Sync scipp/sciline with copier template

.copier-answers.yml

@@ -1,5 +1,5 @@
 # Changes here will be overwritten by Copier; NEVER EDIT MANUALLY
-_commit: bba4103
+_commit: 055c220
 _src_path: gh:scipp/copier_template
 description: Build scientific pipelines for your data
 max_python: '3.12'

.github/workflows/ci.yml

@@ -1,6 +1,3 @@
-# SPDX-License-Identifier: BSD-3-Clause
-# Copyright (c) 2023 Scipp contributors (https://github.com/scipp)
-
 name: CI
 
 on:
@@ -24,15 +21,16 @@ 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'
-      - run: python -m pip install --upgrade pip
-      - run: python -m pip install -r requirements/ci.txt
-      - run: tox -e static
-      - uses: stefanzweifel/git-auto-commit-action@v5
+      - uses: pre-commit/[email protected]
+        with:
+          extra_args: --all-files
+      - uses: pre-commit-ci/[email protected]
+        if: always()
         with:
-          commit_message: Apply automatic formatting
+          msg: Apply automatic formatting
 
   tests:
     name: Tests

.github/workflows/docs.yml

@@ -1,6 +1,3 @@
-# SPDX-License-Identifier: BSD-3-Clause
-# Copyright (c) 2023 Scipp contributors (https://github.com/scipp)
-
 name: Docs
 
 on:
@@ -47,11 +44,12 @@ jobs:
     runs-on: 'ubuntu-22.04'
     steps:
       - run: sudo apt install --yes graphviz pandoc
-      - uses: actions/checkout@v3
+      - 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
@@ -62,12 +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@v4.4.3
+      - uses: JamesIves/github-pages-deploy-action@v4.5.0
         if: ${{ inputs.publish }}
         with:
           branch: gh-pages

.github/workflows/nightly_at_main.yml

@@ -1,6 +1,3 @@
-# SPDX-License-Identifier: BSD-3-Clause
-# Copyright (c) 2023 Scipp contributors (https://github.com/scipp)
-
 name: Nightly test at main branch
 
 on:

.github/workflows/nightly_at_release.yml

@@ -1,6 +1,3 @@
-# SPDX-License-Identifier: BSD-3-Clause
-# Copyright (c) 2023 Scipp contributors (https://github.com/scipp)
-
 name: Nightly tests at latest release
 
 on:

.github/workflows/release.yml

@@ -1,6 +1,3 @@
-# SPDX-License-Identifier: BSD-3-Clause
-# Copyright (c) 2023 Scipp contributors (https://github.com/scipp)
-
 name: Release
 
 on:
@@ -18,7 +15,7 @@ jobs:
     runs-on: 'ubuntu-22.04'
 
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
         with:
           submodules: true
           fetch-depth: 0  # history required so setuptools_scm can determine version
@@ -31,7 +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
@@ -41,11 +38,11 @@ jobs:
     runs-on: 'ubuntu-22.04'
 
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
         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'
 
@@ -56,7 +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
@@ -70,8 +67,8 @@ jobs:
       id-token: write
     if: github.event_name == 'release' && github.event.action == 'published'
     steps:
-      - uses: actions/download-artifact@v3
-      - uses: pypa/[email protected].10
+      - uses: actions/download-artifact@v4
+      - uses: pypa/[email protected].14
 
   upload_conda:
     name: Deploy Conda
@@ -80,7 +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
@@ -104,7 +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

@@ -1,6 +1,3 @@
-# SPDX-License-Identifier: BSD-3-Clause
-# Copyright (c) 2023 Scipp contributors (https://github.com/scipp)
-
 name: Test
 
 on:
@@ -48,16 +45,16 @@ jobs:
     runs-on: ${{ inputs.os-variant }}
 
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
         with:
           ref: ${{ inputs.checkout_ref }}
-      - uses: actions/setup-python@v3
+      - uses: actions/setup-python@v5
         with:
           python-version: ${{ inputs.python-version }}
       - 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

.github/workflows/unpinned.yml

@@ -1,6 +1,3 @@
-# SPDX-License-Identifier: BSD-3-Clause
-# Copyright (c) 2023 Scipp contributors (https://github.com/scipp)
-
 name: Unpinned tests at latest release
 
 on:

.gitignore

@@ -37,3 +37,4 @@ docs/generated/
 *.raw
 *.cif
 *.rcif
+*.ort

conda/meta.yaml

@@ -6,13 +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:
     - python>=3.9
 
+  {% for package in dependencies %}
+    - {% if package == "graphviz" %}python-graphviz{% else %}{{ package }}{% endif %}
+  {% endfor %}
+
+
 test:
   imports:
     - sciline

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/scipp/{{ project|lower }}/releases">older versions</a>).
+Current {{ project }} version: {{ version }} (<a href="https://github.com/{{orgname}}/{{ project|lower }}/releases">older versions</a>).

