Copier update

Author: jl-wynen

.copier-answers.yml

@@ -1,5 +1,5 @@
 # Changes here will be overwritten by Copier; NEVER EDIT MANUALLY
-_commit: afbe5c7
+_commit: 2f9f107
 _src_path: gh:scipp/copier_template
 description: 'Spectroscopy 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
@@ -46,6 +46,7 @@ jobs:
       os-variant: ${{ matrix.os }}
       python-version: ${{ matrix.python.version }}
       tox-env: ${{ matrix.python.tox-env }}
+    secrets: inherit
 
   docs:
     needs: tests
@@ -54,3 +55,4 @@ jobs:
       publish: false
       linkcheck: ${{ contains(matrix.variant.os, 'ubuntu') && github.ref == 'refs/heads/main' }}
       branch: ${{ github.head_ref == '' && github.ref_name || github.head_ref }}
+    secrets: inherit

.github/workflows/docs.yml

@@ -42,6 +42,10 @@ jobs:
   docs:
     name: Build documentation
     runs-on: 'ubuntu-22.04'
+    env:
+        ESS_PROTECTED_FILESTORE_USERNAME: ${{ secrets.ESS_PROTECTED_FILESTORE_USERNAME }}
+        ESS_PROTECTED_FILESTORE_PASSWORD: ${{ secrets.ESS_PROTECTED_FILESTORE_PASSWORD }}
+
     steps:
       - run: sudo apt install --yes graphviz pandoc
       - uses: actions/checkout@v4
@@ -65,7 +69,7 @@ jobs:
           name: docs_html
           path: html/
 
-      - uses: JamesIves/github-pages-deploy-action@v4.6.0
+      - uses: JamesIves/github-pages-deploy-action@v4.6.4
         if: ${{ inputs.publish }}
         with:
           branch: gh-pages

.github/workflows/nightly_at_main.yml

@@ -31,3 +31,4 @@ jobs:
       os-variant: ${{ matrix.os }}
       python-version: ${{ matrix.python.version }}
       tox-env: ${{ matrix.python.tox-env }}
+    secrets: inherit

.github/workflows/nightly_at_release.yml

@@ -38,3 +38,4 @@ jobs:
       python-version: ${{ matrix.python.version }}
       tox-env: ${{ matrix.python.tox-env }}
       checkout_ref: ${{ needs.setup.outputs.release_tag }}
+    secrets: inherit

.github/workflows/test.yml

@@ -41,8 +41,26 @@ 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:
+        ESS_PROTECTED_FILESTORE_USERNAME: ${{ secrets.ESS_PROTECTED_FILESTORE_USERNAME }}
+        ESS_PROTECTED_FILESTORE_PASSWORD: ${{ secrets.ESS_PROTECTED_FILESTORE_PASSWORD }}
 
     steps:
       - uses: actions/checkout@v4

.github/workflows/unpinned.yml

@@ -38,3 +38,4 @@ jobs:
       python-version: ${{ matrix.python.version }}
       tox-env: ${{ matrix.python.tox-env }}
       checkout_ref: ${{ needs.setup.outputs.release_tag }}
+    secrets: inherit

.gitignore

@@ -9,6 +9,7 @@ html
 
 # Environments
 venv
+.venv
 
 # Caches
 .clangd/
@@ -20,6 +21,7 @@ __pycache__/
 .pytest_cache
 .mypy_cache
 docs/generated/
+.ruff_cache
 
 # Editor settings
 .idea/
@@ -38,3 +40,4 @@ 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: v0.4.1
+    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:
@@ -18,16 +19,23 @@ requirements:
   run:
     - python>=3.10
 
+  {# Conda does not allow spaces between package name and version, so remove them #}
   {% for package in dependencies %}
-    - {% if package == "graphviz" %}python-graphviz{% else %}{{ package }}{% endif %}
+    - {% if package == "graphviz" %}python-graphviz{% else %}{{ package|replace(" ", "") }}{% endif %}
   {% endfor %}
 
 
 test:
   imports:
     - ess.spectroscopy
   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/_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 ESSspectroscopy version: {{ version }} (<a href="https://github.com/scipp/essspectroscopy/releases">older versions</a>).

docs/conf.py

@@ -1,12 +1,18 @@
-# -*- coding: utf-8 -*-
+# SPDX-License-Identifier: BSD-3-Clause
+# Copyright (c) 2024 Scipp contributors (https://github.com/scipp)
 
 import doctest
 import os
 import sys
+from importlib.metadata import PackageNotFoundError
 from importlib.metadata import version as get_version
 
+from sphinx.util import logging
+
 sys.path.insert(0, os.path.abspath('.'))
 
