cdf4f",
+   "id": "2",
    "metadata": {},
    "source": [
     "## Recreate reference files using Jochens Amor data reduction software\n",
@@ -60,7 +60,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "a1d7fc35-d958-44ce-83a5-b8d877c47735",
+   "id": "3",
    "metadata": {},
    "source": [
     "## Run essreflectometry on the same files"
@@ -69,7 +69,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "fccf8385-b2ec-4c14-990f-9083a89f46a2",
+   "id": "4",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -103,7 +103,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "5a220b29-5115-4594-9c75-ed0f34be74f7",
+   "id": "5",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -132,7 +132,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "9311bc67-6edf-4f90-9280-f4bee8df9da3",
+   "id": "6",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -147,7 +147,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "64b685cb-654e-46a5-9eae-b9bf76dadb8d",
+   "id": "7",
    "metadata": {},
    "source": [
     "## Plot reflectivity curve comparison"
@@ -156,7 +156,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "8e248ada-0db0-4e9e-a208-64e2ff74c7bb",
+   "id": "8",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -181,7 +181,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "9d97eff4-77cf-4ea1-8be7-1390bebfcb84",
+   "id": "9",
    "metadata": {},
    "source": [
     "## Overlay curves from same sample at different angle, should be on top of each other"
@@ -190,7 +190,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "4758e245-c47a-454c-9788-97b05b49f356",
+   "id": "10",
    "metadata": {},
    "outputs": [],
    "source": [

pyproject.toml

@@ -39,11 +39,18 @@ dependencies = [
   "sciline>=24.6.0",
   "scipp>=24.09.1",  # Fixed new hist/bin API
   "scippneutron>=24.7.0",
+  "scippnexus>=24.9.1",
   "essreduce",
 ]
 
 dynamic = ["version"]
 
+[project.optional-dependencies]
+test = [
+    "pytest",
+    "pooch",
+]
+
 [project.urls]
 "Bug Tracker" = "https://github.com/scipp/essreflectometry/issues"
 "Documentation" = "https://scipp.github.io/essreflectometry"
@@ -65,6 +72,7 @@ filterwarnings = [
   "error",
   'ignore:\n.*Sentinel is not a public part of the traitlets API.*:DeprecationWarning',
   "ignore:.*metadata to be logged in the data array, it is necessary to install the orsopy package.:UserWarning",
+  "ignore:.*A transformation needs a vector attribute. Falling back to returning underlying value.:UserWarning",
 ]
 
 [tool.ruff]
@@ -82,8 +90,8 @@ 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 = ["essreflectometry"]
+fixable = ["B010", "I001", "PT001"]
+isort.known-first-party = ["ess.reflectometry"]
 pydocstyle.convention = "numpy"
 
 [tool.ruff.lint.per-file-ignores]
@@ -114,3 +122,11 @@ 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",
+]

requirements/base.in

@@ -11,4 +11,5 @@ orsopy
 sciline>=24.6.0
 scipp>=24.09.1
 scippneutron>=24.7.0
+scippnexus>=24.9.1
 essreduce

requirements/base.txt

@@ -1,4 +1,4 @@
-# SHA1:c59f85e6dbc38ae7eeef3ce1e4f681c07f43ff24
+# SHA1:3401cd389c29441d88f259ef065f189c2f02bfcb
 #
 # This file is autogenerated by pip-compile-multi
 # To update, run:
@@ -19,27 +19,27 @@ cyclebane==24.6.0
     # via sciline
 cycler==0.12.1
     # via matplotlib
-dask==2024.8.2
+dask==2024.9.0
     # via -r base.in
 decorator==5.1.1
     # via ipython
-essreduce==24.9.0
+essreduce==24.9.1
     # via -r base.in
 exceptiongroup==1.2.2
     # via ipython
 executing==2.1.0
     # via stack-data
-fonttools==4.53.1
+fonttools==4.54.1
     # via matplotlib
-fsspec==2024.6.1
+fsspec==2024.9.0
     # via dask
 graphviz==0.20.3
     # via -r base.in
 h5py==3.11.0
     # via
     #   scippneutron
     #   scippnexus
-importlib-metadata==8.4.0
+importlib-metadata==8.5.0
     # via dask
 ipydatawidgets==4.3.5
     # via pythreejs
@@ -92,11 +92,11 @@ pexpect==4.9.0
     # via ipython
 pillow==10.4.0
     # via matplotlib
-plopp==24.6.0
+plopp==24.9.3
     # via
     #   -r base.in
     #   scippneutron
-prompt-toolkit==3.0.47
+prompt-toolkit==3.0.48
     # via ipython
 ptyprocess==0.7.0
     # via pexpect
@@ -127,10 +127,11 @@ scipp==24.9.1
     #   essreduce
     #   scippneutron
     #   scippnexus
-scippneutron==24.8.0
+scippneutron==24.9.0
     # via -r base.in
-scippnexus==24.8.1
+scippnexus==24.9.1
     # via
+    #   -r base.in
     #   essreduce
     #   scippneutron
 scipy==1.14.1
@@ -163,5 +164,5 @@ wcwidth==0.2.13
     # via prompt-toolkit
 widgetsnbextension==4.0.13
     # via ipywidgets
-zipp==3.20.1
+zipp==3.20.2
     # via importlib-metadata

requirements/basetest.in

@@ -1,5 +1,11 @@
 # Dependencies that are only used by tests.
 # Do not make an environment from this file, use test.txt instead!
+# Add more dependencies in the ``test`` list
+# under ``[project.optional-dependencies]`` section, in ``pyproject.toml``
 
+# Anything above "--- END OF CUSTOM SECTION ---"
+# will not be touched by ``make_base.py``
+# --- END OF CUSTOM SECTION ---
+# The following was generated by 'tox -e deps', DO NOT EDIT MANUALLY!
 pytest
 pooch