docs/conf.py

@@ -3,6 +3,7 @@
 import doctest
 import os
 import sys
+from importlib.metadata import version as get_version
 
 import sciline
 
@@ -23,13 +24,22 @@
     'sphinx.ext.intersphinx',
     'sphinx.ext.mathjax',
     'sphinx.ext.napoleon',
+    'sphinx.ext.viewcode',
     'sphinx_autodoc_typehints',
     'sphinx_copybutton',
     'sphinx_design',
     'nbsphinx',
     'myst_parser',
 ]
 
+try:
+    import sciline.sphinxext.domain_types  # noqa: F401
+
+    extensions.append('sciline.sphinxext.domain_types')
+except ModuleNotFoundError:
+    pass
+
+
 myst_enable_extensions = [
     "amsmath",
     "colon_fence",
@@ -54,6 +64,7 @@
 intersphinx_mapping = {
     'python': ('https://docs.python.org/3', None),
     'numpy': ('https://numpy.org/doc/stable/', None),
+    'scipp': ('https://scipp.github.io/', None),
 }
 
 # autodocs includes everything, even irrelevant API internals. autosummary
@@ -73,6 +84,18 @@
 typehints_defaults = 'comma'
 typehints_use_rtype = False
 
+
+sciline_domain_types_prefix = 'sciline'
+sciline_domain_types_aliases = {
+    'scipp._scipp.core.DataArray': 'scipp.DataArray',
+    'scipp._scipp.core.Dataset': 'scipp.Dataset',
+    'scipp._scipp.core.DType': 'scipp.DType',
+    'scipp._scipp.core.Unit': 'scipp.Unit',
+    'scipp._scipp.core.Variable': 'scipp.Variable',
+    'scipp.core.data_group.DataGroup': 'scipp.DataGroup',
+}
+
+
 # Add any paths that contain templates here, relative to this directory.
 templates_path = ['_templates']
 
@@ -90,10 +113,8 @@
 # built documents.
 #
 
-# The short X.Y version.
-version = sciline.__version__
-# The full version, including alpha/beta/rc tags.
-release = sciline.__version__
+release = get_version("sciline")
+version = ".".join(release.split('.')[:3])  # CalVer
 
 warning_is_error = True
 

docs/conf.py.rej

@@ -0,0 +1,10 @@
+diff a/docs/conf.py b/docs/conf.py	(rejected hunks)
+@@ -133,7 +133,7 @@ html_theme_options = {
+     },
+     "external_links": [
+         {"name": "Scipp", "url": "https://scipp.github.io"},
+-        ],
++    ],
+     "icon_links": [
+         {
+             "name": "GitHub",

docs/developer/index.md

@@ -1,4 +1,4 @@
-# Developer documentation
+# Development
 
 ```{include} ../../CONTRIBUTING.md
 ```

pyproject.toml

@@ -47,6 +47,7 @@ minversion = "7.0"
 addopts = """
 --strict-config
 --strict-markers
+--import-mode=importlib
 -ra
 -v
 """

requirements/base.in

@@ -1,8 +1,4 @@
-# Temporary until questionary (dep of copier) updates
-# See https://github.com/tmbo/questionary/blob/2df265534f3eb77aafcf70902e53e80beb1793e0/pyproject.toml#L36C43-L36C110
-prompt-toolkit==3.0.36
-# Temporary pinned until prompt-tookit conflict is resolved.
-ipython==8.9.0
+# 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/base.in.rej

@@ -0,0 +1,6 @@
+diff a/requirements/base.in b/requirements/base.in	(rejected hunks)
+@@ -5,3 +5,4 @@ prompt-toolkit==3.0.36
+ ipython==8.9.0
+ # --- END OF CUSTOM SECTION ---
+ # The following was generated by 'tox -e deps', DO NOT EDIT MANUALLY!
++

requirements/dev.in

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

requirements/make_base.py

@@ -1,6 +1,3 @@
-# SPDX-License-Identifier: BSD-3-Clause
-# Copyright (c) 2023 Scipp contributors (https://github.com/scipp)
-
 import sys
 from argparse import ArgumentParser
 from pathlib import Path

requirements/make_base.py.rej

@@ -0,0 +1,10 @@
+diff a/requirements/make_base.py b/requirements/make_base.py	(rejected hunks)
+@@ -43,7 +43,7 @@ def write_dependencies(dependency_name: str, dependencies: List[str]) -> None:
+ with open("../pyproject.toml", "rb") as toml_file:
+     pyproject = tomli.load(toml_file)
+     dependencies = pyproject["project"].get("dependencies")
+-    if not dependencies:
++    if dependencies is None:
+         raise RuntimeError("No dependencies found in pyproject.toml")
+     dependencies = [dep.strip().strip('"') for dep in dependencies]
+