+logger = logging.getLogger(__name__)
+
 # General information about the project.
 project = 'ESSspectroscopy'
 copyright = '2024 Scipp contributors'
@@ -34,6 +40,8 @@
     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
 
@@ -111,8 +119,15 @@
 # built documents.
 #
 
-release = get_version("essspectroscopy")
-version = ".".join(release.split('.')[:3])  # CalVer
+try:
+    release = get_version("essspectroscopy")
+    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
 

pyproject.toml

@@ -41,6 +41,11 @@ dependencies = [
 
 dynamic = ["version"]
 
+[project.optional-dependencies]
+test = [
+    "pytest",
+]
+
 [project.urls]
 "Bug Tracker" = "https://github.com/scipp/essspectroscopy/issues"
 "Documentation" = "https://scipp.github.io/essspectroscopy"
@@ -71,14 +76,14 @@ extend-exclude = [
 
 [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"]
+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 = ["essspectroscopy"]
+fixable = ["B010", "I001", "PT001"]
+isort.known-first-party = ["ess.spectroscopy"]
 pydocstyle.convention = "numpy"
 
 [tool.ruff.lint.per-file-ignores]
@@ -109,3 +114,11 @@ 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/basetest.in

@@ -1,4 +1,9 @@
 # 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``
 
-pytest
+# 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!

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)
@@ -43,8 +42,14 @@ def write_dependencies(dependency_name: str, dependencies: List[str]) -> None:
     if dependencies is None:
         raise RuntimeError("No dependencies found in pyproject.toml")
     dependencies = [dep.strip().strip('"') for dep in dependencies]
+    test_dependencies = (
+        pyproject["project"].get("optional-dependencies", {}).get("test", [])
+    )
+    test_dependencies = [dep.strip().strip('"') for dep in test_dependencies]
+
 
 write_dependencies("base", dependencies)
+write_dependencies("basetest", test_dependencies)
 
 
 def as_nightly(repo: str) -> str:
@@ -56,7 +61,8 @@ def as_nightly(repo: str) -> str:
         version = f"cp{sys.version_info.major}{sys.version_info.minor}"
         base = "https://github.com/scipp/scipp/releases/download/nightly/scipp-nightly"
         suffix = "manylinux_2_17_x86_64.manylinux2014_x86_64.whl"
-        return "-".join([base, version, version, suffix])
+        prefix = "scipp @ "
+        return prefix + "-".join([base, version, version, suffix])
     return f"{repo} @ git+https://github.com/{org}/{repo}@main"
 
 

src/ess/spectroscopy/__init__.py

@@ -5,7 +5,7 @@
 import importlib.metadata
 
 try:
-    __version__ = importlib.metadata.version(__package__ or __name__)
+    __version__ = importlib.metadata.version("essspectroscopy")
 except importlib.metadata.PackageNotFoundError:
     __version__ = "0.0.0"
 

tests/package_test.py

@@ -1,7 +1,20 @@
 # SPDX-License-Identifier: BSD-3-Clause
 # Copyright (c) 2024 Scipp contributors (https://github.com/scipp)
+
+"""Tests of package integrity.
+
+Note that addidional imports need to be added for repositories that
+contain multiple packages.
+"""
+
 from ess import spectroscopy as pkg
 
 
 def test_has_version():
     assert hasattr(pkg, '__version__')
+
+
+# This is for CI package tests. They need to run tests with minimal dependencies,
+# that is, without installing pytest. This code does not affect pytest.
+if __name__ == '__main__':
+    test_has_version()