bump requirements

.copier-answers.yml

@@ -1,5 +1,5 @@
 # Changes here will be overwritten by Copier; NEVER EDIT MANUALLY
-_commit: 101e594
+_commit: 75b9a8f
 _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:

.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:
@@ -31,6 +32,13 @@ test:
   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

pyproject.toml

@@ -44,6 +44,12 @@ dependencies = [
 
 dynamic = ["version"]
 
+[project.optional-dependencies]
+test = [
+    "pytest",
+    "pooch",
+]
+
 [project.urls]
 "Bug Tracker" = "https://github.com/scipp/essreflectometry/issues"
 "Documentation" = "https://scipp.github.io/essreflectometry"
@@ -82,8 +88,8 @@ 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 +120,11 @@ 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.txt

@@ -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
     # 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
@@ -53,7 +53,7 @@ jedi==0.19.1
     # via ipython
 jupyterlab-widgets==3.0.13
     # via ipywidgets
-kiwisolver==1.4.6
+kiwisolver==1.4.7
     # via matplotlib
 locket==1.0.0
     # via partd
@@ -92,7 +92,7 @@ pexpect==4.9.0
     # via ipython
 pillow==10.4.0
     # via matplotlib
-plopp==24.6.0
+plopp==24.9.1
     # via
     #   -r base.in
     #   scippneutron
@@ -127,9 +127,9 @@ scipp==24.9.1
     #   essreduce
     #   scippneutron
     #   scippnexus
-scippneutron==24.8.0
+scippneutron==24.9.0
     # via -r base.in
-scippnexus==24.8.1
+scippnexus==24.9.0
     # via
     #   essreduce
     #   scippneutron
@@ -163,5 +163,5 @@ 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

requirements/basetest.txt

@@ -11,25 +11,25 @@ charset-normalizer==3.3.2
     # via requests
 exceptiongroup==1.2.2
     # via pytest
-idna==3.8
+idna==3.10
     # via requests
 iniconfig==2.0.0
     # via pytest
 packaging==24.1
     # via
     #   pooch
     #   pytest
-platformdirs==4.2.2
+platformdirs==4.3.6
     # via pooch
 pluggy==1.5.0
     # via pytest
 pooch==1.8.2
     # via -r basetest.in
-pytest==8.3.2
+pytest==8.3.3
     # via -r basetest.in
 requests==2.32.3
     # via pooch
 tomli==2.0.1
     # via pytest
-urllib3==2.2.2
+urllib3==2.2.3
     # via requests

requirements/ci.txt

@@ -17,28 +17,28 @@ colorama==0.4.6
     # via tox
 distlib==0.3.8
     # via virtualenv
-filelock==3.15.4
+filelock==3.16.1
     # via
     #   tox
     #   virtualenv
 gitdb==4.0.11
     # via gitpython
 gitpython==3.1.43
     # via -r ci.in
-idna==3.8
+idna==3.10
     # via requests
 packaging==24.1
     # via
     #   -r ci.in
     #   pyproject-api
     #   tox
-platformdirs==4.2.2
+platformdirs==4.3.6
     # via
     #   tox
     #   virtualenv
 pluggy==1.5.0
     # via tox
-pyproject-api==1.7.1
+pyproject-api==1.7.2
     # via tox
 requests==2.32.3
     # via -r ci.in
@@ -48,9 +48,9 @@ tomli==2.0.1
     # via
     #   pyproject-api
     #   tox
-tox==4.18.0
+tox==4.19.0
     # via -r ci.in
-urllib3==2.2.2
+urllib3==2.2.3
     # via requests
-virtualenv==20.26.3
+virtualenv==20.26.5
     # via tox

requirements/dev.txt

@@ -26,7 +26,7 @@ arrow==1.3.0
     # via isoduration
 async-lru==2.0.4
     # via jupyterlab
-cffi==1.17.0
+cffi==1.17.1
     # via argon2-cffi-bindings
 copier==9.3.1
     # via -r dev.in
@@ -87,9 +87,9 @@ prometheus-client==0.20.0
     # via jupyter-server
 pycparser==2.22
     # via cffi
-pydantic==2.8.2
+pydantic==2.9.2
     # via copier
-pydantic-core==2.20.1
+pydantic-core==2.23.4
     # via pydantic
 python-json-logger==2.0.7
     # via jupyter-events
@@ -115,7 +115,7 @@ terminado==0.18.1
     #   jupyter-server-terminals
 toposort==1.10
     # via pip-compile-multi
-types-python-dateutil==2.9.0.20240821
+types-python-dateutil==2.9.0.20240906
     # via arrow
 uri-template==1.3.0
     # via jsonschema